@article {pmid37723328, year = {2023}, author = {Sasi, R and Suchithra, TV}, title = {Wastewater microbial diversity versus molecular analysis at a glance: a mini-review.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {37723328}, issn = {1678-4405}, abstract = {Microorganisms play a vital role in biological wastewater treatment by converting organic and toxic materials into harmless substances. Understanding microbial communities' structure, taxonomy, phylogeny, and metabolic activities is essential to improve these processes. Molecular microbial ecology employs molecular techniques to study community profiles and phylogenetic information since culture-dependent approaches have limitations in providing a comprehensive understanding of microbial diversity in a system. Genomic advancements such as DNA hybridization, microarray analysis, sequencing, and reverse sample genome probing have enabled the detailed characterization of microbial communities in wastewater treatment facilities. This mini-review summarizes the current state of knowledge on the diversity of microorganisms in wastewater treatment plants, emphasizing critical microbial processes such as nitrogen and phosphorus removal.}, }
@article {pmid37723166, year = {2023}, author = {Ye, H and Borusak, S and Eberl, C and Krasenbrink, J and Weiss, AS and Chen, SC and Hanson, BT and Hausmann, B and Herbold, CW and Pristner, M and Zwirzitz, B and Warth, B and Pjevac, P and Schleheck, D and Stecher, B and Loy, A}, title = {Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5533}, pmid = {37723166}, issn = {2041-1723}, support = {I2320-B22//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; DOC 69-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.}, }
@article {pmid37722685, year = {2023}, author = {Jacobovitz, MR and Hambleton, EA and Guse, A}, title = {Unlocking the Complex Cell Biology of Coral-Dinoflagellate Symbiosis: A Model Systems Approach.}, journal = {Annual review of genetics}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-genet-072320-125436}, pmid = {37722685}, issn = {1545-2948}, abstract = {Symbiotic interactions occur in all domains of life, providing organisms with resources to adapt to new habitats. A prime example is the endosymbiosis between corals and photosynthetic dinoflagellates. Eukaryotic dinoflagellate symbionts reside inside coral cells and transfer essential nutrients to their hosts, driving the productivity of the most biodiverse marine ecosystem. Recent advances in molecular and genomic characterization have revealed symbiosis-specific genes and mechanisms shared among symbiotic cnidarians. In this review, we focus on the cellular and molecular processes that underpin the interaction between symbiont and host. We discuss symbiont acquisition via phagocytosis, modulation of host innate immunity, symbiont integration into host cell metabolism, and nutrient exchange as a fundamental aspect of stable symbiotic associations. We emphasize the importance of using model systems to dissect the cellular complexity of endosymbiosis, which ultimately serves as the basis for understanding its ecology and capacity to adapt in the face of climate change. Expected final online publication date for the Annual Review of Genetics, Volume 57 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37719127, year = {2023}, author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G}, title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15916}, pmid = {37719127}, issn = {2167-8359}, mesh = {Animals ; Spodoptera ; Larva ; *Bacillus thuringiensis/genetics ; Endotoxins ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.<br><br>METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.<br><br>RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.}, }
@article {pmid37717747, year = {2023}, author = {Farrell, ML and Chueiri, A and Maguire, M and Kovářová, A and Miliotis, G and O'Connor, L and McDonagh, F and Duane, S and Cormican, M and Devane, G and Tuohy, A and DeLappe, N and De Bock, F and Burke, LP and Morris, D}, title = {Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167100}, doi = {10.1016/j.scitotenv.2023.167100}, pmid = {37717747}, issn = {1879-1026}, abstract = {The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.}, }
@article {pmid37717325, year = {2023}, author = {Sandeep, R and Muscolino, JF and Macêdo, WV and Piculell, M and Christensson, M and Poulsen, JS and Nielsen, JL and Vergeynst, L}, title = {Effect of biofilm thickness on the activity and community composition of phosphorus accumulating bacteria in a moving bed biofilm reactor.}, journal = {Water research}, volume = {245}, number = {}, pages = {120599}, doi = {10.1016/j.watres.2023.120599}, pmid = {37717325}, issn = {1879-2448}, abstract = {Can biofilms enhance the rates of phosphorus removal in wastewater treatment? In order to narrow the scientific gap on the effect of biofilm thickness on the activity and microbial community of phosphorus-accumulating bacteria, this study investigated biofilms of 30 to 1000 µm thickness in a moving bed biofilm reactor. Measurements on 5 different biofilm carriers showed that biomass-specific phosphorus release and uptake rates increased as a function of biofilm thickness for biofilms thinner than about 110 µm but were lower for thicker biofilms of about 550-1000 µm. The reduced phosphorus uptake and release rates in the thickest biofilms can result from substrate mass transfer limitations whereas the low activity in the thinnest biofilms can be related to a too high turnover rate in the biofilm due to heterotrophic growth. Additionally, the microbial ecology of the different biofilms confirms the observed phosphorus uptake and release rates. The results from the full-length 16S rRNA gene sequencing of the bacterial community showed that the thicker biofilms were characterized by higher relative abundance (40-58%) of potential phosphorus accumulating genera Zoogloea, Acinetobacter, Dechloromonas and Ca. Accumulibacter. In contrast, the thinner biofilms were dominated by the genus Ferribacterium (34-60%), which might be competing with phosphorus-accumulating bacteria as indicated by the relatively high acetate uptake rates in the thinner biofilms. It is concluded that there is an optimal biofilm thickness of 100-500 µm, at which the phosphorus accumulating bacteria have the highest activity.}, }
@article {pmid37715042, year = {2023}, author = {Candry, P and Chadwick, GL and Caravajal-Arroyo, JM and Lacoere, T and Winkler, MH and Ganigué, R and Orphan, VJ and Rabaey, K}, title = {Trophic interactions shape the spatial organization of medium-chain carboxylic acid producing granular biofilm communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37715042}, issn = {1751-7370}, support = {BOF15/DOC/286//Bijzonder Onderzoeksfonds (Special Research Fund)/ ; BOF19/STA/044//Bijzonder Onderzoeksfonds (Special Research Fund)/ ; #DE-SC0020356//DOE | SC | Biological and Environmental Research (BER)/ ; #DE-SC0020373//DOE | SC | Biological and Environmental Research (BER)/ ; #DE-SC0020373//DOE | SC | Biological and Environmental Research (BER)/ ; }, abstract = {Granular biofilms producing medium-chain carboxylic acids (MCCA) from carbohydrate-rich industrial feedstocks harbor highly streamlined communities converting sugars to MCCA either directly or via lactic acid as intermediate. We investigated the spatial organization and growth activity patterns of MCCA producing granular biofilms grown on an industrial side stream to test (i) whether key functional guilds (lactic acid producing Olsenella and MCCA producing Oscillospiraceae) stratified in the biofilm based on substrate usage, and (ii) whether spatial patterns of growth activity shaped the unique, lenticular morphology of these biofilms. First, three novel isolates (one Olsenella and two Oscillospiraceae species) representing over half of the granular biofilm community were obtained and used to develop FISH probes, revealing that key functional guilds were not stratified. Instead, the outer 150-500 µm of the granular biofilm consisted of a well-mixed community of Olsenella and Oscillospiraceae, while deeper layers were made up of other bacteria with lower activities. Second, nanoSIMS analysis of [15]N incorporation in biofilms grown in normal and lactic acid amended conditions suggested Oscillospiraceae switched from sugars to lactic acid as substrate. This suggests competitive-cooperative interactions may govern the spatial organization of these biofilms, and suggests that optimizing biofilm size may be a suitable process engineering strategy. Third, growth activities were similar in the polar and equatorial biofilm peripheries, leaving the mechanism behind the lenticular biofilm morphology unexplained. Physical processes (e.g., shear hydrodynamics, biofilm life cycles) may have contributed to lenticular biofilm development. Together, this study develops an ecological framework of MCCA-producing granular biofilms that informs bioprocess development.}, }
@article {pmid37713796, year = {2023}, author = {Cai, X and Hu, Y and Zhou, S and Meng, D and Xia, S and Wang, H}, title = {Unraveling bacterial and eukaryotic communities in secondary water supply systems: Dynamics, assembly, and health implications.}, journal = {Water research}, volume = {245}, number = {}, pages = {120597}, doi = {10.1016/j.watres.2023.120597}, pmid = {37713796}, issn = {1879-2448}, abstract = {Secondary water supply systems (SWSSs) are crucial water supply infrastructures for high-rise buildings in metropolitan cities. In recent years, they have garnered public attention due to increased microbial risks. However, our understanding of SWSS microbial ecology, particularly concerning the composition of eukaryotes and the underlying mechanisms driving microbial dynamics and assembly in SWSSs, remains elusive. Herein, we conducted a comprehensive investigation on both eukaryotes and bacteria along the water transportation pathway and across various microbial habitats (water, biofilm, and sediment) in SWSSs. Sequencing results revealed that eukaryotes within SWSSs predominantly consist of protists (average abundance: 31.23%) and metazoans (20.91%), while amoebae accounted for 4.71% of the total. During water transportation from the distribution mains to taps, both bacterial and eukaryotic communities exhibited significant community shifts, and higher degrees of variation were observed for eukaryotic community among different locations within SWSSs. The normalized stochasticity ratio (NST) analysis demonstrated that bacterial community assembly was governed by stochastic processes, while eukaryotic community assembly was primarily shaped by deterministic processes. Within SWSS tanks, bacterial communities significantly varied across water, biofilm, and sediment, whereas eukaryotic communities showed minor differences among these habitats. The co-occurrence networks analysis revealed that tank biofilm and sediment harbored more eukaryote-bacterium linkages than water, suggesting biofilm and sediment might be hotspots for inter-kingdom interactions. We also applied FEAST analysis to track the source of tap water microbiota, results of which showed that household-tap bacteria mainly originated from tank water. In contrast, tank biofilm was identified as the primary microbial source to eukaryotes in household tap water. Additionally, engineering factors such as tank materials significantly affected amoeba community, and the SWSS configuration was found to influence Legionella and Mycobacterium abundances in SWSSs. Overall, results of our study shed light on the microbial ecology in SWSS and provide insights into SWSS management and health risk control.}, }
@article {pmid37712979, year = {2023}, author = {Li, Y and Yang, H and Su, Y and Gong, X and Yao, B and Cheng, L}, title = {Phosphorus Coupled with High Nitrogen Addition Exerts a Great Influence on Soil Bacterial Community in a Semiarid Grassland.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37712979}, issn = {1432-184X}, abstract = {Nitrogen (N) and phosphorus (P) addition, either individually or in combination, has been demonstrated to enhance plant productivity in grassland ecosystems. Soil bacterial community, which is the driver of litter decomposition and nutrient cycling, is assumed to control responses of terrestrial ecosystem structure and function to N and P addition. Using a high-throughput Illumina MiSeq sequencing platform, we conducted a 9-year field experiment of N (0, 5, 10, and 20 g N m[-2] yr[-1]) and P (0 and 10 g P m[-2] yr[-1]) additions in the Inner Mongolian steppes to elucidate long-term effects of N and P addition on soil bacterial richness, diversity and composition. We found that N addition reduced the relative abundance of Acidobacteria, Chloroflexi, and Nitrospirae, while increased that of Bacteroides. The results showed that the bacterial biomarker was enriched in P addition treatments, either individually or combined with N addition. Both N and P addition altered the bacterial community structure, while only N addition greatly decreased bacterial richness and diversity. More importantly, we showed that all of these effects were most significant in N3P treatment (20 g N m[-2] yr[-1] and 10 g P m[-2] yr[-1]), implying that P coupled with a high-level N addition exerted a great influence on soil bacterial community. Structural equation models revealed that N and P addition had a great direct effect on soil bacterial community and an indirect effect on it mainly by changing the litter biomass. Our findings highlighted that severe niche differentiation was induced by P along with a high-level N, further emphasizing the importance of simultaneously evaluating response of soil bacterial community to N and P addition, especially in the context of increasing anthropogenic nutrient additions.}, }
@article {pmid37711620, year = {2023}, author = {Rosel-Pech, C and Pinto-Cardoso, S and Chávez-Torres, M and Montufar, N and Osuna-Padilla, I and Ávila-Ríos, S and Reyes-Terán, G and Aguirre-Alvarado, C and Matías Juan, NA and Pérez-Lorenzana, H and Vázquez-Rosales, JG and Bekker-Méndez, VC}, title = {Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1244473}, pmid = {37711620}, issn = {1664-3224}, abstract = {INTRODUCTION: Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children.<br><br>METHODS: We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata.<br><br>RESULTS: Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively).<br><br>CONCLUSION: The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.}, }
@article {pmid37711139, year = {2023}, author = {Vijay, S and Nair, RR and Sharan, D and Jakkala, K and Ajitkumar, P}, title = {Percoll discontinuous density gradient centrifugation method for the fractionation of the subpopulations of Mycobacterium smegmatis and Mycobacterium tuberculosis from in vitro cultures.}, journal = {MethodsX}, volume = {11}, number = {}, pages = {102344}, pmid = {37711139}, issn = {2215-0161}, abstract = {Bacterial populations in the in vitro laboratory cultures, environment, and patients contain metabolically different subpopulations that respond differently to stress agents, including antibiotics, and emerge as stress tolerant or resistant strains. To contain the emergence of such strains, it is important to study the features of the metabolic status and response of the subpopulations to stress agents. For this purpose, an efficient method is required for the fractionation and isolation of the subpopulations from the cultures. Here we describe in detail the manual setting up of a simple, easy-to-do, reproducibly robust Percoll discontinuous density gradient centrifugation for the fractionation of subpopulations of short-sized cells (SCs) and normal/long-sized cells (NCs) from Mycobacterium smegmatis and Mycobacterium tuberculosis cultures, which we had reported earlier. About 90-98% enrichment was obtained respectively for SCs and NCs for M. smegmatis and 69-67% enrichment was obtained respectively for the SCs and NCs for M. tuberculosis.•The Percoll discontinuous density gradient centrifugation helps the fractionation and isolation of mycobacterial subpopulations that differ in density.•The method offers a consistently reproducible high enrichment of the subpopulations of SCs and NCs from the in vitro cultures of M. smegmatis and M. tuberculosis.•Our earlier reports on the consistency in the differential response of the subpopulations, enriched using the method, to oxidative, nitrite, and antibiotic stress proves its validity.}, }
@article {pmid37708771, year = {2023}, author = {Sentenac, H and Loyau, A and Zoccarato, L and Jassey, VEJ and Grossart, HP and Schmeller, DS}, title = {Biofilm community composition is changing in remote mountain lakes with a relative increase in potentially toxigenic algae.}, journal = {Water research}, volume = {245}, number = {}, pages = {120547}, doi = {10.1016/j.watres.2023.120547}, pmid = {37708771}, issn = {1879-2448}, abstract = {Mountain lakes provide clear drinking water to humankind but are strongly impacted by global change. Benthic biofilms are crucial for maintaining water quality in these oligotrophic lakes, yet little is known about the effects of global change on mountain biofilm communities. By combining analyses of metabarcoding data on 16S and 18S rRNA genes with climatic and environmental data, we investigated global change effects on the composition of biofilm prokaryotic and micro-eukaryotic assemblages in a five-year monitoring program of 26 Pyrenean lakes (2016-2020). Using time-decay relationships and within-lake dissimilarity modelling, we show that the composition of both prokaryotic and micro-eukaryotic biofilm communities significantly shifted and their biodiversity declined from 2016 to 2020. In particular, analyses of temporal trends with linear mixed models indicated an increase in the richness and relative abundance of cyanobacteria, including potentially toxigenic cyanobacteria, and a concomitant decrease in diatom richness and relative abundance. While these compositional shifts may be due to several drivers of global change acting simultaneously on mountain lake biota, water pH and hardness were, from our data, the main environmental variables associated with changes for both prokaryotic and micro-eukaryotic assemblages. Water pH and hardness increased in our lakes over the study period, and are known to increase in Pyrenean lakes due to the intensification of rock weathering as a result of climate change. Given predicted climate trends and if water pH and hardness do cause some changes in benthic biofilms, those changes might be further exacerbated in the future. Such biofilm compositional shifts may induce cascading effects in mountain food webs, threatening the resilience of the entire lake ecosystem. The rise in potentially toxigenic cyanobacteria also increases intoxication risks for humans, pets, wild animals, and livestock that use mountain lakes. Therefore, our study has implications for water quality, ecosystem health, public health, as well as local economies (pastoralism, tourism), and highlights the possible impacts of global change on mountain lakes.}, }
@article {pmid37705860, year = {2024}, author = {Mills, S and Trego, AC and Prevedello, M and De Vrieze, J and O'Flaherty, V and Lens, PNL and Collins, G}, title = {Unifying concepts in methanogenic, aerobic, and anammox sludge granulation.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100310}, pmid = {37705860}, issn = {2666-4984}, abstract = {The retention of dense and well-functioning microbial biomass is crucial for effective pollutant removal in several biological wastewater treatment technologies. High solids retention is often achieved through aggregation of microbial communities into dense, spherical aggregates known as granules, which were initially discovered in the 1980s. These granules have since been widely applied in upflow anaerobic digesters for waste-to-energy conversions. Furthermore, granular biomass has been applied in aerobic wastewater treatment and anaerobic ammonium oxidation (anammox) technologies. The mechanisms underpinning the formation of methanogenic, aerobic, and anammox granules are the subject of ongoing research. Although each granule type has been extensively studied in isolation, there has been a lack of comparative studies among these granulation processes. It is likely that there are some unifying concepts that are shared by all three sludge types. Identifying these unifying concepts could allow a unified theory of granulation to be formed. Here, we review the granulation mechanisms of methanogenic, aerobic, and anammox granular sludge, highlighting several common concepts, such as the role of extracellular polymeric substances, cations, and operational parameters like upflow velocity and shear force. We have then identified some unique features of each granule type, such as different internal structures, microbial compositions, and quorum sensing systems. Finally, we propose that future research should prioritize aspects of microbial ecology, such as community assembly or interspecies interactions in individual granules during their formation and growth.}, }
@article {pmid37702500, year = {2023}, author = {Deng, T and He, Z and Xu, M and Dong, M and Guo, J and Sun, G and Huang, H}, title = {Species' functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning.}, journal = {mBio}, volume = {}, number = {}, pages = {e0156723}, doi = {10.1128/mbio.01567-23}, pmid = {37702500}, issn = {2150-7511}, abstract = {Understanding processes and mechanisms governing microbial community structure and function is a central goal in microbial ecology. Previous studies disentangling the community assembly mechanisms were mainly based on taxonomic diversity but were rarely combined with species' functional traits and interactions. Here, we showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using both culture-independent and culture-dependent technologies. The results showed that species were different in functional traits of nitrate-mediated sulfide and thiosulfate oxidation, which determined their relative abundance in the nitrate-mediated sulfur oxidation systems. Those thiosulfate-oxidizing microbes co-occurred with Thiobacillus by using intermediates (e.g., thiosulfate) secreted by Thiobacillus during sulfide oxidation process. Such metabolic dependencies exerted great effects on community functions. Metabolic dependencies between Thiobacillus and genera that oxidized thiosulfate to more sulfate (e.g., Ciceribacter) sustained high and stable oxidation activities of sulfide to sulfate. In contrast, metabolic dependencies between Thiobacillus and genera that oxidized thiosulfate to tetrathionate (e.g., Pseudoxanthomonas) slowed down the production of sulfate, indicating changes in the metabolic flow. In addition, competitions among species were mostly detrimental to the stability of community function. These results revealed that species' functional traits and interactions were the intrinsic factors determining community structure and functions. This study advances our understanding of microbial community assembly and functions of the nitrate-mediated sulfur oxidation process from the perspectives of species' functional traits and interactions and has important implications for designing and constructing microbiomes with expected functions. IMPORTANCE Understanding the processes and mechanisms governing microbial community assembly and their linkages to ecosystem functioning has long been a core issue in microbial ecology. An in-depth insight still requires combining with analyses of species' functional traits and microbial interactions. Our study showed how species' functional traits and interactions determined microbial community structure and functions by a well-controlled laboratory experiment with nitrate-mediated sulfur oxidation systems using high-throughput sequencing and culture-dependent technologies. The results provided solid evidences that species' functional traits and interactions were the intrinsic factors determining community structure and function. More importantly, our study established quantitative links between community structure and function based on species' functional traits and interactions, which would have important implications for the design and synthesis of microbiomes with expected functions.}, }
@article {pmid37695394, year = {2023}, author = {Wei, N and Tan, J}, title = {Correction to: Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02300-z}, pmid = {37695394}, issn = {1432-184X}, }
@article {pmid37285553, year = {2023}, author = {McKinlay, JB}, title = {Are Bacteria Leaky? Mechanisms of Metabolite Externalization in Bacterial Cross-Feeding.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {277-297}, doi = {10.1146/annurev-micro-032521-023815}, pmid = {37285553}, issn = {1545-3251}, abstract = {The metabolism of a bacterial cell stretches beyond its boundaries, often connecting with the metabolism of other cells to form extended metabolic networks that stretch across communities, and even the globe. Among the least intuitive metabolic connections are those involving cross-feeding of canonically intracellular metabolites. How and why are these intracellular metabolites externalized? Are bacteria simply leaky? Here I consider what it means for a bacterium to be leaky, and I review mechanisms of metabolite externalization from the context of cross-feeding. Despite common claims, diffusion of most intracellular metabolites across a membrane is unlikely. Instead, passive and active transporters are likely involved, possibly purging excess metabolites as part of homeostasis. Re-acquisition of metabolites by a producer limits the opportunities for cross-feeding. However, a competitive recipient can stimulate metabolite externalization and initiate a positive-feedback loop of reciprocal cross-feeding.}, }
@article {pmid37692385, year = {2023}, author = {Fan, R and Liu, Y and Bin, Y and Huang, J and Yi, B and Tang, X and Li, Y and Cai, Y and Yang, Z and Yang, M and Song, J and Pan, Q and Liu, Z and Ghani, MI and Hu, X and Chen, X}, title = {Identification of Colletotrichum aenigma as the new causal agent of leaf blight disease on Aucuba japonica Thunb., and screenings of effective fungicides for its sustainable management.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1222844}, pmid = {37692385}, issn = {1664-302X}, abstract = {Aucuba japonica Thunb is an evergreen woody ornamental plant with significant economic and ecological values. It also produces aucubin, showing a variety of biological activities. It is widely planted in the southwest region of China, including karst landscape areas in Guizhou Province. In January 2022, a serious leaf blight disease was observed on the leaves of A. japonica in the outdoor gardens of Guizhou University, Guiyang, Guizhou, China. The causal agent was identified as Colletotrichum aenigma through amplification and sequencing of the internal transcribed spacer (ITS) region, translation of the chitin synthase (CHS) and actin (ACT) genes, and morphological characterizations. Koch's postulates were confirmed by its pathogenicity on healthy leaves, including re-isolation and identification. To our knowledge, this is the first report of C. aenigma causing leaf blight on A. japonica worldwide. To identify pathogen characteristics that could be utilized for future disease management, the effects of temperature and light on mycelial growth, conidia production, and conidial germination, and the effects of humidity on conidial germination were studied. Optimal temperatures for mycelial growth of C. aenigma BY827 were 25-30°C, while 15°C and 35°C were favorable for conidia production. Concurrently, alternating 10-h light and 14-h dark, proved to be beneficial for mycelial growth and conidial germination. Additionally, conidial germination was enhanced at 90% humidity. In vitro screenings of ten chemical pesticides to assess their efficacy in suppressing C. aenigma representative strain BY827. Among them, difenoconazole showed the best inhibition rate, with an EC50 (concentration for 50% of maximal effect) value of 0.0148 μg/ml. Subsequently, field experiment results showed that difenoconazole had the highest control efficiency on A. japonica leaf blight (the decreasing rate of disease incidence and decreasing rate of disease index were 44.60 and 47.75%, respectively). Interestingly, we discovered that C. aenigma BY827 may develop resistance to mancozeb, which is not reported yet among Colletotrichum spp. strains. In conclusion, our study provided new insights into the causal agent of A. japonica leaf blight, and the effective fungicides evaluated provided an important basis and potential resource for the sustainable control of A. japonica leaf blight caused by C. aenigma in the field.}, }
@article {pmid37607131, year = {2023}, author = {Klapper, FA and Kiel, C and Bellstedt, P and Vyverman, W and Pohnert, G}, title = {Structure Elucidation of the First Sex-Inducing Pheromone of a Diatom.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202307165}, doi = {10.1002/anie.202307165}, pmid = {37607131}, issn = {1521-3773}, support = {FWO G001521N, BOF/GOA No. 01G01715//European Marine Biological Resource Centre Belgium/ ; Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Diatoms are abundant unicellular microalgae, responsible for ≈20 % of global photosynthetic CO2 fixation. Nevertheless, we know little about fundamental aspects of their biology, such as their sexual reproduction. Pheromone-mediated chemical communication is crucial for successful mating. An attraction pheromone was identified in the diatom Seminavis robusta, but metabolites priming cells for sex and synchronizing search and mating behavior remained elusive. These sex-inducing pheromones (SIP) induce cell cycle arrest and trigger the production of the attraction pheromone. Here we describe the challenging structure elucidation of an S. robusta SIP. Guided by metabolomics, a candidate metabolite was identified and elucidated by labeling experiments, NMR, ESI MS[n] analyses, and chemical transformations. The use of negative ion mode MS was essential to decipher the unprecedented hydroxyproline and β-sulfated aspartate-containing cyclic heptapeptide that acts in femtomolar concentrations.}, }
@article {pmid37693795, year = {2021}, author = {Crous, PW and Osieck, ER and Jurjević, &#x17d; and Boers, J and van Iperen, AL and Starink-Willemse, M and Dima, B and Balashov, S and Bulgakov, TS and Johnston, PR and Morozova, OV and Pinruan, U and Sommai, S and Alvarado, P and Decock, CA and Lebel, T and McMullan-Fisher, S and Moreno, G and Shivas, RG and Zhao, L and Abdollahzadeh, J and Abrinbana, M and Ageev, DV and Akhmetova, G and Alexandrova, AV and Altés, A and Amaral, AGG and Angelini, C and Antonín, V and Arenas, F and Asselman, P and Badali, F and Baghela, A and Bañares, A and Barreto, RW and Baseia, IG and Bellanger, JM and Berraf-Tebbal, A and Biketova, AY and Bukharova, NV and Burgess, TI and Cabero, J and Câmara, MPS and Cano-Lira, JF and Ceryngier, P and Chávez, R and Cowan, DA and de Lima, AF and Oliveira, RL and Denman, S and Dang, QN and Dovana, F and Duarte, IG and Eichmeier, A and Erhard, A and Esteve-Raventós, F and Fellin, A and Ferisin, G and Ferreira, RJ and Ferrer, A and Finy, P and Gaya, E and Geering, ADW and Gil-Durán, C and Glässnerová, K and Glushakova, AM and Gramaje, D and Guard, FE and Guarnizo, AL and Haelewaters, D and Halling, RE and Hill, R and Hirooka, Y and Hubka, V and Iliushin, VA and Ivanova, DD and Ivanushkina, NE and Jangsantear, P and Justo, A and Kachalkin, AV and Kato, S and Khamsuntorn, P and Kirtsideli, IY and Knapp, DG and Kochkina, GA and Koukol, O and Kovács, GM and Kruse, J and Kumar, TKA and Kušan, I and Læssøe, T and Larsson, E and Lebeuf, R and Levicán, G and Loizides, M and Marinho, P and Luangsa-Ard, JJ and Lukina, EG and Magaña-Dueñas, V and Maggs-Kölling, G and Malysheva, EF and Malysheva, VF and Martín, B and Martín, MP and Matočec, N and McTaggart, AR and Mehrabi-Koushki, M and Mešić, A and Miller, AN and Mironova, P and Moreau, PA and Morte, A and Müller, K and Nagy, LG and Nanu, S and Navarro-Ródenas, A and Nel, WJ and Nguyen, TH and Nóbrega, TF and Noordeloos, ME and Olariaga, I and Overton, BE and Ozerskaya, SM and Palani, P and Pancorbo, F and Papp, V and Pawłowska, J and Pham, TQ and Phosri, C and Popov, ES and Portugal, A and Pošta, A and Reschke, K and Reul, M and Ricci, GM and Rodríguez, A and Romanowski, J and Ruchikachorn, N and Saar, I and Safi, A and Sakolrak, B and Salzmann, F and Sandoval-Denis, M and Sangwichein, E and Sanhueza, L and Sato, T and Sastoque, A and Senn-Irlet, B and Shibata, A and Siepe, K and Somrithipol, S and Spetik, M and Sridhar, P and Stchigel, AM and Stuskova, K and Suwannasai, N and Tan, YP and Thangavel, R and Tiago, I and Tiwari, S and Tkalčec, Z and Tomashevskaya, MA and Tonegawa, C and Tran, HX and Tran, NT and Trovão, J and Trubitsyn, VE and Van Wyk, J and Vieira, WAS and Vila, J and Visagie, CM and Vizzini, A and Volobuev, SV and Vu, DT and Wangsawat, N and Yaguchi, T and Ercole, E and Ferreira, BW and de Souza, AP and Vieira, BS and Groenewald, JZ}, title = {Fungal Planet description sheets: 1284-1382.}, journal = {Persoonia}, volume = {47}, number = {}, pages = {178-374}, pmid = {37693795}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antartica, Cladosporium austrolitorale from coastal sea sand. Australia, Austroboletus yourkae on soil, Crepidotus innuopurpureus on dead wood, Curvularia stenotaphri from roots and leaves of Stenotaphrum secundatum and Thecaphora stajsicii from capsules of Oxalis radicosa. Belgium, Paraxerochrysium coryli (incl. Paraxerochrysium gen. nov.) from Corylus avellana. Brazil, Calvatia nordestina on soil, Didymella tabebuiicola from leaf spots on Tabebuia aurea, Fusarium subflagellisporum from hypertrophied floral and vegetative branches of Mangifera indica and Microdochium maculosum from living leaves of Digitaria insularis. Canada, Cuphophyllus bondii from a grassland. Croatia, Mollisia inferiseptata from a rotten Laurus nobilis trunk. Cyprus, Amanita exilis on calcareous soil. Czech Republic, Cytospora hippophaicola from wood of symptomatic Vaccinium corymbosum. Denmark, Lasiosphaeria deviata on pieces of wood and herbaceous debris. Dominican Republic, Calocybella goethei among grass on a lawn. France (Corsica), Inocybe corsica on wet ground. France (French Guiana), Trechispora patawaensis on decayed branch of unknown angiosperm tree and Trechispora subregularis on decayed log of unknown angiosperm tree. Germany, Paramicrothecium sambuci (incl. Paramicrothecium gen. nov.) on dead stems of Sambucus nigra. India, Aureobasidium microtermitis from the gut of a Microtermes sp. termite, Laccaria diospyricola on soil and Phylloporia tamilnadensis on branches of Catunaregam spinosa. Iran, Pythium serotinoosporum from soil under Prunus dulcis. Italy, Pluteus brunneovenosus on twigs of broadleaved trees on the ground. Japan, Heterophoma rehmanniae on leaves of Rehmannia glutinosa f. hueichingensis. Kazakhstan, Murispora kazachstanica from healthy roots of Triticum aestivum. Namibia, Caespitomonium euphorbiae (incl. Caespitomonium gen. nov.) from stems of an Euphorbia sp. Netherlands, Alfaria junci, Myrmecridium junci, Myrmecridium juncicola, Myrmecridium juncigenum, Ophioceras junci, Paradinemasporium junci (incl. Paradinemasporium gen. nov.), Phialoseptomonium junci, Sporidesmiella juncicola, Xenopyricularia junci and Zaanenomyces quadripartis (incl. Zaanenomyces gen. nov.), from dead culms of Juncus effusus, Cylindromonium everniae and Rhodoveronaea everniae from Evernia prunastri, Cyphellophora sambuci and Myrmecridium sambuci from Sambucus nigra, Kiflimonium junci, Sarocladium junci, Zaanenomyces moderatricis-academiae and Zaanenomyces versatilis from dead culms of Juncus inflexus, Microcera physciae from Physcia tenella, Myrmecridium dactylidis from dead culms of Dactylis glomerata, Neochalara spiraeae and Sporidesmium spiraeae from leaves of Spiraea japonica, Neofabraea salicina from Salix sp., Paradissoconium narthecii (incl. Paradissoconium gen. nov.) from dead leaves of Narthecium ossifragum, Polyscytalum vaccinii from Vaccinium myrtillus, Pseudosoloacrosporiella cryptomeriae (incl. Pseudosoloacrosporiella gen. nov.) from leaves of Cryptomeria japonica, Ramularia pararhabdospora from Plantago lanceolata, Sporidesmiella pini from needles of Pinus sylvestris and Xenoacrodontium juglandis (incl. Xenoacrodontium gen. nov. and Xenoacrodontiaceae fam. nov.) from Juglans regia. New Zealand, Cryptometrion metrosideri from twigs of Metrosideros sp., Coccomyces pycnophyllocladi from dead leaves of Phyllocladus alpinus, Hypoderma aliforme from fallen leaves Fuscopora solandri and Hypoderma subiculatum from dead leaves Phormium tenax. Norway, Neodevriesia kalakoutskii from permafrost and Variabilispora viridis from driftwood of Picea abies. Portugal, Entomortierella hereditatis from a biofilm covering a deteriorated limestone wall. Russia, Colpoma junipericola from needles of Juniperus sabina, Entoloma cinnamomeum on soil in grasslands, Entoloma verae on soil in grasslands, Hyphodermella pallidostraminea on a dry dead branch of Actinidia sp., Lepiota sayanensis on litter in a mixed forest, Papiliotrema horticola from Malus communis, Paramacroventuria ribis (incl. Paramacroventuria gen. nov.) from leaves of Ribes aureum and Paramyrothecium lathyri from leaves of Lathyrus tuberosus. South Africa, Harzia combreti from leaf litter of Combretum collinum ssp. sulvense, Penicillium xyleborini from Xyleborinus saxesenii, Phaeoisaria dalbergiae from bark of Dalbergia armata, Protocreopsis euphorbiae from leaf litter of Euphorbia ingens and Roigiella syzygii from twigs of Syzygium chordatum. Spain, Genea zamorana on sandy soil, Gymnopus nigrescens on Scleropodium touretii, Hesperomyces parexochomi on Parexochomus quadriplagiatus, Paraphoma variabilis from dung, Phaeococcomyces kinklidomatophilus from a blackened metal railing of an industrial warehouse and Tuber suaveolens in soil under Quercus faginea. Svalbard and Jan Mayen, Inocybe nivea associated with Salix polaris. Thailand, Biscogniauxia whalleyi on corticated wood. UK, Parasitella quercicola from Quercus robur. USA, Aspergillus arizonicus from indoor air in a hospital, Caeliomyces tampanus (incl. Caeliomyces gen. nov.) from office dust, Cippumomyces mortalis (incl. Cippumomyces gen. nov.) from a tombstone, Cylindrium desperesense from air in a store, Tetracoccosporium pseudoaerium from air sample in house, Toxicocladosporium glendoranum from air in a brick room, Toxicocladosporium losalamitosense from air in a classroom, Valsonectria portsmouthensis from air in men's locker room and Varicosporellopsis americana from sludge in a water reservoir. Vietnam, Entoloma kovalenkoi on rotten wood, Fusarium chuoi inside seed of Musa itinerans, Micropsalliota albofelina on soil in tropical evergreen mixed forests and Phytophthora docyniae from soil and roots of Docynia indica. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Osieck ER, Jurjević Ž, et al. 2021. Fungal Planet description sheets: 1284-1382. Persoonia 47: 178-374. https://doi.org/10.3767/persoonia.2021.47.06.}, }
@article {pmid37692384, year = {2023}, author = {Mermans, F and Mattelin, V and Van den Eeckhoudt, R and García-Timermans, C and Van Landuyt, J and Guo, Y and Taurino, I and Tavernier, F and Kraft, M and Khan, H and Boon, N}, title = {Opportunities in optical and electrical single-cell technologies to study microbial ecosystems.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233705}, pmid = {37692384}, issn = {1664-302X}, abstract = {New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.}, }
@article {pmid37692382, year = {2023}, author = {Amon, CER and Fossou, RK and Ebou, AET and Koua, DK and Kouadjo, CG and Brou, YC and Voko Bi, DRR and Cowan, DA and Zézé, A}, title = {The core bacteriobiome of Côte d'Ivoire soils across three vegetation zones.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1220655}, doi = {10.3389/fmicb.2023.1220655}, pmid = {37692382}, issn = {1664-302X}, abstract = {The growing understanding that soil bacteria play a critical role in ecosystem servicing has led to a number of large-scale biogeographical surveys of soil microbial diversity. However, most of such studies have focused on northern hemisphere regions and little is known of either the detailed structure or function of soil microbiomes of sub-Saharan African countries. In this paper, we report the use of high-throughput amplicon sequencing analyses to investigate the biogeography of soil bacteria in soils of Côte d'Ivoire. 45 surface soil samples were collected from Côte d'Ivoire, representing all major biomes, and bacterial community composition was assessed by targeting the V4-V5 hypervariable region of the 16S ribosomal RNA gene. Causative relationships of both soil physicochemical properties and climatic data on bacterial community structure were infered. 48 phyla, 92 classes, 152 orders, 356 families, and 1,234 genera of bacteria were identified. The core bacteriobiome consisted of 10 genera ranked in the following order of total abundance: Gp6, Gaiella, Spartobacteria_genera_incertae_sedis, WPS-1_genera_incertae_sedis, Gp4, Rhodoplanes, Pseudorhodoplanes, Bradyrhizobium, Subdivision3_genera_incertae_sedis, and Gp3. Some of these genera, including Gp4 and WPS-1_genera_incertae_sedis, were unequally distributed between forest and savannah areas while other taxa (Bradyrhizobium and Rhodoplanes) were consistently found in all biomes. The distribution of the core genera, together with the 10 major phyla, was influenced by several environmental factors, including latitude, pH, Al and K. The main pattern of distribution that was observed for the core bacteriobiome was the vegetation-independent distribution scheme. In terms of predicted functions, all core bacterial taxa were involved in assimilatory sulfate reduction, while atmospheric dinitrogen (N2) reduction was only associated with the genus Bradyrhizobium. This work, which is one of the first such study to be undertaken at this scale in Côte d'Ivoire, provides insights into the distribution of bacterial taxa in Côte d'Ivoire soils, and the findings may serve as biological indicator for land management in Côte d'Ivoire.}, }
@article {pmid37691494, year = {2023}, author = {Mödl, B and Awad, M and Zwolanek, D and Scharf, I and Schwertner, K and Milovanovic, D and Moser, D and Schmidt, K and Pjevac, P and Hausmann, B and Krauß, D and Mohr, T and Svinka, J and Kenner, L and Casanova, E and Timelthaler, G and Sibilia, M and Krieger, S and Eferl, R}, title = {Defects in microvillus crosslinking sensitize to colitis and inflammatory bowel disease.}, journal = {EMBO reports}, volume = {}, number = {}, pages = {e57084}, doi = {10.15252/embr.202357084}, pmid = {37691494}, issn = {1469-3178}, support = {DOC 59-833//Austrian Science Fund (FWF)/ ; P35069-B//Austrian Science Fund (FWF)/ ; P32900-B//Austrian Science Fund (FWF)/ ; P33430//Austrian Science Fund (FWF)/ ; ERC-2015-AdG TNT-Tumors 694883//EC | European Research Council (ERC)/ ; 766214//EC | Horizon 2020 Framework Programme (H2020)/ ; }, abstract = {Intestinal epithelial cells are covered by the brush border, which consists of densely packed microvilli. The Intermicrovillar Adhesion Complex (IMAC) links the microvilli and is required for proper brush border organization. Whether microvillus crosslinking is involved in the intestinal barrier function or colitis is currently unknown. We investigate the role of microvillus crosslinking in colitis in mice with deletion of the IMAC component CDHR5. Electron microscopy shows pronounced brush border defects in CDHR5-deficient mice. The defects result in severe mucosal damage after exposure to the colitis-inducing agent DSS. DSS increases the permeability of the mucus layer and brings bacteria in direct contact with the disorganized brush border of CDHR5-deficient mice. This correlates with bacterial invasion into the epithelial cell layer which precedes epithelial apoptosis and inflammation. Single-cell RNA sequencing data of patients with ulcerative colitis reveals downregulation of CDHR5 in enterocytes of diseased areas. Our results provide experimental evidence that a combination of microvillus crosslinking defects with increased permeability of the mucus layer sensitizes to inflammatory bowel disease.}, }
@article {pmid37690780, year = {2023}, author = {Cantu-Jungles, TM and Hamaker, BR}, title = {Tuning expectations to reality: don't expect increased gut microbiota diversity with dietary fiber.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2023.09.001}, pmid = {37690780}, issn = {1541-6100}, abstract = {Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping the gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.}, }
@article {pmid37689957, year = {2023}, author = {Wang, S and De Paepe, K and Van de Wiele, T and Fu, X and Wang, S and Zhang, B and Huang, Q}, title = {Starch-entrapped microspheres enhance gut microbiome-mediated anti-obesity effects of resistant starch in high-fat diet induced obese C57BL/6J mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113215}, doi = {10.1016/j.foodres.2023.113215}, pmid = {37689957}, issn = {1873-7145}, mesh = {Animals ; Mice ; Mice, Inbred C57BL ; *Resistant Starch ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Dysbiosis ; Microspheres ; Obesity ; Starch/pharmacology ; Amylose ; }, abstract = {The prevalence of obesity is growing worldwide and has been extensively linked to gut microbiota dysbiosis. In addition to exercise and physical activity, fiber-rich foods may be a first-line prophylactic to manage obesity. This study investigated in vivo dietary intervention with high-amylose maize starch (HAMS) and starch-entrapped microspheres (MS) to treat high-fat diet induced metabolic disorder and gut microbiome dysbiosis in mice. MS more efficiently controlled body weight as well as adipose tissue mass compared to HAMS. Furthermore, MS significantly reduced blood glucose, insulin, lipid and pro-inflammatory cytokine levels compared to the high-fat diet, while the effects of HAMS were less pronounced. The MS-altered gut microbiota composition favoring Streptococcaceae, Bacilli, Firmicutes and unclassified Clostridiales was predicted to promote fatty acid, pantothenate and Coenzyme A biosynthesis. In line with this, elevated fecal short chain fatty acid (SCFA), in particular, propionate concentration was observed in MS-fed mice. Our study provides novel insights into the mechanistic action of MS on intestinal homeostasis, providing a basis for future dietary therapeutic applications.}, }
@article {pmid37688636, year = {2023}, author = {Garrido, AG and Machado, LF and Pereira, CM and Abrantes, DP and Calderon, EN and Zilberberg, C}, title = {Marine Heatwave Caused Differentiated Dysbiosis in Photosymbiont Assemblages of Corals and Hydrocorals During El Niño 2015/2016.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37688636}, issn = {1432-184X}, abstract = {Reef corals have been threatened by climate change, with more frequent and intense bleaching events leading to extensive coral mortality and loss of coral cover worldwide. In the face of this, the corals' photosymbiont assemblages have received special attention as a key to better understand the bleaching process and its recovery. To assess the effects of thermal anomalies, the coral Mussismilia harttii and the hydrocoral Millepora alcicornis were monitored through the El Niño 2015/2016 at a Southwestern Atlantic (SWA) coral reef. A severe bleaching event (57% of colonies bleached) was documented, triggered by a < 3 °C-week heatwave, but no mortality was detected. The hydrocoral was more susceptible than the scleractinian, displaying bleaching symptoms earlier and experiencing a longer and more intense bleaching event. The composition of photosymbionts in the M. alcicornis population was affected only at the rare biosphere level (< 5% relative abundance), with the emergence of new symbionts after bleaching. Conversely, a temporary dysbiosis was observed in the M. harttii population, with one of the dominant symbiodiniaceans decreasing in relative abundance at the peak of the bleaching, which negatively affected the total β-diversity. After colonies' complete recovery, symbiodiniaceans' dominances returned to normal levels in both hosts. These results highlight critical differences in how the two coral species cope with bleaching and contribute to the understanding of the role of photosymbionts throughout the bleaching-recovery process.}, }
@article {pmid37687396, year = {2023}, author = {Galinytė, D and Balčiūnaitė-Murzienė, G and Karosienė, J and Morudov, D and Naginienė, R and Baranauskienė, D and Šulinskienė, J and Kudlinskienė, I and Savickas, A and Savickienė, N}, title = {Determination of Heavy Metal Content: Arsenic, Cadmium, Mercury, and Lead in Cyano-Phycocyanin Isolated from the Cyanobacterial Biomass.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {17}, pages = {}, pmid = {37687396}, issn = {2223-7747}, abstract = {Cyano-phycocyanin (C-PC) is a light-absorbing biliprotein found in cyanobacteria, commonly known as blue-green algae. Due to its antioxidative, anti-inflammatory, and anticancer properties, this protein is a promising substance in medicine and pharmaceuticals. However, cyanobacteria tend to bind heavy metals from the environment, making it necessary to ensure the safety of C-PC for the development of pharmaceutical products, with C-PC isolated from naturally collected cyanobacterial biomass. This study aimed to determine the content of the most toxic heavy metals, arsenic (As), cadmium (Cd), mercury (Hg), and lead (Pb) in C-PC isolated from different cyanobacterial biomasses collected in the Kaunas Lagoon during 2019-2022, and compare them with the content of heavy metals in C-PC isolated from cultivated Spirulina platensis (S. platensis). Cyanobacteria of Aphanizomenon flos-aquae (A. flos-aquae) dominated the biomass collected in 2019, while the genus Microcystis dominated the biomasses collected in the years 2020 and 2022. Heavy metals were determined using inductively coupled plasma mass spectrometry (ICP-MS). ICP-MS analysis revealed higher levels of the most investigated heavy metals (Pb, Cd, and As) in C-PC isolated from the biomass with the dominant Microcystis spp. compared to C-PC isolated from the biomass with the predominant A. flos-aquae. Meanwhile, C-PC isolated from cultivated S. platensis exhibited lower concentrations of As and Pb than C-PC isolated from naturally collected cyanobacterial biomass.}, }
@article {pmid37687181, year = {2023}, author = {Tom, A and Jacob, J and Mathews, M and Rajagopal, R and Alfarhan, A and Barcelo, D and Narayanankutty, A}, title = {Synthesis of Bis-Chalcones and Evaluation of Its Effect on Peroxide-Induced Cell Death and Lipopolysaccharide-Induced Cytokine Production.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {17}, pages = {}, doi = {10.3390/molecules28176354}, pmid = {37687181}, issn = {1420-3049}, abstract = {Plant secondary metabolites are important sources of biologically active compounds with wide pharmacological potentials. Among the different classes, the chalcones form integral pharmacologically active agents. Natural chalcones and bis-chalcones exhibit high antioxidant and anti-inflammatory properties in various experiments. Studies are also underway to explore more biologically active bis-chalcones by chemical synthesis of these compounds. In this study, the effects of six synthetic bis-chalcones were evaluated in intestinal epithelial cells (IEC-6); further, the anti-inflammatory potentials were studied in lipopolysaccharide-induced cytokine production in macrophages. The synthesized bis-chalcones differ from each other first of all by the nature of the aromatic cores (functional group substitution, and their position) and by the size of a central alicycle. The exposure of IEC-6 cells to peroxide radicals reduced the cell viability; however, pre-treatment with the bis-chalcones improved the cell viability in these cells. The mechanism of action was observed to be the increased levels of glutathione and antioxidant enzyme activities. Further, these bis-chalcones also inhibited the LPS-stimulation-induced inflammatory cytokine production in RAW 264.7 macrophages. Overall, the present study indicated the cytoprotective and anti-inflammatory abilities of synthetic bis-chalcones.}, }
@article {pmid37684546, year = {2023}, author = {Liu, N and Huang, Z and Fang, Y and Dong, Z}, title = {Impacts of Thermal Drainage on Bacterial Diversity and Community Construction in Tianwan Nuclear Power Plant.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37684546}, issn = {1432-184X}, abstract = {As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes.}, }
@article {pmid37684545, year = {2023}, author = {Huang, R and Tang, C and Zhao, Y and Liu, L and Chen, J and Shi, Z and Yan, Z}, title = {Unveiling the Biochar-Respiratory Growth of Methanosarcina acetivorans Involving Extracellular Polymeric Substances.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37684545}, issn = {1432-184X}, support = {22008142//National Natural Science Foundation of China/ ; ZR2022YQ31//Natural Science Foundation of Shandong Province/ ; BK20200232//Natural Science Foundation of Jiangsu Province/ ; Qilu Youth Talent Program//Shandong University/ ; }, abstract = {Biochar can be applied to diverse natural and engineered anaerobic systems. Biochar plays biogeochemical roles during its production, storage, and environmental dynamics, one of which is related to the global methane flux governed by methanotrophs and methanogens. Our understanding of relevant mechanisms is currently limited to the roles of biochar in methanotrophic growth, but less is known about the roles of biochar in methanogenic growth. Here, we demonstrated that biochar enhanced the methanogenic growth of a model methanogen, Methanosarcina acetivorans, and the role of biochar as an electron acceptor during methanogenic growth was confirmed, which is referred to as biochar-respiratory growth. The biochar-respiratory growth of M. acetivorans promoted the secretion of extracellular polymeric substances (EPS) with augmented electron transfer capabilities, and the removal of EPS significantly attenuated extracellular electron transfer. Identification and quantification of prosthetic cofactors for EPS suggest an important role of flavin and F420 in extracellular electron transfer. Transcriptomic analysis provided additional insights into the biochar-respiratory growth of M. acetivorans, showing that there was a positive response in transcriptional regulation to the favorable growth environment provided by biochar, which stimulated global methanogenesis. Our results shed more light on the in situ roles of biochar in the ecophysiology of methanogens in diverse anaerobic environments.}, }
@article {pmid37682693, year = {2023}, author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Withall, DM and Wäckers, F and Birkett, MA and Jacquemyn, H and Lievens, B}, title = {Effects of root inoculation of entomopathogenic fungi on olfactory-mediated behavior and life history traits of the parasitoid Aphidius ervi (Haliday) (Hymenoptera: Braconidae).}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.7762}, pmid = {37682693}, issn = {1526-4998}, abstract = {BACKGROUND: Although most biological control programs use multiple biological agents to manage pest species, to date only a few programs have combined the use of agents from different guilds. Using sweet pepper (Capsicum annuum L.), the entomopathogenic fungus Akanthomyces muscarius ARSEF 5128, the tobacco peach aphid Myzus persicae var. nicotianae and the aphid parasitoid Aphidius ervi as the experimental model, we explored whether root inoculation with an entomopathogenic fungus is compatible with parasitoid wasps for enhanced biocontrol of aphids.<br><br>RESULTS: In dual-choice behavior experiments, A. ervi was significantly attracted to the odor of M. persicae-infested C. annuum plants that had been inoculated with A. muscarius, compared to non-inoculated infested plants. There was no significant difference in attraction to the odor of uninfested plants. Myzus persicae-infested plants inoculated with A. muscarius emitted significantly higher amounts of indole, (E)-nerolidol, (3E,7E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene (TMTT) and one unidentified terpene compared to non-inoculated infested plants. Coupled gas chromatography-electroantennography (GC-EAG), using the antennae of A. ervi, confirmed physiological activity of these elevated compounds. Inoculation of plants with A. muscarius did not affect parasitism rate nor parasitoid longevity, but significantly increased the speed of mummy formation in parasitized aphids on fungus-inoculated plants.<br><br>CONCLUSION: Our data suggest that root inoculation of C. annuum with A. muscarius ARSEF 5128 alters the olfactory-mediated behavior of parasitoids, but has little effect on parasitism efficiency or life history parameters. However, increased attraction of parasitoids towards M. persicae-infested plants when inoculated by entomopathogenic fungi can accelerate host localization and hence improve biocontrol efficacy. This article is protected by copyright. All rights reserved.}, }
@article {pmid37680522, year = {2023}, author = {You, Y and Zhang, W and Cai, M and Guo, Q and Wang, J and Cai, Y and Lin, J}, title = {Discovery of fecal microbial signatures in patients with ankylosing spondylitis.}, journal = {Archives of rheumatology}, volume = {38}, number = {2}, pages = {217-229}, pmid = {37680522}, issn = {2618-6500}, abstract = {OBJECTIVES: This study aimed to investigate the characteristics of the gut microbiota in Chinese patients with ankylosing spondylitis (AS) and healthy controls in Quanzhou aiming to explore the correlation between microbiome changes and AS activities.<br><br>PATIENTS AND METHODS: In this study, high-throughput sequencing of the gene of 16S ribosomal RNA (16S rRNA) in fecal samples from 40 AS patients and 40 healthy controls, for a total of 80 participants (70 males, 10 females; mean age 33.7&#xb1;10.7 years; range, 15 to 58 years), was conducted between January 2018 and January 2019. Alpha and beta diversity were analyzed using the QIIME (Quantitative Insights Into Microbial Ecology) software, and differences were analyzed using Student's t-test, linear discriminant analysis coupled with effect size and Metastats. Finally, a correlation network was constructed using Pearson's analysis.<br><br>RESULTS: The alpha index values of the AS group were not significantly different from those of the control group. At the genus level, eight genera, Ruminiclostridium_9, Fusicatenibacter, Adlercreutzia, CAG-56, Intestinimonas, Lachnospira, Bacteroides, and Pseudoflavonifractor, were significantly enriched in patients with AS, whereas the abundance of uncultured_bacterium_f_Saccharimonadaceae, Prevotella_7, uncultured_bacterium_f_ Enterobacteriaceae, Cronobacter, Prevotellaceae_NK3B31_group, and Weissella were significantly decreased in patients with AS. In addition, diseaserelated gut microbial communities were detected in patients with AS.<br><br>CONCLUSION: We found differences in the gut microbiome between the patients with AS and controls and identified potential disease activity-related bacterial communities.}, }
@article {pmid37676325, year = {2023}, author = {Sun, P and Wang, M and Zheng, W and Li, S and Zhu, X and Chai, X and Zhao, S}, title = {Unbalanced diets enhance the complexity of gut microbial network but destabilize its stability and resistance.}, journal = {Stress biology}, volume = {3}, number = {1}, pages = {20}, pmid = {37676325}, issn = {2731-0450}, abstract = {Stability is a fundamental ecological property of the gut microbiota and is associated with host health. Numerous studies have shown that unbalanced dietary components disturb the gut microbial composition and thereby contribute to the onset and progression of disease. However, the impact of unbalanced diets on the stability of the gut microbiota is poorly understood. In the present study, four-week-old mice were fed a plant-based diet high in refined carbohydrates or a high-fat diet for four weeks to simulate a persistent unbalanced diet. We found that persistent unbalanced diets significantly reduced the gut bacterial richness and increased the complexity of bacterial co-occurrence networks. Furthermore, the gut bacterial response to unbalanced diets was phylogenetically conserved, which reduced network modularity and enhanced the proportion of positive associations between community taxon, thereby amplifying the co-oscillation of perturbations among community species to destabilize gut microbial communities. The disturbance test revealed that the gut microbiota of mice fed with unbalanced diets was less resistant to antibiotic perturbation and pathogenic bacteria invasion. This study may fill a gap in the mechanistic understanding of the gut microbiota stability in response to diet and provide new insights into the gut microbial ecology.}, }
@article {pmid37676037, year = {2023}, author = {Danevčič, T and Spacapan, M and Dragoš, A and Kovács, &#xc1;T and Mandic-Mulec, I}, title = {DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0090823}, doi = {10.1128/spectrum.00908-23}, pmid = {37676037}, issn = {2165-0497}, abstract = {Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.}, }
@article {pmid37675430, year = {2023}, author = {Edwards, J and Hoffbeck, C and West, AG and Pas, A and Taylor, MW}, title = {16S rRNA gene-based microbiota profiles from diverse avian faeces are largely independent of DNA preservation and extraction method.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1239167}, pmid = {37675430}, issn = {1664-302X}, abstract = {The avian gut microbiota has been the subject of considerable recent attention, with potential implications for diverse fields such as the poultry industry, microbial ecology, and conservation. Faecal microbiotas are frequently used as a non-invasive proxy for the gut microbiota, however the extraction of high-quality microbial DNA from avian faeces has often proven challenging. Here we aimed to evaluate the performance of two DNA preservation methods (95% ethanol and RNAlater) and five extraction approaches (IndiSpin Pathogen Kit, QIAamp PowerFecal Pro DNA Kit, MicroGEM PrepGEM Bacteria Kit, ZymoBIOMICS DNA Miniprep Kit, and an in-house phase separation-based method) for studying the avian gut microbiota. Systematic testing of the efficacy of these approaches on faecal samples from an initial three avian species (chicken, ostrich, and the flightless parrot kākāpō) revealed substantial differences in the quality, quantity and integrity of extracted DNA, but negligible influence of applied method on 16S rRNA gene-based microbiota profiles. Subsequent testing with a selected combination of preservation and extraction method on 10 further phylogenetically and ecologically diverse avian species reiterated the efficacy of the chosen approach, with bacterial community structure clustering strongly by technical replicates for a given avian species. Our finding that marked differences in extraction efficacy do not appear to influence 16S rRNA gene-based bacterial community profiles provides an important foundation for ongoing research on the avian gut microbiota.}, }
@article {pmid37674014, year = {2023}, author = {Cornish, CM and Bergholz, P and Schmidt, K and Sweetman, J}, title = {How Benthic Sediment Microbial Communities Respond to Glyphosate and Its Metabolite: a Microcosm Experiment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37674014}, issn = {1432-184X}, abstract = {Glyphosate is the most commonly used agricultural herbicide in the world. In aquatic ecosystems, glyphosate often adsorbs to benthic substrates or is metabolized and degraded by microorganisms. The effects of glyphosate on microbial communities vary widely as microorganisms respond differently to exposure. To help understand the impacts of glyphosate on the sediment microbiome, we conducted a microcosm experiment examining the responses of benthic sediment microbial communities to herbicide treatments. Sediments from a prairie pothole wetland were collected, and 16S rRNA gene sequencing was used to analyze community composition 2-h and 14-days after a single treatment of low (0.07 ppm), medium (0.7 ppm), or high (7 ppm) glyphosate, aminomethylphosphonic acid (glyphosate metabolite), or a glyphosate-based commercial formula. We found no significant differences in microbial community composition across treatments, concentration levels, or day of sampling. These findings suggest that microbial species in the Prairie Pothole Region of North America may be tolerant to glyphosate exposure.}, }
@article {pmid37671861, year = {2023}, author = {Roller, BRK and Hellerschmied, C and Wu, Y and Miettinen, TP and Gomez, AL and Manalis, SR and Polz, MF}, title = {Single-cell mass distributions reveal simple rules for achieving steady-state growth.}, journal = {mBio}, volume = {}, number = {}, pages = {e0158523}, doi = {10.1128/mbio.01585-23}, pmid = {37671861}, issn = {2150-7511}, abstract = {Optical density is a proxy of total biomass concentration and is commonly used for measuring the growth of bacterial cultures. However, there is a misconception that exponential optical density growth is equivalent to steady-state population growth. Many cells comprise a culture and individuals can differ from one another. Hallmarks of steady-state population growth are stable frequency distributions of cellular properties over time, something total biomass growth alone cannot quantify. Using single-cell mass sensors paired with optical density measurements, we explore when steady-state population growth prevails in typical batch cultures. We find the average cell mass of Escherichia coli and Vibrio cyclitrophicus growing in several media increases by 0.5-1 orders of magnitude within a few hours of inoculation, and that time-invariant mass distributions are only achieved for short periods when cultures are inoculated with low initial biomass concentrations from overnight cultures. These species achieve an effective steady-state after approximately 2.5-4 total biomass doublings in rich media, which can be decomposed to 1 doubling of cell number and 1.5-3 doublings of average cell mass. We also show that typical batch cultures in rich media depart steady-state early in their growth curves at low cell and biomass concentrations. Achieving steady-state population growth in batch culture is a delicate balancing act, so we provide general guidance for commonly used rich media. Quantifying single-cell mass outside of steady-state population growth is an important first step toward understanding how microbes grow in their natural context, where fluctuations pervade at the scale of individuals. IMPORTANCE Microbiologists have watched clear liquid turn cloudy for over 100 years. While the cloudiness of a culture is proportional to its total biomass, growth rates from optical density measurements are challenging to interpret when cells change size. Many bacteria adjust their size at different steady-state growth rates, but also when shifting between starvation and growth. Optical density cannot disentangle how mass is distributed among cells. Here, we use single-cell mass measurements to demonstrate that a population of cells in batch culture achieves a stable mass distribution for only a short period of time. Achieving steady-state growth in rich medium requires low initial biomass concentrations and enough time for individual cell mass accumulation and cell number increase via cell division to balance out. Steady-state growth is important for reliable cell mass distributions and experimental reproducibility. We discuss how mass variation outside of steady-state can impact physiology, ecology, and evolution experiments.}, }
@article {pmid37669892, year = {2023}, author = {Hellal, J and Barthelmebs, L and Bérard, A and Cébron, A and Cheloni, G and Colas, S and Cravo-Laureau, C and De Clerck, C and Gallois, N and Hery, M and Martin-Laurent, F and Martins, J and Morin, S and Palacios, C and Pesce, S and Richaume, A and Vuilleumier, S}, title = {Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad102}, pmid = {37669892}, issn = {1574-6941}, abstract = {Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment and also play key roles in the fate of pollutants through the degradation, transformation and transfer of organic or inorganic compounds. They are thus crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.}, }
@article {pmid37668400, year = {2023}, author = {Du, H and Pan, J and Zhang, C and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and Qu, W and Jiang, C and Tian, Y and He, Z and Liu, Y and Li, M}, title = {Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0157723}, doi = {10.1128/spectrum.01577-23}, pmid = {37668400}, issn = {2165-0497}, abstract = {As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.}, }
@article {pmid37668159, year = {2023}, author = {Van den Eeckhoudt, R and Christiaens, AS and Ceyssens, F and Vangalis, V and Verstrepen, KJ and Boon, N and Tavernier, F and Kraft, M and Taurino, I}, title = {Full-electric microfluidic platform to capture, analyze and selectively release single cells.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3lc00645j}, pmid = {37668159}, issn = {1473-0189}, abstract = {Current single-cell technologies require large and expensive equipment, limiting their use to specialized labs. In this paper, we present for the first time a microfluidic device which demonstrates a combined method for full-electric cell capturing, analyzing, and selectively releasing with single-cell resolution. All functionalities are experimentally demonstrated on Saccharomyces cerevisiae. Our microfluidic platform consists of traps centered around a pair of individually accessible coplanar electrodes, positioned under a microfluidic channel. Using this device, we validate our novel Two-Voltage method for trapping single cells by positive dielectrophoresis (pDEP). Cells are attracted to the trap when a high voltage (VH) is applied. A low voltage (VL) holds the already trapped cell in place without attracting additional cells, allowing full control over the number of trapped cells. After trapping, the cells are analyzed by broadband electrochemical impedance spectroscopy. These measurements allow the detection of single cells and the extraction of cell parameters. Additionally, these measurements show a strong correlation between average phase change and cell size, enabling the use of our system for size measurements in biological applications. Finally, our device allows selectively releasing trapped cells by turning off the pDEP signal in their trap. The experimental results show the techniques potential as a full-electric single-cell analysis tool with potential for miniaturization and automation which opens new avenues towards small-scale, high throughput single-cell analysis and sorting lab-on-CMOS devices.}, }
@article {pmid37667323, year = {2023}, author = {Rodríguez-Pastor, R and Hasik, AZ and Knossow, N and Bar-Shira, E and Shahar, N and Gutiérrez, R and Zaman, L and Harrus, S and Lenski, RE and Barrick, JE and Hawlena, H}, title = {Bartonella infections are prevalent in rodents despite efficient immune responses.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {315}, pmid = {37667323}, issn = {1756-3305}, support = {DEB-1813069//National Science Foundation/ ; 1391/15//Israel Science Foundation/ ; }, mesh = {Animals ; *Bartonella Infections/epidemiology/veterinary ; *Bartonella ; Immunoglobulin G ; Kinetics ; Immunity ; }, abstract = {BACKGROUND: Pathogens face strong selection from host immune responses, yet many host populations support pervasive pathogen populations. We investigated this puzzle in a model system of Bartonella and rodents from Israel's northwestern Negev Desert. We chose to study this system because, in this region, 75-100% of rodents are infected with Bartonella at any given time, despite an efficient immunological response. In this region, Bartonella species circulate in three rodent species, and we tested the hypothesis that at least one of these hosts exhibits a waning immune response to Bartonella, which allows reinfections.<br><br>METHODS: We inoculated captive animals of all three rodent species with the same Bartonella strain, and we quantified the bacterial dynamics and Bartonella-specific immunoglobulin G antibody kinetics over a period of 139&#xa0;days after the primary inoculation, and then for 60&#xa0;days following reinoculation with the same strain.<br><br>RESULTS: Contrary to our hypothesis, we found a strong, long-lasting immunoglobulin G antibody response, with protective immunological memory in all three rodent species. That response prevented reinfection upon exposure of the rodents to the same Bartonella strain.<br><br>CONCLUSIONS: This study constitutes an initial step toward understanding how the interplay between traits of Bartonella and their hosts influences the epidemiological dynamics of these pathogens in nature.}, }
@article {pmid37667132, year = {2023}, author = {Lv, H and Li, X and He, D and Chen, X and Liu, M and Lan, Y and Zhao, J and Wang, H and Yan, Z}, title = {Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37667132}, issn = {1432-184X}, abstract = {The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.}, }
@article {pmid37666974, year = {2023}, author = {Lin, Q and Li, L and De Vrieze, J and Li, C and Fang, X and Li, X}, title = {Functional conservation of microbial communities determines composition predictability in anaerobic digestion.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37666974}, issn = {1751-7370}, abstract = {A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH4 production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.}, }
@article {pmid37664629, year = {2023}, author = {Simon, LM and Flocco, C and Burkart, F and Methner, A and Henke, D and Rauer, L and Müller, CL and Vogel, J and Quaisser, C and Overmann, J and Simon, S}, title = {Microbial fingerprints reveal interaction between museum objects, curators, and visitors.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107578}, pmid = {37664629}, issn = {2589-0042}, abstract = {Microbial communities reside at the interface between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To investigate this, we selected objects from the Museum für Naturkunde and the Pergamonmuseum in Berlin, Germany, varying in material and size. Using swabs, we collected 126 samples from natural and cultural heritage objects, which were analyzed through 16S rRNA sequencing. By comparing the microbial composition of touched and untouched objects, we identified a microbial signature associated with human skin microbes. Applying this signature to cultural heritage objects, we identified areas with varying degrees of exposure to human contact on the Ishtar gate and Sam'al gate lions. Furthermore, we differentiated objects touched by two different individuals. Our findings demonstrate that the microbiome of museum objects provides insights into the level of human contact, crucial for conservation, heritage science, and potentially provenance research.}, }
@article {pmid37217203, year = {2023}, author = {Dundore-Arias, JP and Michalska-Smith, M and Millican, M and Kinkel, LL}, title = {More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes.}, journal = {Annual review of phytopathology}, volume = {61}, number = {}, pages = {403-423}, doi = {10.1146/annurev-phyto-021021-041457}, pmid = {37217203}, issn = {1545-2107}, abstract = {Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.}, }
@article {pmid37662195, year = {2023}, author = {Hoang, DQ and Wilson, LR and Scheftgen, AJ and Suen, G and Currie, CR}, title = {Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.25.554838}, pmid = {37662195}, abstract = {UNLABELLED: Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio , Lacunisphaera , and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37-3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.<br><br>ABSTRACT IMPORTANCE: A generalizable diversity-disturbance relationship (DDR) of microbial communities remains a contentious topic. Various microbial systems have different DDRs. Rather than finding support or refuting specific DDRs, we investigated the underlying factors that lead to different DDRs. In this study, we measured a cellulose-enriched microbial community's response to a range of disturbance frequencies from high to low, across two different substrates: cellulose and glucose. We demonstrate that the community displays a unimodal DDR when grown on cellulose, and a monotonically increasing DDR when grown on glucose. Our findings suggest that the same community can display different DDRs. These results suggest that the range of DDRs we observe across different microbial systems may be due to the nutritional resources microbial communities can access and the interactions between bacteria and their environment.}, }
@article {pmid37658881, year = {2023}, author = {Owashi, Y and Minami, T and Kikuchi, T and Yoshida, A and Nakano, R and Kageyama, D and Adachi-Hagimori, T}, title = {Microbiome of Zoophytophagous Biological Control Agent Nesidiocoris tenuis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37658881}, issn = {1432-184X}, abstract = {Many insects are associated with endosymbionts that influence the feeding, reproduction, and distribution of their hosts. Although the small green mirid, Nesidiocoris tenuis (Reuter) (Hemiptera: Miridae), a zoophytophagous predator that feeds on plants as well as arthropods, is a globally important biological control agent, its microbiome has not been sufficiently studied. In the present study, we assessed the microbiome variation in 96 N. tenuis individuals from 14 locations throughout Japan, based on amplicon sequencing of the 16S ribosomal RNA gene. Nine major bacteria associated with N. tenuis were identified: Rickettsia, two strains of Wolbachia, Spiroplasma, Providencia, Serratia, Pseudochrobactrum, Lactococcus, and Stenotrophomonas. Additionally, a diagnostic PCR analysis for three typical insect reproductive manipulators, Rickettsia, Wolbachia, and Spiroplasma, was performed on a larger sample size (n = 360) of N. tenuis individuals; the most prevalent symbiont was Rickettsia (69.7%), followed by Wolbachia (39.2%) and Spiroplasma (6.1%). Although some symbionts were co-infected, their prevalence did not exhibit any specific tendency, such as a high frequency in specific infection combinations. The infection frequency of Rickettsia was significantly correlated with latitude and temperature, while that of Wolbachia and Spiroplasma was significantly correlated with host plants. The predominance of these bacteria and the absence of obligate symbionts suggested that the N. tenuis microbiome is typical for predatory arthropods rather than sap-feeding insects. Rickettsia and Wolbachia were vertically transmitted rather than horizontally transmitted from the prey. The functional validation of each symbiont would be warranted to develop N. tenuis as a biological control agent.}, }
@article {pmid37659544, year = {2023}, author = {Kazmi, SSUH and Saqib, HSA and Pastorino, P and Grossart, HP and Yaseen, ZM and Abualreesh, MH and Liu, W and Wang, Z}, title = {Influence of the antibiotic nitrofurazone on community dynamics of marine periphytic ciliates: Evidence from community-based bioassays.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166687}, doi = {10.1016/j.scitotenv.2023.166687}, pmid = {37659544}, issn = {1879-1026}, abstract = {Marine periphytic ciliates play a pivotal role in shaping coastal ecosystems dynamics, thereby acting as robust biological indicators of aquatic ecosystem health and functionality. However, the understanding of the effects of veterinary antibiotics on composition and structure of periphytic ciliate communities remains limited. Therefore, this research investigates the influence of the veterinary antibiotic nitrofurazone on the community dynamics of marine periphytic ciliates through bioassay experiments conducted over a one-year cycle. Various concentrations of nitrofurazone were administered to the tested ciliate assemblages, and subsequent changes in community composition, abundance, and diversity were quantitatively analyzed. The research revealed significant alterations in periphytic ciliate communities following exposure to nitrofurazone. Concentration-dependent (0-8 mg L[-1]) decrease in ciliates abundance, accompanied by shifts in species composition, community structure, and community patterns were observed. Comprehensive assessment of diversity metrics indicated significant changes in species richness and evenness in the presence of nitrofurazone, potentially disrupting the stability of ciliate communities. Furthermore, nitrofurazone significantly influenced the community structure of ciliates in all seasons (winter: R[2] = 0.489; spring: R[2] = 0.666; summer: R[2] = 0.700, autumn: R[2] = 0.450), with high toxic potential in treatments 4 and 8 mg L[-1]. Differential abundances of ciliates varied across seasons and nitrofurazone treatments, some orders like Pleurostomatida were consistently affected, while others (i.e., Strombidida and Philasterida) showed irregular distributions or were evenly affected (e.g., Urostylida and Synhymeniida). Retrieved contrasting patterns between nitrofurazone and community responses underscore the broad response repertoire exhibited by ciliates to antibiotic exposure, suggesting potential cascading effects on associated ecological processes in the periphyton community. These findings significantly enhance the understanding of the ecological impacts of nitrofurazone on marine periphytic ciliate communities, emphasizing the imperative for vigilant monitoring and regulation of veterinary antibiotics to protect marine ecosystem health and biodiversity. Further research is required to explore the long-term effects of nitrofurazone exposure and evaluate potential strategies to reduce the ecological repercussions of antibiotics in aquatic environments, with a particular focus on nitrofurazone.}, }
@article {pmid37659520, year = {2023}, author = {Schulz, G and van Beusekom, JEE and Jacob, J and Bold, S and Schöl, A and Ankele, M and Sanders, T and Dähnke, K}, title = {Low discharge intensifies nitrogen retention in rivers - A case study in the Elbe River.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166740}, doi = {10.1016/j.scitotenv.2023.166740}, pmid = {37659520}, issn = {1879-1026}, abstract = {Eutrophication due to excessive nutrient inputs is a major threat to coastal ecosystems worldwide, causing harmful algae blooms, seagrass loss and hypoxia. Decisions to combat eutrophication in the North Sea were made in the 1980s. Despite significant improvements during recent decades, high nitrogen loads and resulting eutrophication problems remain. In this study, long-term changes in nitrogen inputs to the Elbe Estuary (Germany) were characterized based on nitrogen data provided by the Elbe River Basin Community from 1985 to 2019. Additionally, surface water samples were taken at the weir separating the river from the estuary from 2011 to 2021 to characterize dissolved inorganic nitrogen concentrations and nitrate stable isotope composition. The findings suggest a close coupling of river discharge with the riverine nitrogen cycle. Nitrogen loads decreased disproportionately with decreasing discharge. This decrease is due to intensified nitrogen retention in the Elbe catchment, which can double nitrogen retention compared to average discharge conditions. Phytoplankton growth was enhanced by long residence times and high light availability at low water levels. This suggests that the recent decreases in nitrogen loads in the Elbe River were not only a result of management measures in the catchment but were also amplified by a recent long-lasting drought in the catchment. Based on projections from the Intergovernmental Panel on Climate Change, more frequent and extensive droughts are anticipated, which may lead to future seasonal shifts to nitrate limitation in the lower Elbe River.}, }
@article {pmid37658593, year = {2023}, author = {Ahmmed, MK and Bhowmik, S and Ahmmed, F and Giteru, SG and Islam, SS and Hachem, M and Hussain, MA and Kanwugu, ON and Agyei, D and Defoirdt, T}, title = {Utilisation of probiotics for disease management in giant freshwater prawn (Macrobrachium rosenbergii): Administration methods, antagonistic effects and immune response.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfd.13850}, pmid = {37658593}, issn = {1365-2761}, support = {//Bijzonder Onderzoeksfonds UGent/ ; //University of Otago/ ; //Ural Federal University/ ; }, abstract = {The giant freshwater prawn (Macrobrachium rosenbergii) is a high-yielding prawn variety well-received worldwide due to its ability to adapt to freshwater culture systems. Macrobrachium rosenbergii is an alternative to shrimp typically obtained from marine and brackish aquaculture systems. However, the use of intensive culture systems can lead to disease outbreaks, particularly in larval and post-larval stages, caused by pathogenic agents such as viruses, bacteria, fungi, yeasts and protozoans. White tail disease (viral), white spot syndrome (viral) and bacterial necrosis are examples of economically significant diseases. Given the increasing antibiotic resistance of disease-causing microorganisms, probiotics have emerged as promising alternatives for disease control. Probiotics are live active microbes that are introduced into a target host in an adequate number or dose to promote its health. In the present paper, we first discuss the diseases that occur in M. rosenbergii production, followed by an in-depth discussion on probiotics. We elaborate on the common methods of probiotics administration and explain the beneficial health effects of probiotics as immunity enhancers. Moreover, we discuss the antagonistic effects of probiotics on pathogenic microorganisms. Altogether, this paper provides a comprehensive overview of disease control in M. rosenbergii aquaculture through the use of probiotics, which could enhance the sustainability of prawn culture.}, }
@article {pmid37657296, year = {2023}, author = {Fu, S and Zhang, Y and Wang, R and Qiu, Z and Song, W and Yang, Q and Shen, L}, title = {A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118737}, doi = {10.1016/j.jenvman.2023.118737}, pmid = {37657296}, issn = {1095-8630}, abstract = {Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.}, }
@article {pmid37656873, year = {2023}, author = {Cantoran, A and Maillard, F and Baldrian, P and Kennedy, PG}, title = {Defining a core microbial necrobiome associated with decomposing fungal necromass.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad098}, pmid = {37656873}, issn = {1574-6941}, abstract = {Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.}, }
@article {pmid37656196, year = {2023}, author = {Fagre, AC and Islam, A and Reeves, WK and Kading, RC and Plowright, RK and Gurley, ES and McKee, CD}, title = {Bartonella Infection in Fruit Bats and Bat Flies, Bangladesh.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37656196}, issn = {1432-184X}, abstract = {Bats harbor diverse intracellular Bartonella bacteria, but there is limited understanding of the factors that influence transmission over time. Investigation of Bartonella dynamics in bats could reveal general factors that control transmission of multiple bat-borne pathogens, including viruses. We used molecular methods to detect Bartonella DNA in paired bat (Pteropus medius) blood and bat flies in the family Nycteribiidae collected from a roost in Faridpur, Bangladesh between September 2020 and January 2021. We detected high prevalence of Bartonella DNA in bat blood (35/55, 64%) and bat flies (59/60, 98%), with sequences grouping into three phylogenetic clades. Prevalence in bat blood increased over the study period (33% to 90%), reflecting an influx of juvenile bats in the population and an increase in the prevalence of bat flies. Discordance between infection status and the clade/genotype of detected Bartonella was also observed in pairs of bats and their flies, providing evidence that bat flies take blood meals from multiple bat hosts. This evidence of bat fly transfer between hosts and the changes in Bartonella prevalence during a period of increasing nycteribiid density support the role of bat flies as vectors of bartonellae. The study provides novel information on comparative prevalence and genetic diversity of Bartonella in pteropodid bats and their ectoparasites, as well as demographic factors that affect Bartonella transmission and potentially other bat-borne pathogens.}, }
@article {pmid37655448, year = {2023}, author = {Wang, Y and Li, Q and Zhang, J and Liu, P and Zheng, H and Chen, L and Wang, Z and Tan, C and Zhang, M and Zhang, H and Miao, W and Wang, Y and Xuan, X and Yi, G and Wang, P}, title = {Ring1a protects against colitis through regulating mucosal immune system and colonic microbial ecology.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2251646}, doi = {10.1080/19490976.2023.2251646}, pmid = {37655448}, issn = {1949-0984}, abstract = {Inflammatory bowel disease (IBD) represents a prominent chronic immune-mediated inflammatory disorder, yet its etiology remains poorly comprehended, encompassing intricate interactions between genetics, immunity, and the gut microbiome. This study uncovers a novel colitis-associated risk gene, namely Ring1a, which regulates the mucosal immune response and intestinal microbiota. Ring1a deficiency exacerbates colitis by impairing the immune system. Concomitantly, Ring1a deficiency led to a Prevotella genus-dominated pathogenic microenvironment, which can be horizontally transmitted to co-housed wild type (WT) mice, consequently intensifying dextran sodium sulfate (DSS)-induced colitis. Furthermore, we identified a potential mechanism linking the altered microbiota in Ring1aKO mice to decreased levels of IgA, and we demonstrated that metronidazole administration could ameliorate colitis progression in Ring1aKO mice, likely by reducing the abundance of the Prevotella genus. We also elucidated the immune landscape of DSS colitis and revealed the disruption of intestinal immune homeostasis associated with Ring1a deficiency. Collectively, these findings highlight Ring1a as a prospective candidate risk gene for colitis and suggest metronidazole as a potential therapeutic option for clinically managing Prevotella genus-dominated colitis.}, }
@article {pmid37655346, year = {2023}, author = {Gutierrez, T and Liu, H}, title = {Editorial: Rising stars in aquatic microbiology: 2022.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1265720}, doi = {10.3389/fmicb.2023.1265720}, pmid = {37655346}, issn = {1664-302X}, }
@article {pmid37653502, year = {2023}, author = {Zehentner, B and Scherer, S and Neuhaus, K}, title = {Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {243}, pmid = {37653502}, issn = {1471-2180}, abstract = {Analysis of genome wide transcription start sites (TSSs) revealed an unexpected complexity since not only canonical TSS of annotated genes are recognized by RNA polymerase. Non-canonical TSS were detected antisense to, or within, annotated genes as well new intergenic (orphan) TSS, not associated with known genes. Previously, it was hypothesized that many such signals represent noise or pervasive transcription, not associated with a biological function. Here, a modified Cappable-seq protocol allows determining the primary transcriptome of the enterohemorrhagic E. coli O157:H7 EDL933 (EHEC). We used four different growth media, both in exponential and stationary growth phase, replicated each thrice. This yielded 19,975 EHEC canonical and non-canonical TSS, which reproducibly occurring in three biological replicates. This questions the hypothesis of experimental noise or pervasive transcription. Accordingly, conserved promoter motifs were found upstream indicating proper TSSs. More than 50% of 5,567 canonical and between 32% and 47% of 10,355 non-canonical TSS were differentially expressed in different media and growth phases, providing evidence for a potential biological function also of non-canonical TSS. Thus, reproducible and environmentally regulated expression suggests that a substantial number of the non-canonical TSSs may be of unknown function rather than being the result of noise or pervasive transcription.}, }
@article {pmid37653010, year = {2023}, author = {Gralka, M and Pollak, S and Cordero, OX}, title = {Genome content predicts the carbon catabolic preferences of heterotrophic bacteria.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37653010}, issn = {2058-5276}, support = {542395//Simons Foundation/ ; 599207//Simons Foundation/ ; 542395//Simons Foundation/ ; }, abstract = {Heterotrophic bacteria-bacteria that utilize organic carbon sources-are taxonomically and functionally diverse across environments. It is challenging to map metabolic interactions and niches within microbial communities due to the large number of metabolites that could serve as potential carbon and energy sources for heterotrophs. Whether their metabolic niches can be understood using general principles, such as a small number of simplified metabolic categories, is unclear. Here we perform high-throughput metabolic profiling of 186 marine heterotrophic bacterial strains cultured in media containing one of 135 carbon substrates to determine growth rates, lag times and yields. We show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic (sugars) or gluconeogenic (amino and organic acids) carbon sources. This preference is encoded by the total number of genes found in pathways that feed into the two modes of carbon utilization and can be predicted using a simple linear model based on gene counts. This allows for coarse-grained descriptions of microbial communities in terms of prevalent modes of carbon catabolism. The sugar-acid preference is also associated with genomic GC content and thus with the carbon-nitrogen requirements of their encoded proteome. Our work reveals how the evolution of bacterial genomes is structured by fundamental constraints rooted in metabolism.}, }
@article {pmid37652144, year = {2023}, author = {Low, KE and Tingley, JP and Klassen, L and King, ML and Xing, X and Watt, C and Hoover, SER and Gorzelak, M and Abbott, DW}, title = {Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108245}, doi = {10.1016/j.biotechadv.2023.108245}, pmid = {37652144}, issn = {1873-1899}, abstract = {Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.}, }
@article {pmid37650927, year = {2023}, author = {Ho, HVN and Dunigan, DD and Salsbery, ME and Agarkova, IV and Al Ameeli, Z and Van Etten, JL and DeLong, JP}, title = {Viral Chemotaxis of Paramecium Bursaria Altered by Algal Endosymbionts.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37650927}, issn = {1432-184X}, support = {1736030//Directorate for Biological Sciences/ ; 1736030//Directorate for Biological Sciences/ ; 1736030//Directorate for Biological Sciences/ ; }, abstract = {Chemotaxis is widespread across many taxa and often aids resource acquisition or predator avoidance. Species interactions can modify the degree of movement facilitated by chemotaxis. In this study, we investigated the influence of symbionts on Paramecium bursaria's chemotactic behavior toward chloroviruses. To achieve this, we performed choice experiments using chlorovirus and control candidate attractors (virus stabilization buffer and pond water). We quantified the movement of Paramecia grown with or without algal and viral symbionts toward each attractor. All Paramecia showed some chemotaxis toward viruses, but cells without algae and viruses showed the most movement toward viruses. Thus, the endosymbiotic algae (zoochlorellae) appeared to alter the movement of Paramecia toward chloroviruses, but it was not clear that ectosymbiotic viruses (chlorovirus) also had this effect. The change in behavior was consistent with a change in swimming speed, but a change in attraction remains possible. The potential costs and benefits of chemotactic movement toward chloroviruses for either the Paramecia hosts or its symbionts remain unclear.}, }
@article {pmid37649628, year = {2023}, author = {Levante, A and Bertani, G and Marrella, M and Mucchetti, G and Bernini, V and Lazzi, C and Neviani, E}, title = {The microbiota of Mozzarella di Bufala Campana PDO cheese: a study across the manufacturing process.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1196879}, pmid = {37649628}, issn = {1664-302X}, abstract = {INTRODUCTION: Mozzarella di Bufala Campana PDO cheese (MBC) is a globally esteemed Italian cheese. The traditional cheesemaking process of MBC relies on natural whey starter culture, water buffalo's milk, and the local agroecosystem.<br><br>METHODS: In this study, the microbial ecology of intermediate samples of MBC production, coming from two dairies with slightly different cheesemaking technology (dairy M large producer, and dairy C medium-small), was investigated using 16S rRNA amplicon sequencing. This research aimed to provide insights into the dynamics of microbial consortia involved in various cheesemaking steps.<br><br>RESULTS AND DISCUSSION: All samples, except for raw buffalo milk, exhibited a core microbiome predominantly composed of Streptococcus spp. and Lactobacillus spp., albeit with different ratios between the two genera across the two MBC producers. Notably, the microbiota of the brine from both dairies, analyzed using 16S amplicon sequencing for the first time, was dominated by the Lactobacillus and Streptococcus genera, while only dairy C showed the presence of minor genera such as Pediococcus and Lentilactobacillus. Intriguingly, the final mozzarella samples from both producers displayed an inversion in the dominance of Lactobacillus spp. over Streptococcus spp. in the microbiota compared to curd samples, possibly attributable to the alleviation of thermal stress following the curd stretching step. In conclusion, the different samples from the two production facilities did not exhibit significant differences in terms of the species involved in MBC cheesemaking. This finding confirms that the key role in the MBC cheesemaking process lies with a small-sized microbiome primarily composed of Streptococcus and Lactobacillus spp.}, }
@article {pmid37649327, year = {2023}, author = {Mariën, Q and Regueira, A and Ganigué, R}, title = {Steerable isobutyric and butyric acid production from CO2 and H2 by Clostridium luticellarii.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14321}, pmid = {37649327}, issn = {1751-7915}, support = {ERDF (UE)//Galician Competitive Research Group/ ; GRC ED431C 2021/37//Galician Competitive Research Group/ ; BOF19/STA/044//Bijzonder Onderzoeksfonds UGent/ ; 1SC5722N//Fonds Wetenschappelijk Onderzoek/ ; ED481B-2021-012//Xunta de Galicia/ ; }, abstract = {Clostridium luticellarii is a recently discovered acetogen that is uniquely capable of producing butyric and isobutyric acid from various substrates (e.g. methanol), but it is unclear which factors influence its (iso)butyric acid production from H2 and CO2 . We aimed to investigate the autotrophic metabolism of C. luticellarii by identifying the necessary growth conditions and examining the effects of pH and metabolite levels on product titers and selectivity. Results show that autotrophic growth of C. luticellarii requires the addition of complex nutrient sources and the absence of shaking conditions. Further experiments combined with thermodynamic calculations identified pH as a key parameter governing the direction of metabolic fluxes. At circumneutral pH (~6.5), acetic acid is the sole metabolic end product but C. luticellarii possesses the unique ability to co-oxidize organic acids such as valeric acid under high H2 partial pressures (>1 bar). Conversely, mildly acidic pH (≤5.5) stimulates the production of butyric and isobutyric acid while partly halting the oxidation of organic acids. Additionally, elevated acetic acid concentrations stimulated butyric and isobutyric acid production up to a combined selectivity of 53 ± 3%. Finally, our results suggest that isobutyric acid is produced by a reversible isomerization of butyric acid, but valeric and caproic acid are not isomerized. These combined insights can inform future efforts to optimize and scale-up the production of valuable chemicals from CO2 using C. luticellarii.}, }
@article {pmid37643688, year = {2023}, author = {McEvoy, N and O'Connor, A and McDonagh, F and Lonappan, AM and Farrell, ML and Kovarova, A and Burke, L and Ryan, K and Hallahan, B and Miliotis, G}, title = {Complete genome of an inhibitor resistant blaTEM-30 encoding Escherichia coli sequence type 127 isolate identified in human saliva with a high genotypic virulence load.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2023.08.014}, pmid = {37643688}, issn = {2213-7173}, abstract = {OBJECTIVES: Escherichia coli ST 127 is a pandemic clone that belongs to the extraintestial pathogenic (ExPEC) family, associated with urinary tract infections and bloodstream infections. Here, we report the complete genome of an E. coli ST127 isolate which was identified in the saliva of a patient with Treatment Resistant Schizophrenia (TRS) exhibting no signs of infection. The objective of this work is to determine the mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and virulence factors (VFs) that contribute to the pathogenicity of such ST127 isolates.<br><br>METHODS: Whole-genome sequencing (WGS) of isolate GABEEC10 was performed using DNABseq and Nanopore MinION platforms. Hybrid assembly of GABEEC10 was conducted with Unicycler v 0.5.0. and annotated using PROKKA v1.14.5. Comparative genomics and phylogenomics were conducted using average nucleotide identity (ANI) and approximately-maximum-likelihood phylogenetic inference. ARGs, VFs and serotyping were identified with Abricate v1.0.0 using CARD, vfdb and EcOH databases respectively.<br><br>RESULTS: E. coli salivary isolate GABEEC10 was identfied to belong to phylogroup B2 and have a serotype of O6 H31 with a total genome length of 4 940 530 bp and a mean GC content of 50.40 %. GABEEC10 was identified to have a highly virulent genotype with the presence of 84 VFs in addition to 44 ARGs, including an acquired blaTEM-30. The strain was identified to additionally carry four mobilisable plasmids.<br><br>CONCLUSION: We report the complete genome of E. coli GABAEEC10 that can be used to aid in understanding the pathogenicity, drug resistance and dissemination of the emerging pandemic lineage ST 127.}, }
@article {pmid37640259, year = {2023}, author = {Ikeda, T and Ogawa, T and Aono, T}, title = {Dethiobiotin uptake and utilization by bacteria possessing bioYB operon.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104131}, doi = {10.1016/j.resmic.2023.104131}, pmid = {37640259}, issn = {1769-7123}, abstract = {Biotin is an essential vitamin for all organisms. Some bacteria cannot synthesize biotin and live by acquiring biotin from the environment. Bacterial biotin transporters (BioY) are classified into three mechanistic types. The first forms the BioMNY complex with ATPase (BioM) and transmembrane protein (BioN). The second relies on a promiscuous energy coupling module. The third functions independently. One-third of bioY genes spread in bacteria cluster with bioM and bioN on the genomes, and the rest does not. Interestingly, some bacteria have the bioY gene clustering with bioB gene, which encodes biotin synthase, an enzyme that converts dethiobiotin to biotin, on their genome. This bioY-bioB cluster is observed even though these bacteria cannot synthesize biotin. Azorhizobium caulinodans ORS571, a rhizobium of tropical legume Sesbania rostrata, is one of such bacteria. In this study using this bacterium, we demonstrated that the BioY linked to BioB could transport not only biotin but also dethiobiotin, and the combination of BioY and BioB contributed to the growth of A. caulinodans ORS571 in a biotin-deficient but dethiobiotin-sufficient environment. We propose that such environment universally exists in the natural world, and the identification of such environment will be a new subject in the field of microbial ecology.}, }
@article {pmid37639796, year = {2023}, author = {Mei, Z and Fu, Y and Wang, F and Xiang, L and Hu, F and Harindintwali, JD and Wang, M and Virta, M and Hashsham, SA and Jiang, X and Tiedje, JM}, title = {Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132388}, doi = {10.1016/j.jhazmat.2023.132388}, pmid = {37639796}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.}, }
@article {pmid37637623, year = {2023}, author = {Ratna, HVK and Jeyaraman, M and Yadav, S and Jeyaraman, N and Nallakumarasamy, A}, title = {Is Dysbiotic Gut the Cause of Low Back Pain?.}, journal = {Cureus}, volume = {15}, number = {7}, pages = {e42496}, pmid = {37637623}, issn = {2168-8184}, abstract = {Low back pain (LBP) is the foremost cause of disability that affects the day-to-day activities of millions of people worldwide. The putative trigger of LBP is linked to the gut microbiome (GM) and its dysbiotic environment. With the concept of GM, various disease pathogenesis has been revisited with plausible crosstalks and micromolecular mimicry. In the normal intervertebral disc (IVD), Firmicutes and Actinobacteria were found in abundance. The blood-disc barrier protects IVD from systemic infection, resists inflammation, and halts the immune surveillance of the inner aspects of IVD. The insights into microbial ecology will broaden our horizons in GM and IVD degeneration in LBP cases. However, an improved understanding of GM and back pain has to be explored in large-scale individuals with varied timescales to validate the above findings. The role of GM (diet, prebiotics, probiotics, and fecal microbiota transplantation) in pain modulation can form novel therapies in cases of LBP.}, }
@article {pmid37637134, year = {2023}, author = {White, C and Antell, E and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, W and Alvarez-Cohen, L}, title = {Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1243410}, pmid = {37637134}, issn = {1664-302X}, abstract = {Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4[+]:NO2[-], where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4[+]:NO2[-] ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4[+]:NO2[-] ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4[+]:NO2[-] ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.}, }
@article {pmid37637113, year = {2023}, author = {Huang, J and Li, J and Zhou, W and Cheng, Y and Li, J}, title = {Effect of different rice transplanting patterns on microbial community in water, sediment, and Procambarus clarkii intestine in rice-crayfish system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233815}, pmid = {37637113}, issn = {1664-302X}, abstract = {Although the microbial ecology of integrated rice-crayfish farming systems is receiving increasing attention with the expanding application area in China, the effects of rice transplanting patterns on the microbial community of water, sediment and Procambarus clarkii intestine in rice-crayfish system has yet to be determined. This study explored the microbial community present in water, sediment and intestine samples from three transplant patterns (rice crayfish with wide-narrow row transplanting, rice-crayfish with normal transplanting and pond-crayfish, abbreviated as RC-W, RC, and PC, respectively) using high-throughput sequencing. The results showed that the dominant microbial taxa from sediment, surrounding water, and intestine at phylum level were Proteobacteria, Chloroflexi, Cyanobacteria, Actinobacteria, Bacteroidetes. The patterns of rice transplanting had significant effects on microbial biodiversity and species composition in surrounding water. The OTUs community richness of water under RC group was significantly higher than that of PC group and RC-W group. The OTU relative abundance of top 10 operational taxonomic units had significantly different (p < 0.05) in the water samples from the three groups. The intestinal OTU community richness of Procambarus clarkii in the three groups was positively correlated with the community richness of water. The proximity between intestinal and water samples in PCA diagram indicated that their species composition was more similar. The results also showed that rice transplanting patterns can affect intestinal microbial biodiversity of Procambarus clarkii and the intestinal microbial biodiversity correlated with water bodies. Although the intestinal microbial diversity of crayfish in RC-W group was lower than that in RC group, the relative abundance of potential pathogenic bacteria, such as Vibrio, Aeromonas, in intestine of the crayfish in the RC-W group was significantly decreased under rice wide-narrow row transplanting model. Redundancy analysis revealed that environmental parameters, such as pH, DO, nitrate, which regulate the composition of microbial community structures. This study provides an understanding for microbial response to different rice transplanting pattern in rice-crayfish farming system.}, }
@article {pmid37635954, year = {2024}, author = {Romans-Casas, M and Feliu-Paradeda, L and Tedesco, M and Hamelers, HVM and Bañeras, L and Balaguer, MD and Puig, S and Dessì, P}, title = {Selective butyric acid production from CO2 and its upgrade to butanol in microbial electrosynthesis cells.}, journal = {Environmental science and ecotechnology}, volume = {17}, number = {}, pages = {100303}, pmid = {37635954}, issn = {2666-4984}, abstract = {Microbial electrosynthesis (MES) is a promising carbon utilization technology, but the low-value products (i.e., acetate or methane) and the high electric power demand hinder its industrial adoption. In this study, electrically efficient MES cells with a low ohmic resistance of 15.7 mΩ m[2] were operated galvanostatically in fed-batch mode, alternating periods of high CO2 and H2 availability. This promoted acetic acid and ethanol production, ultimately triggering selective (78% on a carbon basis) butyric acid production via chain elongation. An average production rate of 14.5 g m[-2] d[-1] was obtained at an applied current of 1.0 or 1.5 mA cm[-2], being Megasphaera sp. the key chain elongating player. Inoculating a second cell with the catholyte containing the enriched community resulted in butyric acid production at the same rate as the previous cell, but the lag phase was reduced by 82%. Furthermore, interrupting the CO2 feeding and setting a constant pH2 of 1.7-1.8 atm in the cathode compartment triggered solventogenic butanol production at a pH below 4.8. The efficient cell design resulted in average cell voltages of 2.6-2.8 V and a remarkably low electric energy requirement of 34.6 kWhel kg[-1] of butyric acid produced, despite coulombic efficiencies being restricted to 45% due to the cross-over of O2 and H2 through the membrane. In conclusion, this study revealed the optimal operating conditions to achieve energy-efficient butyric acid production from CO2 and suggested a strategy to further upgrade it to valuable butanol.}, }
@article {pmid37635262, year = {2023}, author = {Zhai, X and Castro-Mejía, JL and Gobbi, A and Aslampaloglou, A and Kot, W and Nielsen, DS and Deng, L}, title = {The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {193}, pmid = {37635262}, issn = {2049-2618}, support = {201906870027//China Scholarship Council/ ; 36242//Villum Fonden/ ; 23145//Villum Fonden/ ; }, abstract = {BACKGROUND: There is an increasing interest in investigating the human gut virome for its influence on the gut bacterial community and its putative influence on the trajectory towards health or disease. Most gut virome studies are based on sequencing of stored fecal samples. However, relatively little is known about how conventional storage buffers and storage conditions affect the infectivity of bacteriophages and influence the downstream metavirome sequencing.<br><br>RESULTS: We demonstrate that the infectivity and genome recovery rate of different spiked bacteriophages (T4, c2 and Phi X174) are variable and highly dependent on storage buffers. Regardless of the storage temperature and timespan, all tested phages immediately lost 100% (DNA/RNA Shield) or more than 90% (StayRNA and RNAlater) of their infectivity. Generally, in SM buffer at 4&#xa0;&#xb0;C phage infectivity was preserved for up to 30 days and phage DNA integrity was maintained for up to 100&#xa0;days. While in CANVAX, the most effective buffer, all spiked phage genomes were preserved for at least 100&#xa0;days. Prolonged storage time (500&#xa0;days) at -&#xa0;80&#xa0;&#xb0;C impacted viral diversity differently in the different buffers. Samples stored in CANVAX or DNA/RNA Shield buffer had the least shifts in metavirome composition, after prolonged storage, but they yielded more contigs classified as "uncharacterised". Moreover, in contrast to the SM buffer, these storage buffers yielded a higher fraction of bacterial DNA in metavirome-sequencing libraries. We demonstrated that the latter was due to inactivation of the DNases employed to remove extra-cellular DNA during virome extraction. The latter could be partly avoided by employing additional washing steps prior to virome extraction.<br><br>CONCLUSION: Fecal sample storage buffers and storage conditions (time and temperature) strongly influence bacteriophage infectivity and viral composition as determined by plaque assay and metavirome sequencing. The choice of buffer had a larger effect than storage temperature and storage time on the quality of the viral sequences and analyses. Based on these results, we recommend storage of fecal virome samples at in SM buffer at 4&#xa0;&#xb0;C for the isolation of viruses and at -&#xa0;80&#xa0;&#xb0;C for metagenomic applications if practically feasible (i.e., access to cold storage). For fecal samples stored in other buffers, samples should be cleared of these buffers before viral extraction and sequencing. Video Abstract.}, }
@article {pmid37635076, year = {2023}, author = {Barman, D and Dkhar, MS}, title = {Purification and characterization of moderately thermostable raw-starch digesting α-amylase from endophytic Streptomyces mobaraensis DB13 associated with Costus speciosus.}, journal = {The Journal of general and applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2323/jgam.2023.08.001}, pmid = {37635076}, issn = {1349-8037}, abstract = {Endophytic actinobacteria are known to produce various enzymes with potential industrial applications. Alpha-amylase is an important class of industrial enzyme with a multi-dimensional utility. The present experiment was designed to characterize a moderately thermostable α-amylase producing endophytic Streptomyces mobaraensis DB13 isolated from Costus speciosus (J. Koenig) Sm. The enzyme was purified using 60% ammonium sulphate precipitation, dialysis, and Sephadex G-100 column chromatography. Based on 12% SDS-PAGE, the molecular weight of the purified α-amylase was estimated to be 55 kDa. The maximum α-amylase activity was achieved at pH 7.0, 50°C and it retained 80% of its activity at both pH 7.0 and 8.0 after incubation for 2 h. The α-mylase activity is strongly enhanced by Ca[2+], Mg[2+], and inhibited by Ba[2+]. The activity remains stable in the presence of Tween-80, SDS, PMSF, and Triton X-100; however, β-mercaptoethanol, EDTA, and H2O2 reduced the activity. The kinetic parameters Km and Vmax values for this α-amylase were calculated as 2.53 mM and 29.42 U/mL respectively. The α-amylase had the ability to digest various raw starches at a concentration of 10 mg/mL at pH 7.0, 50°C, where maize and rice are the preferred substrates. The digestion starts after 4 h of incubation, which reaches maximum after 48 h of incubation. These results suggest that S. mobaraensis DB13 is a potential source of moderately thermostable α-amylase enzyme, that effciently hydrolyzes raw starch. It suggesting that this α-amylase is a promising candidate to be use for industrial purposes.}, }
@article {pmid37633274, year = {2023}, author = {Pérez-Cobas, AE and Ginevra, C and Rusniok, C and Jarraud, S and Buchrieser, C}, title = {The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101167}, doi = {10.1016/j.xcrm.2023.101167}, pmid = {37633274}, issn = {2666-3791}, abstract = {Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.}, }
@article {pmid37633148, year = {2023}, author = {Guo, T and Wang, T and Chen, L and Zheng, B}, title = {Whole-grain highland barley premade biscuit prepared by hot-extrusion 3D printing: Printability and nutritional assessment.}, journal = {Food chemistry}, volume = {432}, number = {}, pages = {137226}, doi = {10.1016/j.foodchem.2023.137226}, pmid = {37633148}, issn = {1873-7072}, abstract = {In this study, to explore the possibility of applying whole-grain highland barley (HB) in functional food, HB premade biscuit was created by hot-extrusion 3D printing (HEP) for the first time, and its printability and nutritional functions were evaluated. The rheology results showed 20% (w/w) HB suspension with 9% corn oil addition had better printability due to the formation of a structure with higher elasticity and stronger resistance to deformation. Moreover, the obtained premade biscuit had lower predicted glycemic index (pGI) and starch digestibility. Meanwhile, in vivo experiment results showed it could affect the glycolipid metabolism, ameliorate the high fat diet (HFD)-induced metabolic disorders and maintain the balance of the gut microbial ecology. This could be attributed to the decrease in Firmicutes/Bacteroidetes ratio and the proliferation of propionate-producing probiotics, especially Veilonella, Weissella and Desulfovibrio. Overall, this study could provide basic data and innovative approaches to prepare nutritional whole-grain foods.}, }
@article {pmid37632540, year = {2023}, author = {Seward, J and Bräuer, S and Beckett, P and Roy-Léveillée, P and Emilson, E and Watmough, S and Basiliko, N}, title = {Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37632540}, issn = {1432-184X}, abstract = {Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.}, }
@article {pmid37630470, year = {2023}, author = {Won, S and Shin, C and Kang, HY}, title = {Potential Self-Attenuation of Arsenic by Indigenous Microorganisms in the Nakdong River.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630470}, issn = {2076-2607}, support = {NRF- 2020R1I1A3068585//National Research Foundation of Korea/ ; }, abstract = {The toxic element arsenic (As) has become the major focus of global research owing to its harmful effects on human health, resulting in the establishment of several guidelines to prevent As contamination. The widespread industrial use of As has led to its accumulation in the environment, increasing the necessity to develop effective remediation technologies. Among various treatments, such as chemical, physical, and biological treatments, used to remediate As-contaminated environments, biological methods are the most economical and eco-friendly. Microbial oxidation of arsenite (As(III)) to arsenate (As(V)) is a primary detoxification strategy for As remediation as it reduces As toxicity and alters its mobility in the environment. Here, we evaluated the self-detoxification potential of microcosms isolated from Nakdong River water by investigating the autotrophic and heterotrophic oxidation of As(III) to As(V). Experimental data revealed that As(III) was oxidized to As(V) during the autotrophic and heterotrophic growth of river water microcosms. However, the rate of oxidation was significantly higher under heterotrophic conditions because of the higher cell growth and density in an organic-matter-rich environment compared to that under autotrophic conditions without the addition of external organic matter. At an As(III) concentration > 5 mM, autotrophic As(III) oxidation remained incomplete, even after an extended incubation time. This inhibition can be attributed to the toxic effect of the high contaminant concentration on bacterial growth and the acidification of the growth medium with the oxidation of As(III) to As(V). Furthermore, we isolated representative pure cultures from both heterotrophic- and autotrophic-enriched cultures. The new isolates revealed new members of As(III)-oxidizing bacteria in the diversified bacterial community. This study highlights the natural process of As attenuation within river systems, showing that microcosms in river water can detoxify As under both organic-matter-rich and -deficient conditions. Additionally, we isolated the bacterial strains HTAs10 and ATAs5 from the microcosm which can be further investigated for potential use in As remediation systems. Our findings provide insights into the microbial ecology of As(III) oxidation in river ecosystems and provide a foundation for further investigations into the application of these bacteria for bioremediation.}, }
@article {pmid37624441, year = {2023}, author = {Pinheiro Alves de Souza, Y and Schloter, M and Weisser, W and Schulz, S}, title = {Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37624441}, issn = {1432-184X}, abstract = {Despite its enormous importance for ecosystem services, factors driving microbial recolonization of soils after disturbance are still poorly understood. Here, we compared the microbial recolonization patterns of a disturbed, autoclaved soil using different amounts of the original non-disturbed soil as inoculum. By using this approach, we manipulated microbial biomass, but did not change microbial diversity of the inoculum. We followed the development of a new soil microbiome after reinoculation over a period of 4 weeks using a molecular barcoding approach as well as qPCR. Focus was given on the assessment of bacteria and archaea. We could show that 1 week after inoculation in all inoculated treatments bacterial biomass exceeded the values from the original soil as a consequence of high dissolved organic carbon (DOC) concentrations in the disturbed soil resulting from the disturbance. This high biomass was persistent over the complete experimental period. In line with the high DOC concentrations, in the first 2 weeks of incubation, copiotrophic bacteria dominated the community, which derived from the inoculum used. Only in the disturbed control soils which did not receive a microbial inoculum, recolonization pattern differed. In contrast, archaeal biomass did not recover over the experimental period and recolonization was strongly triggered by amount of inoculated original soil added. Interestingly, the variability between replicates of the same inoculation density decreased with increasing biomass in the inoculum, indicating a deterministic development of soil microbiomes if higher numbers of cells are used for reinoculation.}, }
@article {pmid37624156, year = {2023}, author = {Cao, Y and Wang, R and Liu, Y and Li, Y and Jia, L and Yang, Q and Zeng, X and Li, X and Wang, Q and Wang, R and Riaz, L}, title = {Improved Calculations of Heavy Metal Toxicity Coefficients for Evaluating Potential Ecological Risk in Sediments Based on Seven Major Chinese Water Systems.}, journal = {Toxics}, volume = {11}, number = {8}, pages = {}, pmid = {37624156}, issn = {2305-6304}, support = {U1904205//Key Project of the National Natural Science Foundation of China-Henan Joint Fund/ ; NSFC 42277409//National Natural Science Foundation of China/ ; 22B180006//Educational Commission of the Henan Province of China/ ; 21A180014//Key Project of Natural Science of the Education Department of Henan Province of China/ ; 212102110322//Science and Technology Project of Henan Province/ ; }, abstract = {Several methods have been used to assess heavy metal contamination in sediments. However, an assessment that considers both composite heavy metal speciation and concentration is necessary to accurately study ecological risks. This study improved the potential ecological risk index method and calculated the toxicity coefficients of seven heavy metals: Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn). The newly calculated toxicity coefficients were validated by using previously published heavy metal distribution data of the Henan section of the Yellow River. The calculation procedure is based on the principle that the abundance of heavy metals in the environment and their bioavailable forms affect the toxicity of heavy metals. The toxicity coefficients for the seven heavy metals were calculated as follows: As = 10, Cd = 20, Cr = 5, Cu = 2, Ni = 5, Pb = 5, Zn = 1. Ecological risk assessment of the Henan section of the Yellow River using the improved toxicity coefficients revealed that the ecological risk of Cd and total heavy metals is higher than previous calculations, reaching the strength and moderate risk levels, respectively. The improved potential ecological risk index method is more sensitive to heavy metal pollution and thus provides a better indication of ecological risk. This is a necessary improvement to provide more accurate pollution assessments.}, }
@article {pmid37620628, year = {2023}, author = {Chen, X and Li, Q and Chen, D and Zhao, L and Xiao, C}, title = {Restoration Measures of Fencing after Tilling Guided Succession of Grassland Soil Microbial Community Structure to Natural Grassland in the Sanjiangyuan Agro-pasture Ecotone of the Qinghai-Tibetan Plateau.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37620628}, issn = {1432-184X}, support = {2019QZKK040104//the Second Tibetan Plateau Scientific Expedition and Research (STEP) Program/ ; 2021FY100705//the Special Project on National Science and Technology Basic Resources Investigation of China/ ; 31770501//the National Natural Science Foundation of China/ ; }, abstract = {In the fragile Sanjiangyuan (SJY) agro-pasture ecotone of the Qinghai-Tibetan Plateau (QTP), planting and fencing have been used to alleviate grassland degradation and to provide high-quality grass seeds for the implementation of the project of "grain for green". The soil microbe is the major driving factor in maintaining plant productivity and soil nutrient cycling. However, few studies have explored the effects of planting and fencing on soil microorganisms in the SJY agro-pasture ecotone. We explored the effects of tilling (TG) and fencing after tilling (FTG) on soil microbial communities to reveal the effects of restoration measures on soil microbes and to provide a reference in assessing and improving ecosystem structure. The results showed that restoration measures increased soil microbial species diversity and significantly changed their community structure. We found, the microbial composition was more complex under FTG, and its fungal variability was higher and more similar to that of natural grassland. Additionally, restoration measures resulted in fungal co-occurrence network was more edges, higher density, larger diameter and more positive interactions. This was due to the management of the vegetation-soil microenvironment by FTG inducing a differentiation of microbial community structure. In summary, the implementation of FTG could change the microenvironment in the SJY agro-pasture ecotone, so that variation in the structure of microbial community tended toward that of natural grassland, and increased the stability of microbial co-occurrence network, which was more obvious in the fungal community. HIGHLIGHTS: • Restoration measures have changed the vegetation characteristics and soil microenvironment. • Fencing after tilling (FTG) has brought the microenvironment closer to natural grassland. • FTG significantly increased microbial unique ASVs. The number of fungal unique ASVs was similar to that of natural grassland. • FTG resulted in changes in microbial community structure towards natural grasslands and increased the stability of the microbial co-occurrence network, which was more apparent in the fungal community.}, }
@article {pmid37620398, year = {2023}, author = {De Micco, V and Amitrano, C and Mastroleo, F and Aronne, G and Battistelli, A and Carnero-Diaz, E and De Pascale, S and Detrell, G and Dussap, CG and Ganigué, R and Jakobsen, &#xd8;M and Poulet, L and Van Houdt, R and Verseux, C and Vlaeminck, SE and Willaert, R and Leys, N}, title = {Plant and microbial science and technology as cornerstones to Bioregenerative Life Support Systems in space.}, journal = {NPJ microgravity}, volume = {9}, number = {1}, pages = {69}, pmid = {37620398}, issn = {2373-8065}, abstract = {Long-term human space exploration missions require environmental control and closed Life Support Systems (LSS) capable of producing and recycling resources, thus fulfilling all the essential metabolic needs for human survival in harsh space environments, both during travel and on orbital/planetary stations. This will become increasingly necessary as missions reach farther away from Earth, thereby limiting the technical and economic feasibility of resupplying resources from Earth. Further incorporation of biological elements into state-of-the-art (mostly abiotic) LSS, leading to bioregenerative LSS (BLSS), is needed for additional resource recovery, food production, and waste treatment solutions, and to enable more self-sustainable missions to the Moon and Mars. There is a whole suite of functions crucial to sustain human presence in Low Earth Orbit (LEO) and successful settlement on Moon or Mars such as environmental control, air regeneration, waste management, water supply, food production, cabin/habitat pressurization, radiation protection, energy supply, and means for transportation, communication, and recreation. In this paper, we focus on air, water and food production, and waste management, and address some aspects of radiation protection and recreation. We briefly discuss existing knowledge, highlight open gaps, and propose possible future experiments in the short-, medium-, and long-term to achieve the targets of crewed space exploration also leading to possible benefits on Earth.}, }
@article {pmid37619629, year = {2023}, author = {Wang, SH and Yuan, SW and Che, FF and Wan, X and Wang, YF and Yang, DH and Yang, HJ and Zhu, D and Chen, P}, title = {Strong bacterial stochasticity and fast fungal turnover in Taihu Lake sediments, China.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116954}, doi = {10.1016/j.envres.2023.116954}, pmid = {37619629}, issn = {1096-0953}, abstract = {Understanding the assembly and turnover of microbial communities is crucial for gaining insights into the diversity and functioning of lake ecosystems, a fundamental and central issue in microbial ecology. The ecosystem of Taihu Lake has been significantly jeopardized due to urbanization and industrialization. In this study, we examined the diversity, assembly, and turnover of bacterial and fungal communities in Taihu Lake sediment. The results revealed strong bacterial stochasticity and fast fungal turnover in the sediment. Significant heterogeneity was observed among all sediment samples in terms of environmental factors, especially ORP, TOC, and TN, as well as microbial community composition and alpha diversity. For instance, the fungal richness index exhibited an approximate 3-fold variation. Among the environmental factors, TOC, TN, and pH had a more pronounced influence on the bacterial community composition compared to the fungal community composition. Interestingly, species replacement played a dominant role in microbial beta diversity, with fungi exhibiting a stronger pattern. In contrast, stochastic processes governed the community assembly of both bacteria and fungi, but were more pronounced for bacteria (R[2] = 0.7 vs. 0.5). These findings deepen the understanding of microbial assembly and turnover in sediments under environmental stress and provide essential insights for maintaining the multifunctionality of lake ecosystems.}, }
@article {pmid37615431, year = {2023}, author = {Armour, CR and Sovacool, KL and Close, WL and Topçuoğlu, BD and Wiens, J and Schloss, PD}, title = {Machine learning classification by fitting amplicon sequences to existing OTUs.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0033623}, doi = {10.1128/msphere.00336-23}, pmid = {37615431}, issn = {2379-5042}, abstract = {The ability to use 16S rRNA gene sequence data to train machine learning classification models offers the opportunity to diagnose patients based on the composition of their microbiome. In some applications, the taxonomic resolution that provides the best models may require the use of de novo operational taxonomic units (OTUs) whose composition changes when new data are added. We previously developed a new reference-based approach, OptiFit, that fits new sequence data to existing de novo OTUs without changing the composition of the original OTUs. While OptiFit produces OTUs that are as high quality as de novo OTUs, it is unclear whether this method for fitting new sequence data into existing OTUs will impact the performance of classification models relative to models trained and tested only using de novo OTUs. We used OptiFit to cluster sequences into existing OTUs and evaluated model performance in classifying a dataset containing samples from patients with and without colonic screen relevant neoplasia (SRN). We compared the performance of this model to standard methods including de novo and database-reference-based clustering. We found that using OptiFit performed as well or better in classifying SRNs. OptiFit can streamline the process of classifying new samples by avoiding the need to retrain models using reclustered sequences. IMPORTANCE There is great potential for using microbiome data to aid in diagnosis. A challenge with de novo operational taxonomic unit (OTU)-based classification models is that 16S rRNA gene sequences are often assigned to OTUs based on similarity to other sequences in the dataset. If data are generated from new patients, the old and new sequences must be reclustered to OTUs and the classification model retrained. Yet there is a desire to have a single, validated model that can be widely deployed. To overcome this obstacle, we applied the OptiFit clustering algorithm to fit new sequence data to existing OTUs allowing for reuse of the model. A random forest model implemented using OptiFit performed as well as the traditional reassign and retrain approach. This result shows that it is possible to train and apply machine learning models based on OTU relative abundance data that do not require retraining or the use of a reference database.}, }
@article {pmid37614461, year = {2023}, author = {Kandeel, SA and Megahed, AA}, title = {Editorial: Infectious diseases, microbial ecology, and antimicrobial resistance dynamics in food animals.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1266980}, pmid = {37614461}, issn = {2297-1769}, }
@article {pmid37610498, year = {2023}, author = {Wei, N and Tan, J}, title = {Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37610498}, issn = {1432-184X}, support = {030869//Holden Arboretum/ ; LEQSF(2023-26)-RD-A-14//Louisiana Board of Regents/ ; LEQSF(2023-26)-RD-A-14//Louisiana Board of Regents/ ; 10635//Gordon and Betty Moore Foundation/ ; }, abstract = {To understand how microbiota influence plant populations in nature, it is important to examine the biogeographic distribution of plant-associated microbiomes and the underlying mechanisms. However, we currently lack a fundamental understanding of the biogeography of plant microbiomes across populations and the environmental and host genetic factors that shape their distribution. Leveraging the broad distribution and extensive genetic variation in duckweeds (the Lemna species complex), we identified key factors that governed plant microbiome diversity and compositional variation geographically. In line with the microbial biogeography of free-living microbiomes, we observed higher bacterial richness in temperate regions relative to lower latitudes in duckweed microbiomes (with 10% higher in temperate populations). Our analyses revealed that higher temperature and sodium concentration in aquatic environments showed a negative impact on duckweed bacterial richness, whereas temperature, precipitation, pH, and concentrations of phosphorus and calcium, along with duckweed genetic variation, influenced the biogeographic variation of duckweed bacterial community composition. Analyses of plant microbiome assembly processes further revealed that niche-based selection played an important role (26%) in driving the biogeographic variation of duckweed bacterial communities, alongside the contributions of dispersal limitation (33%) and drift (39%). These findings add significantly to our understanding of host-associated microbial biogeography and provide important insights for predicting plant microbiome vulnerability and resilience under changing climates and intensifying anthropogenic activities.}, }
@article {pmid37608162, year = {2023}, author = {Fecchio, A and Bell, JA and Williams, EJ and Dispoto, JH and Weckstein, JD and de Angeli Dutra, D}, title = {Co-infection with Leucocytozoon and Other Haemosporidian Parasites Increases with Latitude and Altitude in New World Bird Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37608162}, issn = {1432-184X}, support = {DEB-1503804//National Science Foundation/ ; }, abstract = {Establishing how environmental gradients and host ecology drive spatial variation in infection rates and diversity of pathogenic organisms is one of the central goals in disease ecology. Here, we identified the predictors of concomitant infection and lineage richness of blood parasites in New Word bird communities. Our multi-level Bayesian models revealed that higher latitudes and elevations played a determinant role in increasing the probability of a bird being co-infected with Leucocytozoon and other haemosporidian parasites. The heterogeneity in both single and co-infection rates was similarly driven by host attributes and temperature, with higher probabilities of infection in heavier migratory host species and at cooler localities. Latitude, elevation, host body mass, migratory behavior, and climate were also predictors of Leucocytozoon lineage richness across the New World avian communities, with decreasing parasite richness at higher elevations, rainy and warmer localities, and in heavier and resident host species. Increased parasite richness was found farther from the equator, confirming a reverse Latitudinal Diversity Gradient pattern for this parasite group. The increased rates of Leucocytozoon co-infection and lineage richness with increased latitude are in opposition with the pervasive assumption that pathogen infection rates and diversity are higher in tropical host communities.}, }
@article {pmid37607924, year = {2023}, author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M}, title = {Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5090}, pmid = {37607924}, issn = {2041-1723}, mesh = {*Fusariosis ; *Microbiota ; *Fusarium ; Metagenome ; Hydrogen-Ion Concentration ; }, abstract = {Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.}, }
@article {pmid37606945, year = {2023}, author = {Ricks, KD and Ricks, NJ and Yannarell, AC}, title = {Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes.}, journal = {The American naturalist}, volume = {202}, number = {3}, pages = {276-287}, doi = {10.1086/725393}, pmid = {37606945}, issn = {1537-5323}, mesh = {Humans ; *Salinity ; Acclimatization ; *Infertility ; Phenotype ; Soil ; }, abstract = {AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.}, }
@article {pmid37606696, year = {2023}, author = {Theodorescu, M and Bucur, R and Bulzu, PA and Faur, L and Levei, EA and Mirea, IC and Cadar, O and Ferreira, RL and Souza-Silva, M and Moldovan, OT}, title = {Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37606696}, issn = {1432-184X}, abstract = {Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.}, }
@article {pmid37604894, year = {2023}, author = {Utzeri, VJ and Cilli, E and Fontani, F and Zoboli, D and Orsini, M and Ribani, A and Latorre, A and Lissovsky, AA and Pillola, GL and Bovo, S and Gruppioni, G and Luiselli, D and Fontanesi, L}, title = {Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13635}, pmid = {37604894}, issn = {2045-2322}, support = {RFO//University of Bologna/ ; RFO//University of Bologna/ ; RFO//University of Bologna/ ; COST Action RGB-Net//European Union/ ; }, abstract = {Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.}, }
@article {pmid37604501, year = {2023}, author = {Kuzyk, SB and Messner, K and Plouffe, J and Ma, X and Wiens, K and Yurkov, V}, title = {Diverse aerobic anoxygenic phototrophs synthesize bacteriochlorophyll in oligotrophic rather than copiotrophic conditions, suggesting ecological niche.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16482}, pmid = {37604501}, issn = {1462-2920}, support = {1501//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {While investigating aerobic anoxygenic phototrophs (AAP) from Lake Winnipeg's bacterial community, over 500 isolates were obtained. Relatives of 20 different species were examined simultaneously, identifying conditions for optimal growth or pigment production to determine features that may unify this group of phototrophs. All were distributed among assorted α-Proteobacterial families including Erythrobacteraceae, Sphingomonadaceae, Sphingosinicellaceae, Acetobacteraceae, Methylobacteriaceae, and Rhodobacteraceae. Major phenotypic characteristics matched phylogenetic association, including pigmentation, morphology, metal transformations, tolerances, lipid configurations, and enzyme activities, which distinctly separated each taxonomic family. While varying pH and temperature had a limited independent impact on pigment production, bacteriochlorophyll synthesis was distinctly promoted under low nutrient conditions, whereas copiotrophy repressed its production but enhanced carotenoid yield. New AAP diversity was also reported by revealing strains related to non-phototrophic Rubellimicrobium and Sphingorhabdus, as well as spread throughout Roseomonas, Sphingomonas, and Methylobacterium/Methylorubrum, which previously only had a few known photosynthetic members. This study exemplified the overwhelming diversity of AAP in a single aquatic environment, confirming cultivation continues to be of importance in microbial ecology to discover functionality in both new and previously reported cohorts of bacteria as specific laboratory conditions were required to promote aerobic bacteriochlorophyll production.}, }
@article {pmid37603734, year = {2023}, author = {Lee, H and Bloxham, B and Gore, J}, title = {Resource competition can explain simplicity in microbial community assembly.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {35}, pages = {e2212113120}, doi = {10.1073/pnas.2212113120}, pmid = {37603734}, issn = {1091-6490}, abstract = {Predicting the composition and diversity of communities is a central goal in ecology. While community assembly is considered hard to predict, laboratory microcosms often follow a simple assembly rule based on the outcome of pairwise competitions. This assembly rule predicts that a species that is excluded by another species in pairwise competition cannot survive in a multispecies community with that species. Despite the empirical success of this bottom-up prediction, its mechanistic origin has remained elusive. In this study, we elucidate how this simple pattern in community assembly can emerge from resource competition. Our geometric analysis of a consumer-resource model shows that trio community assembly is always predictable from pairwise outcomes when one species grows faster than another species on every resource. We also identify all possible trio assembly outcomes under three resources and find that only two outcomes violate the assembly rule. Simulations demonstrate that pairwise competitions accurately predict trio assembly with up to 100 resources and the assembly of larger communities containing up to twelve species. We then further demonstrate accurate quantitative prediction of community composition using the harmonic mean of pairwise fractions. Finally, we show that cross-feeding between species does not decrease assembly rule prediction accuracy. Our findings highlight that simple community assembly can emerge even in ecosystems with complex underlying dynamics.}, }
@article {pmid37601377, year = {2023}, author = {Flocco, CG and Methner, A and Burkart, F and Geppert, A and Overmann, J}, title = {Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1197837}, pmid = {37601377}, issn = {1664-302X}, abstract = {Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.}, }
@article {pmid37597041, year = {2023}, author = {Cleary, DFR and de Voogd, NJ and Stuij, TM and Swierts, T and Oliveira, V and Polónia, ARM and Louvado, A and Gomes, NCM and Coelho, FJRC}, title = {A Study of Sponge Symbionts from Different Light Habitats.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37597041}, issn = {1432-184X}, abstract = {The amount of available light plays a key role in the growth and development of microbial communities. In the present study, we tested to what extent sponge-associated prokaryotic communities differed between specimens of the sponge species Cinachyrella kuekenthali and Xestospongia muta collected in dimly lit (caves and at greater depths) versus illuminated (shallow water) habitats. In addition to this, we also collected samples of water, sediment, and another species of Cinachyrella, C. alloclada. Overall, the biotope (sponge host species, sediment, and seawater) proved the major driver of variation in prokaryotic community composition. The light habitat, however, also proved a predictor of compositional variation in prokaryotic communities of both C. kuekenthali and X. muta. We used an exploratory technique based on machine learning to identify features (classes, orders, and OTUs), which distinguished X. muta specimens sampled in dimly lit versus illuminated habitat. We found that the classes Alphaproteobacteria and Rhodothermia and orders Puniceispirillales, Rhodospirillales, Rhodobacterales, and Thalassobaculales were associated with specimens from illuminated, i.e., shallow water habitat, while the classes Dehalococcoidia, Spirochaetia, Entotheonellia, Nitrospiria, Schekmanbacteria, and Poribacteria, and orders Sneathiellales and Actinomarinales were associated with specimens sampled from dimly lit habitat. There was, however, considerable variation within the different light habitats highlighting the importance of other factors in structuring sponge-associated bacterial communities.}, }
@article {pmid37594520, year = {2023}, author = {Martínez, LT and Marchant, M and Díaz, RTA and Arrojo, M&#xc1; and Muñoz, P}, title = {Benthic Foraminifera as Pollution Biomarkers: a Morphological Approach.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37594520}, issn = {1432-184X}, support = {1130511//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 170124//Fondo de Equipamiento Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, abstract = {Coastal areas are often intervened by anthropic activities, which increase the contamination of toxic agents such as heavy metals. This causes adverse morphological effects on benthic microorganisms, such as foraminifera. This group is one of the most susceptible to environmental deterioration, so they can be used as pollution biomarkers by identifying shell abnormalities. Therefore, 28 sediment samples from northern Chile were analyzed, calculating the Abnormality Index-FAI and its spatio-temporal distributions in benthic foraminifera, as well as the minimum and maximum abnormality percentages and their relationship with heavy metal concentrations, using a generalized non-linear model and a principal component analysis. The results indicated a proportion of abnormal shells within the ranges described for polluted areas conditions, revealing environmental stress conditions. This reflected a change in the environmental conditions in the most recent sediments of the bay. The highest FAI values were observed to the southwest of the bay, caused by the local current system. The species Bolivina seminuda, Buliminella elegantissima, and Epistominella exigua presented a greater number of deformities, allowing them to be used as contamination biomarkers. A significant correlation was found between Ti, Mn, Ni, Va, and Ba with decreased chamber sizes, wrong coiling, scars, and number of abnormality types. This suggests the effect of the particular geochemical conditions of the area on the heavy metals that cause toxic effects on foraminifera. These analyses are an efficient tool for identifying the effects of environmental stress before they occur in higher organisms, mitigating the environmental impact on marine biodiversity.}, }
@article {pmid37594170, year = {2023}, author = {Hambleton, EA}, title = {How corals get their nutrients.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37594170}, issn = {2050-084X}, mesh = {Animals ; *Nutrients ; *Anthozoa ; Cell Wall ; }, abstract = {Algae living inside corals provide sugars for their host by digesting their own cell walls.}, }
@article {pmid37590550, year = {2022}, author = {de Almeida, OGG and De Martinis, ECP}, title = {Multitargeted Analyses are Instrumental for Microbial Ecology Studies.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {187}, pages = {}, doi = {10.3791/64789}, pmid = {37590550}, issn = {1940-087X}, }
@article {pmid37586176, year = {2023}, author = {Bai, X and Dinkla, IJT and Muyzer, G}, title = {Shedding light on the total and active core microbiomes in slow sand filters for drinking water production.}, journal = {Water research}, volume = {243}, number = {}, pages = {120404}, doi = {10.1016/j.watres.2023.120404}, pmid = {37586176}, issn = {1879-2448}, abstract = {Slow sand filters (SSF) are widely used in the production of drinking water as a last barrier in the removal of pathogens. This removal mainly depends on the 'Schmutzdecke', a biofilm-like layer on the surface of the sand bed. Most previous studies focused on the total community as revealed by DNA analysis rather than on the active community, which may lead to an incorrect understanding of the SSF ecology. In the current study, we determined and compared the DNA- (total) and RNA-displayed (active) communities in the Schmutzdecke layer from 10 full-scale slow sand filters and further explored the SSF core microbiome in terms of both presence (DNA) and activity (RNA). Discrepancies were observed between the total and the active community, although there was a consistent grouping in the PCoA analysis. The DNA-displayed community may be somewhat inflated, while the RNA-displayed community could reveal low abundance (or rare) but active community members. The overall results imply that both DNA (presence) and RNA (activity) data should be considered to prevent the underestimation of organisms of functional importance but lower abundance. Microbial communities of studied mature Schmutzdecke were shaped by the influent water. Nevertheless, a core microbiome was shared by the mature Schmutzdeckes from independent filters, representing the dominant and consistent microbial community composition in slow sand filters. In the DNA samples, a total of 33 VSC families ('very strict core', with a relative abundance >0.1% and 100% prevalence) were observed across all filters. Among the RNA samples, there were 18 VSC families, including 16 families that overlapped with the DNA VSC families and 2 unique RNA VSC families. The core microbial community structure was influenced by the operational parameters, including the Schmutzdecke age and the sand size, and was less influenced by water flow. In addition, indicator organisms ('biomarkers') for the Schmutzdecke age, which show the longest duration that SSF can maintain a good operation, were observed in our study. The abundant presence of bacteria belonging to bacteriap25 and Caldilineaceae was associated with older Schmutzdeckes, revealing longer periods of stable operation performance of the filter, while the high abundance of bacteria belonging to Bdellovibrionaceae and Bryobacteraceae related to short periods of stable operation performance.}, }
@article {pmid37579703, year = {2023}, author = {Li, Z and Wang, J and Fan, J and Yue, H and Zhang, X}, title = {Marine toxin domoic acid alters protistan community structure and assembly process in sediments.}, journal = {Marine environmental research}, volume = {191}, number = {}, pages = {106131}, doi = {10.1016/j.marenvres.2023.106131}, pmid = {37579703}, issn = {1879-0291}, abstract = {Domoic acid (DA)-producing algal blooms have been the issue of worldwide concerns in recent decades, but there has never been any attempt to investigate the effects of DA on microbial ecology in marine environments. Protists are considered to be key regulators of microbial activity, community structure and evolution, we therefore explore the effect of DA on the ecology of protists via metagenome in this work. The results indicate that trace amounts of DA can act as a stressor to alter alpha and beta diversity of protistan community. Among trophic functional groups, consumers and phototrophs are negative responders of DA, implying DA is potentially capable of functional-level effects in the ocean. Moreover, microecological theory reveals that induction of DA increases the role of deterministic processes in microbial community assembly, thus altering the biotic relationships and successional processes in symbiotic patterns. Finally, we demonstrate that the mechanism by which DA shapes protistan ecological network is by acting on phototrophs, which triggers cascading effects in networks and eventually leading to shifts in ecological succession of protists. Overall, our results present the first perspective regarding the effects of DA on marine microbial ecology, which will supplement timely information on the ecological impacts of DA in the ocean.}, }
@article {pmid37573698, year = {2023}, author = {Song, Y and Zhang, S and Lu, J and Duan, R and Chen, H and Ma, Y and Si, T and Luo, M}, title = {Reed restoration decreased nutrients in wetlands with dredged sediments: Microbial community assembly and function in rhizosphere.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118700}, doi = {10.1016/j.jenvman.2023.118700}, pmid = {37573698}, issn = {1095-8630}, abstract = {Using dredged sediments as substrate for aquatic plants is a low-cost and ecological friendly way for in situ aquatic ecological restoration. However, the limited information available about how aquatic plant restoration affects the microbial ecology and nutrients in dredged sediments. In this study, nutrient contents, enzyme activities, and bacterial and archaeal communities in vertical sediment layers were determined in bulk and reed zones of wetlands constructed with dredged sediments in west Lake Taihu for three years. Reed restoration significantly decreased total nitrogen, total phosphorus, and organic carbon contents and increased alkaline phosphatase, urease, and sucrase activities compared to bulk area. Bacterial communities in vertical sediment layers had higher similarity in reed zone in comparison to bulk zone, and many bacterial and archaeal genera were only detected in reed rhizosphere zones. Compared with the bulk zone, the reed restoration area has a higher abundance of phylum Actinobacteriota, Hydrothermarchaeota, and class α-proteobacteria. The assembly process of the bacterial and archaeal communities was primarily shaped by dispersal limitation (67.03% and 32.97%, respectively), and stochastic processes were enhanced in the reed recovery area. Network analysis show that there were more complicated interactions among bacteria and archaea and low-abundance taxa were crucial in maintaining the microbial community stability in rhizosphere of reed zone. PICRUST2 analysis demonstrate that reed restoration promotes metabolic pathways related to C and N cycle in dredged sediments. These data highlight that using dredged sediments as substrates for aquatic plants can transform waste material into a valuable resource, enhancing the benefits to the environment.}, }
@article {pmid37567875, year = {2023}, author = {Molbert, N and Ghanavi, HR and Johansson, T and Mostadius, M and Hansson, MC}, title = {An evaluation of DNA extraction methods on historical and roadkill mammalian specimen.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13080}, pmid = {37567875}, issn = {2045-2322}, mesh = {Animals ; *Chloroform ; *DNA/genetics ; Phenol ; Phenols ; Mammals/genetics ; Silicon Dioxide ; }, abstract = {Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.}, }
@article {pmid37567306, year = {2023}, author = {Schroll, M and Liu, L and Einzmann, T and Keppler, F and Grossart, HP}, title = {Methane accumulation and its potential precursor compounds in the oxic surface water layer of two contrasting stratified lakes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166205}, doi = {10.1016/j.scitotenv.2023.166205}, pmid = {37567306}, issn = {1879-1026}, abstract = {Methane (CH4) supersaturation in oxygenated waters is a widespread phenomenon despite the traditional perception of strict anoxic methanogenesis. This notion has recently been challenged by successive findings of processes and mechanisms that produce CH4 in oxic environments. While some of the processes contributing to the vertical accumulation of CH4 in the oxygenated upper water layers of freshwater lakes have been identified, temporal variations as well as drivers are still poorly understood. In this study, we investigated the accumulation of CH4 in oxic water layers of two contrasting lakes in Germany: Lake Willersinnweiher (shallow, monomictic, eutrophic) and Lake Stechlin (deep, dimictic, mesotrophic) from 2019 to 2020. The dynamics of isotopic values of CH4 and the role of potential precursor compounds of oxic CH4 production were explored. During the study period, persistent strong CH4 supersaturation (relative to air) was observed in the surface waters, mostly concentrated around the thermocline. The magnitude of vertical CH4 accumulation strongly varied over season and was generally more pronounced in shallow Lake Willersinnweiher. In both lakes, increases in CH4 concentrations from the surface to the thermocline mostly coincided with an enrichment in [13]C-CH4 and [2]H-CH4, indicating a complex interaction of multiple processes such as CH4 oxidation, CH4 transport from littoral sediments and oxic CH4 production, sustaining and controlling this CH4 supersaturation. Furthermore, incubation experiments with [13]C and [2]H labelled methylated P-, N- and C- compounds clearly showed that methylphosphonate, methylamine and methionine acted as potent precursors of accumulating CH4 and at least partly sustained CH4 supersaturation. This highlights the need to better understand the mechanisms underlying CH4 accumulation by focusing on production and transport pathways of CH4 and its precursor compounds, e.g., produced via phytoplankton. Such knowledge forms the foundation to better predict aquatic CH4 dynamics and its subsequent rates of emissions to the atmosphere.}, }
@article {pmid37564072, year = {2023}, author = {Michoud, G and Kohler, TJ and Ezzat, L and Peter, H and Nattabi, JK and Nalwanga, R and Pramateftaki, P and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and Marasco, R and Daffonchio, D and Bourquin, M and Busi, SB and Battin, TJ}, title = {The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa.}, journal = {Royal Society open science}, volume = {10}, number = {8}, pages = {230329}, pmid = {37564072}, issn = {2054-5703}, abstract = {The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.}, }
@article {pmid37563275, year = {2023}, author = {Epp Schmidt, D and Maul, JE and Yarwood, SA}, title = {Quantitative Amplicon Sequencing Is Necessary to Identify Differential Taxa and Correlated Taxa Where Population Sizes Differ.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37563275}, issn = {1432-184X}, support = {1828910//NSF/ ; }, abstract = {High-throughput, multiplexed-amplicon sequencing has become a core tool for understanding environmental microbiomes. As researchers have widely adopted sequencing, many open-source analysis pipelines have been developed to compare microbiomes using compositional analysis frameworks. However, there is increasing evidence that compositional analyses do not provide the information necessary to accurately interpret many community assembly processes. This is especially true when there are large gradients that drive distinct community assembly processes. Recently, sequencing has been combined with Q-PCR (among other sources of total quantitation) to generate "Quantitative Sequencing" (QSeq) data. QSeq more accurately estimates the true abundance of taxa, is a more reliable basis for inferring correlation, and, ultimately, can be more reliably related to environmental data to infer community assembly processes. In this paper, we use a combination of published data sets, synthesis, and empirical modeling to offer guidance for which contexts QSeq is advantageous. As little as 5% variation in total abundance among experimental groups resulted in more accurate inference by QSeq than compositional methods. Compositional methods for differential abundance and correlation unreliably detected patterns in abundance and covariance when there was greater than 20% variation in total abundance among experimental groups. Whether QSeq performs better for beta diversity analysis depends on the question being asked, and the analytic strategy (e.g., what distance metric is being used); for many questions and methods, QSeq and compositional analysis are equivalent for beta diversity analysis. QSeq is especially useful for taxon-specific analysis; QSeq transformation and analysis should be the default for answering taxon-specific questions of amplicon sequence data. Publicly available bioinformatics pipelines should incorporate support for QSeq transformation and analysis.}, }
@article {pmid37555066, year = {2023}, author = {Mashamaite, L and Lebre, PH and Varliero, G and Maphosa, S and Ortiz, M and Hogg, ID and Cowan, DA}, title = {Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203216}, pmid = {37555066}, issn = {1664-302X}, abstract = {INTRODUCTION: The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica.<br><br>METHODS: We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons.<br><br>RESULTS AND DISCUSSION: Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.}, }
@article {pmid37552473, year = {2023}, author = {Jiang, Z and Liu, S and Zhang, D and Sha, Z}, title = {The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37552473}, issn = {1432-184X}, abstract = {To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.}, }
@article {pmid37550791, year = {2023}, author = {Pitiriga, V and Bakalis, J and Theodoridou, K and Dimitroulia, E and Saroglou, G and Tsakris, A}, title = {Comparison of microbial colonization rates between central venous catheters and peripherally inserted central catheters.}, journal = {Antimicrobial resistance and infection control}, volume = {12}, number = {1}, pages = {74}, pmid = {37550791}, issn = {2047-2994}, mesh = {Humans ; *Central Venous Catheters/adverse effects ; *Catheterization, Central Venous/adverse effects/methods ; Retrospective Studies ; Critical Illness ; *Catheter-Related Infections/prevention &amp; control ; Risk Factors ; *Sepsis ; *Anti-Infective Agents ; }, abstract = {BACKGROUND: Central venous catheters (CVCs) and peripherally inserted central catheters (PICCs), have been widely used as intravascular devices in critically ill patients. However, they might evoke complications, such as catheter colonization that has been considered as predisposing factor for central line-associated bloodstream infections (CLABSIs). Although numerous studies have compared the risk of bloodstream infections between PICCs and CVCs, comparative studies on their colonization rates are limited.<br><br>OBJECTIVES: The episodes of catheter colonization in critically ill patients with CVCs or PICCs were retrospectively analysed during a two-year period in a Greek tertiary care hospital and colonization rates, microbial profiles and antimicrobial susceptibility&#xa0;patterns were compared.<br><br>METHODS: Clinical and laboratory data of consecutive hospitalized critically-ill patients who underwent PICC and CVC placement between May 2017-May 2019 were analysed. All catheters were examined by the semiquantitative culture technique for bacterial pathogens, either as a routine process after catheter removal or after suspicion of infection. Species identification and antimicrobial resistance patterns were determined by the Vitek2 automated system.<br><br>RESULTS: During the survey period a total of 122/1187 (10.28%) catheter colonization cases were identified among CVCs and 19/639 (2.97%) cases among PICCs (p&#x2009;=&#x2009;0.001). The colonization rate was 12.48/1000 catheter-days for the&#xa0;CVC group and 1.71/1000 catheter-days for the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). The colonization rate per 1000 catheter-days due to multidrug-resistant organisms (MDROs) was 3.85 in all study cases, 7.26 (71/122) in the&#xa0;CVC group and 0.63 (7/19) in the&#xa0;PICC group (p&#x2009;<&#x2009;0.001). Within the&#xa0;CVC group, the most common microorganism isolated was MDR Acinetobacter baumannii (n&#x2009;=&#x2009;38, 31.1%) followed by MDR Klebsiella pneumoniae (n&#x2009;=&#x2009;20, 16.4%). In the&#xa0;PICC group, the predominant microorganism isolated was Candida spp. (n&#x2009;=&#x2009;5, 23.8%) followed by MDR K. pneumoniae and MDR A. baumannii in equal numbers (n&#x2009;=&#x2009;3, 14.2%).<br><br>CONCLUSION: PICC lines were associated with significantly lower colonization rates comparing to the&#xa0;CVC&#xa0;ones. In addition, patterns of microbial colonization revealed a trend over the predominance of MDR gram-negatives in CVCs suggesting that PICCs might be a&#xa0;safer alternative for prolonged inpatient intravascular access. Prevention programs directed by local microbial ecology may diminish catheter colonization rates and CLABSIs.}, }
@article {pmid37550373, year = {2023}, author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van de Peer, Y and Olsen, JL and Reusch, TBH}, title = {Author Correction: Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41477-023-01504-y}, pmid = {37550373}, issn = {2055-0278}, }
@article {pmid37548146, year = {2023}, author = {Ruiz, J and de Celis, M and Diaz-Colunga, J and Vila, JC and Benitez-Dominguez, B and Vicente, J and Santos, A and Sanchez, A and Belda, I}, title = {Predictability of the community-function landscape in wine yeast ecosystems.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {e11613}, doi = {10.15252/msb.202311613}, pmid = {37548146}, issn = {1744-4292}, support = {ECOPROSPECTOR-101088469/ERC_/European Research Council/International ; }, abstract = {Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most ecologically and industrially relevant traits exhibit phylogenetic signal, allowing functional traits in wine yeast communities to be predicted from taxonomy. Furthermore, we demonstrate that the quantitative contributions of individual wine yeast strains to the function of complex communities followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing theoretical questions in functional ecology, our results and methodologies can provide a blueprint for rationally managing microbial processes of biotechnological relevance.}, }
@article {pmid37547726, year = {2023}, author = {Gibson, E and Zimmerman, NB}, title = {Urban biogeography of fungal endophytes across San Francisco.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15454}, pmid = {37547726}, issn = {2167-8359}, mesh = {Humans ; Endophytes/genetics ; Cities ; San Francisco ; Hot Temperature ; *Fungi, Unclassified ; Plants/microbiology ; Trees/microbiology ; *Microbiota ; }, abstract = {In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.}, }
@article {pmid37544074, year = {2023}, author = {Fu, S and Wang, R and Zhang, J and Xu, Z and Yang, X and Yang, Q}, title = {Temporal variability of microbiome in the different plankton hosts revealed distinct environmental persistence of Vibrio parahaemolyticus in shrimp farms.}, journal = {Microbiological research}, volume = {275}, number = {}, pages = {127464}, doi = {10.1016/j.micres.2023.127464}, pmid = {37544074}, issn = {1618-0623}, abstract = {Plankton-bacteria interactions may play essential roles in maintaining the persistence of pathogenic Vibrio spp. However, the actual plankton host of the toxigenic Vibrio parahaemolyticus that harbors thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) remains unclear. To answer this question, we measured the abundance of toxigenic and nontoxigenic Vibrio parahaemolyticus in different types of plankton by most probable number (MPN)-PCR. We next investigated the dynamics of the microbiomes of rearing water, copepods, Chlorella, four predominant diatom genera (Nitzschia, Melosira, Skeletonema and Chaetoceros) and the gut of the shrimp in two recirculated shrimp farming systems from April to September using high-throughput 16 S rRNA amplicon sequencing. The survival of trh-positive and trh-negative V. parahaemolyticus in seawater and different plankton hosts was examined under low temperature and starvation conditions. The results showed that copepods harbored the highest proportion of trh-positive V. parahaemolyticus, followed by diatoms. Chitinous diatoms (CD) harbored a high proportion of Vibrionaceae, of which a high abundance of V. parahaemolyticus was found in summer. In contrast, Vibrio spp. is rarely found in Chlorella and nonchitinous diatoms. Taxon-specific associations were also observed, including a relatively high abundance of Vibrio and Halodesulfovibrio on copepods and covariation of Aeromonas and Bacillus inside the Chlorella. The survival assays showed that, in comparison to trh-negative V. parahaemolyticus, trh-positive V. parahaemolyticus showed better survival in copepods and CD under starvation conditions and maintained high persistence in the above hosts at low temperature. In conclusion, the results herein suggested that chitinous plankton might provide protection for V. parahaemolyticus, especially trh-positive V. parahaemolyticus, and improve their persistence under harsh conditions. Our study provided in-depth insights into the persistence of V. parahaemolyticus in the environment, which would promote targeted disease prevention measures.}, }
@article {pmid37543702, year = {2023}, author = {Tang, L and O'Dwyer, J and Kimyon, &#xd6; and Manefield, MJ}, title = {Microbial community composition of food waste before anaerobic digestion.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12703}, pmid = {37543702}, issn = {2045-2322}, mesh = {Anaerobiosis ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; *Microbiota/genetics ; Bacteria/genetics ; Bioreactors/microbiology ; Methane ; Sewage/microbiology ; }, abstract = {Anaerobic digestion is widely used to process and recover value from food waste. Commercial food waste anaerobic digestion facilities seek improvements in process efficiency to enable higher throughput. There is limited information on the composition of microbial communities in food waste prior to digestion, limiting rational exploitation of the catalytic potential of microorganisms in pretreatment processes. To address this knowledge gap, bacterial and fungal communities in food waste samples from a commercial anaerobic digestion facility were characterised over 3 months. The abundance of 16S rRNA bacterial genes was approximately five orders of magnitude higher than the abundance of the fungal intergenic spacer (ITS) sequence, suggesting the numerical dominance of bacteria over fungi in food waste before anaerobic digestion. Evidence for the mass proliferation of bacteria in food waste during storage prior to anaerobic digestion is presented. The composition of the bacterial community shows variation over time, but lineages within the Lactobacillaceae family are consistently dominant. Nitrogen content and pH are correlated to community variation. These findings form a foundation for understanding the microbial ecology of food waste and provide opportunities to further improve the throughput of anaerobic digestion.}, }
@article {pmid37542810, year = {2023}, author = {De Paepe, J and Garcia Gragera, D and Arnau Jimenez, C and Rabaey, K and Vlaeminck, SE and Gòdia, F}, title = {Continuous cultivation of microalgae yields high nutrient recovery from nitrified urine with limited supplementation.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118500}, doi = {10.1016/j.jenvman.2023.118500}, pmid = {37542810}, issn = {1095-8630}, abstract = {Microalgae can play a key role in the bioeconomy, particularly in combination with the valorisation of waste streams as cultivation media. Urine is an example of a widely available nutrient-rich waste stream, and alkaline stabilization and subsequent full nitrification in a bioreactor yields a stable nitrate-rich solution. In this study, such nitrified urine served as a culture medium for the edible microalga Limnospira indica. In batch cultivation, nitrified urine without additional supplements yielded a lower biomass concentration, nutrient uptake and protein content compared to modified Zarrouk medium, as standard medium. To enhance the nitrogen uptake efficiency and biomass production, nitrified urine was supplemented with potentially limiting elements. Limited amounts of phosphorus (36 mg L[-1]), magnesium (7.9 mg L[-1]), calcium (12.2 mg L[-1]), iron (2.0 mg L[-1]) and EDTA (88.5 mg Na2-EDTA.2H2O L[-1]) rendered the nitrified urine matrix as effective as modified Zarrouk medium in terms of biomass production (OD750 of 1.2), nutrient uptake (130 mg N L[-1]) and protein yield (47%) in batch culture. Urine precipitates formed by alkalinisation could in principle supply enough phosphorus, calcium and magnesium, requiring only external addition of iron, EDTA and inorganic carbon. Subsequently, the suitability of supplemented nitrified urine as a culture medium was confirmed in continuous Limnospira cultivation in a CSTR photobioreactor. This qualifies nitrified urine as a valuable and sustainable microalgae growth medium, thereby creating novel nutrient loops on Earth and in Space, i.e., in regenerative life support systems for human deep-space missions.}, }
@article {pmid37542791, year = {2023}, author = {van den Bergh, SG and Chardon, I and Meima-Franke, M and Costa, OYA and Korthals, GW and de Boer, W and Bodelier, PLE}, title = {The intrinsic methane mitigation potential and associated microbes add product value to compost.}, journal = {Waste management (New York, N.Y.)}, volume = {170}, number = {}, pages = {17-32}, doi = {10.1016/j.wasman.2023.07.027}, pmid = {37542791}, issn = {1879-2456}, abstract = {Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 &amp; ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h[-1] g dw compost[-1] and 25.19 ± 6.75 pmol h[-1] g dw compost[-1], respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.}, }
@article {pmid37542538, year = {2023}, author = {Niu, J and Chen, D and Shang, C and Xiao, L and Wang, Y and Zeng, W and Zheng, X and Chen, Z and Du, X and Chen, X}, title = {Niche Differentiation of Biofilm Microorganisms in a Full-scale Municipal Drinking Water Distribution System in China and Their Implication for Biofilm Control.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37542538}, issn = {1432-184X}, abstract = {Biofilms on the inner surface of a drinking water distribution system (DWDS) affect water quality and stability. Understanding the niche differentiation of biofilm microbial communities is necessary for the efficient control of DWDS biofilms. However, biofilm studies are difficult to conduct in the actual DWDS because of inaccessibility to the pipes buried underground. Taking the opportunity of infrastructure construction and relevant pipeline replacement in China, biofilms in a DWDS (a water main and its branch pipes) were collected in situ, followed by analysis on the abundances and community structures of bacterial and archaeal using quantitative PCR and high-throughput sequencing, respectively. Results showed that archaea were detected only in the biofilms of the water main, with a range of 9.4×10[3]~1.1×10[5] copies/cm[2]. By contrast, bacteria were detected in the biofilms of branch pipes and the distal part of the water main, with a range of 8.8×10[3]~9.6×10[6] copies/cm[2]. Among the biofilm samples, the archaeal community in the central part of the water main showed the highest richness and diversity. Nitrosopumilus was found to be predominant (86.22%) in the biofilms of the proximal part of the water main. However, Methanobrevibacter (87.15%) predominated in the distal part of the water main. The bacterial community of the water main and branch pipes was primarily composed of Firmicutes and Proteobacteria at the phylum level, respectively. Regardless of archaea or bacteria, only few operational taxonomic units (OTUs) (<0.5% of total OTUs) were shared by all the biofilms, indicating the niche differentiation of biofilm microorganisms. Moreover, the high Mn content in the biofilms of the distal sampling location (D3) in the water main was linked to the predominance of Bacillus. Functional gene prediction revealed that the proportion of infectious disease-related genes was 0.44-0.67% in the tested biofilms. Furthermore, functional genes related to the resistance of the bacterial community to disinfections and antibiotics were detected in all the samples, that is, glutathione metabolism-relating genes (0.14-0.65%) and beta-lactam resistance gene (0.01-0.05%). The results of this study indicate the ubiquity of archaea and bacteria in the biofilms of water main and branch pipes, respectively, and pipe diameters could be a major influencing factor on bacterial community structure. In the water main, the key finding was the predominant existence of archaea, particularly Nitrosopumilus and methanogen. Hence, their routine monitoring and probable influences on water quality in pipelines with large diameter should be given more attention. Besides, since Mn-related Bacillus and suspected pathogenic Enterococcus were detected in the biofilm, supplementation of disinfectant may be a feasible strategy for inhibiting their growth and ensuring water quality. In addition, the monitoring on their abundance variation could help to determine the frequency and methods of pipeline maintenance.}, }
@article {pmid37542537, year = {2023}, author = {Ren, Z and Ye, S and Li, H and Huang, X and Chen, L and Cao, S and Chen, T}, title = {Biological Interactions and Environmental Influences Shift Microeukaryotes in Permafrost Active Layer Soil Across the Qinghai-Tibet Plateau.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37542537}, issn = {1432-184X}, abstract = {Permafrost active layer soils are harsh environments with thaw/freeze cycles and sub-zero temperatures, harboring diverse microorganisms. However, the distribution patterns, assembly mechanism, and driving forces of soil microeukaryotes in permafrost remain largely unknown. In this study, we investigated microeukaryotes in permafrost active layer across the Qinghai-Tibet Plateau (QTP) using 18S rRNA gene sequencing. The results showed that the microbial eukaryotic communities were dominated by Nematozoa, Ciliophora, Ascomycota, Cercozoa, Arthropoda, and Basidiomycota in terms of relative abundance and operational taxonomic unit (OTU) richness. Nematozoa had the highest relative abundance, while Ciliophora had the highest OTU richness. These phyla had strong interactions between each other. Their alpha diversity and community structure were differently influenced by the factors associated to location, climate, and soil properties, particularly the soil properties. Significant but weak distance-decay relationships with different slopes were established for the communities of these dominant phyla, except for Basidiomycota. According to the null model, community assemblies of Nematozoa and Cercozoa were dominated by heterogeneous selection, Ciliophora and Ascomycota were dominated by dispersal limitation, while Arthropoda and Basidiomycota were highly dominated by non-dominant processes. The assembly mechanisms can be jointly explained by biotic interactions, organism treats, and environmental influences. Modules in the co-occurrence network of the microeukaryotes were composed by members from different taxonomic groups. These modules also had interactions and responded to different environmental factors, within which, soil properties had strong influences on these modules. The results suggested the importance of biological interactions and soil properties in structuring microbial eukaryotic communities in permafrost active layer soil across the QTP.}, }
@article {pmid37541415, year = {2023}, author = {He, Q and Yan, X and Wang, H and Ji, Y and Li, J and Liu, L and Bi, P and Xu, P and Xu, B and Ma, J}, title = {Towards a better understanding of the anaerobic/oxic/anoxic-aerobic granular sludge process (AOA-AGS) for simultaneous low-strength wastewater treatment and in situ sludge reduction from ambient to winter temperatures.}, journal = {Environmental research}, volume = {236}, number = {Pt 2}, pages = {116822}, doi = {10.1016/j.envres.2023.116822}, pmid = {37541415}, issn = {1096-0953}, abstract = {The new anaerobic/oxic/anoxic-aerobic granular sludge (AOA-AGS) merits the advantages of effective carbon utilization and low-carbon treatment. However, low temperature poses stressing concerns and the resisting mechanism remains much unknown. Herein, an AOA-AGS process was configured for simultaneous nitrification, denitrification and phosphorus removal (SNDPR) with low-strength wastewater from ambient (>15 °C) to winter temperatures (<15 °C). Results showed that simultaneously advanced nutrients removal, and dramatic in situ sludge reduction (Yobs of 0.093 g MLSS/g COD) were gained regardless of seasonally decreasing temperatures. Winter temperatures even amplified Candidatus Competibacter predominating from 20.11% to 34.74%, which laid the core basis for endogenous denitrification, sludge minimization and temperature resistance. A removal model was thus proposed given the observed functional groups, and doubts were also raised for future investigations. This study would aid a better understanding on the microbial ecology and engineering aspects of the new AOA-AGS process treating low-strength wastewater at low temperatures.}, }
@article {pmid37537784, year = {2023}, author = {Guan, X and Zhao, Z and Jiang, J and Fu, L and Liu, J and Pan, Y and Gao, S and Wang, B and Chen, Z and Wang, X and Sun, H and Jiang, B and Dong, Y and Zhou, Z}, title = {Succession and assembly mechanisms of seawater prokaryotic communities along an extremely wide salinity gradient.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13188}, pmid = {37537784}, issn = {1758-2229}, support = {2022JH2/101300155//Applied Basic Research Project of Liaoning Province/ ; 2022XTCX0504//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; 2021RT08//Innovation and Entrepreneurship Program for High-level Talent of Dalian/ ; 2021921071//Liaoning BaiQianWan Talents Program/ ; }, abstract = {Salinity is an important environmental factor in microbial ecology for affecting the microbial communities in diverse environments. Understanding the salinity adaptation mechanisms of a microbial community is a significant issue, while most previous studies only covered a narrow salinity range. Here, variations in seawater prokaryotic communities during the whole salt drying progression (salinity from 3% to 25%) were investigated. According to high-throughput sequencing results, the diversity, composition, and function of seawater prokaryotic communities varied significantly along the salinity gradient, expressing as decreased diversity, enrichment of some halophilic archaea, and powerful nitrate reduction in samples with high salt concentrations. More importantly, a sudden and dramatic alteration of prokaryotic communities was observed when salinity reached 16%, which was recognized as the change point. Combined with the results of network analysis, we found the increasing of complexity but decreasing of stability in prokaryotic communities when salinity exceeded the change point. Moreover, prokaryotic communities became more deterministic when salinity exceeded the change point due to the niche adaptation of halophilic species. Our study showed that substantial variations in seawater prokaryotic communities along an extremely wide salinity gradient, and also explored the underlying mechanisms regulating these changes.}, }
@article {pmid37537681, year = {2023}, author = {Mendes, LW and Raaijmakers, JM and de Hollander, M and Sepo, E and Gómez Expósito, R and Chiorato, AF and Mendes, R and Tsai, SM and Carrión, VJ}, title = {Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {68}, pmid = {37537681}, issn = {2524-6372}, support = {2014/03217-3, 2015/00251-9, 2020/00469-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 408191/2018-0, 307670/2021-0, 302591/2019-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.185941/2018-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.<br><br>RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.<br><br>CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.}, }
@article {pmid37535084, year = {2023}, author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW}, title = {Correction to: Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02281-z}, pmid = {37535084}, issn = {1432-184X}, }
@article {pmid37535083, year = {2023}, author = {Šaraba, V and Milovanovic, J and Nikodinovic-Runic, J and Budin, C and de Boer, T and Ciric, M}, title = {Brackish Groundwaters Contain Plastic- and Cellulose-Degrading Bacteria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37535083}, issn = {1432-184X}, abstract = {The selected brackish groundwater occurrences in the geotectonic regions of Inner Dinarides of western Serbia (Obrenovačka Banja) and Serbian crystalline core (Lomnički Kiseljak and Velika Vrbnica) were sampled for isolation and identification of plastic- and lignocellulose-degrading bacteria, as well as for the assessment of their enzymatic potential. The examined occurrences belong to the cold and warm (subthermal), weakly alkaline, neutral, and weakly acidic groundwater, and their genetic types are HCO3-Na + K and HCO3-Ca, Mg. The most abundant genera identified by next-generation 16S sequencing of cultivated groundwater samples belong to Aeromonas and Exiguobacterium. Of isolates screened on plastic and lignocellulosic substrates, 85.3% demonstrated growth and/or degrading activity on at least one tested substrate, with 27.8% isolates degrading plastic substrate Impranil® DLN-SD (SD), 1.9% plastic substrate bis(2-hydroxyethyl)terephthalate, and 5.6% carboxymethyl cellulose (CMC). Isolates degrading SD that were identified by 16S rDNA sequencing belonged to genera Stenotrophomonas, Flavobacterium, Pantoea, Enterobacter, Pseudomonas, Serratia, Acinetobacter, and Proteus, while isolates degrading CMC belonged to genera Rhizobium and Shewanella. All investigated brackish groundwaters harbor bacteria with potential in degradation of plastics or cellulose. Taking into account that microplastics contamination of groundwater resources is becoming a significant problem, the finding of plastic-degrading bacteria may have potential in bioremediation treatments of polluted groundwater. Subterranean ecosystems, which are largely untapped resources of biotechnologically relevant enzymes, are not traditionally considered the environment of choice for screening for plastic- and cellulose-degrading bacteria and therefore deserve a special attention from this aspect.}, }
@article {pmid37533451, year = {2023}, author = {Pandey, S and Kim, ES and Cho, JH and Song, M and Doo, H and Kim, S and Keum, GB and Kwak, J and Ryu, S and Choi, Y and Kang, J and Lee, JJ and Kim, HB}, title = {Swine gut microbiome associated with non-digestible carbohydrate utilization.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1231072}, pmid = {37533451}, issn = {2297-1769}, abstract = {Non-digestible carbohydrates are an unavoidable component in a pig's diet, as all plant-based feeds contain different kinds of non-digestible carbohydrates. The major types of non-digestible carbohydrates include non-starch polysaccharides (such as cellulose, pectin, and hemicellulose), resistant starch, and non-digestible oligosaccharides (such as fructo-oligosaccharide and xylo-oligosaccharide). Non-digestible carbohydrates play a significant role in balancing the gut microbial ecology and overall health of the swine by promoting the production of short chain fatty acids. Although non-digestible carbohydrates are rich in energy, swine cannot extract this energy on their own due to the absence of enzymes required for their degradation. Instead, they rely on gut microbes to utilize these carbohydrates for energy production. Despite the importance of non-digestible carbohydrate degradation, limited studies have been conducted on the swine gut microbes involved in this process. While next-generation high-throughput sequencing has aided in understanding the microbial compositions of the swine gut, specific information regarding the bacteria involved in non-digestible carbohydrate degradation remains limited. Therefore, it is crucial to investigate and comprehend the bacteria responsible for the breakdown of non-digestible carbohydrates in the gut. In this mini review, we have discussed the major bacteria involved in the fermentation of different types of non-digestible carbohydrates in the large intestine of swine, shedding light on their potential roles and contributions to swine nutrition and health.}, }
@article {pmid37532947, year = {2023}, author = {Jabir, T and Jain, A and Vipindas, PV and Krishnan, KP}, title = {Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37532947}, issn = {1432-184X}, abstract = {Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3[+]) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.}, }
@article {pmid37531050, year = {2023}, author = {Zhang, D and Sun, J and Wang, D and Peng, S and Wang, Y and Lin, X and Yang, X and Hua, Q and Wu, P}, title = {Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37531050}, issn = {1614-7499}, support = {BK20201110//Natural Science Foundation of Jiangsu Province/ ; 2021BEE02025//Key Research and Development Program of Ningxia/ ; NMKJXM202009//Science and Technology Major Project of Inner Mongolia/ ; }, abstract = {Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.}, }
@article {pmid37528183, year = {2023}, author = {Wang, L and Wang, J and Yuan, J and Tang, Z and Wang, J and Zhang, Y}, title = {Long-Term Organic Fertilization Strengthens the Soil Phosphorus Cycle and Phosphorus Availability by Regulating the pqqC- and phoD-Harboring Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37528183}, issn = {1432-184X}, abstract = {The pqqC and phoD genes encode pyrroloquinoline quinone synthase and alkaline phosphomonoesterase (ALP), respectively. These genes play a crucial role in regulating the solubilization of inorganic phosphorus (Pi) and the mineralization of organic phosphorus (Po), making them valuable markers for P-mobilizing bacterial. However, there is limited understanding of how the interplay between soil P-mobilizing bacterial communities and abiotic factors influences P transformation and availability in the context of long-term fertilization scenarios. We used real-time polymerase chain reaction and high-throughput sequencing to explore the characteristics of soil P-mobilizing bacterial communities and their relationships with key physicochemical properties and P fractions under long-term fertilization scenarios. In a 38-year fertilization experiment, six fertilization treatments were selected. These treatments were sorted into three groups: the non-P-amended group, including no fertilization and mineral NK fertilizer; the sole mineral-P-amended group, including mineral NP and NPK fertilizer; and the organically amended group, including sole organic fertilizer and organic fertilizer plus mineral NPK fertilizer. The organically amended group significantly increased soil labile P (Ca2-P and enzyme-P) and Olsen-P content and proportion but decreased non-labile P (Ca10-P) proportion compared with the sole mineral-P-amended group, indicating enhanced P availability in the soil. Meanwhile, the organically amended group significantly increased soil ALP activity and pqqC and phoD gene abundances, indicating that organic fertilization promotes the activity and abundance of microorganisms involved in P mobilization processes. Interestingly, the organically amended group dramatically reshaped the community structure of P-mobilizing bacteria and increased the relative abundance of Acidiphilium, Panacagrimonas, Hansschlegelia, and Beijerinckia. These changes had a greater positive impact on ALP activity, labile P, and Olsen-P content compared to the abundance of P-mobilizing genes alone, indicating their importance in driving P mobilization processes. Structural equation modeling indicated that soil organic carbon and Po modulated the relationship between P-mobilizing bacterial communities and labile P and Olsen-P, highlighting the influence of SOC and Po on the functioning of P-mobilizing bacteria and their impact on P availability. Overall, our study demonstrates that organic fertilization has the potential to reshape the structure of P-mobilizing bacterial communities, leading to increased P mobilization and availability in the soil. These findings contribute to our understanding of the mechanisms underlying P cycling in agricultural systems and provide valuable insights for enhancing microbial P mobilization through organic fertilization.}, }
@article {pmid37527741, year = {2023}, author = {Antonelli, P and Peruzzo, A and Mancin, M and Boscolo Anzoletti, A and Dall'Ara, S and Orsini, M and Bordin, P and Arcangeli, G and Zanolin, B and Barco, L and Losasso, C}, title = {Tetrodotoxin in bivalve mollusks: An integrated study towards the comprehension of the influencing factors of a newly native phenomenon.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139682}, doi = {10.1016/j.chemosphere.2023.139682}, pmid = {37527741}, issn = {1879-1298}, abstract = {Tetrodotoxins (TTXs) are potent neurotoxins named after the Tetraodontidae fish family. The ingestion of TTX-contaminated flesh can cause neurotoxic symptoms and can lead to death. In 2017 symptoms the European Food Safety Authority (EFSA) recognized the threat to food safety resulting from TTX exposure via food consumption and, thus, proposed a safety limit of 44 μg/kg of TTX in marine gastropods and bivalves. To date, however, TTXs have not yet been included in the list of biotoxins to be monitored within the European Union, even though, in a few cases, levels of TTX found were higher than the EFSA limit. The origin of TTX production is debated and the roles of both biotic and abiotic factors on TTX-mediated toxic events remain unclear. In order to meet these knowledge requests the present study was aimed to investigate the role of seawater temperature, pH, water conductivity, and oxygen saturation, along with the marine phytoplankton community and the bacterial community of mussels and oysters on the accumulation of TTX and analogues in the bivalves. Abiotic parameters were measured by means of a multi-parametric probe, phytoplankton community was analyzed by optic microscopy while microbial community was described by amplicon metataxonomic sequencing, TTXs concentration in the collected matrices were measured by HILIC-MS/MS. A possible role of seawater pH and temperature, among the investigated abiotic factors, in regulating the occurrence of TTXs was found. Regarding biotic variables, a possible influence of Vibrio, Shewanella and Flavobacteriaceae in the occurrence of TTXs was found. Concurrently, Prorocentrum cordatum cell numbers were correlated to the incidence of TTX in mussels. The results herein collected suggest that environmental variables play a consistent part in the occurrence of TTX in the edible bivalve habitats, and there are also indications of a potential role played by specific bacteria taxa in association with phytoplankton.}, }
@article {pmid37527740, year = {2023}, author = {Wang, Y and Gao, Y and Lu, X and Gadow, SI and Zhuo, G and Hu, W and Song, Y and Zhen, G}, title = {Bioelectrochemical anaerobic membrane bioreactor enables high methane production from methanolic wastewater: Roles of microbial ecology and microstructural integrity of anaerobic biomass.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {139676}, doi = {10.1016/j.chemosphere.2023.139676}, pmid = {37527740}, issn = {1879-1298}, abstract = {The disintegration of anaerobic sludge and blockage of membrane pores has impeded the practical application of anaerobic membrane bioreactor (AnMBR) in treating methanolic wastewater. In this study, bioelectrochemical system (BES) was integrated into AnMBR to alleviate sludge dispersion and membrane fouling as well as enhance bioconversion of methanol. Bioelectrochemical regulation effect induced by BES enhanced methane production rate from 4.94 ± 0.52 to 5.39 ± 0.37 L/Lreactor/d by accelerating the enrichment of electroactive microorganisms and the agglomeration of anaerobic sludge via the adhesive and chemical bonding force. 16 S rRNA gene high-throughput sequencing demonstrated that bioelectrochemical stimulation had modified the metabolic pathways by regulating the key functional microbial communities. Methanogenesis via the common methylotrophic Methanomethylovorans was partially substituted by the hydrogenotrophic Candidatus_Methanofastidiosum, etc. The metabolic behaviors of methanol are bioelectrochemistry-dependent, and controlling external voltage is thus an effective strategy for ensuring robust electron transfer, low membrane fouling, and long-term process stability.}, }
@article {pmid37525505, year = {2023}, author = {Effelsberg, N and Kobusch, I and Schollenbruch, H and Linnemann, S and Bang, C and Franke, A and Köck, R and Boelhauve, M and Mellmann, A}, title = {Pilot study on nasal microbiota dynamics and MRSA carriage of a pig cohort housed on straw bedding.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.15136}, pmid = {37525505}, issn = {1365-2958}, support = {01KI2009A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01KI2009B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) can be transmitted between pigs and humans on farms. Hence, the reduction of MRSA carriage in pigs could decrease the risk of zoonotic transmission. Recently, straw bedding has been found to significantly reduce MRSA carriage in pigs. The mechanisms behind this effect remain unclear but changes in the nasal microbiome may play a role. In this exploratory study, the nasal microbiota of pigs kept on straw was examined using V1/V2 16S rRNA gene sequencing. Nasal swabs were collected from 13 pigs at six different time points during the course of a full fattening cycle resulting in 74 porcine samples. In addition, straw samples were collected at each time point. Eleven out of 13 pigs were MRSA positive at housing-in. We found a strong temporal pattern in the microbial communities. Both microbial diversity and abundance of Staphylococcus species peaked in week 5 after introduction to the straw stable decreased in week 10, when all pigs turned MRSA-negative, and increased again toward the end of the fattening period. These findings show that the introduction of pigs into a new environment has a huge impact on their nasal microbiota, which might lead to unfavorable conditions for MRSA. Moreover, other Staphylococcus species may play a role in eliminating MRSA carriage. We designed a follow-up study including two different husbandry systems to further assess these effects.}, }
@article {pmid37523041, year = {2023}, author = {Li, S and Young, T and Archer, S and Lee, K and Alfaro, AC}, title = {Gut microbiome resilience of green-lipped mussels, Perna canaliculus, to starvation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37523041}, issn = {1618-1905}, abstract = {Host gut microbiomes play an important role in animal health and resilience to conditions, such as malnutrition and starvation. These host-microbiome relationships are poorly understood in the marine mussel Perna canaliculus, which experiences significant variations in food quantity and quality in coastal areas. Prolonged starvation may be a contributory factor towards incidences of mass mortalities in farmed mussel populations, resulting in highly variable production costs and unreliable market supplies. Here, we examine the gut microbiota of P. canaliculus in response to starvation and subsequent re-feeding using high-throughput amplicon sequencing of the 16S rRNA gene. Mussels showed no change in bacterial species richness when subjected to a 14-day starvation, followed by re-feeding/recovery. However, beta bacteria diversity revealed significant shifts (PERMANOVA p-value < 0.001) in community structure in the starvation group and no differences in the subsequent recovery group (compared to the control group) once they were re-fed, highlighting their recovery capability and resilience. Phylum-level community profiles revealed an elevation in dominance of Proteobacteria (ANCOM-BC p-value <0.001) and Bacteroidota (ANCOM-BC p-value = 0.04) and lower relative abundance of Cyanobacteria (ANCOM-BC p-value = 0.01) in the starvation group compared to control and recovery groups. The most abundant genus-level shifts revealed relative increases of the heterotroph Halioglobus (p-value < 0.05) and lowered abundances of the autotroph Synechococcus CC9902 in the starvation group. Furthermore, a SparCC correlation network identified co-occurrence of a cluster of genera with elevated relative abundance in the starved mussels that were positively correlated with Synechococcus CC9902. The findings from this work provide the first insights into the effect of starvation on the resilience capacity of Perna canaliculus gut microbiota, which is of central importance to understanding the effect of food variation and limitation in farmed mussels.}, }
@article {pmid37520283, year = {2023}, author = {Wentzien, NM and Fernández-González, AJ and Villadas, PJ and Valverde-Corredor, A and Mercado-Blanco, J and Fernández-López, M}, title = {Thriving beneath olive trees: The influence of organic farming on microbial communities.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {3575-3589}, pmid = {37520283}, issn = {2001-0370}, abstract = {Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 10[6] ± 1.62 × 10[5] (CM) to 4.54 × 10[6] ± 8.07 × 10[5] (OM) copies of the 18 S rRNA gene g[-1] soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.}, }
@article {pmid37516570, year = {2023}, author = {Parizadeh, M and Arrieta, MC}, title = {The global human gut microbiome: genes, lifestyles, and diet.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2023.07.002}, pmid = {37516570}, issn = {1471-499X}, abstract = {A growing number of human gut microbiome studies consistently describe differences between human populations. Here, we review how factors related to host genetics, ethnicity, lifestyle, and geographic location help explain this variation. Studies from contrasting environmental scenarios point to diet and lifestyle as the most influential. The effect of human migration and displacement demonstrates how the microbiome adapts to newly adopted lifestyles and contributes to the profound biological and health consequences attributed to migration. This information strongly suggests against a universal scale for healthy or dysbiotic gut microbiomes, and prompts for additional microbiome population surveys, particularly from less industrialized nations. Considering these important differences will be critical for designing strategies to diagnose and restore dysbiosis in various human populations.}, }
@article {pmid37515622, year = {2023}, author = {Mi, JX and Liu, KL and Ding, WL and Zhang, MH and Wang, XF and Shaukat, A and Rehman, MU and Jiao, XL and Huang, SC}, title = {Comparative analysis of the gut microbiota of wild wintering whooper swans (Cygnus Cygnus), captive black swans (Cygnus Atratus), and mute swans (Cygnus Olor) in Sanmenxia Swan National Wetland Park of China.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37515622}, issn = {1614-7499}, support = {No. 32202876//National Natural Science Foundation of China/ ; No. 30501374//Special Support Fund for High-level Talents of Henan Agricultural University/ ; }, abstract = {The gastrointestinal microbiota, a complex ecosystem, is involved in the physiological activities of hosts and the development of diseases. Birds occupy a critical ecological niche in the ecosystem, performing a variety of ecological functions and possessing a complex gut microbiota composition. However, the gut microbiota of wild and captive birds has received less attention in the same region. We profiled the fecal gut microbiome of wild wintering whooper swans (Cygnus Cygnus; Cyg group, n = 25), captive black swans (Cygnus Atratus; Atr group, n = 20), and mute swans (Cygnus Olor; Olor group, n = 30) using 16S rRNA gene sequencing to reveal differences in the gut microbial ecology. The results revealed that the three species of swans differed significantly in terms of the alpha and beta diversity of their gut microbiota, as measured by ACE, Chao1, Simpson and Shannon indices, principal coordinates analysis (PCoA) and non-metricmulti-dimensional scaling (NMDS) respectively. Based on the results of the linear discriminant analysis effect size (LEfSe) and random forest analysis, we found that there were substantial differences in the relative abundance of Gottschalkia, Trichococcus, Enterococcus, and Kurthia among the three groups. Furthermore, an advantageous pattern of interactions between microorganisms was shown by the association network analysis. Among these, Gottschalkia had the higher area under curve (AUC), which was 0.939 (CI = 0.879-0.999), indicating that it might be used as a biomarker to distinguish between wild and captive black swans. Additionally, PICRUSt2 predictions indicated significant differences in gut microbiota functions between wild and captive trumpeter swans, with the gut microbiota functions of Cyg group focusing on carbohydrate metabolism, membrane transport, cofactor, and vitamin metabolism pathways, the Atr group on lipid metabolism, and the Olor group on cell motility, amino acid metabolism, and replication and repair pathways. These findings showed that the gut microbiota of wild and captive swans differed, which is beneficial to understand the gut microecology of swans and to improve regional wildlife conservation strategies.}, }
@article {pmid37512939, year = {2023}, author = {Mourgela, RN and Kioukis, A and Pourjam, M and Lagkouvardos, I}, title = {Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512939}, issn = {2076-2607}, abstract = {The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.}, }
@article {pmid37512925, year = {2023}, author = {St-Pierre, B and Perez Palencia, JY and Samuel, RS}, title = {Impact of Early Weaning on Development of the Swine Gut Microbiome.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512925}, issn = {2076-2607}, support = {Hatch projects SD00H719-20 and SD00H682-19//South Dakota State University Agricultural Experiment Station / USDA National Institute of Food and Agriculture/ ; }, abstract = {Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.}, }
@article {pmid37512843, year = {2023}, author = {Cowan, DA and Cary, SC and DiRuggiero, J and Eckardt, F and Ferrari, B and Hopkins, DW and Lebre, PH and Maggs-Kölling, G and Pointing, SB and Ramond, JB and Tribbia, D and Warren-Rhodes, K}, title = {'Follow the Water': Microbial Water Acquisition in Desert Soils.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/microorganisms11071670}, pmid = {37512843}, issn = {2076-2607}, support = {80256//National Research Foundation/ ; }, abstract = {Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.}, }
@article {pmid37511881, year = {2023}, author = {Walther-Antonio, M and Schulze-Makuch, D}, title = {The Hypothesis of a "Living Pulse" in Cells.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/life13071506}, pmid = {37511881}, issn = {2075-1729}, abstract = {Motility is a great biosignature and its pattern is characteristic for specific microbes. However, motion does also occur within the cell by the myriads of ongoing processes within the cell and the exchange of gases and nutrients with the outside environment. Here, we propose that the sum of these processes in a microbial cell is equivalent to a pulse in complex organisms and suggest a first approach to measure the "living pulse" in microorganisms. We emphasize that if a "living pulse" can be shown to exist, it would have far-reaching applications, such as for finding life in extreme environments on Earth and in extraterrestrial locations, as well as making sure that life is not present where it should not be, such as during medical procedures and in the food processing industry.}, }
@article {pmid37511821, year = {2023}, author = {Schulze-Makuch, D and Irwin, LN}, title = {Life Unknown: Preliminary Scheme for a Magnetotrophic Organism.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/life13071446}, pmid = {37511821}, issn = {2075-1729}, abstract = {No magnetotrophic organism on Earth is known to use magnetic fields as an energy source or the storage of information. However, a broad diversity of life forms is sensitive to magnetic fields and employs them for orientation and navigation, among other purposes. If the magnetic field strength were much larger, such as that on planets around neutron stars or magnetars, metabolic energy could be obtained from these magnetic fields in principle. Here, we introduce three hypothetical models of magnetotrophic organisms that obtain energy via the Lorentz force. Even if an organism uses magnetic fields only as an energy source, but otherwise is relying on biochemistry, this organism would be by definition a magnetotrophic form of life as we do not know it.}, }
@article {pmid37511182, year = {2023}, author = {Turbant, F and Waeytens, J and Blache, A and Esnouf, E and Raussens, V and Węgrzyn, G and Achouak, W and Wien, F and Arluison, V}, title = {Interactions and Insertion of Escherichia coli Hfq into Outer Membrane Vesicles as Revealed by Infrared and Orientated Circular Dichroism Spectroscopies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, doi = {10.3390/ijms241411424}, pmid = {37511182}, issn = {1422-0067}, support = {101004806//Trans-National Access (TNA) of Molecular-Scale Biophysics Research Infrastructure (MOSBRI)/ ; 08254//IEA/PICS CNRS/ ; ANR-11-IDEX-0003-02//Investissements d'Avenir &#xbb; program, through the "ADI 2021 Paris Saclay/ ; 2016/21/N/NZ1/02850//National Science Center Poland/ ; 531-D020-D242-23//University of Gdansk/ ; }, abstract = {The possible carrier role of Outer Membrane Vesicles (OMVs) for small regulatory noncoding RNAs (sRNAs) has recently been demonstrated. Nevertheless, to perform their function, these sRNAs usually need a protein cofactor called Hfq. In this work we show, by using a combination of infrared and circular dichroism spectroscopies, that Hfq, after interacting with the inner membrane, can be translocated into the periplasm, and then be exported in OMVs, with the possibility to be bound to sRNAs. Moreover, we provide evidence that Hfq interacts with and is inserted into OMV membranes, suggesting a role for this protein in the release of sRNA outside the vesicle. These findings provide clues to the mechanism of host-bacteria interactions which may not be defined solely by protein-protein and protein-outer membrane contacts, but also by the exchange of RNAs, and in particular sRNAs.}, }
@article {pmid37509218, year = {2023}, author = {Li, G and Jin, Y and Chen, B and Lin, A and Wang, E and Xu, F and Hu, G and Xiao, C and Liu, H and Hou, X and Zhang, B and Song, J}, title = {Exploring the Relationship between the Gut Mucosal Virome and Colorectal Cancer: Characteristics and Correlations.}, journal = {Cancers}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/cancers15143555}, pmid = {37509218}, issn = {2072-6694}, support = {Nos. 81873553//National Natural Science Foundation of China/ ; Nos. 81800465//National Natural Science Foundation of China/ ; }, abstract = {The fecal virome has been reported to be associated with CRC. However, little is known about the mucosal virome signature in CRC. This study aimed to determine the viral community within CRC tissues and their contributions to colorectal carcinogenesis. Colonic mucosal biopsies were harvested from patients with CRC (biopsies of both neoplasia and adjacent normal tissue (CRC-A)) and healthy controls (HC). The shot-gun metagenomic sequencing of virus-like particles (VLPs) was performed on the biopsies. Viral community, functional pathways, and their correlations to clinical data were analyzed. Fluorescence in situ hybridizations (FISH) for the localization of viruses in the intestine was performed, as well as quantitative PCR for the detection of Torque teno virus load in human mucosal VLP DNA. A greater number and proportion of core species were found in CRC tissues than in CRC-A and HC tissues. The diversity of the mucosal virome in CRC tissues was significantly increased compared to that in HC and CRC-A tissues. The mucosal virome signature of CRC tissues were significantly different from those of HC and CRC-A tissues at the species level. The abundances of eukaryotic viruses from the Anelloviridae family and its sub-species Torque teno virus (TTV) were significantly higher in CRC patients than in HC. Furthermore, increased levels of TTV in the intestinal lamina propria were found in the CRC group. Multiple viral functions of TTV associated with carcinogenesis were enriched in CRC tissues. We revealed for the first time that the mucosal virobiota signature of CRC is characterized by a higher diversity and more eukaryotic viruses. The enrichment of TTV species in CRC tissues suggests that they may play an oncogenic role in CRC. Targeting eukaryotic viruses in the gut may provide novel strategies for the prevention and treatment of CRC.}, }
@article {pmid37507629, year = {2023}, author = {Daba, G and Daelemans, R and Berecha, G and Geerinck, MWJ and Verreth, C and Crauwels, S and Lievens, B and Honnay, O}, title = {Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37507629}, issn = {1618-1905}, abstract = {Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.}, }
@article {pmid37507489, year = {2023}, author = {Daraz, U and Erhunmwunse, AS and Dubeux, JCB and Mackowiak, C and Guerra, VA and Hsu, CM and Ma, J and Li, Y and Yang, X and Liao, HL and Wang, XB}, title = {Soil Bacterial Communities Across Seven Rhizoma Peanut Cultivars (Arachis glabrata Benth.) Respond to Seasonal Variation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37507489}, issn = {1432-184X}, abstract = {Soil microorganisms play key roles in soil nutrient transformations and have a notable effect on plant growth and health. Different plant genotypes can shape soil microbial patterns via the secretion of root exudates and volatiles, but it is uncertain how a difference in soil microorganisms induced by crop cultivars will respond to short-term seasonal variations. A field experiment was conducted to assess the changes in soil bacterial communities of seven rhizoma peanut (Arachis glabrata Benth, RP) cultivars across two growing seasons, April (Spring season) and October (Fall season). Soils' bacterial communities were targeted using 16S rRNA gene amplicon sequencing. Bacterial community diversity and taxonomic composition among rhizoma peanut cultivars were significantly affected by seasons, cultivars, and their interactions (p < 0.05). Alpha diversity, as estimated by the OTU richness and Simpson index, was around onefold decrease in October than in April across most of the RP cultivars, while the soils from Arblick and Latitude had around one time higher alpha diversity in both seasons compared with other cultivars. Beta diversity differed significantly in April (R = 0.073, p < 0.01) and October (R = 0.084, p < 0.01) across seven cultivars. Bacterial dominant taxa (at phylum and genus level) were strongly affected by seasons and varied towards more dominant groups that have functional potentials involved in nutrient cycling from April to October. A large shift in water availability induced by season variations in addition to host cultivar's effects can explain the observed patterns in diversity, composition, and co-occurrence of bacterial taxa. Overall, our results demonstrate an overriding effect of short-term seasonal variations on soil bacterial communities associated with different crop cultivars. The findings suggest that season-induced shifts in environmental conditions could exert stronger impacts on soil microorganisms than the finer-scale rhizosphere effect from crop cultivars, and consequently influence largely microbe-mediated soil processes and crop health in agricultural ecosystems.}, }
@article {pmid37507488, year = {2023}, author = {Gonçalves, OS and Santana, MF}, title = {Uncovering the Secrets of Slow-Growing Bacteria in Tropical Savanna Soil Through Isolation and Genomic Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37507488}, issn = {1432-184X}, abstract = {One gram of soil holds ten billion bacteria of thousands of different species, but most remain unknown, and one of the serious issues is intrinsic to slow-growing bacteria. In this study, we aimed to isolate and characterize slow-growing bacteria from Brazilian Cerrado soil. Over a period of 4 weeks, we conducted an incubation process and selected a total of 92 isolates. These isolates, consisting mostly of slow-growing bacteria, have the ability to thrive in low-water conditions and possess features that promote plant growth. To identify the isolated bacteria, we performed 16S rRNA sequencing analysis and found that the slow-growing strains were genetically similar to known bacterial species but also belonged to a novel group of species. The new strains identified were Caballeronia sp., Neobacillus sp., Bradyrhizobium sp., and high GC Gram-positive species. Furthermore, we conducted growth experiments using various culture media and temperature conditions. These experiments revealed an extended lag phase for five strains, indicating their slow growth characteristics. Genomic analysis of these five slow-growing bacteria showed their potential to participate in biogeochemical cycles, metabolize various carbohydrates, encode proteins with a role in promoting plant growth and have biosynthetic potential for secondary metabolites. Taken together, our findings reveal the untapped potential of slow-growing bacteria in tropical savanna soils.}, }
@article {pmid37507453, year = {2023}, author = {Villela, H and Modolon, F and Schultz, J and Delgadillo-Ordoñez, N and Carvalho, S and Soriano, AU and Peixoto, RS}, title = {Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12273}, pmid = {37507453}, issn = {2045-2322}, abstract = {Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.}, }
@article {pmid37507436, year = {2023}, author = {Melaugh, G and Martinez, VA and Baker, P and Hill, PJ and Howell, PL and Wozniak, DJ and Allen, RJ}, title = {Distinct types of multicellular aggregates in Pseudomonas aeruginosa liquid cultures.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {52}, pmid = {37507436}, issn = {2055-5008}, support = {EP/J007404//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/J007404//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/J007404//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; RGY0081/2012//Human Frontier Science Program (HFSP)/ ; RGY0081/2012//Human Frontier Science Program (HFSP)/ ; }, abstract = {Pseudomonas aeruginosa forms suspended multicellular aggregates when cultured in liquid media. These aggregates may be important in disease, and/or as a pathway to biofilm formation. The polysaccharide Psl and extracellular DNA (eDNA) have both been implicated in aggregation, but previous results depend strongly on the experimental conditions. Here we develop a quantitative microscopy-based method for assessing changes in the size distribution of suspended aggregates over time in growing cultures. For exponentially growing cultures of P. aeruginosa PAO1, we find that aggregation is mediated by cell-associated Psl, rather than by either eDNA or secreted Psl. These aggregates arise de novo within the culture via a growth process that involves both collisions and clonal growth, and Psl non-producing cells do not aggregate with producers. In contrast, we find that stationary phase (overnight) cultures contain a different type of multicellular aggregate, in which both eDNA and Psl mediate cohesion. Our findings suggest that the physical and biological properties of multicellular aggregates may be very different in early-stage vs late-stage bacterial cultures.}, }
@article {pmid37505287, year = {2023}, author = {Feckler, A and Baudy-Groh, P and Friedrichs, L and Gonçalves, S and Lüderwald, S and Risse-Buhl, U and Bundschuh, M}, title = {Diatoms Reduce Decomposition of and Fungal Abundance on Less Recalcitrant Leaf Litter via Negative Priming.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37505287}, issn = {1432-184X}, support = {2017-0507//Vetenskapsr&#xe5;det/ ; 2017-0507//Vetenskapsr&#xe5;det/ ; }, abstract = {Heterotrophic microbial decomposers colonize submerged leaf litter in close spatial proximity to periphytic algae that exude labile organic carbon during photosynthesis. These exudates are conjectured to affect microbial decomposers' abundance, resulting in a stimulated (positive priming) or reduced (negative priming) leaf litter decomposition. Yet, the occurrence, direction, and intensity of priming associated with leaf material of differing recalcitrance remains poorly tested. To assess priming, we submerged leaf litter of differing recalcitrance (Alnus glutinosa [alder; less recalcitrant] and Fagus sylvatica [beech; more recalcitrant]) in microcosms and quantified bacterial, fungal, and diatom abundance as well as leaf litter decomposition over 30 days in absence and presence of light. Diatoms did not affect beech decomposition but reduced alder decomposition by 20% and alder-associated fungal abundance by 40% in the treatments including all microbial groups and light, thus showing negative priming. These results suggest that alder-associated heterotrophs acquired energy from diatom exudates rather than from leaf litter. Moreover, it is suggested that these heterotrophs have channeled energy to alternative (reproductive) pathways that may modify energy and nutrient availability for the remaining food web and result in carbon pools protected from decomposition in light-exposed stream sections.}, }
@article {pmid37500801, year = {2023}, author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ}, title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37500801}, issn = {2058-5276}, support = {PR1603/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RA3432/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BE6703/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1553211//National Science Foundation (NSF)/ ; }, abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.}, }
@article {pmid37496156, year = {2022}, author = {Wolfsberger, W and Chhugani, K and Shchubelka, K and Frolova, A and Salyha, Y and Zlenko, O and Arych, M and Dziuba, D and Parkhomenko, A and Smolanka, V and Gümüş, ZH and Sezgin, E and Diaz-Lameiro, A and Toth, VR and Maci, M and Bortz, E and Kondrashov, F and Morton, PM and Łabaj, PP and Romero, V and Hlávka, J and Mangul, S and Oleksyk, TK}, title = {Scientists without borders: lessons from Ukraine.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37496156}, issn = {2047-217X}, mesh = {Humans ; Ukraine ; }, abstract = {Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades' worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.}, }
@article {pmid37491575, year = {2023}, author = {Kim, JM and Yoo, SY and An, JS and Woo, JJ and Cho, YD and Park, HE and Karm, MH}, title = {Effect of a multichannel oral irrigator on periodontal health and the oral microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12043}, pmid = {37491575}, issn = {2045-2322}, mesh = {Humans ; Administration, Oral ; Dental Plaque Index ; *Microbiota ; *Periodontal Diseases ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Oral biofilms or dental plaques are one of the major etiological factors for diverse oral diseases. We aimed to evaluate the effect of a multichannel oral irrigator (MCOI) on periodontal health in 29 participants randomly divided into two groups: the MCOI group and the control group. To evaluate the effect of the MCOI on periodontal health, the modified Quigley Hein Plaque Index (PI), Mühlemann-Son Sulcus Bleeding Index (SBI), bleeding on probing (BOP), and swelling were evaluated and compared before and after MCOI use for 3 days. Although PI and SBI showed statistically significant increases in the control group, the MCOI group showed no significant changes in either parameter. Moreover, the percentage of BOP was significantly lower in the MCOI group. Saliva samples were analyzed by 16s rRNA amplicon sequencing to investigate changes in the oral microbiome. Sequencing results showed that Porphyromonas spp. were significantly increased in the control group, whereas no significant change was detected in the MCOI group. Using the MCOI, enriched populations and functional pathways were detected in pioneer species comprising non-mutans streptococci. These findings provide evidence of the effectiveness of the MCOI in maintaining periodontal health and a healthy microbial ecology in the oral cavity.}, }
@article {pmid37486583, year = {2023}, author = {Zaman, R and Antonioli, F and Shah, A and Ullah, A and May, C and Klutsch, JG and Erbilgin, N}, title = {A Pine in Distress: How Infection by Different Pathogenic Fungi Affect Lodgepole Pine Chemical Defenses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37486583}, issn = {1432-184X}, abstract = {In North America, lodgepole pine is frequently subjected to attacks by various biotic agents that compromise its ability to defend against subsequent attacks by insect herbivores. We investigated whether infections of lodgepole pine by different pathogenic fungal species have varying effects on its defense chemistry. We selected two common pathogens, Atropellis canker, Atropellis piniphila, and western gall rust, Endocronartium harknessii, affecting mature lodgepole pine trees in western Canada. We also included three ophiostomatoid fungi Grosmannia clavigera, Ophiostoma montium, and Leptographium longiclavatum associated with the mountain pine beetle (Dendroctonus ponderosae), because they are commonly used to investigate induced defenses of host trees of bark beetles. We collected phloem samples from lodgepole pines infected with the rust or the canker and healthy lodgepole pines in the same stand. We also inoculated mature lodgepole pines with the three fungal symbionts and collected phloem samples 2 weeks later when the defense chemistry was at its highest level. Different fungal species differentially altered the terpene chemistry of lodgepole pine trees. E. harknessii and the fungal symbionts altered the terpene chemistry in a similar pattern while trees responded to the infection by the A. piniphila differently. Our study highlights the importance of considering specific biotic stress agents in tree susceptibility or resistance to the subsequent attacks by insect herbivores, such as mountain pine beetle.}, }
@article {pmid37485515, year = {2023}, author = {Němečková, K and Mareš, J and Procházková, L and Culka, A and Košek, F and Wierzchos, J and Nedbalová, L and Dudák, J and Tymlová, V and Žemlička, J and Kust, A and Zima, J and Nováková, E and Jehlička, J}, title = {Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1175066}, pmid = {37485515}, issn = {1664-302X}, abstract = {In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.}, }
@article {pmid37485507, year = {2023}, author = {Thiele, S and Vader, A and Thomson, S and Saubrekka, K and Petelenz, E and Müller, O and Bratbak, G and Øvreås, L}, title = {Seasonality of the bacterial and archaeal community composition of the Northern Barents Sea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213718}, pmid = {37485507}, issn = {1664-302X}, abstract = {The Barents Sea is a transition zone between the Atlantic and the Arctic Ocean. The ecosystem in this region is highly variable, and a seasonal baseline of biological factors is needed to monitor the effects of global warming. In this study, we report the results from the investigations of the bacterial and archaeal community in late winter, spring, summer, and early winter along a transect through the northern Barents Sea into the Arctic Ocean east of Svalbard using 16S rRNA metabarcoding. Winter samples were dominated by members of the SAR11 clade and a community of nitrifiers, namely Cand. Nitrosopumilus and LS-NOB (Nitrospinia), suggest a prevalence of chemoautotrophic metabolisms. During spring and summer, members of the Gammaproteobacteria (mainly members of the SAR92 and OM60(NOR5) clades, Nitrincolaceae) and Bacteroidia (mainly Polaribacter, Formosa, and members of the NS9 marine group), which followed a succession based on their utilization of different phytoplankton-derived carbon sources, prevailed. Our results indicate that Arctic marine bacterial and archaeal communities switch from carbon cycling in spring and summer to nitrogen cycling in winter and provide a seasonal baseline to study the changes in these processes in response to the effects of climate change.}, }
@article {pmid37485503, year = {2023}, author = {Van Holm, W and Lauwens, K and De Wever, P and Schuermans, A and Zayed, N and Pamuk, F and Saghi, M and Fardim, P and Bernaerts, K and Boon, N and Teughels, W}, title = {Probiotics for oral health: do they deliver what they promise?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1219692}, pmid = {37485503}, issn = {1664-302X}, abstract = {Probiotics have demonstrated oral health benefits by influencing the microbiome and the host. Although promising, their current use is potentially constrained by several restrictions. One such limiting factor lies in the prevailing preparation of a probiotic product. To commercialize the probiotic, a shelf stable product is achieved by temporarily inactivating the live probiotic through drying or freeze drying. Even though a lyophilized probiotic can be kept dormant for an extended period of time, their viability can be severely compromised, making their designation as probiotics questionable. Additionally, does the application of an inactive probiotic directly into the oral cavity make sense? While the dormancy may allow for survival on its way towards the gut, does it affect their capacity for oral colonisation? To evaluate this, 21 probiotic product for oral health were analysed for the number of viable (probiotic), culturable (CFU) and dead (postbiotic) cells, to verify whether the commercial products indeed contain what they proclaim. After isolating and uniformly lyophilizing three common probiotic species in a simple yet effective lyoprotective medium, the adhesion to saliva covered hydroxyapatite discs of lyophilized probiotics was compared to fresh or reactivated lyophilized probiotics. Unfortunately, many of the examined products failed to contain the claimed amounts of viable cells, but also the strains used were inadequately characterized and lacked clinical evidence for that unknown strain, questioning their label of a 'probiotic'. Additionally, lyophilized probiotics demonstrated low adhesive capacity compared to their counterparts, prompting the question of why fresh or reactivated probiotics are not currently used.}, }
@article {pmid37482337, year = {2023}, author = {Santás-Miguel, V and Arias-Estévez, M and Rodríguez-Seijo, A and Arenas-Lago, D}, title = {Use of metal nanoparticles in agriculture. A review on the effects on plant germination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122222}, doi = {10.1016/j.envpol.2023.122222}, pmid = {37482337}, issn = {1873-6424}, abstract = {Agricultural nanotechnology has become a powerful tool to help crops and improve agricultural production in the context of a growing world population. However, its application can have some problems with the development of harvests, especially during germination. This review evaluates nanoparticles with essential (Cu, Fe, Ni and Zn) and non-essential (Ag and Ti) elements on plant germination. In general, the effect of nanoparticles depends on several factors (dose, treatment time, application method, type of nanoparticle and plant). In addition, pH and ionic strength are relevant when applying nanoparticles to the soil. In the case of essential element nanoparticles, Fe nanoparticles show better results in improving nutrient uptake, improving germination, and the possibility of magnetic properties could favor their use in the removal of pollutants. In the case of Cu and Zn nanoparticles, they can be beneficial at low concentrations, while their excess presents toxicity and negatively affects germination. About nanoparticles of non-essential elements, both Ti and Ag nanoparticles can be helpful for nutrient uptake. However, their potential effects depend highly on the crop type, particle size and concentration. Overall, nanotechnology in agriculture is still in its early stages of development, and more research is needed to understand potential environmental and public health impacts.}, }
@article {pmid37482010, year = {2023}, author = {Pan, Y and Sun, RZ and Wang, Y and Chen, GL and Fu, YY and Yu, HQ}, title = {Carbon source shaped microbial ecology, metabolism and performance in denitrification systems.}, journal = {Water research}, volume = {243}, number = {}, pages = {120330}, doi = {10.1016/j.watres.2023.120330}, pmid = {37482010}, issn = {1879-2448}, abstract = {The limited information on microbial interactions and metabolic patterns in denitrification systems, especially those fed with different carbon sources, has hindered the establishment of ecological linkages between microscale connections and macroscopic reactor performance. In this work, denitrification performance, metabolic patterns, and ecological structure were investigated in parallel well-controlled bioreactors with four representative carbon sources, i.e., methanol, glycerol, acetate, and glucose. After long-term acclimation, significant differences were observed among the four bioreactors in terms of denitrification rates, organic utilization, and heterotrophic bacterial yields. Different carbon sources induced the succession of denitrifying microbiota toward different ecological structures and exhibited distinct metabolic patterns. Methanol-fed reactors showed distinctive microbial carbon utilization pathways and a more intricate microbial interaction network, leading to significant variations in organic utilization and metabolite production compared to other carbon sources. Three keystone taxa belonging to the Verrucomicrobiota phylum, SJA-15 order and the Kineosphaera genus appeared as network hubs in the methanol, glycerol, and acetate-fed systems, playing essential roles in their ecological functions. Several highly connected species were also identified within the glucose-fed system. The close relationship between microbial metabolites, ecological structures, and system performances suggests that this complex network relationship may greatly contribute to the efficient operation of bioreactors.}, }
@article {pmid37482007, year = {2023}, author = {Wang, M and Wang, X and Zhou, S and Chen, Z and Chen, M and Feng, S and Li, J and Shu, W and Cao, B}, title = {Strong succession in prokaryotic association networks and community assembly mechanisms in an acid mine drainage-impacted riverine ecosystem.}, journal = {Water research}, volume = {243}, number = {}, pages = {120343}, doi = {10.1016/j.watres.2023.120343}, pmid = {37482007}, issn = {1879-2448}, abstract = {Acid mine drainage (AMD) serves as an ideal model system for investigating microbial ecology, interaction, and assembly mechanism in natural environments. While previous studies have explored the structure and function of microbial communities in AMD, the succession patterns of microbial association networks and underlying assembly mechanisms during natural attenuation processes remain elusive. Here, we investigated prokaryotic microbial diversity and community assembly along an AMD-impacted river, from the extremely acidic, heavily polluted headwaters to the nearly neutral downstream sites. Microbial diversity was increased along the river, and microbial community composition shifted from acidophile-dominated to freshwater taxa-dominated communities. The complexity and relative modularity of the microbial networks were also increased, indicating greater network stability during succession. Deterministic processes, including abiotic selection of pH and high contents of sulfur and iron, governed community assembly in the headwaters. Although the stochasticity ratio was increased downstream, manganese content, microbial negative cohesion, and relative modularity played important roles in shaping microbial community structure. Overall, this study provides valuable insights into the ecological processes that govern microbial community succession in AMD-impacted riverine ecosystems. These findings have important implications for in-situ remediation of AMD contamination.}, }
@article {pmid37480518, year = {2023}, author = {O'Brien, L and Siboni, N and Seymour, JR and Balzer, M and Mitrovic, S}, title = {Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37480518}, issn = {1432-184X}, abstract = {Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.}, }
@article {pmid37480517, year = {2023}, author = {Aguado-López, D and Bartolomé, C and Lopes, AR and Henriques, D and Segura, SK and Maside, X and Pinto, MA and Higes, M and Martín-Hernández, R}, title = {Frequent Parasitism of Apis mellifera by Trypanosomatids in Geographically Isolated Areas with Restricted Beekeeping Movements.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37480517}, issn = {1432-184X}, support = {project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; project No. SBPLY/19/180501/000334//Consejer&#xed;a de Educaci&#xf3;n, Cultura y Deportes, of the Junta de Castilla - La Mancha (European Regional development Fund)/ ; Grant no. PRE2018-084878, RTA2017-00004-C02-01//Ministerio de Asuntos Econ&#xf3;micos y Transformaci&#xf3;n Digital/ ; program COMPETE 2020-POCI//Programa Operacional para a Competividade e Internacionaliza&#xe7;&#xe3;o/ ; program COMPETE 2020-POCI//Programa Operacional para a Competividade e Internacionaliza&#xe7;&#xe3;o/ ; program COMPETE 2020-POCI//Programa Operacional para a Competividade e Internacionaliza&#xe7;&#xe3;o/ ; project BeeHappy (POCI-01-0145-FEDER-029871)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; project BeeHappy (POCI-01-0145-FEDER-029871)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; project BeeHappy (POCI-01-0145-FEDER-029871)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/143627/2019//Funda&#xe7;ao para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0007/2021//SusTEC/ ; LA/P/0007/2021//SusTEC/ ; LA/P/0007/2021//SusTEC/ ; INCRECYT program//European Social Funds/ ; }, abstract = {Trypanosomatids form a group of high prevalence protozoa that parasitise honey bees, with Lotmaria passim as the predominant species worldwide. However, the knowledge about the ecology of trypanosomatids in isolated areas is limited. The Portuguese archipelagos of Madeira and Azores provide an interesting setting to investigate these parasites because of their geographic isolation, and because they harbour honey bee populations devoid of two major enemies: Varroa destructor and Nosema ceranae. Hence, a total of 661 honey bee colonies from Madeira and the Azores were analysed using different molecular techniques, through which we found a high prevalence of trypanosomatids despite the isolation of these islands. L. passim was the predominant species and, in most colonies, was the only one found, even on islands free of V. destructor and/or N. ceranae with severe restrictions on colony movements to prevent the spread of them. However, islands with V. destructor had a significantly higher prevalence of L. passim and, conversely, islands with N. ceranae did not shown any significant correlation with the trypanosomatid. Crithidia bombi was detected in Madeira and on three islands of the Azores, almost always coincident with L. passim. By contrast, Crithidia mellificae was not detected in any sample. A high-throughput sequencing analysis distinguished two main haplotypes of L. passim, which accounted for 98% of the total sequence reads. This work suggests that L. passim and C. bombi are parasites that have been associated with honey bees predating the spread of V. destructor and N. ceranae.}, }
@article {pmid37479828, year = {2023}, author = {Ravindhiran, R and Sivarajan, K and Sekar, JN and Murugesan, R and Dhandapani, K}, title = {Listeria monocytogenes an Emerging Pathogen: a Comprehensive Overview on Listeriosis, Virulence Determinants, Detection, and Anti-Listerial Interventions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37479828}, issn = {1432-184X}, abstract = {Listeria monocytogenes, the third most deleterious zoonotic pathogen, is a major causative agent of animal and human listeriosis, an infection related to the consumption of contaminated food products. Even though, this pathogen has been responsible for the outbreaks of foodborne infections in the early 1980s, the major outbreaks have been reported during the past two decades. Listeriosis infection in the host is a rare but life-threatening disease with major public health and economic implications. Extensive reports on listeriosis outbreaks are associated with milk and milk products, meat and meat products, and fresh produce. This bacterium can adapt to any environmental and stress conditions, making it a prime causative agent for major foodborne diseases. The pathogen could survive an antibiotic treatment and persist in the host cell, thereby escaping the standard diagnostic practices. The current review strives to provide concise information on the epidemiology, serotypes, and pathogenesis of the L. monocytogenes to decipher the knowledge on the endurance of the pathogen inside the host and food products as a vehicle for Listeria contaminations. In addition, various detection methods for Listeria species from food samples and frontline regimens of L. monocytogenes treatment have also been discussed.}, }
@article {pmid37479827, year = {2023}, author = {Hirata, K and Asahi, T and Kataoka, K}, title = {Spatial and Sexual Divergence of Gut Bacterial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37479827}, issn = {1432-184X}, abstract = {The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut compartments, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut bacteriome of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by their gut compartments rather than sex. The species richness and diversity analyses revealed large difference in the bacterial communities between the gut compartments while minor differences were observed between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the gut compartment dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.}, }
@article {pmid37478594, year = {2023}, author = {Tang, Y and Wang, C and Holm, PE and Hansen, HCB and Brandt, KK}, title = {Impacts of biochar materials on copper speciation, bioavailability, and toxicity in chromated copper arsenate polluted soil.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132067}, doi = {10.1016/j.jhazmat.2023.132067}, pmid = {37478594}, issn = {1873-3336}, abstract = {Trace element polluted soils pose risks to human and environmental health. Biochar can decrease trace element bioavailability in soils, but their resulting ability to reduce soil toxicity may vary significantly depending on feedstocks used, pyrolysis conditions, and the target pollutants. Chromated copper arsenate (CCA) polluted sites are common, but only very few types of biochar have been tested for these sites. Hence, we tested fourteen well-characterized biochar materials for their ability to bind Cu and reduce toxicity in a CCA polluted soil in a 56-day experiment. Biochar (1%, wt/wt) increased plant (wheat, Triticum aestivum L.) shoot and root growth by 6-58% and 0-73%, reduced soil toxicity to Arthrobacter globiformis by 7-55%, decreased bioavailable Cu (Pseudomonas fluorescens bioreporter) by 5-65%, and decreased free Cu[2+] ion activities by 27-89%. The A. globiformis solid-contact test constituted a sensitive ecotoxicological endpoint and deserves further attention for assessment of soil quality. Oil seed rape straw biochar generally performed better than other tested biochar materials. Biochar performance was positively correlated with its high cation exchange capacity, multiple surface functional groups, and high nitrogen and phosphorus content. Our results pave the way for future selection of feedstocks for creation of modified biochar materials with optimal performance in CCA polluted soil.}, }
@article {pmid37476672, year = {2023}, author = {Zhang, Y and Wang, R}, title = {The human gut phageome: composition, development, and alterations in disease.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213625}, pmid = {37476672}, issn = {1664-302X}, abstract = {The human gastrointestinal tract is colonized by a large number of microorganisms, including bacteria, archaea, viruses, and eukaryotes. The bacterial community has been widely confirmed to have a significant impact on human health, while viruses, particularly phages, have received less attention. Phages are viruses that specifically infect bacteria. They are abundant in the biosphere and exist in a symbiotic relationship with their host bacteria. Although the application of high-throughput sequencing and bioinformatics technology has greatly improved our understanding of the genomic diversity, taxonomic composition, and spatio-temporal dynamics of the human gut phageome, there is still a large portion of sequencing data that is uncharacterized. Preliminary studies have predicted that the phages play a crucial role in driving microbial ecology and evolution. Prior to exploring the function of phages, it is necessary to address the obstacles that hinder establishing a comprehensive sequencing database with sufficient biological properties and understanding the impact of phage-bacteria interactions on human health. In this study, we provide an overview of the human gut phageome, including its composition, structure, and development. We also explore the various factors that may influence the phageome based on current research, including age, diet, ethnicity, and geographical location. Additionally, we summarize the relationship between the phageome and human diseases, such as IBD, IBS, obesity, diabetes, and metabolic syndrome.}, }
@article {pmid37474781, year = {2023}, author = {Yu, L and Khachaturyan, M and Matschiner, M and Healey, A and Bauer, D and Cameron, B and Cusson, M and Emmett Duffy, J and Joel Fodrie, F and Gill, D and Grimwood, J and Hori, M and Hovel, K and Hughes, AR and Jahnke, M and Jenkins, J and Keymanesh, K and Kruschel, C and Mamidi, S and Menning, DM and Moksnes, PO and Nakaoka, M and Pennacchio, C and Reiss, K and Rossi, F and Ruesink, JL and Schultz, ST and Talbot, S and Unsworth, R and Ward, DH and Dagan, T and Schmutz, J and Eisen, JA and Stachowicz, JJ and Van De Peer, Y and Olsen, JL and Reusch, TBH}, title = {Ocean current patterns drive the worldwide colonization of eelgrass (Zostera marina).}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, pmid = {37474781}, issn = {2055-0278}, abstract = {Currents are unique drivers of oceanic phylogeography and thus determine the distribution of marine coastal species, along with past glaciations and sea-level changes. Here we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Two west-to-east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present there for ~243 ky (thousand years). Mediterranean populations were founded ~44 kya, while extant distributions along western and eastern Atlantic shores were founded at the end of the Last Glacial Maximum (~19 kya), with at least one major refuge being the North Carolina region. The recent colonization and five- to sevenfold lower genomic diversity of the Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.}, }
@article {pmid37470815, year = {2023}, author = {Lee, K and Bogdanova, A and Missaoui, A}, title = {Host Genetic Background Effect on Vertical Seed Transmission of Epichloë Endophyte Strains in Tall Fescue.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37470815}, issn = {1432-184X}, abstract = {Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass widely grown for forage and turf. Tall fescue lives in association with a fungal endophyte that helps the grass overcome abiotic and biotic stressors. The endophyte is asexual and transmits vertically from the tall fescue plant to the next generation through the seed. Producers of endophyte-infected tall fescue must have endophyte infection in at least 70% of their seed. Therefore, endophyte seed transmission is vital in breeding and seed production. Transfer of endophytes from their native host to different backgrounds of elite tall fescue cultivars can lead to a low seed transmission of the endophyte to the seed. This study screened 23 previously uncharacterized endophyte strains for transmissibility when artificially inoculated into continental and Mediterranean-type host tall fescue. We found no correlation between the rate of successful inoculation and the seed transmission rate of the endophyte in the new host. Nor did the seed transmission rate of the endophyte strains in their native host correlate with the seed transmission rate of the endophyte in the new host. Five strains exhibited seed transmission above 70% in both Mediterranean and Continental host backgrounds and will be characterized further for potential use in cultivar development.}, }
@article {pmid37469593, year = {2023}, author = {Riedel, T and Bunk, B and Schröttner, P}, title = {Editorial: Characterization of rare and recently first described human pathogenic bacteria.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1212627}, pmid = {37469593}, issn = {2235-2988}, mesh = {Humans ; *Bacteria/genetics ; *Genome, Bacterial ; }, }
@article {pmid37468677, year = {2023}, author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ}, title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37468677}, issn = {1751-7370}, support = {PR1603/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.}, }
@article {pmid37466247, year = {2023}, author = {Avasthi, I and Lerner, H and Grings, J and Gräber, C and Schleheck, D and Cölfen, H}, title = {Biodegradable Mineral Plastics.}, journal = {Small methods}, volume = {}, number = {}, pages = {e2300575}, doi = {10.1002/smtd.202300575}, pmid = {37466247}, issn = {2366-9608}, support = {//Carl-Zeiss Foundation/ ; }, abstract = {Mineral plastics are a promising class of bio-inspired materials that offer exceptional properties, like self-heal ability, stretchability in the hydrogel state, and high hardness, toughness, transparency, and non-flammability in the dry state along with reversible transformation into the hydrogel by addition of water. This enables easy reshape-ability and recycling like the solubility in mild acids to subsequently form mineral plastics again by base addition. However, current mineral plastics rely on petrochemistry, are hardly biodegradable, and thus persistent in nature. This work presents the next generation of mineral plastics, which are bio-based and biodegradable, making them a promising, new class of polymers for the development of environmentally friendly materials. Physically cross-linked (poly)glutamic-acid (PGlu)-based mineral plastics are synthesized using various alcohol-water mixtures, metal ion ratios and molecular weights. The rheological properties are easily adjusted using these parameters. The general procedure involves addition of equimolar solution of CaCl2 to PGlu in equal volumes followed by addition of iPrOH (iPrOH:H2 O = 1:1) under vigorous stirring conditions. The ready biodegradability of PGlu/CaFe mineral plastic is confirmed in this study where the elements N, Ca, and Fe present in it tend to act as additional nutrients, supporting the growth of microorganisms and consequently, promoting the biodegradation process.}, }
@article {pmid37459919, year = {2023}, author = {Wang, L and Zhu, L and Liang, C and Huang, X and Liu, Z and Huo, J and Zhang, Y and Zhang, Y and Chen, L and Xu, H and Li, X and Xu, L and Kuang, M and Wong, CC and Yu, J}, title = {Targeting N6-methyladenosine reader YTHDF1 with siRNA boosts anti-tumor immunity in NASH-HCC by inhibiting EZH2-IL-6 axis.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2023.06.021}, pmid = {37459919}, issn = {1600-0641}, abstract = {BACKGROUND &amp; AIMS: RNA N[6]-Methyladenosine (m[6]A) reader protein YTHDF1 has been implicated in cancer; however, its role in hepatocellular carcinoma (HCC), especially in nonalcoholic steatohepatitis-associated HCC (NASH-HCC), remains unknown. Here, we investigated the functional role and molecular mechanism of YTHDF1 on NASH-HCC and its interplay with tumor immune microenvironment.<br><br>METHODS: Hepatocyte specific Ythdf1 overexpression mice was subjected to dietary models of NASH-HCC. Tumor infiltrating immune cells were profiled with single-cell RNA sequencing (scRNA-seq), flow cytometry, and immunostaining. The molecular target of YTHDF1 was elucidated with RNA-sequencing, m[6]A-sequencing, YTHDF1 RNA immunoprecipitation (RIP) sequencing, proteomics, and ribosome-profiling. Ythdf1 in NASH-HCC models was targeted by lipid nanoparticles (LNP)-encapsulated siYthdf1.<br><br>RESULTS: YTHDF1 is overexpressed in tumor tissues than adjacent peri-tumor tissues from NASH-HCC patients. Liver specific Ythdf1 overex pression drives tumorigenesis in dietary models of spontaneous NASH-HCC. scRNA-seq and flow cytometry unraveled that Ythdf1 induced accumulation of myeloid-derived suppressor cells (MDSCs) and suppressed cytotoxic CD8[+] T cell function. Mechanistically, Ythdf1 expression in NASH-HCC cells induced the secretion of IL-6, which mediated MDSCs recruitment and activation, leading to CD8[+] T cell dysfunction. Integrated m[6]A-seq, RIP-seq, and ribo-seq have identified EZH2 mRNA as a key YTHDF1 target. YTHDF1 binds to m[6]A-modified EZH2 mRNA and promotes EZH2 translation. EZH2 in turn increased expression and secretion of IL-6. Ythdf1 knockout synergized with anti-PD-1 treatment to suppress tumor growth in NASH-HCC allografts. Furthermore, therapeutic targeting of Ythdf1 using LNP encapsulated siRNA significantly increased efficacy of anti-PD-1 blockade in NASH-HCC allografts.<br><br>CONCLUSIONS: We identified that YTHDF1 promotes NASH-HCC tumorigenesis via EZH2-IL-6 signaling, which recruits and activates MDSCs to cause cytotoxic CD8[+] T cell dysfunction. YTHDF1 may be a novel therapeutic target to improve response to anti-PD-1 immunotherapy for NASH-HCC.}, }
@article {pmid37459796, year = {2023}, author = {Sabbe, K and D'Haen, L and Boon, N and Ganigué, R}, title = {Predicting the performance of chain elongating microbiomes through flow cytometric fingerprinting.}, journal = {Water research}, volume = {243}, number = {}, pages = {120323}, doi = {10.1016/j.watres.2023.120323}, pmid = {37459796}, issn = {1879-2448}, abstract = {As part of the circular bio-economy paradigm shift, waste management and valorisation practices have moved away from sanitation and towards the production of added-value compounds. Recently, the development of mixed culture bioprocess for the conversion of waste(water) to platform chemicals, such as medium chain carboxylic acids, has attracted significant interest. Often, the microbiology of these novel bioprocesses is less diverse and more prone to disturbances, which can lead to process failure. This issue can be tackled by implementing an advanced monitoring strategy based on the microbiology of the process. In this study, flow cytometry was used to monitor the microbiology of lactic acid chain elongation for the production of caproic acid, and assess its performance both qualitatively and quantitatively. Two continuous stirred tank reactors for chain elongation were monitored flow cytometrically for over 336 days. Through community typing, four specific community types could be identified and correlated to both a specific functionality and genotypic diversity. Additionally, the machine-learning algorithms trained in this study demonstrated the ability to predict production rates of, amongst others, caproic acid with high accuracy in the present (R[2] > 0.87) and intermediate accuracy in the near future (R[2] > 0.63). The identification of specific community types and the development of predictive algorithms form the basis of advanced bioprocess monitoring based on flow cytometry, and have the potential to improve bioprocess control and optimization, leading to better product quality and yields.}, }
@article {pmid37458953, year = {2023}, author = {Vélez-Martínez, GA and Reyes-Ardila, WL and Duque-Zapata, JD and Rugeles-Silva, PA and Muñoz Flórez, JE and López-Álvarez, D}, title = {Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37458953}, issn = {1618-1905}, abstract = {The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.}, }
@article {pmid37458790, year = {2023}, author = {Huang, S and Lentendu, G and Fujinuma, J and Shiono, T and Kubota, Y and Mitchell, EAD}, title = {Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37458790}, issn = {1432-184X}, support = {182531/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.}, }
@article {pmid37458590, year = {2023}, author = {Masuda, T and Inomura, K and Mareš, J and Kodama, T and Shiozaki, T and Matsui, T and Suzuki, K and Takeda, S and Deutsch, C and Prášil, O and Furuya, K}, title = {Coexistence of Dominant Marine Phytoplankton Sustained by Nutrient Specialization.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0400022}, doi = {10.1128/spectrum.04000-22}, pmid = {37458590}, issn = {2165-0497}, abstract = {Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, but the basis for their coexistence has not been quantitatively demonstrated. Here, we combine in situ microcosm experiments and an ecological model to show that this coexistence can be sustained by specialization in the uptake of distinct nitrogen (N) substrates at low-level concentrations that prevail in subtropical environments. In field incubations, the response of both Prochlorococcus and Synechococcus to nanomolar N amendments demonstrates N limitation of growth in both populations. However, Prochlorococcus showed a higher affinity to ammonium, whereas Synechococcus was more adapted to nitrate uptake. A simple ecological model demonstrates that the differential nutrient preference inferred from field experiments with these genera may sustain their coexistence. It also predicts that as the supply of NO3[-] decreases, as expected under climate warming, the dominant genera should undergo a nonlinear shift from Synechococcus to Prochlorococcus, a pattern that is supported by subtropical field observations. Our study suggests that the evolution of differential nutrient affinities is an important mechanism for sustaining the coexistence of genera and that climate change is likely to shift the relative abundance of the dominant plankton genera in the largest biomes in the ocean. IMPORTANCE Our manuscript addresses the following fundamental question in microbial ecology: how do different plankton using the same essential nutrients coexist? Prochlorococcus and Synechococcus are the two dominant picocyanobacteria in the low-nutrient surface waters of the subtropical ocean, which support a significant amount of marine primary production. The geographical distributions of these two organisms are largely overlapping, but the basis for their coexistence in these biomes remains unclear. In this study, we combined in situ microcosm experiments and an ecosystem model to show that the coexistence of these two organisms can arise from specialization in the uptake of distinct nitrogen substrates; Prochlorococcus prefers ammonium, whereas Synechococcus prefers nitrate when these nutrients exist at low concentrations. Our framework can be used for simulating and predicting the coexistence in the future ocean and may provide hints toward understanding other similar types of coexistence.}, }
@article {pmid37458207, year = {2023}, author = {Seto, M and Kondoh, M}, title = {Microbial redox cycling enhances ecosystem thermodynamic efficiency and productivity.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.14287}, pmid = {37458207}, issn = {1461-0248}, support = {JPMEERF20214103//Environmental Restoration and Conservation Agency/ ; JP19H05641//Japan Society for the Promotion of Science/ ; JP19K06853//Japan Society for the Promotion of Science/ ; JP21H05315//Japan Society for the Promotion of Science/ ; JP22K06390//Japan Society for the Promotion of Science/ ; JP23H04652//Japan Society for the Promotion of Science/ ; }, abstract = {Microbial life in low-energy ecosystems relies on individual energy conservation, optimizing energy use in response to interspecific competition and mutualistic interspecific syntrophy. Our study proposes a novel community-level strategy for increasing energy use efficiency. By utilizing an oxidation-reduction (redox) reaction network model that represents microbial redox metabolic interactions, we investigated multiple species-level competition and cooperation within the network. Our results suggest that microbial functional diversity allows for metabolic handoffs, which in turn leads to increased energy use efficiency. Furthermore, the mutualistic division of labour and the resulting complexity of redox pathways actively drive material cycling, further promoting energy exploitation. Our findings reveal the potential of self-organized ecological interactions to develop efficient energy utilization strategies, with important implications for microbial ecosystem functioning and the co-evolution of life and Earth.}, }
@article {pmid37454793, year = {2023}, author = {Qi, L and Li, R and Wu, Y and Ibeanusi, V and Chen, G}, title = {Spatial distribution and assembly processes of bacterial communities in northern Florida freshwater springs.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116584}, doi = {10.1016/j.envres.2023.116584}, pmid = {37454793}, issn = {1096-0953}, abstract = {Freshwater microorganisms are an essential component of the global biogeochemical cycle and a significant contributory factor in water quality. Unraveling the mechanisms controlling microbial community spatial distribution is crucial for the assessment of water quality and health of aquatic ecosystems. This research provided a comprehensive analysis of microbial communities in Florida freshwater springs. The 16 S rRNA gene sequencing and bioinformatics analyses revealed the bacterial compositional heterogeneity as well as numerous unique ASVs and biomarkers in different springs. Statistical analysis showed both geographic distance and environmental variables contributed to regional bacterial community variation, while nitrate was the dominant environmental stressor that shaped the bacterial communities. The phylogenetic bin-based null model characterized both deterministic and stochastic factors contributing to community assembly in Florida springs, with the majority of bins dominated by ecological drift. Mapping of predicted pathways to the MetaCyc database revealed the inconsistency between microbial taxonomic and functional profiles, implying the functional redundancy pattern. Collectively, our work sheds insights into the microbial spatial distribution, community assembly, and function traits in one of the world's most productive aquifers. Therefore, this work provides a unique view of the health of Florida's artesian springs and offers new perspectives for freshwater quality assessment and sustainable management.}, }
@article {pmid37453005, year = {2023}, author = {Nagpal, S and Mande, SS}, title = {Environmental insults and compensative responses: when microbiome meets cancer.}, journal = {Discover. Oncology}, volume = {14}, number = {1}, pages = {130}, pmid = {37453005}, issn = {2730-6011}, support = {PhD Sponsorship//Tata Consultancy Services/ ; }, abstract = {Tumor microenvironment has recently been ascribed a new hallmark-the polymorphic microbiome. Accumulating evidence regarding the tissue specific territories of tumor-microbiome have opened new and interesting avenues. A pertinent question is regarding the functional consequence of the interface between host-microbiome and cancer. Given microbial communities have predominantly been explored through an ecological perspective, it is important that the foundational aspects of ecological stress and the fight to 'survive and thrive' are accounted for tumor-micro(b)environment as well. Building on existing evidence and classical microbial ecology, here we attempt to characterize the ecological stresses and the compensative responses of the microorganisms inside the tumor microenvironment. What insults would microbes experience inside the cancer jungle? How would they respond to these insults? How the interplay of stress and microbial quest for survival would influence the fate of tumor? This work asks these questions and tries to describe this underdiscussed ecological interface of the tumor and its microbiota. It is hoped that a larger scientific thought on the importance of microbial competition sensing vis-à-vis tumor-microenvironment would be stimulated.}, }
@article {pmid37452612, year = {2023}, author = {Hoque, E and Fritscher, J}, title = {Are anaerobic fungi crucial hidden players of microbiomes in anoxic environment?.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-24}, doi = {10.1080/1040841X.2023.2224425}, pmid = {37452612}, issn = {1549-7828}, abstract = {Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research.}, }
@article {pmid37452527, year = {2023}, author = {Soder-Walz, JM and Wasmund, K and Deobald, D and Vicent, T and Adrian, L and Marco-Urrea, E}, title = {Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16464}, pmid = {37452527}, issn = {1462-2920}, support = {//European Regional Development Fund/ ; 2021-SGR-01008//Generalitat de Catalunya, Consolidated Research Group/ ; PID2019-103989RB-I00//Spanish Ministry of Economy and Competitiveness State Research Agency/ ; }, abstract = {Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.}, }
@article {pmid37449414, year = {2023}, author = {Ni, G and Leung, PM and Daebeler, A and Guo, J and Hu, S and Cook, P and Nicol, GW and Daims, H and Greening, C}, title = {Nitrification in acidic and alkaline environments.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20220194}, pmid = {37449414}, issn = {1744-1358}, abstract = {Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.}, }
@article {pmid37446198, year = {2023}, author = {Gu, X and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, Q and Fu, L and Li, J}, title = {Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37446198}, issn = {1422-0067}, support = {RFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; RFSOCC2023-2025//Jiang Li/ ; }, abstract = {Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.}, }
@article {pmid37442613, year = {2023}, author = {Demarquest, G and Lajoie, G}, title = {Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad079}, pmid = {37442613}, issn = {1574-6941}, abstract = {Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.}, }
@article {pmid37440561, year = {2023}, author = {Fiedler, S and Schrader, H and Theobalt, N and Hofmann, I and Geiger, T and Arndt, D and Wanke, R and Schwaiger, J and Blutke, A}, title = {Standardized tissue sampling guidelines for histopathological and molecular analyses of rainbow trout (Oncorhynchus mykiss) in ecotoxicological studies.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288542}, pmid = {37440561}, issn = {1932-6203}, abstract = {In ecotoxicology, evaluation of toxicities and no observed effect concentrations (NOEC) of test compounds in experimental fish is commonly based on molecular-, biochemical- and analytical chemistry analyses of organ/tissue samples and the assessment of (histo-) pathological lesions. Standardization of organ/tissue sampling locations, sample numbers, and sample processing contributes to warrant the reproducibility and inter- and intra-study comparability of analysis results. The present article provides the first comprehensive tissue sampling guidelines specifically adapted to rainbow trout (Oncorhynchus mykiss) as a frequently used fish species in ecotoxicological studies. A broad spectrum of ~40 different organs and tissues is covered. Appropriate sampling locations, sample sizes and sample numbers for subsequent routine histopathological evaluation (all organs/tissue) and for molecular analyses (~30 organs/tissues) are described in detail and illustrated with schematic drawings and representative macroscopic and histological images. These field-proven sampling guidelines were developed based on the pertinent literature and practical experience in ecotoxicological fish studies. They are intended to serve as a standard reference for any routine ecotoxicological study using rainbow trout as a test system. A broad application of the featured tissue sampling procedures will help to improve the reproducibility of analyses and to reduce inter- and intra-study variability induced by sampling bias and (normal) inter-sample morphological variation, and will therefore provide a robust basis for reliable characterization of toxicity and NOEC identification of diverse test substances and aquatic pollutants.}, }
@article {pmid37438876, year = {2023}, author = {Basile, A and Heinken, A and Hertel, J and Smarr, L and Li, W and Treu, L and Valle, G and Campanaro, S and Thiele, I}, title = {Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2226921}, pmid = {37438876}, issn = {1949-0984}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Microbiota ; Inflammation ; Liver ; Anti-Bacterial Agents ; Escherichia coli ; }, abstract = {We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual's dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual's gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics.}, }
@article {pmid37438797, year = {2023}, author = {Nguyen, LH and Okin, D and Drew, DA and Battista, VM and Jesudasen, SJ and Kuntz, TM and Bhosle, A and Thompson, KN and Reinicke, T and Lo, CH and Woo, JE and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Das Adhikari, U and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, MB and Kwon, DS and Huttenhower, C and Chan, AT and Lai, PS}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {49}, pmid = {37438797}, issn = {1756-994X}, support = {K23DK125838/DK/NIDDK NIH HHS/United States ; K01DK120742/BC/NCI NIH HHS/United States ; }, mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.<br><br>METHODS: We profiled 127 hospitalized patients with COVID-19 (n&#x2009;=&#x2009;79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.<br><br>RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.<br><br>CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, }
@article {pmid37438590, year = {2023}, author = {Nava, V and Chandra, S and Aherne, J and Alfonso, MB and Antão-Geraldes, AM and Attermeyer, K and Bao, R and Bartrons, M and Berger, SA and Biernaczyk, M and Bissen, R and Brookes, JD and Brown, D and Cañedo-Argüelles, M and Canle, M and Capelli, C and Carballeira, R and Cereijo, JL and Chawchai, S and Christensen, ST and Christoffersen, KS and de Eyto, E and Delgado, J and Dornan, TN and Doubek, JP and Dusaucy, J and Erina, O and Ersoy, Z and Feuchtmayr, H and Frezzotti, ML and Galafassi, S and Gateuille, D and Gonçalves, V and Grossart, HP and Hamilton, DP and Harris, TD and Kangur, K and Kankılıç, GB and Kessler, R and Kiel, C and Krynak, EM and Leiva-Presa, &#xc0; and Lepori, F and Matias, MG and Matsuzaki, SS and McElarney, Y and Messyasz, B and Mitchell, M and Mlambo, MC and Motitsoe, SN and Nandini, S and Orlandi, V and Owens, C and Özkundakci, D and Pinnow, S and Pociecha, A and Raposeiro, PM and Rõõm, EI and Rotta, F and Salmaso, N and Sarma, SSS and Sartirana, D and Scordo, F and Sibomana, C and Siewert, D and Stepanowska, K and Tavşanoğlu, &#xdc;N and Tereshina, M and Thompson, J and Tolotti, M and Valois, A and Verburg, P and Welsh, B and Wesolek, B and Weyhenmeyer, GA and Wu, N and Zawisza, E and Zink, L and Leoni, B}, title = {Plastic debris in lakes and reservoirs.}, journal = {Nature}, volume = {619}, number = {7969}, pages = {317-322}, pmid = {37438590}, issn = {1476-4687}, mesh = {Ecosystem ; *Lakes/chemistry ; *Plastics/analysis/classification ; *Water Pollution/analysis/statistics &amp; numerical data ; Surveys and Questionnaires ; Urbanization ; *Water Supply ; Human Activities ; }, abstract = {Plastic debris is thought to be widespread in freshwater ecosystems globally[1]. However, a lack of comprehensive and comparable data makes rigorous assessment of its distribution challenging[2,3]. Here we present a standardized cross-national survey that assesses the abundance and type of plastic debris (>250 μm) in freshwater ecosystems. We sample surface waters of 38 lakes and reservoirs, distributed across gradients of geographical position and limnological attributes, with the aim to identify factors associated with an increased observation of plastics. We find plastic debris in all studied lakes and reservoirs, suggesting that these ecosystems play a key role in the plastic-pollution cycle. Our results indicate that two types of lakes are particularly vulnerable to plastic contamination: lakes and reservoirs in densely populated and urbanized areas and large lakes and reservoirs with elevated deposition areas, long water-retention times and high levels of anthropogenic influence. Plastic concentrations vary widely among lakes; in the most polluted, concentrations reach or even exceed those reported in the subtropical oceanic gyres, marine areas collecting large amounts of debris[4]. Our findings highlight the importance of including lakes and reservoirs when addressing plastic pollution, in the context of pollution management and for the continued provision of lake ecosystem services.}, }
@article {pmid37436063, year = {2023}, author = {Smets, W and Chock, MK and Walsh, CM and Vanderburgh, CQ and Kau, E and Lindow, SE and Fierer, N and Koskella, B}, title = {Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome.}, journal = {mBio}, volume = {}, number = {}, pages = {e0111123}, doi = {10.1128/mbio.01111-23}, pmid = {37436063}, issn = {2150-7511}, abstract = {Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.}, }
@article {pmid37434715, year = {2023}, author = {Trexler, RV and Van Goethem, MW and Goudeau, D and Nath, N and Malmstrom, RR and Northen, TR and Couradeau, E}, title = {BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1176751}, pmid = {37434715}, issn = {1664-302X}, abstract = {Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.}, }
@article {pmid37433981, year = {2023}, author = {Gomes, AFF and de Almeida, LG and Cônsoli, FL}, title = {Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37433981}, issn = {1432-184X}, support = {140835/2019-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2010/13714-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2011/50877-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, abstract = {Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.}, }
@article {pmid37433980, year = {2023}, author = {Candelori, A and Di Giuseppe, G and Villalobo, E and Sjödin, A and Vallesi, A}, title = {Bipolar Biogeographical Distribution of Parafrancisella Bacteria Carried by the Ciliate Euplotes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37433980}, issn = {1432-184X}, support = {PNRA18_00152//PNRA (Programma Nazionale di Ricerca in Antartide)/ ; PNRA18_00152//PNRA (Programma Nazionale di Ricerca in Antartide)/ ; }, abstract = {Parafrancisella adeliensis, a Francisella-like endosymbiont, was found to reside in the cytoplasm of an Antarctic strain of the bipolar ciliate species, Euplotes petzi. To inquire whether Euplotes cells collected from distant Arctic and peri-Antarctic sites host Parafrancisella bacteria, wild-type strains of the congeneric bipolar species, E. nobilii, were screened for Parafrancisella by in situ hybridization and 16S gene amplification and sequencing. Results indicate that all Euplotes strains analyzed contained endosymbiotic bacteria with 16S nucleotide sequences closely similar to the P. adeliensis 16S gene sequence. This finding suggests that Parafrancisella/Euplotes associations are not endemic to Antarctica, but are common in both the Antarctic and Arctic regions.}, }
@article {pmid37432727, year = {2023}, author = {Wang, J and Shi, K and Jing, Z and Ge, Y}, title = {Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c02181}, pmid = {37432727}, issn = {1520-5851}, abstract = {Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.}, }
@article {pmid37432469, year = {2023}, author = {DiPietro, AG and Bryant, SA and Zanger, MM and Williamson, KE}, title = {Understanding Viral Impacts in Soil Microbial Ecology Through the Persistence and Decay of Infectious Bacteriophages.}, journal = {Current microbiology}, volume = {80}, number = {9}, pages = {276}, pmid = {37432469}, issn = {1432-0991}, abstract = {Marine bacteriophages have been well characterized in terms of decay rates, population dynamics in relation to their hosts, and their impacts on biogeochemical cycles in the global ocean. Knowledge in soil bacteriophage ecology lags considerably behind, with few studies documenting population dynamics with hosts and even fewer reporting phage decay rates. By using sterile soil or aquatic microcosms inoculated with single bacteriophage isolates, phage decay rates (loss of infectivity over time) were determined, independent of host interactions, for 5 model phage isolates. Decay rates varied by phage from 0.11-2.07% h[-1] in soils to 0.07-0.28% h[-1] in aquatic microcosms. For phages incubated in both soil and aquatic microcosms, the observed decay rate was consistently higher in soil microcosms than in aquatic microcosms by at least a factor of two. However, when decay rates for soil phage isolates in the present study were compared to those reported for marine and freshwater phage isolates from previous studies, the decay constants for soil phages were, on average, 4 times lower than those for aquatic phages. Slower rates of phage decay in soils indicate a lower turnover rate, which may have subsequent and potentially far-reaching impacts on virus-mediated mortality and bacterial activity. The wide range of decay rates observed in the present study and the lack of information on this critical aspect of virus-host dynamics in soil emphasizes the need for continued research in this field.}, }
@article {pmid37431054, year = {2022}, author = {Seo, H and Lee, S and Park, H and Jo, S and Kim, S and Rahim, MA and Ul-Haq, A and Barman, I and Lee, Y and Seo, A and Kim, M and Jung, IY and Song, HY}, title = {Characteristics and Microbiome Profiling of Korean Gochang Bokbunja Vinegar by the Fermentation Process.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, doi = {10.3390/foods11203308}, pmid = {37431054}, issn = {2304-8158}, support = {2021040D288//Gochang Bokbunja vinegar Research Project/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; }, abstract = {As NGS (next-generation sequencing) technology develops, metagenomics-based microbial ecology, that is, microbiome research, has recently led to the science of fermented food. Based on the above technology, a study was conducted to understand the characteristics of vinegar made from bokbunja, a local crop in Gochang-gun, Korea. Physicochemical characteristics of vinegar, organic acid analysis, microbial community analysis, and electronic tongue analysis were explored while fermenting the vinegar for 70 days under eight fermentation conditions according to the concentration of bokbunja liquid (100% or 50%), type of fermenter (porcelain jar or stainless container), and fermentation environment (natural outdoor conditions or temperature/oxygen controlled). As a result, distinct microbial community patterns were found in the stage of acetic acid fermentation and, accordingly, this fermentation of Gochang vinegar is classified into three categories. Vinegar prepared by the traditional method of outdoor fermentation using jars showed characteristics of "Acetobacter (42.1%)/Lactobacillus (56.9%) fusion fermentation". Under conditions where oxygen and temperature were controlled indoors using jars, characteristics of "Komagataeibacter (90.2%) fermentation" were found. "Lactobacillus (92.2%) fermentation" characteristics were discovered under natural outdoor conditions using stainless steel containers. These fermentation pattern differences were related to taxonomic phylogenetic diversity, which was also considered involved in determining organic acid production and taste. These results will be helpful as a scientific basis for understanding the fermentation characteristics of Gochang vinegar and developing high-value-added traditional vinegar products.}, }
@article {pmid37428189, year = {2023}, author = {Rellegadla, S and Prajapat, G and Jain, S and Agrawal, A}, title = {Microbial communities succession post to polymer flood demonstrate a role in enhanced oil recovery.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37428189}, issn = {1432-0614}, support = {IMP/2018/000589//SERB Department of Science and Technology/ ; BT/PR25132/NER/95/1034/2017//Department of Biotechnology, Ministry of Science and Technology, India/ ; 09/1131(0028)/2019-EMR-I//CSIR India/ ; }, abstract = {The role of indigenous microbial communities in residual oil extraction following a recovery process is not well understood. This study investigated the dynamics of resident microbial communities in oil-field simulating sand pack bioreactors after the polymer flooding stage resumed with waterflooding and explored their contribution to the oil extraction process. The microbial community succession was studied through high-throughput sequencing of 16S rRNA genes. The results revealed alternating dominance of minority populations, including Dietzia sps., Acinetobacter sps., Soehngenia sps., and Paracoccus sps., in each bioreactor following the flooding process. Additionally, the post-polymer waterflooding stage led to higher oil recovery, with hydroxyethylcellulose, tragacanth gum, and partially hydrolyzed polyacrylamide polymer-treated bioreactors yielding additional recovery of 4.36%, 5.39%, and 3.90% residual oil in place, respectively. The dominant microbial communities were previously reported to synthesize biosurfactants and emulsifiers, as well as degrade and utilize hydrocarbons, indicating their role in aiding the recovery process. However, the correlation analysis of the most abundant taxa showed that some species were more positively correlated with the oil recovery process, while others acted as competitors for the carbon source. The study also found that higher biomass favored the plugging of high permeability zones in the reservoir, facilitating the dislodging of crude oil in new channels. In conclusion, this study suggests that microbial populations significantly shift upon polymer treatment and contribute synergistically to the oil recovery process depending on the characteristics of the polymers injected. KEY POINTS: • Post-polymer flooded microbial ecology shows unique indigenous microbial consortia. • Injected polymers are observed to act as enrichment substrates by resident communities. • The first study to show successive oil recovery stage post-polymer flood without external influence.}, }
@article {pmid37426976, year = {2023}, author = {Wang, M and Cernava, T}, title = {Editorial: The phyllosphere microbiome.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1234843}, pmid = {37426976}, issn = {1664-462X}, }
@article {pmid37423403, year = {2023}, author = {Melo-Bolívar, JF and Ruiz-Pardo, RY and Quintanilla Carvajal, MX and Díaz, LE and Alzate, JF and Junca, H and Rodríguez Orjuela, JA and Villamil Diaz, LM}, title = {Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {108928}, doi = {10.1016/j.fsi.2023.108928}, pmid = {37423403}, issn = {1095-9947}, abstract = {The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.}, }
@article {pmid37354976, year = {2023}, author = {Kable, ME and Chin, EL and Huang, L and Stephensen, CB and Lemay, DG}, title = {Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2023.06.025}, pmid = {37354976}, issn = {1541-6100}, abstract = {BACKGROUND: Lactase persistence (LP) is a heritable trait in which lactose can be digested throughout adulthood. Lactase nonpersistent (LNP) individuals who consume lactose may experience microbial adaptations in response to undigested lactose.<br><br>OBJECTIVES: The objective of the study was to estimate lactose from foods reported in the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) and determine the interaction between lactose consumption, LP genotype, and gut microbiome in an observational cross-sectional study of healthy adults in the United States (US).<br><br>METHODS: Average daily lactose consumption was estimated for 279 healthy US adults, genotyped for the lactase gene -13910G>A polymorphism (rs4988235) by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. Analysis of covariance was used to identify whether the A genotype (LP) influenced lactose and total dairy consumption, with total energy intake and weight as covariates. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300 bp paired-end) and analyzed using Quantitative Insights Into Microbial Ecology (QIIME)2 (version 2019.10). Differential abundances of bacterial taxa were analyzed using DESeq2 likelihood ratio tests.<br><br>RESULTS: Across a diverse set of ethnicities, LP subjects consumed more lactose than LNP subjects. Lactobacillaceae abundance was highest in LNP subjects who consumed more than 12.46 g/d (upper tercile). Within Caucasians and Hispanics, family Lachnospiraceae was significantly enriched in the gut microbiota of LNP individuals consuming the upper tercile of lactose across both sexes.<br><br>CONCLUSIONS: Elevated lactose consumption in individuals with the LNP genotype is associated with increased abundance of family Lactobacillaceae and Lachnospriaceae, taxa that contain multiple genera capable of utilizing lactose. This trial was registered on clinicaltrials.gov as NCT02367287.}, }
@article {pmid37422225, year = {2023}, author = {Villar-dePablo, M and Ascaso, C and Rodríguez-Pérez, E and Urizal, M and Wierzchos, J and Pérez-Ortega, S and de Los Ríos, A}, title = {Innovative approaches to accurately assess the effectiveness of biocide-based treatments to fight biodeterioration of Cultural Heritage monuments.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {165318}, doi = {10.1016/j.scitotenv.2023.165318}, pmid = {37422225}, issn = {1879-1026}, abstract = {The development of diagnostic methods to accurately assess the effects of treatments on lithobiont colonization remains a challenge for the conservation of Cultural Heritage monuments. In this study, we tested the efficacy of biocide-based treatments on microbial colonization of a dolostone quarry, in the short and long-term, using a dual analytical strategy. We applied a metabarcoding approach to characterize fungal and bacterial communities over time, integrated with microscopy techniques to analyze the interactions of microorganisms with the substrate and evaluate the effectiveness. These communities were dominated by the bacterial phyla Actinobacteriota, Proteobacteria and Cyanobacteria, and the fungal order Verrucariales, which include taxa previously reported as biodeteriogenic agents and observed here associated with biodeterioration processes. Following the treatments, changes over time in the abundance profiles depend on taxa. While Cyanobacteriales, Cytophagales and Verrucariales decreased in abundance, other groups, such as Solirubrobacteriales, Thermomicrobiales and Pleosporales increased. These patterns could be related not only to the specific effects of the biocide on the different taxa, but also to different recolonization abilities of those organisms. The different susceptibility to treatments could be associated with the inherent cellular properties of different taxa, but differences in biocide penetration to endolithic microhabitats could be involved. Our results demonstrate the importance of both removing epilithic colonization and applying biocides to act against endolithic forms. Recolonization processes could also explain some of the taxon-dependent responses, especially in the long-term. Taxa showing resistance, and those benefiting from nutrient accumulation in the form of cellular debris following treatments, may have an advantage in colonizing treated areas, pointing to the need for long-term monitoring of a wide range of taxa. This study highlights the potential utility of combining metabarcoding and microscopy to analyze the effects of treatments and design appropriate strategies to combat biodeterioration and establish preventive conservation protocols.}, }
@article {pmid37419360, year = {2023}, author = {Martin-Pozas, T and Fernandez-Cortes, A and Cuezva, S and Cañaveras, JC and Benavente, D and Duarte, E and Saiz-Jimenez, C and Sanchez-Moral, S}, title = {New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain).}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {165218}, doi = {10.1016/j.scitotenv.2023.165218}, pmid = {37419360}, issn = {1879-1026}, abstract = {In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.}, }
@article {pmid37419243, year = {2023}, author = {Loyola-Fonseca, SC and Campello, AF and Rodrigues, RCV and Alves, FRF and Brasil, SC and Vilela, CLS and Gonçalves, LS and Provenzano, JC and Siqueira, JF and Rôças, IN}, title = {Disinfection and shaping of Vertucci class II root canals after preparation with two instrument systems and supplementary ultrasonic activation of sodium hypochlorite.}, journal = {Journal of endodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joen.2023.06.017}, pmid = {37419243}, issn = {1878-3554}, abstract = {INTRODUCTION: This study compared disinfection and shaping after root canal preparation with either XP-endo Shaper or TruNatomy instrument systems, supplemented by ultrasonic activation of sodium hypochlorite (NaOCl) with either stainless-steel (SS) or nickel-titanium (NiTi) inserts.<br><br>METHODS: Mesial roots from mandibular molars with Vertucci class II configuration were divided into two groups (n=24) based on anatomically paired micro-computed tomography (micro-CT) analyses. Pre and postpreparation micro-CT scans were obtained to evaluate the shaping performance. The canals were contaminated with a mixed bacterial culture for 30 days and then subjected to preparation with either XP-endo Shaper or TruNatomy instruments using NaOCl irrigation. Supplementary ultrasonic activation of NaOCl was conducted using either an SS (TruNatomy group) or NiTi (XP-endo Shaper group) insert. Bacteriological samples were taken from the canals before preparation (S1), after preparation (S2), and after the supplementary approach (S3). Bacterial reduction was evaluated using a quantitative real-time polymerase chain reaction.<br><br>RESULTS: Preparation with both instrument systems significantly reduced bacterial counts (P < .01). After preparation, 36% (TruNatomy) and 35% (XP-endo Shaper) were negative for bacteria. These values increased to 59% and 65% after ultrasonic activation with the SS and NiTi inserts, respectively. The quantitative data in S2 showed that XP-endo Shaper promoted a significantly higher bacterial reduction than TruNatomy (P < .05). No significant intragroup differences were observed after ultrasonic activation (P > .05), probably because the SS insert promoted a significantly higher S2-to-S3 reduction than the NiTi insert (P < .01). Micro-CT analysis revealed no significant differences in the unprepared areas between the groups (P > .05).<br><br>CONCLUSION: The XP-endo Shaper caused a significantly higher bacterial reduction than TruNatomy in Vertucci class II canals. Better antibacterial results after ultrasonic activation were observed for the SS ultrasonic inserts than for the NiTi inserts.}, }
@article {pmid37418833, year = {2023}, author = {Crump, BC and Bowen, JL}, title = {The Microbial Ecology of Estuarine Ecosystems.}, journal = {Annual review of marine science}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-marine-022123-101845}, pmid = {37418833}, issn = {1941-0611}, abstract = {Human civilization relies on estuaries, and many estuarine ecosystem services are provided by microbial communities. These services include high rates of primary production that nourish harvests of commercially valuable species through fisheries and aquaculture, the transformation of terrestrial and anthropogenic materials to help ensure the water quality necessary to support recreation and tourism, and mutualisms that maintain blue carbon accumulation and storage. Research on the ecology that underlies microbial ecosystem services in estuaries has expanded greatly across a range of estuarine environments, including water, sediment, biofilms, biological reefs, and stands of seagrasses, marshes, and mangroves. Moreover, the application of new molecular tools has improved our understanding of the diversity and genomic functions of estuarine microbes. This review synthesizes recent research on microbial habitats in estuaries and the contributions of microbes to estuarine food webs, elemental cycling, and interactions with plants and animals, and highlights novel insights provided by recent advances in genomics. Expected final online publication date for the Annual Review of Marine Science, Volume 16 is January 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37417553, year = {2023}, author = {Jansma, J and Thome, NU and Schwalbe, M and Chatziioannou, AC and Elsayed, SS and van Wezel, GP and van den Abbeele, P and van Hemert, S and El Aidy, S}, title = {Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: a network theory approach.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2232506}, doi = {10.1080/19490976.2023.2232506}, pmid = {37417553}, issn = {1949-0984}, abstract = {The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, the molecular mechanisms involved in such therapies are often not well understood, particularly when targeting the small intestinal microbiota. In this study, we investigated the effects of a probiotic formula (Ecologic®825) on the adult human small intestinal ileostoma microbiota. The results showed that supplementation with the probiotic formula led to a reduction in the growth of pathobionts, such as Enterococcaceae and Enterobacteriaceae, and a decrease in ethanol production. These changes were associated with significant alterations in nutrient utilization and resistance to perturbations. These probiotic mediated alterations which coincided with an initial increase in lactate production and decrease in pH were followed by a sharp increase in the levels of butyrate and propionate. Moreover, the probiotic formula increased the production of multiple N-acyl amino acids in the stoma samples. The study demonstrates the utility of network theory in identifying novel microbiota-targeted therapies and improving existing ones. Overall, the findings provide insights into the dynamic molecular mechanisms underlying probiotic therapies, which can aid in the development of more effective treatments for a range of conditions.}, }
@article {pmid37415044, year = {2023}, author = {King, NG and Uribe, R and Moore, PJ and Earp, HS and Gouraguine, A and Hinostroza, D and Perez-Matus, A and Smith, K and Smale, DA}, title = {Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37415044}, issn = {1432-184X}, abstract = {Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.}, }
@article {pmid37415043, year = {2023}, author = {Shao, Q and Lin, Z and Xu, Z and Zhu, Z and Zhou, C and Yan, X}, title = {Integrated Biogeography and Assembly Mechanisms of Microeukaryotic Communities in Coastal Waters Near Shellfish Cultivation.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37415043}, issn = {1432-184X}, support = {2022J195//Natural Science Foundation of Ningbo/ ; 2022S116//Public Welfare Science and Technology Project of Ningbo/ ; 2018YFD0900702//National Key Research and Development Program of China/ ; }, abstract = {The Lianjiang coast in the East China Sea is a typical subtropical marine ecosystem, and shellfish cultivation occupies almost all of the available tidal flats. Many studies have investigated the effects of shellfish cultivation on benthic organisms and sediments, while the impact of shellfish cultivation on plankton ecosystems is still poorly understood. This study investigated the biogeographical patterns of microeukaryotic communities from Lianjiang coastal waters in four seasons using 18S ribosomal RNA gene amplicon sequencing. Microeukaryotes were mainly comprised of Dinoflagellata, Diatomea, Arthropoda, Ciliophora, Chlorophyta, Protalveolata, Cryptophyceae, and Ochrophyta, and presented significant differences in three habitats (the aquaculture area, confluent area, and offshore area) and four seasons. Similarity percentage analysis revealed that Paracalanus parvus, Heterocapsa rotundata, Bestiolina similis, and five additional key taxa contributed to spatio-temporal differences. Seasonal environmental and spatial factors explained 27.47% of microeukaryotic community variation on average, with 11.11% of the variation shared. Environmental variables, particularly depth, pH, and nitrite concentration, were strongly associated with the microeukaryotic community compositions. The neutral community model further demonstrated that stochastic processes were sufficient in shaping substantial variation in microeukaryotic communities across four seasons, which may reveal the remaining unexplained microeukaryotic community variation. We further divided four seasons into the aquaculture stages and non-aquaculture stages, and speculated that aquaculture activities may increase the dispersal limitation of microeukaryotes in coastal waters, especially for the big bodied-microbes like Arthropoda. The results provide a better understanding of the biogeographical patterns, processes, and mechanisms of microeukaryotic communities near shellfish cultivation.}, }
@article {pmid37408642, year = {2023}, author = {Kasahara, K and Leygeber, M and Seiffarth, J and Ruzaeva, K and Drepper, T and Nöh, K and Kohlheyer, D}, title = {Enabling oxygen-controlled microfluidic cultures for spatiotemporal microbial single-cell analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1198170}, pmid = {37408642}, issn = {1664-302X}, abstract = {Microfluidic cultivation devices that facilitate O2 control enable unique studies of the complex interplay between environmental O2 availability and microbial physiology at the single-cell level. Therefore, microbial single-cell analysis based on time-lapse microscopy is typically used to resolve microbial behavior at the single-cell level with spatiotemporal resolution. Time-lapse imaging then provides large image-data stacks that can be efficiently analyzed by deep learning analysis techniques, providing new insights into microbiology. This knowledge gain justifies the additional and often laborious microfluidic experiments. Obviously, the integration of on-chip O2 measurement and control during the already complex microfluidic cultivation, and the development of image analysis tools, can be a challenging endeavor. A comprehensive experimental approach to allow spatiotemporal single-cell analysis of living microorganisms under controlled O2 availability is presented here. To this end, a gas-permeable polydimethylsiloxane microfluidic cultivation chip and a low-cost 3D-printed mini-incubator were successfully used to control O2 availability inside microfluidic growth chambers during time-lapse microscopy. Dissolved O2 was monitored by imaging the fluorescence lifetime of the O2-sensitive dye RTDP using FLIM microscopy. The acquired image-data stacks from biological experiments containing phase contrast and fluorescence intensity data were analyzed using in-house developed and open-source image-analysis tools. The resulting oxygen concentration could be dynamically controlled between 0% and 100%. The system was experimentally tested by culturing and analyzing an E. coli strain expressing green fluorescent protein as an indirect intracellular oxygen indicator. The presented system allows for innovative microbiological research on microorganisms and microbial ecology with single-cell resolution.}, }
@article {pmid37406718, year = {2023}, author = {Lv, T and Wang, D and Hui, J and Cheng, W and Ai, H and Qin, L and Huang, M and Feng, M and Wu, Y}, title = {Effect of return activated sludge diversion ratio on phosphorus removal performance in side-stream enhanced biological phosphorus removal (S2EBPR) process.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116546}, doi = {10.1016/j.envres.2023.116546}, pmid = {37406718}, issn = {1096-0953}, abstract = {In this study, a lab-scale continuous flow side-stream enhanced biological phosphorus (P) removal (S2EBPR) reactor was operated for 247 days treating synthetic wastewater with influent carbon to phosphorus (C/P) ratio of 25.0 g COD/g P and influent PO4[3-]P of 7.4 ± 0.3 mg P/L. The effect of the return activated sludge (RAS) diversion ratio on S2EBPR reactor was investigated by comparing P removal performance, microbial activity, and community structure. The results showed that the RAS diversion ratio of 8.0%, by yielding a side-stream sludge retention time (SRTSS) of ∼60 h, resulted in the lowest effluent PO4[3-]P concentration of 0.5 ± 0.3 mg P/L. The results of in situ process profiles and ex situ P release and uptake batch tests under different RAS diversion conditions showed that the more anaerobic P release was obtained in the side-stream reactor, the higher the P removal efficiency and EBPR activity were achieved. The stoichiometric ratios observed in EBPR activity tests indicated a polyphosphate accumulating organisms (PAOs) metabolism mainly dependent on the glycolysis pathway. The results of microbial ecology analysis revealed that the optimized SRTSS would give a competitive advantage to PAOs in the S2EBPR process. By obtaining statistically reliable results, this study would provide guidance for wastewater treatment plants to achieve optimal P removal performance in S2EBPR configuration.}, }
@article {pmid37406090, year = {2023}, author = {Pollak, S}, title = {Plant DNA in feces as a nutritional crystal ball.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {29}, pages = {e2309172120}, doi = {10.1073/pnas.2309172120}, pmid = {37406090}, issn = {1091-6490}, }
@article {pmid37405949, year = {2023}, author = {Almeida-Silva, F and Van de Peer, Y}, title = {Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.}, journal = {Molecular biology and evolution}, volume = {40}, number = {7}, pages = {}, pmid = {37405949}, issn = {1537-1719}, abstract = {Angiosperms have a complex history of whole-genome duplications (WGDs), with varying numbers and ages of WGD events across clades. These WGDs have greatly affected the composition of plant genomes due to the biased retention of genes belonging to certain functional categories following their duplication. In particular, regulatory genes and genes encoding proteins that act in multiprotein complexes have been retained in excess following WGD. Here, we inferred protein-protein interaction (PPI) networks and gene regulatory networks (GRNs) for seven well-characterized angiosperm species and explored the impact of both WGD and small-scale duplications (SSDs) in network topology by analyzing changes in frequency of network motifs. We found that PPI networks are enriched in WGD-derived genes associated with dosage-sensitive intricate systems, and strong selection pressures constrain the divergence of WGD-derived genes at the sequence and PPI levels. WGD-derived genes in network motifs are mostly associated with dosage-sensitive processes, such as regulation of transcription and cell cycle, translation, photosynthesis, and carbon metabolism, whereas SSD-derived genes in motifs are associated with response to biotic and abiotic stress. Recent polyploids have higher motif frequencies than ancient polyploids, whereas WGD-derived network motifs tend to be disrupted on the longer term. Our findings demonstrate that both WGD and SSD have contributed to the evolution of angiosperm GRNs, but in different ways, with WGD events likely having a more significant impact on the short-term evolution of polyploids.}, }
@article {pmid37405460, year = {2023}, author = {Suzuki, K and Katashima, K and Miki, T and Igarashi, H and Xu, Q and Ohkubo, S and Iwaishi, S and Harada, N}, title = {Bacterial Community Composition Under Paddy Conditions Is More Strongly Affected by the Difference in Soil Type than by Field Management.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37405460}, issn = {1432-184X}, abstract = {In this study, we aimed to investigate the effects of soil type and field management on bacterial communities in paddy soils, taking into account the differences in soil physicochemical properties. We collected soil samples from 51 paddy fields in six prefectures in Japan. The paddy fields were managed under organic regimes (26 fields), natural-farming regimes (12 fields), or conventional regimes (13 fields). The paddy fields were classified into four soil types: andosol, gray lowland soil, gley soil, and gray upland soil. Soil DNA was extracted from the soil samples collected 2 to 10 weeks after the flooding, and the 16S rRNA gene amplicon sequencing analysis was performed. The bacterial community compositions were dominated by the phylum Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, and Firmicutes in all fields. The difference in soil type had significant effects on α-diversities of the bacterial communities, although the field management had no effect. The soil bacterial communities in the gley soils and gray upland soils individually formed different groups from those in the other soils, while the andosol and gray lowland soils tended to form relatively similar bacterial communities. On the other hand, the effects of the field management were estimated to be smaller than those of soil type. The β-diversity of the bacterial community compositions were significantly correlated with soil pH, total nitrogen content, total carbon content, and divalent iron content. Our results suggest that the soil microbial community in paddy fields may be strongly influenced by soil physiochemical properties derived from differences in soil type.}, }
@article {pmid37404190, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0017723}, doi = {10.1128/aem.00177-23}, pmid = {37404190}, issn = {1098-5336}, abstract = {Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.}, }
@article {pmid37404136, year = {2023}, author = {Li, H and Zhou, H and Yang, S and Dai, X}, title = {Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0070123}, doi = {10.1128/aem.00701-23}, pmid = {37404136}, issn = {1098-5336}, abstract = {Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.}, }
@article {pmid37402057, year = {2023}, author = {Hkiri, N and Aounallah, F and Fouzai, K and Chouchani, C and Asses, N}, title = {Ability of marine-derived fungi isolated from polluted saline environment for enzymatic hydrocarbon remediation.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {37402057}, issn = {1678-4405}, abstract = {Marine-derived fungi have attracted much attention due to their ability to present a new biosynthetic diversity. About 50 fungal isolates were obtained from Tunisian Mediterranean seawater and then screened for the presence of lignin-peroxidase (LiP), manganese-dependent peroxidase (MnP), and laccase (Lac) activities. The results obtained from both qualitative and quantitative assays showed that four of marine fungi isolates had a high potential to produce lignin-degrading enzymes. They were characterized taxonomically by a molecular method, based on international spacer (ITS) rDNA sequence analysis, as Chaetomium jodhpurense (MH667651.1), Chaetomium maderasense (MH665977.1), Paraconiothyrium variabile (MH667653.1), and Phoma betae (MH667655.1) which have been reported as producers of ligninolytic enzyme in the literature. The enzymatic activities and culture conditions were optimized using a Fractional Factorial design (2 [7- 4]). Then, fungal strains were incubated with the addition of 1% of crude oil in 50% of seawater for 25 days to evaluate their abilities to simultaneously degrade hydrocarbon compounds and to produce ligninolytic enzymes. The strain P. variabile exhibited the highest crude oil degradation rate (48.3%). Significant production of ligninolytic enzymes was recorded during the degradation process, which reached 2730 U/L for the MnP, 410 U/L for LiP, and 168.5 U/L for Lac. The FTIR and GC-MS analysis confirmed that the isolates rapidly biodegrade crude oil under ecological and economic conditions.}, }
@article {pmid37401933, year = {2023}, author = {Chen, L and Xin, X and Li, J and Han, C and Xiong, W and Luo, Y and Sun, R and Zhang, J}, title = {Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37401933}, issn = {1432-184X}, support = {42177332//National Natural Science Foundation of China/ ; XDA24020104 and XDA28020203//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 2022YFD1500203 and 2022YFD1500401//National Key Research and Development Program of China/ ; 2023325//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; CARS-03-15 and CARS-52//China Agriculture Research System/ ; }, abstract = {Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with [13]C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased [13]C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and [13]C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial [13]C assimilation (i.e., [13]C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.}, }
@article {pmid37396621, year = {2023}, author = {Moens, F and Vandevijver, G and De Blaiser, A and Larsson, A and Spreafico, F and Augustijns, P and Marzorati, M}, title = {The Dynamic Intestinal Absorption Model (Diamod®), an in vitro tool to study the interconnected kinetics of gastrointestinal solubility, supersaturation, precipitation, and intestinal permeation processes of oral drugs.}, journal = {International journal of pharmaceutics: X}, volume = {5}, number = {}, pages = {100177}, pmid = {37396621}, issn = {2590-1567}, abstract = {This study aimed at developing the Diamod® as a dynamic gastrointestinal transfer model with physically interconnected permeation. The Diamod® was validated by studying the impact of the intraluminal dilution of a cyclodextrin-based itraconazole solution and the negative food effect for indinavir sulfate for which clinical data are available demonstrating that the systemic exposure was strongly mediated by interconnected solubility, precipitation, and permeation processes. The Diamod® accurately simulated the impact of water intake on the gastrointestinal behavior of a Sporanox® solution. Water intake significantly decreased the duodenal solute concentrations of itraconazole as compared to no intake of water. Despite this duodenal behavior the amount of permeated itraconazole was not affected by water intake as observed in vivo. Next to this, the Diamod® accurately simulated the negative food effect for indinavir sulfate. Different fasted and fed state experiments demonstrated that this negative food effect was mediated by an increased stomach pH, entrapment of indinavir in colloidal structures and the slower gastric emptying of indinavir under fed state conditions. Therefore, it can be concluded that the Diamod® is a useful in vitro model to mechanistically study the gastrointestinal performance of drugs.}, }
@article {pmid37395875, year = {2023}, author = {Simon, MP and Schatz, M and Böhm, L and Papp, I and Grossart, HP and Andersen, TJ and Bálint, M and Düring, RA}, title = {Dissent in the sediment? Lake sediments as archives of short- and long-range impact of anthropogenic activities in northeastern Germany.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37395875}, issn = {1614-7499}, support = {DFG BA 4843/2-1//Deutsche Forschungsgemeinschaft/ ; K314/2020//Deutsche Forschungsgemeinschaft/ ; K314/2020//Leibniz-Gemeinschaft/ ; }, abstract = {The suitability of lake sediment cores to reconstruct past inputs, regional pollution, and usage patterns of pesticides has been shown previously. Until now, no such data exist for lakes in eastern Germany. Therefore, 10 sediment cores (length 1 m) of 10 lakes in eastern Germany, the territory of the former German Democratic Republic (GDR), were collected and cut into 5-10-mm layers. In each layer, concentrations of trace elements (TEs) As, Cd, Cr, Cu, Ni, Pb, S, and Zn, as well as of organochlorine pesticides (OCPs), i.e., dichlorodiphenyltrichloroethane (DDT) and hexachlorocyclohexane (HCH), were analyzed. A miniaturized solid-liquid extraction technique in conjunction with headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) was used for the latter. The progression of TE concentrations over time is uniform. It follows a trans-regional pattern and is indicative of activity and policy making in West Germany before 1990 instead of those in the GDR. Of OCPs, only transformation products of DDT were found. Congener ratios indicate a mainly aerial input. In the lakes' profiles, several regional features and responses to national policies and measures are visible. Dichlorodiphenyldichloroethane (DDD) concentrations reflect the history of DDT use in the GDR. Lake sediments proved to be suitable to archive short- and long-range impacts of anthropogenic activity. Our data can be used to complement and validate other forms of environmental pollution long-term monitoring and to check for the efficiency of pollution countermeasures in the past.}, }
@article {pmid37393557, year = {2023}, author = {Madrigal-Trejo, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Valdivia-Anistro, JA and Eguiarte, LE and Souza, V}, title = {A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37393557}, issn = {1432-184X}, support = {IG200319//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; 970341//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; R20F009//http://dx.doi.org/10.13039/501100020884/ ; }, abstract = {Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from [Formula: see text]1-4% to [Formula: see text]33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.}, }
@article {pmid37392205, year = {2023}, author = {Woźniak, M and Tyśkiewicz, R and Siebielec, S and Gałązka, A and Jaroszuk-Ściseł, J}, title = {Metabolic Profiling of Endophytic Bacteria in Relation to Their Potential Application as Components of Multi-Task Biopreparations.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37392205}, issn = {1432-184X}, abstract = {Agricultural crops are exposed to various abiotic and biotic stresses that can constrain crop productivity. Focusing on a limited subset of key groups of organisms has the potential to facilitate the monitoring of the functions of human-managed ecosystems. Endophytic bacteria can enhance plant stress resistance and can help plants to cope with the negative impacts of stress factors through the induction of different mechanisms, influencing plant biochemistry and physiology. In this study, we characterise endophytic bacteria isolated from different plants based on their metabolic activity and ability to synthesise 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD), the activity of hydrolytic exoenzymes, the total phenolic compounds (TPC) and iron-complexing compounds (ICC). Test GEN III MicroPlate indicated that the evaluated endophytes are highly metabolically active, and the best used substrates were amino acids, which may be important in selecting potential carrier components for bacteria in biopreparations. The ACCD activity of strain ES2 (Stenotrophomonas maltophilia) was the highest, whereas that of strain ZR5 (Delftia acidovorans) was the lowest. Overall, the obtained results indicated that ∼91.3% of the isolates were capable of producing at least one of the four hydrolytic enzymes. In addition, most of the tested strains produced ICC and TPC, which play a significant role in reducing stress in plants. The results of this study suggest that the tested endophytic bacterial strains can potentially be used to mitigate climate change-associated stresses in plants and to inhibit plant pathogens.}, }
@article {pmid37392204, year = {2023}, author = {Berçot, MR and Queiroz, PRM and Grynberg, P and Togawa, R and Martins, &#xc9;S and Rocha, GT and Monnerat, RG}, title = {Distribution and Genetic Diversity of Genes from Brazilian Bacillus thuringiensis Strains Toxic to Agricultural Insect Pests Revealed by Real-Time PCR.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37392204}, issn = {1432-184X}, abstract = {Bacillus thuringiensis is a Gram-positive aerobic bacterium and the most used biopesticide worldwide. Given the importance of B. thuringiensis strain characterization for the development of new bioinsecticides or transgenic events and the identification and classification of new B. thuringiensis genes and strains to understand its distribution and diversity, this work is aimed at creating a gene identification system based on qPCR reactions utilizing core B. thuringiensis genes cry1, cry2, cry3, cry4, cry5, app6, cry7, cry8, cry9, cry10, cry11, vpb1, vpa2, vip3, cyt1, and cyt2 for the characterization of 257 strains of B. thuringiensis. This system was based on the Invertebrate Bacteria Collection from Embrapa Genetic Resources and Biotechnology and analyzed (a) the degree of correlation between the distribution of these strains and the origin of the substrate from which the strain was isolated and (b) between its distribution and geoclimatic conditions. This study made it possible to observe that the cry1, cry2, and vip3A/B genes occur homogeneously in the Brazilian territory, and some genes are found in specific regions. The biggest reservoir of variability is within B. thuringiensis strains in each region, and it is suggested that both geoclimatic conditions and regional crops interfere with the genetic diversity of the B. thuringiensis strains present in the region, and B. thuringiensis strains can constantly exchange genetic information.}, }
@article {pmid37391884, year = {2023}, author = {Grosicki, GJ and Pugh, J and Wosinska, L and Quilter, K and Mattimoe, D and Allen, J and Joyce, SA and O'Sullivan, O and Close, GL}, title = {Ultra-Endurance Triathlon Competition Shifts Fecal Metabolome Independent of Changes to Microbiome Composition.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {}, number = {}, pages = {}, doi = {10.1152/japplphysiol.00024.2023}, pmid = {37391884}, issn = {1522-1601}, support = {SFI/12/RC/2273//Science Foundation Ireland Centres Grant/ ; No. 3358//SFI: EU Joint Programme Initiative CABALA for Health/ ; DAFM 17-RD-US-ROI//Ireland Department of Agriculture, Food and the Marine/ ; 16/RC/3835//VistaMilk/ ; }, abstract = {Understanding changes to gut microbiota composition and metabolic output in response to acute exercise may be necessary for understanding the mechanisms mediating the long-term health and performance benefits of exercise. Our primary objective was to characterize acute changes in the fecal microbiome and metabolome following participation in an ultra-endurance (3.9km swim, 180.2km bike, 42.2km run) triathlon. An exploratory aim was to determine associations between athlete-specific factors (race performance [i.e., completion time] and lifetime years of endurance training) with pre-race gut microbiota and metabolite profiles. Stool samples from 12 triathletes (9M/3F; 43±14 yrs, 23±2 kg/m[2]) were collected ≤48 hours before and the first bowel movement following race completion. Intra- and inter-individual diversity of bacterial species and individual bacterial taxa were unaltered following race completion (P>0.05). However, significant reductions (P<0.05) in free and secondary bile acids (DCA, 12-ketoLCA) and short-chain fatty acids (butyric and pivalic acids), and significant increases (P<0.05) in long-chain fatty acids (oleic and palmitoleic acids) were observed. Exploratory analyses revealed several associations between pre-race bacterial taxa and fecal metabolites with race performance and lifetime history of endurance training (P<0.05). These findings suggest that 1) acute ultra-endurance exercise shifts microbial metabolism independent of changes to community composition and 2) athlete performance level and training history relate to resting-state gut microbial ecology.}, }
@article {pmid37391045, year = {2023}, author = {Abele, M and Doll, E and Bayer, FP and Meng, C and Lomp, N and Neuhaus, K and Scherer, S and Kuster, B and Ludwig, C}, title = {Unified workflow for the rapid and in-depth characterization of bacterial proteomes.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {}, number = {}, pages = {100612}, doi = {10.1016/j.mcpro.2023.100612}, pmid = {37391045}, issn = {1535-9484}, abstract = {Bacteria are the most abundant and diverse organisms among the kingdoms of life. Due to this excessive variance, finding a unified, comprehensive, and safe workflow for quantitative bacterial proteomics is challenging. In this study, we have systematically evaluated and optimized sample preparation, mass spectrometric data acquisition, and data analysis strategies in bacterial proteomics. We investigated workflow performances on six representative species with highly different physiologic properties to mimic bacterial diversity. The best sample preparation strategy was a cell lysis protocol in 100% trifluoroacetic acid followed by an in-solution digest. Peptides were separated on a 30-minute linear microflow liquid chromatography gradient and analyzed in data-independent acquisition mode. Data analysis was performed with DIA-NN using a predicted spectral library. Performance was evaluated according to the number of identified proteins, quantitative precision, throughput, costs, and biological safety. With this rapid workflow, over 40% of all encoded genes were detected per bacterial species. We demonstrated the general applicability of our workflow on a set of 23 taxonomically and physiologically diverse bacterial species. We could confidently identify over 45,000 proteins in the combined dataset, of which 30,000 have not been experimentally validated. Our work thereby provides a valuable resource for the microbial scientific community. Finally, we grew Escherichia coli and Bacillus cereus in replicates under twelve different cultivation conditions to demonstrate the high-throughput suitability of the workflow. The proteomic workflow we present in this manuscript does not require any specialized equipment or commercial software and can be easily applied by other laboratories to support and accelerate the proteomic exploration of the bacterial kingdom.}, }
@article {pmid37389724, year = {2023}, author = {Das, S and Roy, R and Paul, P and Chakraborty, P and Chatterjee, S and Malik, M and Sarkar, S and Das Gupta, A and Maiti, D and Tribedi, P}, title = {Piperine, a Plant Alkaloid, Exhibits Efficient Disintegration of the Pre-existing Biofilm of Staphylococcus aureus: a Step Towards Effective Management of Biofilm Threats.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37389724}, issn = {1559-0291}, support = {R&amp;D/2020/F2//The Neotia University/ ; }, abstract = {Staphylococcus aureus causes a range of chronic infections in humans by exploiting its biofilm machinery and drug-tolerance property. Although several strategies have been proposed to eradicate biofilm-linked issues, here, we have explored whether piperine, a bioactive plant alkaloid, can disintegrate an already existing Staphylococcal biofilm. Towards this direction, the cells of S. aureus were allowed to develop biofilm first followed by treatment with the test concentrations (8 and 16 µg/mL) of piperine. In this connection, several assays such as total protein recovery assay, crystal violet assay, extracellular polymeric substances (EPS) measurement assay, fluorescein diacetate hydrolysis assay, and fluorescence microscopic image analysis confirmed the biofilm-disintegrating property of piperine against S. aureus. Piperine reduced the cellular auto-aggregation by decreasing the cell surface hydrophobicity. On further investigation, we observed that piperine could down regulate the dltA gene expression that might reduce the cell surface hydrophobicity of S. aureus. It was also observed that the piperine-induced accumulation of reactive oxygen species (ROS) could enhance biofilm disintegration by decreasing the cell surface hydrophobicity of the test organism. Together, all the observations suggested that piperine could be used as a potential molecule for the effective management of the pre-existing biofilm of S. aureus.}, }
@article {pmid37387230, year = {2023}, author = {Falkenberg, R and Sigl, L and Fochler, M}, title = {From 'making lists' to conducting 'well-rounded' studies: Epistemic re-orientations in soil microbial ecology.}, journal = {Social studies of science}, volume = {}, number = {}, pages = {3063127231179700}, doi = {10.1177/03063127231179700}, pmid = {37387230}, issn = {1460-3659}, abstract = {Soil microbial ecology is a relatively young research field that became established around the middle of the 20th century and has grown considerably since then. We analyze two epistemic re-orientations in the field, asking how possibilities for creating do-able problems within current conditions of research governance and researchers' collective sense-making about new, more desirable modes of research were intertwined in these developments. We show that a first re-orientation towards molecular omics studies was comparably straightforward to bring about, because it allowed researchers to gain resources for their work and to build careers-in other words, to create do-able problems. Yet, over time this mode of research developed into a scientific bandwagon from which researchers found it difficult to depart, even as they considered this kind of work as producing mostly descriptive studies rather than exploring interesting and important ecological questions. Researchers currently wish to re-orient their field again, towards a new mode of conducting 'well-rounded' interdisciplinary and ecologically-relevant studies. This re-orientation is, however, not easy to put into practice. In contrast to omics studies, this new mode of research does not easily enable the creation of do-able problems for two reasons. First, it is not as readily 'packaged' and hence more difficult to align with institutional and funding frameworks as well as with demands for productivity and career building. Second, while the first re-orientation was part of a broader exciting bandwagon across the life sciences and promised apparent discoveries, the current re-orientation goes along with a different sense of novelty, exploring complex environmental relations and building an understanding at the intersection of disciplines, instead of pushing a clearly circumscribed frontier. Ultimately, our analysis raises questions about whether current conditions of research governance structurally privilege particular kinds of scientific re-orientation over others.}, }
@article {pmid37387175, year = {2023}, author = {Grover, S and Markin, A and Anderson, TK and Eulenstein, O}, title = {Phylogenetic diversity statistics for all clades in a phylogeny.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {Supplement_1}, pages = {i177-i184}, pmid = {37387175}, issn = {1367-4811}, support = {/NH/NIH HHS/United States ; 75N93021C00015/HH/HHS/United States ; }, abstract = {The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.}, }
@article {pmid37383638, year = {2023}, author = {McAtee, TB and Pinnell, LJ and Powledge, SA and Wolfe, CA and Morley, PS and Richeson, JT}, title = {Effects of respiratory virus vaccination and bovine respiratory disease on the respiratory microbiome of feedlot cattle.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203498}, pmid = {37383638}, issn = {1664-302X}, abstract = {INTRODUCTION: The objectives of this study were to evaluate the impacts of two modified-live virus (MLV) vaccination protocols and respiratory disease (BRD) occurrence on the microbial community composition of the nasopharynx in feedlot cattle.<br><br>METHODS: The treatment groups included in this randomized controlled trial included: 1) no viral respiratory vaccination (CON), 2) intranasal, trivalent, MLV respiratory vaccine in addition to a parenteral BVDV type I and II vaccine (INT), and 3) parenteral, pentavalent, MLV respiratory vaccination against the same agents (INJ). Calves (n = 525) arrived in 5 truckload blocks and were stratified by body weight, sex, and presence of a pre-existing identification ear-tag. A total of 600 nasal swab samples were selected for DNA extraction and subsequent 16S rRNA gene sequencing to characterize the microbiome of the upper respiratory tract. Nasal swabs collected on d 28 from healthy cattle were used to evaluate the impact of vaccination on upper respiratory tract (URT) microbial communities.<br><br>RESULTS: Firmicutes were less abundant in INT calves (n = 114; P < 0.05) and this difference was attributed to decreased relative abundance (RA) of Mycoplasma spp. (P = 0.04). Mannheimia and Pasteurella had lower RA in INT (P < 0.05). The microbiome in healthy animals on d 28 had increased Proteobacteria (largely Moraxella spp.) and decreased Firmicutes (comprised almost exclusively of Mycoplasma spp.) compared to animals that were treated for or died from BRD (P < 0.05). Cattle that died had a greater RA of Mycoplasma spp. in their respiratory microbiome on d 0 (P < 0.02). Richness was similar on d 0 and 28, but diversity increased for all animals on d 28 (P>0.05).}, }
@article {pmid37383354, year = {2023}, author = {Kim, S and Kwak, J and Song, M and Cho, J and Kim, ES and Keum, GB and Doo, H and Pandey, S and Cho, JH and Ryu, S and Kim, S and Im, YM and Kim, HB}, title = {Effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and intestinal microbiome in weaned pigs.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1140718}, pmid = {37383354}, issn = {2297-1769}, abstract = {INTRODUCTION: This study was conducted to evaluate the effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and gut microbiome in weaned pigs.<br><br>METHODS: A total of 300 crossbred pigs [(Landrace &#xd7; Yorkshire]&#x2009;&#xd7;&#x2009;Duroc; 8.87&#x2009;&#xb1;&#x2009;0.34&#x2009; kg of average initial body weight [BW]; 4&#x2009; weeks of age) were divided into two dietary treatments (15 pigs/pen, 10 replicates/treatment) using a randomized complete block design (block&#x2009;=&#x2009;BW): control (CON) and the effective microorganism (MEM). The CON was not treated, while the MEM was treated with the mixture of L. casei (1 &#xd7; 10[7]&#x2009;CFU/mL) and S. cerevisiae (1 &#xd7; 10[7]&#x2009;CFU/mL) at 3&#x2009;mL/pig/day for 4&#x2009; weeks via the drinking water supply. Two feces and one blood sample from the randomly selected pigs in each pen were collected on D1 and D28 after weaning. Pigs were individually weighed, and pen feed intakes were recorded to evaluate pig growth performance. For the gut microbiome analysis, 16S rRNA gene hypervariable regions (V5 to V6) were sequenced using the Illumina MiSeq platform, and Quantitative Insight into Microbial Ecology (QIIME) and Microbiome Helper pipeline were used for 16S rRNA gene sequence analysis.<br><br>RESULTS AND DISCUSSION: The daily weight gain and feed efficiency of MEM were significantly higher than those of CON (p&#x2009;<&#x2009;0.001). There were no significant differences in hematological parameters and immune responses between CON and MEM. However, MEM had significantly lower Treponema genus, whereas significantly higher Lactobacillus and Roseburia genera compared to CON. Overall, our data showed that L. casei and S. cerevisiae mixture could promote growth performance through the modulation of gut microbiota in pigs. This study will help to understand the correlation between the growth performance and the gut microbiome.}, }
@article {pmid37382454, year = {2023}, author = {Liu, W and Cui, X and Wang, X and Shen, C and Ji, L and Zhang, M and Wong, MH and Zhang, J and Shan, S}, title = {Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019823}, doi = {10.1128/msystems.00198-23}, pmid = {37382454}, issn = {2379-5077}, abstract = {Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.}, }
@article {pmid37382302, year = {2023}, author = {Puente-Sánchez, F and Hoetzinger, M and Buck, M and Bertilsson, S}, title = {Exploring environmental intra-species diversity through non-redundant pangenome assemblies.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13826}, pmid = {37382302}, issn = {1755-0998}, support = {892961//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; 2019-02336//Svenska Forskningsr&#xe5;det Formas/ ; 2017-04422//Vetenskapsr&#xe5;det/ ; 2018-05973//Vetenskapsr&#xe5;det/ ; }, abstract = {At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.}, }
@article {pmid37379878, year = {2023}, author = {Abel, SM and Wu, F and Primpke, S and Gerdts, G and Brandt, A}, title = {Journey to the deep: plastic pollution in the hadal of deep-sea trenches.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {122078}, doi = {10.1016/j.envpol.2023.122078}, pmid = {37379878}, issn = {1873-6424}, abstract = {The global increase of plastic production, linked with an overall plastic misuse and waste mismanagement, leads to an inevitable increase of plastic debris that ends up in our oceans. One of the major sinks of this pollution is the deep-sea floor, which is hypothesized to accumulate in its deepest points, the hadal trenches. Little is known about the magnitude of pollution in these trenches, given the remoteness of these environments, numerous factors influencing the input and sinking behavior of plastic debris from shallower environments. This study represents to the best of our knowledge the largest survey of (macro)plastic debris sampled at hadal depths, down to 9600 m. Industrial packaging and material assignable to fishing activities were the most common debris items in the Kuril Kamchatka trench, most likely deriving from long-distance transport by the Kuroshio extension current (KE) or from regional marine traffic and fishing activities. The chemical analysis by (Attenuated Total Reflection Fourier transform infrared (ATR-FTIR) spectroscopy revealed that the main polymers detected were polyethylene (PE), polypropylene (PP) and nylon. Plastic waste is reaching the depths of the trench, although some of the items were only partially broken down. This finding suggests that complete breakdown into secondary microplastics (MP) may not always occur at the sea surface or though the water column. Due to increased brittleness, plastic debris may break apart upon reaching the hadal trench floor where plastic degrading factors were thought to be, coming off. The KKT's remote location and high sedimentation rates make it a potential site for high levels of plastic pollution, potentially making it one of the world's most heavily contaminated marine areas and an oceanic plastic deposition zone.}, }
@article {pmid37378294, year = {2023}, author = {Xie, P and Huang, K and Deng, A and Mo, P and Xiao, F and Wu, F and Xiao, D and Wang, Y}, title = {The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1111087}, pmid = {37378294}, issn = {1664-302X}, abstract = {Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.}, }
@article {pmid37375921, year = {2023}, author = {Qi, Y and Ma, L and Ghani, MI and Peng, Q and Fan, R and Hu, X and Chen, X}, title = {Effects of Drought Stress Induced by Hypertonic Polyethylene Glycol (PEG-6000) on Passiflora edulis Sims Physiological Properties.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37375921}, issn = {2223-7747}, support = {2021-229, HZJD [2022]001//Guizhou Provincial Science and Technology Program/ ; Guike AA21196003//Science and Technology Base &amp; Talent Project of Guangxi Province/ ; 2021YFD1100303-3//National Key Research and Development Program of China/ ; 2019-04//Guizhou University Cultivation Project/ ; }, abstract = {Passion fruit is known to be sensitive to drought, and in order to study the physiological and biochemical changes that occur in passion fruit seedlings under drought stress, a hypertonic polyethylene glycol (PEG) solution (5%, 10%, 15%, and 20%) was used to simulate drought stress in passion fruit seedlings. We explored the physiological changes in passion fruit seedlings under drought stress induced by PEG to elucidate their response to drought stress and provide a theoretical basis for drought-resistant cultivation of passion fruit seedlings. The results show that drought stress induced by PEG had a significant effect on the growth and physiological indices of passion fruit. Drought stress significantly decreased fresh weight, chlorophyll content, and root vitality. Conversely, the contents of soluble protein (SP), proline (Pro), and malondialdehyde (MDA) increased gradually with the increasing PEG concentration and prolonged stress duration. After nine days, the SP, Pro and MDA contents were higher in passion fruit leaves and roots under 20% PEG treatments compared with the control. Additionally, with the increase in drought time, the activities of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) showed an increasing trend and then a decreasing trend, and they reached the highest value at the sixth day of drought stress. After rehydration, SP, Pro and MDA contents in the leaves and roots of passion fruit seedlings was reduced. Among all the stress treatments, 20% PEG had the most significant effect on passion fruit seedlings. Therefore, our study demonstrated sensitive concentrations of PEG to simulate drought stress on passion fruit and revealed the physiological adaptability of passion fruit to drought stress.}, }
@article {pmid37199998, year = {2023}, author = {Getz, EW and Lanclos, VC and Kojima, CY and Cheng, C and Henson, MW and Schön, ME and Ettema, TJG and Faircloth, BC and Thrash, JC}, title = {The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0017923}, doi = {10.1128/msystems.00179-23}, pmid = {37199998}, issn = {2379-5077}, support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation/ ; OCE-1945279, EF-2125191//National Science Foundation/ ; }, abstract = {Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning order-level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to the Pelagibacterales is highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to the Pelagibacterales. We used a new isolate genome, recently released single-amplified genomes and metagenome-assembled genomes, and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with the recruitment of metagenomes spanning the open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade and support the contention that this group represents a taxonomic family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in the transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa. IMPORTANCE One goal of marine microbiologists is to uncover the roles various microorganisms are playing in biogeochemical cycles. Success in this endeavor relies on differentiating groups of microbes and circumscribing their relationships. An early-diverging group (subclade V) of the most abundant bacterioplankton, SAR11, has recently been proposed as a separate lineage that does not share a most recent common ancestor. But beyond phylogenetics, little has been done to evaluate how these organisms compare with SAR11. Our work leverages dozens of new genomes to demonstrate the similarities and differences between subclade V and SAR11. In our analysis, we also establish that subclade V is synonymous with a group of bacteria established from 16S rRNA gene sequences, AEGEAN-169. Subclade V/AEGEAN-169 has clear metabolic distinctions from SAR11 and their shared traits point to remarkable convergent evolution if they do not share a most recent common ancestor.}, }
@article {pmid37195192, year = {2023}, author = {Wang, J and Pan, Z and Yu, J and Zhang, Z and Li, YZ}, title = {Global assembly of microbial communities.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0128922}, doi = {10.1128/msystems.01289-22}, pmid = {37195192}, issn = {2379-5077}, support = {32070030//National Natural Science Foundation of China (NSFC)/ ; 2018YFA0900400, 2018YFA0901704//MOST | National Key Research and Development Program of China (NKPs)/ ; ZR2022QC229//Science Foundation for Youths of Shandong Province/ ; 2022M711918//China Postdoctoral Science Foundation/ ; SDCX-ZG-20220201//Postdoctoral Innovation Project of Shandong Province ()/ ; 32201303//National Natural Science Foundation of China (NSFC)/ ; }, abstract = {Different habitats harbor different microbial communities with elusive assembly mechanisms. This study comprehensively investigated the global assembly mechanisms of microbial communities and effects of community-internal influencing factors using the Earth Microbiome Project (EMP) data set. We found that deterministic and stochastic processes contribute approximately equally to global microbial community assembly, and, specifically, deterministic processes generally play a major role in free-living and plant-associated (but not plant corpus) environments, while stochastic processes are the major contributor in animal-associated environments. In contrast with the assembly of microorganisms, the assembly of functional genes, predicted from PICRUSt, is mainly attributed to deterministic processes in all microbial communities. The sink and source microbial communities are normally assembled using similar mechanisms, and the core microorganisms are specific to different environment types. On a global scale, deterministic processes are positively related to the community alpha diversity, microbial interaction degree and bacterial predatory-specific gene abundance. Our analysis provides a panoramic picture and regularities of global and environment-typical microbial community assemblies. IMPORTANCE With the development of sequencing technologies, the research topic of microbial ecology has evolved from the analysis of community composition to community assembly, including the relative contribution of deterministic and stochastic processes for the formation and maintenance of community diversity. Many studies have reported the microbial assembly mechanisms in various habitats, but the assembly regularities of global microbial communities remain unknown. In this study, we analyzed the EMP data set using a combined pipeline to explore the assembly mechanisms of global microbial communities, microbial sources to construct communities, core microbes in different environment types, and community-internal factors influencing assembly. The results provide a panoramic picture and rules of global and environment-typical microbial community assemblies, which enhances our understandings of the mechanisms globally controlling community diversity and species coexistence.}, }
@article {pmid37375077, year = {2023}, author = {Xu, ZS and Ju, T and Yang, X and Gänzle, M}, title = {A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/microorganisms11061575}, pmid = {37375077}, issn = {2076-2607}, support = {Food Microbiology and Probiotics//Canada Research Chairs/ ; Accelerate Fellowship//Mitacs/ ; }, abstract = {Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.}, }
@article {pmid37375028, year = {2023}, author = {Villeneuve, K and Turcotte-Blais, V and Lazar, CS}, title = {Effect of Snowmelt on Groundwater Bacterial Community Composition and Potential Role of Surface Environments as Microbial Seed Bank in Two Distinct Aquifers from the Region of Quebec, Canada.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/microorganisms11061526}, pmid = {37375028}, issn = {2076-2607}, support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; Aquatic Environmental Genomics//Canada Research Chairs/ ; }, abstract = {Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiomes in two distinct aquifers located in the region of Vaudreuil-Soulanges (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested a low contribution of surface environments to the groundwater microbiome except for in the months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers.}, }
@article {pmid37375009, year = {2023}, author = {Satari, L and Iglesias, A and Porcar, M}, title = {The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/microorganisms11061507}, pmid = {37375009}, issn = {2076-2607}, support = {ID101000470//European Union (MICRO4BIOGAS project)/ ; }, abstract = {As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental-often extreme-selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the "build environment" microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches.}, }
@article {pmid37374902, year = {2023}, author = {Heczko, P and Kozień, &#x141; and Strus, M}, title = {Special Issue "An Update on Lactobacillus": Editorial.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/microorganisms11061400}, pmid = {37374902}, issn = {2076-2607}, abstract = {As indicated in the introduction to this Special Issue, as of 2020, the original genus Lactobacillus comprised over 260 recognized species, a figure which is probably much higher now [...].}, }
@article {pmid37369788, year = {2023}, author = {Fukui, Y and Abe, M and Kobayashi, M}, title = {Effects of Hyphomonas Strains on the Growth of Red Algae Pyropia Species by Attaching Specifically to Their Rhizoids.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37369788}, issn = {1432-184X}, abstract = {Bacteria and marine macroalgae form close associations, while various bacteria affect the morphogenesis and growth of macroalgae. Hyphomonas strains exhibit normal morphogenetic activity in protoplasts of the red alga Pyropia yezoensis (nori). However, the effects of the bacteria on the growth of Pyropia from protoplast cells to regenerated thalli remain unknown. Here, we assessed the growth of P. yezoensis and Pyropia tenera using combined cultures of three Hyphomonas strains (LNM10-16, SCM-2, and LNM-9) and three algal media (artificial seawater with vitamins, artificial seawater, and natural seawater) over 7 weeks. Third week after culture, the three Hyphomonas strains showed almost similar levels of normal growth activity for both Pyropia species. However, at 7 weeks, significant differences were observed among the three Hyphomonas strains in terms of length, length-to-width ratio, and normal morphology of Pyropia thalli. LNM10-16 significantly promoted the thalli length and length-to-width ratios of both Pyropia species in artificial seawater without vitamins and natural seawater, compared with the other two Hyphomonas strains. P. yezoensis cultured in artificial seawater with vitamins showed a much higher demand for LNM10-16 in development of the thalli length than P. tenera. These results may be explained by differences in the growth activities of Hyphomonas strains and the nutrient requirements of Pyropia species. Furthermore, the bacteria were more specifically attached to the rhizoid surfaces of both species. This study is the first to reveal that Hyphomonas strains affect the growth of Pyropia species by attaching to their rhizoids.}, }
@article {pmid37365511, year = {2023}, author = {Chang, Y and Sun, H and Liu, S and He, Y and Zhao, S and Wang, J and Wang, T and Zhang, J and Gao, J and Yang, Q and Li, M and Zhao, X}, title = {Identification of BBX gene family and its function in the regulation of microtuber formation in yam.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {354}, pmid = {37365511}, issn = {1471-2164}, support = {5101049470215//Postdoctor Initiative Foundation of Henan Normal University/ ; 21A180013//Colleges and Universities in Henan Province Key Scientific Research Project Funding Scheme/ ; CARS-21//Agriculture Research System of China/ ; 224200510011//The Zhongyuan high level talents special support plan-Science and Technology Innovation Leading Talents/ ; 2021YFD1600100//Special National Key Research and Development Plan/ ; 81274019//National Natural Science Foundation of China/ ; 5201049160163//Henan Normal University and Wen County People's Government Jointly Build National Yam Germplasm Resource Garden Project/ ; }, mesh = {*Dioscorea/genetics/metabolism ; Gene Expression Profiling ; Multigene Family ; Photoperiod ; Circadian Rhythm ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism ; }, abstract = {BBX proteins play important roles in all of the major light-regulated developmental processes. However, no systematic analysis of BBX gene family regarding the regulation of photoperiodic microtuber formation has been previously performed in yam. In this study, a systematic analysis on the BBX gene family was conducted in three yam species, with the results, indicating that this gene plays a role in regulating photoperiodic microtuber formation. These analyses included identification the BBX gene family in three yam species, their evolutionary relationships, conserved domains, motifs, gene structure, cis-acting elements, and expressional patterns. Based on these analyses, DoBBX2/DoCOL5 and DoBBX8/DoCOL8 showing the most opposite pattern of expression during microtuber formation were selected as candidate genes for further investigation. Gene expression analysis showed DoBBX2/DoCOL5 and DoBBX8/DoCOL8 were highest expressed in leaves and exhibited photoperiod responsive expression patterns. Besides, the overexpression of DoBBX2/DoCOL5 and DoBBX8/DoCOL8 in potato accelerated tuber formation under short-day (SD) conditions, whereas only the overexpression of DoBBX8/DoCOL8 enhanced the accelerating effect of dark conditions on tuber induction. Tuber number was increased in DoBBX8/DoCOL8 overexpressing plants under dark, as well as in DoBBX2/DoCOL5 overexpressing plants under SD. Overall, the data generated in this study may form the basis of future functional characterizations of BBX genes in yam, especially regarding their regulation of microtuber formation via the photoperiodic response pathway.}, }
@article {pmid37364132, year = {2023}, author = {Schleyer, G and Kuhlisch, C and Ziv, C and Ben-Dor, S and Malitsky, S and Schatz, D and Vardi, A}, title = {Lipid biomarkers for algal resistance to viral infection in the ocean.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {27}, pages = {e2217121120}, doi = {10.1073/pnas.2217121120}, pmid = {37364132}, issn = {1091-6490}, support = {101053543//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 735079//Simons Foundation (SF)/ ; 731065//EC | Horizon 2020 Framework Programme (H2020)/ ; }, mesh = {Humans ; *Viruses ; Phytoplankton/metabolism ; *Haptophyta/metabolism ; *Virus Diseases ; Biomarkers/metabolism ; Oceans and Seas ; Lipids ; }, abstract = {Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to identify lipid biomarkers for the resistance of the bloom-forming alga Emiliania huxleyi to its specific virus, E. huxleyi virus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistant E. huxleyi strains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers in E. huxleyi isolates collected from induced E. huxleyi blooms and in samples collected during an open-ocean E. huxleyi bloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition of E. huxleyi cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and coevolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.}, }
@article {pmid37362850, year = {2023}, author = {McDonagh, F and Cormican, M and Morris, D and Burke, L and Singh, NK and Venkateswaran, K and Miliotis, G}, title = {Medical Astro-Microbiology: Current Role and Future Challenges.}, journal = {Journal of the Indian Institute of Science}, volume = {}, number = {}, pages = {1-26}, doi = {10.1007/s41745-023-00360-1}, pmid = {37362850}, issn = {0970-4140}, abstract = {The second and third decades of the twenty-first century are marked by a flourishing of space technology which may soon realise human aspirations of a permanent multiplanetary presence. The prevention, control and management of infection with microbial pathogens is likely to play a key role in how successful human space aspirations will become. This review considers the emerging field of medical astro-microbiology. It examines the current evidence regarding the risk of infection during spaceflight via host susceptibility, alterations to the host's microbiome as well as exposure to other crew members and spacecraft's microbiomes. It also considers the relevance of the hygiene hypothesis in this regard. It then reviews the current evidence related to infection risk associated with microbial adaptability in spaceflight conditions. There is a particular focus on the International Space Station (ISS), as one of the only two crewed objects in low Earth orbit. It discusses the effects of spaceflight related stressors on viruses and the infection risks associated with latent viral reactivation and increased viral shedding during spaceflight. It then examines the effects of the same stressors on bacteria, particularly in relation to changes in virulence and drug resistance. It also considers our current understanding of fungal adaptability in spaceflight. The global public health and environmental risks associated with a possible re-introduction to Earth of invasive species are also briefly discussed. Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars. Overall, this review summarises much of our current understanding of medical astro-microbiology and identifies significant knowledge gaps.}, }
@article {pmid37356531, year = {2023}, author = {Wang, H and Lin, L and Zhang, L and Han, P and Ju, F}, title = {Microbiome assembly mechanism and functional potential in enhanced biological phosphorus removal system enriched with Tetrasphaera-related polyphosphate accumulating organisms.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116494}, doi = {10.1016/j.envres.2023.116494}, pmid = {37356531}, issn = {1096-0953}, abstract = {Tetrasphaera-related polyphosphate accumulating organisms (PAOs) are the key functional guilds for enhanced biological phosphorus removal (EBPR) systems. Their enrichment can be enhanced by the nitrification inhibitor allylthiourea (ATU). However, the underlying assembly mechanism and the functional potential of the EBPR microbiome regulated by ATU are unclear. This study investigates the effect of ATU on microbiome assembly and function by closely following the microbiota dynamics in an EBPR system enriched with Tetrasphaera-related PAOs for 288-days before, during and after ATU addition. The results showed that ATU addition increased microbiota structural similarity and compositional convergence, and increased determinism in the assembly of EBPR microbiome. During exposure to ATU, Tetrasphaera-related PAOs were governed by homogeneous selection and the dominant species revealed by 16 S rRNA gene-based phylogenetic analysis shifted from clade III to clade I. Meanwhile, ATU supply promoted significant enrichment of functional genes involved in phosphate transport (pit) and polyphosphate synthesis and degradation (ppk1 and ppk2), whereas both Nitrosomonas and ammonia monooxygenase-encoding genes (amoA/B/C) assignable to this group of nitrifying bacteria decreased. Moreover, ATU addition relieved the significant abundance correlation between filamentous bacteria Ca. Promineofilum and denitrifying Brevundimonas (FDR-adjusted P < 0.01), damaging their potential synergic or cooperative interactions, thus weakening their competitiveness against Tetrasphaera-related PAOs. Notably, ATU withdrawn created opportunistic conditions for the unexpected explosive growth and predominance of Thiothrix filaments, leading to a serious bulking event. Our study provides new insights into the microbial ecology of Tetrasphaera-related PAOs in EBPR system, which could guide the establishment of an efficient microbiota for EBPR.}, }
@article {pmid37356163, year = {2023}, author = {Yuan, W and Xu, EG and Li, L and Zhou, A and Peijnenburg, WJGM and Grossart, HP and Liu, W and Yang, Y}, title = {Tracing and trapping micro- and nanoplastics: Untapped mitigation potential of aquatic plants?.}, journal = {Water research}, volume = {242}, number = {}, pages = {120249}, doi = {10.1016/j.watres.2023.120249}, pmid = {37356163}, issn = {1879-2448}, abstract = {Micro- and nanoplastics are emerging concerns due to their environmental ubiquity and currently largely unknown ecological impacts. Leveraging on a recently developed method using europium-doped polystyrene particles (PS-Eu), our present work aimed to accurately trace the uptake and transport of micro- and nanoplastics in aquatic plants and shed insights into the potential of different aquatic plants for trapping and removal of plastics from water environment. Seedlings of Vallisneria denseserrulata Makino (submerged plant), Iris tectorum Maxim (emergent plant), and Eichhornia crassipes Solms (floating plant) were exposed to 100 nm and 2 μm PS-Eu in freshwater (5 μg/mL) or sediments (5 μg/g) for 8 weeks. Fluorescence imaging clearly evidenced that PS-Eu mainly accumulated in the intercellular space and were transported from roots to leaves via the apoplastic path and vascular bundle. Mass spectrum analysis demonstrated that up to 6250 μg/g nanoplastics were trapped in aquatic plants (mainly in roots) with a bioconcentration factor of 306.5, depending on exposure routes and plant species. Owing to their excellent capture capability and high tolerance to plastic exposures, floating plants like E. crassipes are promising for immobilizing and removing fine plastics from the water environment.}, }
@article {pmid37350274, year = {2023}, author = {Rupp, ME and Van Schooneveld, TC and Starlin, R and Quick, J and Snyder, GM and Passaretti, CL and Stevens, MP and Cawcutt, K}, title = {Hospital return-to-work practices for healthcare providers infected with severe acute respiratory coronavirus virus 2 (SARS-CoV-2).}, journal = {Infection control and hospital epidemiology}, volume = {}, number = {}, pages = {1-4}, doi = {10.1017/ice.2023.133}, pmid = {37350274}, issn = {1559-6834}, abstract = {A survey of academic medical-center hospital epidemiologists indicated substantial deviation from Centers for Disease Control and Prevention guidance regarding healthcare providers (HCPs) recovering from coronavirus disease 2019 (COVID-19) returning to work. Many hospitals continue to operate under contingency status and have HCPs return to work earlier than recommended.}, }
@article {pmid37348760, year = {2023}, author = {Eudy, BJ and Odle, J and Lin, X and Maltecca, C and Walter, KR and McNulty, NP and Fellner, V and Jacobi, SK}, title = {Dietary Prebiotic Oligosaccharides and Arachidonate Alter the Fecal Microbiota and Mucosal Lipid Composition of Suckling Pigs.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2023.06.019}, pmid = {37348760}, issn = {1541-6100}, abstract = {BACKGROUND: Early intestinal development is important to infant vitality and optimal formula composition can promote gut health.<br><br>OBJECTIVES: The objectives were to evaluate the effects of arachidonate (ARA) and/or prebiotic oligosaccharide (PRE) supplementation in formula on the development of the microbial ecosystem and colonic health parameters.<br><br>METHODS: Newborn piglets were fed four formulas containing ARA (0.5 versus 2.5% of dietary fatty acids) and PRE (0 versus 8g/L, containing a 1:1 mixture of galactooligosaccharides (GOS) and polydextrose (PDX)) in a 2x2 factorial design for 22 days. Fecal samples were collected weekly and analyzed for relative microbial abundance. Intestinal samples were collected on day 22 and analyzed for mucosal fatty acids, pH, and short-chain fatty acids (SCFAs).<br><br>RESULTS: PRE supplementation significantly increased genera within Bacteroidetes and Firmicutes including Anaerostipes, Mitsuokella, Prevotella, Clostridium IV, and Bulleidia, and resulted in progressive separation from controls as determined by Principal Coordinates Analysis. Concentrations of SCFA increased from 70.98 to 87.37 mM, with an accompanying reduction in colonic pH. ARA supplementation increased the ARA content of the colonic mucosa from 2.35% to 5.34% of total fatty acids. PRE supplementation also altered mucosal fatty acid composition, resulting in increased linoleic acid (11.52% to 16.33% of total fatty acids) and ARA (2.35% to 5.16% of total fatty acids).<br><br>CONCLUSIONS: Prebiotic supplementation during the first 22 days of life altered the gut microbiota of piglets and increased the abundance of specific bacterial genera. These changes correlated with increased SCFA, which may benefit intestinal development. Although dietary ARA did not alter the microbiota, it increased the ARA content of the colonic mucosa, which may support intestinal development and epithelial repair. Prebiotic supplementation also increased unsaturation of fatty acids in the colonic mucosa. Although the mechanism requires further investigation, it may be related to altered microbial ecology or biohydrogenation of fatty acids.}, }
@article {pmid37347668, year = {2023}, author = {Verbeelen, T and Van Houdt, R and Leys, N and Ganigué, R and Mastroleo, F}, title = {RNA extraction protocol from low-biomass bacterial Nitrosomonas europaea and Nitrobacter winogradskyi cultures for whole transcriptome studies.}, journal = {STAR protocols}, volume = {4}, number = {3}, pages = {102358}, doi = {10.1016/j.xpro.2023.102358}, pmid = {37347668}, issn = {2666-1667}, abstract = {RNA-sequencing for whole transcriptome analysis requires high-quality RNA in adequate amounts, which can be difficult to generate with low-biomass-producing bacteria where sample volume is limited. We present an RNA extraction protocol for low-biomass-producing autotrophic bacteria Nitrosomonas europaea and Nitrobacter winogradskyi cultures. We describe steps for sample collection, lysozyme-based enzymatic lysis, and a commercial silica-column-based RNA extraction. We then detail evaluation of RNA yield and quality for downstream applications such as RNA-Seq. For complete details on the use and execution of this protocol, please refer to Verbeelen et al.[1].}, }
@article {pmid37346753, year = {2023}, author = {Petrin, S and Wijnands, L and Benincà, E and Mughini-Gras, L and Delfgou-van Asch, EHM and Villa, L and Orsini, M and Losasso, C and Olsen, JE and Barco, L}, title = {Assessing phenotypic virulence of Salmonella enterica across serovars and sources.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1184387}, pmid = {37346753}, issn = {1664-302X}, abstract = {INTRODUCTION: Whole genome sequencing (WGS) is increasingly used for characterizing foodborne pathogens and it has become a standard typing technique for surveillance and research purposes. WGS data can help assessing microbial risks and defining risk mitigating strategies for foodborne pathogens, including Salmonella enterica.<br><br>METHODS: To test the hypothesis that (combinations of) different genes can predict the probability of infection [P(inf)] given exposure to a certain pathogen strain, we determined P(inf) based on invasion potential of 87 S. enterica strains belonging to 15 serovars isolated from animals, foodstuffs and human patients, in an in vitro gastrointestinal tract (GIT) model system. These genomes were sequenced with WGS and screened for genes potentially involved in virulence. A random forest (RF) model was applied to assess whether P(inf) of a strain could be predicted based on the presence/absence of those genes. Moreover, the association between P(inf) and biofilm formation in different experimental conditions was assessed.<br><br>RESULTS AND DISCUSSION: P(inf) values ranged from 6.7E-05 to 5.2E-01, showing variability both among and within serovars. P(inf) values also varied between isolation sources, but no unambiguous pattern was observed in the tested serovars. Interestingly, serovars causing the highest number of human infections did not show better ability to invade cells in the GIT model system, with strains belonging to other serovars displaying even higher infectivity. The RF model did not identify any virulence factor as significant P(inf) predictors. Significant associations of P(inf) with biofilm formation were found in all the different conditions for a limited number of serovars, indicating that the two phenotypes are governed by different mechanisms and that the ability to form biofilm does not correlate with the ability to invade epithelial cells. Other omics techniques therefore seem more promising as alternatives to identify genes associated with P(inf), and different hypotheses, such as gene expression rather than presence/absence, could be tested to explain phenotypic virulence [P(inf)].}, }
@article {pmid37345931, year = {2023}, author = {Aldeguer-Riquelme, B and Antón, J and Santos, F}, title = {Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0021523}, doi = {10.1128/msystems.00215-23}, pmid = {37345931}, issn = {2379-5077}, abstract = {The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.}, }
@article {pmid37343911, year = {2023}, author = {Andrade, L and P Ryan, M and P Burke, L and Hynds, P and Weatherill, J and O'Dwyer, J}, title = {Assessing antimicrobial and metal resistance genes in Escherichia coli from domestic groundwater supplies in rural Ireland.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121970}, doi = {10.1016/j.envpol.2023.121970}, pmid = {37343911}, issn = {1873-6424}, abstract = {Natural ecosystems can become significant reservoirs and/or pathways for antimicrobial resistance (AMR) dissemination, with the potential to affect nearby microbiological, animal, and ultimately human communities. This is further accentuated in environments that provide direct human exposure, such as drinking water. To date, however, few studies have investigated AMR dissemination potential and the presence of co-selective stressors (e.g., metals/metalloids) in groundwater environments of human health significance. Accordingly, the present study analysed samples from rural (drinking) groundwater supplies (i.e., private wells) in the Republic of Ireland, where land use is dominated by livestock grazing activities. In total, 48 Escherichia coli isolates tested phenotypically for antimicrobial susceptibility in an earlier study were further subject to whole genome sequencing (WGS) and corresponding water samples were further analysed for trace metal/metalloid concentrations. Eight isolates (i.e., 16.7%) were genotypically resistant to antimicrobials, confirming prior phenotypic results through the identification of ten antimicrobial resistance genes (ARGs); namely: aph(3″)-lb (strA; n=7), aph(6)-Id (strA; n = 6), blaTEM (n = 6), sul2 (n = 6), tetA (n = 4), floR (n = 2), dfrA5 (n = 1), tetB (n = 1), and tetY (n = 1). Additional bioinformatic analysis revealed that all ARGs were plasmid-borne, except for two of the six sul2 genes, and that 31.2% of all tested isolates (n = 15) and 37.5% of resistant ones (n = 3) carried virulence genes. Study results also found no significant relationships between metal concentrations and ARG abundance. Additionally, just one genetic linkage was identified between ARGs and a metal resistance gene (MRG), namely merA, a mercury-resistant gene found on the same plasmid as blaTEM, dfrA5, strA, strB, and sul2 in the only isolate of inferred porcine (as opposed to bovine) origin. Overall, findings suggest that ARG (and MRG) acquisition may be occurring prior to groundwater ingress, and are likely a legacy issue arising from agricultural practices.}, }
@article {pmid37342144, year = {2023}, author = {Wilberts, L and Rojas-Preciado, N and Jacquemyn, H and Lievens, B}, title = {Fungal strain and crop cultivar affect growth of sweet pepper plants after root inoculation with entomopathogenic fungi.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1196765}, pmid = {37342144}, issn = {1664-462X}, abstract = {As endophytes, entomopathogenic fungi can protect plants against biotic and abiotic stresses and at the same time promote plant growth and plant health. To date, most studies have investigated whether Beauveria bassiana can enhance plant growth and plant health, while only little is known about other entomopathogenic fungi. In this study, we evaluated whether root inoculation of the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128, B. bassiana ARSEF 3097 and Cordyceps fumosorosea ARSEF 3682 can promote plant growth of sweet pepper (Capsicum annuum L.), and whether effects are cultivar-dependent. Plant height, stem diameter, number of leaves, canopy area, and plant weight were assessed four weeks following inoculation in two independent experiments using two cultivars of sweet pepper (cv. 'IDS RZ F1' and cv. 'Maduro'). Results showed that the three entomopathogenic fungi were able to enhance plant growth, particularly canopy area and plant weight. Further, results showed that effects significantly depended on cultivar and fungal strain, with the strongest fungal effects obtained for cv. 'IDS RZ F1', especially when inoculated with C. fumosorosea. We conclude that inoculation of sweet pepper roots with entomopathogenic fungi can stimulate plant growth, but effects depend on fungal strain and crop cultivar.}, }
@article {pmid36872509, year = {2023}, author = {Munley, JA and Kelly, LS and Park, G and Gillies, GS and Pons, EE and Kannan, KB and Whitley, EM and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM}, title = {Multicompartmental traumatic injury induces sex-specific alterations in the gut microbiome.}, journal = {The journal of trauma and acute care surgery}, volume = {95}, number = {1}, pages = {30-38}, doi = {10.1097/TA.0000000000003939}, pmid = {36872509}, issn = {2163-0763}, abstract = {BACKGROUND: Previous preclinical studies have demonstrated an altered gut microbiome after traumatic injury; however, the impact of sex on dysbiosis remains unknown. We hypothesized that the "pathobiome" phenotype induced by multicompartmental injuries and chronic stress is host sex specific with unique microbiome signatures.<br><br>METHODS: Male and proestrus female Sprague-Dawley rats (n = 8/group) aged 9 weeks to 11 weeks were subjected to either multicompartmental injury (PT) (lung contusion, hemorrhagic shock, cecectomy, bifemoral pseudofractures), PT plus 2 hours daily chronic restraint stress (PT/CS) or naive controls. Fecal microbiome was measured on Days 0 and 2 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology bioinformatics analyses. Microbial alpha-diversity was assessed using Chao1 (number of different unique species) and Shannon (species richness and evenness) indices. Beta-diversity was assessed using principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin and lipopolysaccharide binding protein. Histologic evaluation of ileum and colon tissues was scored for injury by a blinded pathologist. Analyses were performed in GraphPad and R, with significance defined as p < 0.05 between males versus females.<br><br>RESULTS: At baseline, females had significantly elevated alpha-diversity (Chao1, Shannon indices) compared with males (p < 0.05) which was no longer present 2 days postinjury in PT and PT/CS. Beta-diversity also differed significantly between males and females after PT (p = 0.01). At Day 2, the microbial composition in PT/CS females was dominated by Bifidobacterium , whereas PT males demonstrated elevated levels of Roseburia (p < 0.01). The PT/CS males had significantly elevated ileum injury scores compared with females (p = 0.0002). Plasma occludin was higher in PT males compared with females (p = 0.004); plasma lipopolysaccharide binding protein was elevated in PT/CS males (p = 0.03).<br><br>CONCLUSION: Multicompartmental trauma induces significant alterations in microbiome diversity and taxa, but these signatures differ by host sex. These findings suggest that sex is an important biological variable that may influence outcomes after severe trauma and critical illness.}, }
@article {pmid37339946, year = {2023}, author = {Ma, L and Liu, KW and Li, Z and Hsiao, YY and Qi, Y and Fu, T and Tang, GD and Zhang, D and Sun, WH and Liu, DK and Li, Y and Chen, GZ and Liu, XD and Liao, XY and Jiang, YT and Yu, X and Hao, Y and Huang, J and Zhao, XW and Ke, S and Chen, YY and Wu, WL and Hsu, JL and Lin, YF and Huang, MD and Li, CY and Huang, L and Wang, ZW and Zhao, X and Zhong, WY and Peng, DH and Ahmad, S and Lan, S and Zhang, JS and Tsai, WC and Van de Peer, Y and Liu, ZJ}, title = {Diploid and tetraploid genomes of Acorus and the evolution of monocots.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3661}, pmid = {37339946}, issn = {2041-1723}, abstract = {Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.}, }
@article {pmid37338413, year = {2023}, author = {Bittleston, LS and Wolock, CJ and Maeda, J and Infante, V and Ané, JM and Pierce, NE and Pringle, A}, title = {Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0081223}, doi = {10.1128/aem.00812-23}, pmid = {37338413}, issn = {1098-5336}, abstract = {Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.}, }
@article {pmid37338363, year = {2023}, author = {Ye, L and Yang, X and Zhang, B and Zhou, J and Tian, H and Zhang, X and Li, X}, title = {Seasonal Succession of Fungal Communities in Native Truffle (Tuber indicum) Ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0019523}, doi = {10.1128/aem.00195-23}, pmid = {37338363}, issn = {1098-5336}, abstract = {Truffles are a rare underground fungus and one of the most expensive, and sought-after kitchen ingredients in the world. Microbial ecology plays an important role in the annual growth cycle of truffles, but fungal communities in native truffle ecosystems are still largely unknown, especially for Tuber indicum from China. In this study, the spatial and temporal dynamics of soil physicochemical properties and fungal communities were described associated with four T. indicum-producing plots (TPPs) and one non-truffle-producing plot in four successive growing seasons. A total of 160 biological samples were collected, 80 of which were used for the determination of 10 soil physicochemical indices and 80 for Illumina-based analysis of the fungal microbiome. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. Ascomycetes, Basidiomycetes, and Mucormycoides dominated. The core microbiome work on the microecological changes in TPPs, and the identified core members contribute to the seasonal succession of communities. The genus Tuber occupies a central position in healthy TPPs. There was a strong correlation between soil physicochemical properties and fungal communities. The genus Tuber showed a positive correlation with Ca, Mg, and total nitrogen, but a negative correlation with total phosphorus and available potassium. This study describes the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum, and highlights the succession of core communities in truffle plots, which contribute to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China. IMPORTANCE The spatial and temporal dynamics of soil physicochemical properties and fungal communities associated with four Tuber indicum-producing plots and one non truffle producing plot in four different growing seasons are described. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. This study examines the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum and highlights the succession of core communities in truffle plots, which contributes to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China.}, }
@article {pmid37338299, year = {2023}, author = {Hurst, JH and Kelly, MS}, title = {Leveraging the human microbiota to target bacterial respiratory pathogens: new paths toward an expanded antimicrobial armamentarium.}, journal = {mBio}, volume = {}, number = {}, pages = {e0085423}, doi = {10.1128/mbio.00854-23}, pmid = {37338299}, issn = {2150-7511}, abstract = {Acute respiratory infections are the most frequent infections across the lifespan and are the leading infectious cause of death among children globally. Bacterial respiratory infections are routinely treated with antibiotics, nearly all of which are derived from microbial natural products. Unfortunately, antibiotic-resistant bacteria are an increasingly frequent cause of respiratory infections, and there are few new antibiotics in development that target these pathogens. In the article by Stubbendieck et al., the authors identified Rothia species that demonstrate in vitro and ex vivo growth inhibition of the respiratory pathobiont Moraxella catarrhalis. The authors present experiments suggesting that this activity is mediated at least in part through the secretion of a novel peptidoglycan endopeptidase that targets the M. catarrhalis cell wall. In this commentary, we discuss these findings in the context of the urgent threat of antimicrobial resistance and highlight the promise of the human respiratory microbiota as a source of novel biotherapeutics.}, }
@article {pmid37336018, year = {2023}, author = {Liu, H and Wang, Y and Shi, X}, title = {Co-existing antibiotics alter the enantioselective dissipation characteristics of zoxamide and drive combined impact on soil microenvironment.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118340}, doi = {10.1016/j.jenvman.2023.118340}, pmid = {37336018}, issn = {1095-8630}, abstract = {Co-existence of antibiotics (ABX) in soil may expand the environmental harm of pesticide pollution. Our study investigated the combined effects of five antibiotics chlortetracycline (CTC), oxytetracycline (OTC), tetracycline (TC), sulfamethoxazole (SMX), enrofloxacin (ENR) on enantioselective fate of zoxamide (ZXM) and soil health. The results showed that S-(+)-ZXM preferentially dissipated in soil. ABX prolonged dissipation half-life and reduced enantioselectivity of ZXM. Soil was detected to be more acidic after long-term treatment of ZXM and ABX. Lowest soil available N, P, K were found in ZXM + SMX, ZXM + OTC and ZXM + SMX groups at 80 days, respectively. ABX had demonstrated effective promotion of catalase (S-CAT), urease (S-UE) and negative impact on dehydrogenase (S-DHA), sucrase (S-SC) activities. Bacteria Lysobacter, Sphingomonas and fungus Mortierella were identified as the most dominant genera, which possessed as potential microbial resources for removal of composite pollution from ZXM and ABX. SMX and TC, SMX, ENR, respectively, contributed to the alteration of bacteria and fungi community abundance. Soil acidity, available N and enzyme activity showed stronger correlations with bacteria and fungi compared to other environmental factors. Our findings highlighted the interactions between ZXM and ABX from the perspective of soil microenvironment changes. Moreover, a theoretical basis for the mechanism was actively provided.}, }
@article {pmid37333658, year = {2023}, author = {Schultz, J and Modolon, F and Peixoto, RS and Rosado, AS}, title = {Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1167718}, pmid = {37333658}, issn = {1664-302X}, abstract = {More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.}, }
@article {pmid37331053, year = {2023}, author = {Araujo, FF and Salvador, GLO and Lupatini, GC and Pereira, APA and Costa, RM and de Aviz, RO and de Alcantara Neto, F and Mendes, LW and Araujo, ASF}, title = {Exploring the diversity and composition of soil microbial communities in different soybean-maize management systems.}, journal = {Microbiological research}, volume = {274}, number = {}, pages = {127435}, doi = {10.1016/j.micres.2023.127435}, pmid = {37331053}, issn = {1618-0623}, abstract = {Soybean-maize are cultivated in different management systems, such as no-tillage and pastures, which presents potential to add organic residues, and it can potentially impacts the soil microbial community present in these systems. Thus, this study aimed to examine the effects of different soybean-maize management practices on the diversity and composition of soil microbial communities. Specifically, 16 S rRNA amplicon sequencing was used to investigate whether the use of pasture species in a fallowing system influences microbial communities in a soybean-maize rotation system, as compared to conventional tillage and no-tillage systems. The results indicate that the inclusion of the pasture species Urochloa brizantha in soybean-maize management systems leads to distinct responses within the soil microbial community. It was found that different soybean-maize management systems, particularly those with U. brizantha, affected the microbial community, likely due to the management applied to this pasture species. The system with 3 years of fallowing before soybean-maize showed the lowest microbial richness (∼2000 operational taxonomic units) and diversity index (∼6.0). Proteobacteria (∼30%), Acidobacteria (∼15%), and Verrucomicrobia (∼10%) were found to be the most abundant phyla in the soil under tropical native vegetation, while soils under cropland had an increased abundance of Firmicutes (∼30% to ∼50%) and Actinobacteria (∼30% to ∼35%). To summarize, this study identified the impacts of various soybean-maize management practices on the soil microbial community and emphasized the advantages of adding U. brizantha as a fallow species.}, }
@article {pmid37333959, year = {2020}, author = {Zeibich, L and Guhl, J and Drake, HL}, title = {Impact of water content and dietary organic carbon richness on gut bacteria in the earthworm Lumbricus terrestris.}, journal = {FEMS microbes}, volume = {1}, number = {1}, pages = {xtaa002}, pmid = {37333959}, issn = {2633-6685}, abstract = {Many higher and lower animal gut ecosystems have complex resident microbial communities. In contrast, ingested soil is the primary source of the gut microbial diversity of earthworms, invertebrates of fundamental importance to the terrestrial biosphere. Earthworms also harbor a few endemic bacteria including Tenericutes-affiliated Candidatus Lumbricincola of unknown function. Gut microbes are subject to nutrient fluctuations due to dilution effects during gut passage, the nutrient richness of the anoxic gut, and dietary organic carbon, factors that could alter their activity/detection. This study's objective was to assess the potential impact of these factors on the occurrence and activity of ingested and endemic bacteria in gut content of Lumbricus terrestris. Fermentation product profiles of anoxic undiluted and diluted gut content treatments were similar, suggesting that experimental increase in water content and nutrient dilution had marginal impact on fermentation. However, 16S ribosomal Ribonucleic Acid (16S rRNA) sequence abundances indicated that stimulated bacterial taxa were not identical in undiluted and diluted treatments, with dominate potentially functionally redundant phylotypes being affiliated to the Firmicutes, Fusobacteria and Proteobacteria. Although the earthworm-associated Tenericutes were not stimulated in these treatments, the occurrence of three Tenericutes-affiliated phylotypes varied with the organic carbon richness of the earthworm diet, with two phylotypes being associated with high organic carbon richness. 16S rRNA sequence abundances indicated that other dominant gut taxa also varied with dietary organic carbon richness. These findings illustrate that functionally redundant ingested bacteria and earthworm-associated Tenericutes might be influenced by nutrient fluctuations in the gut and organic carbon richness of the earthworm diet.}, }
@article {pmid37327546, year = {2023}, author = {Ostermeyer, P and Folens, K and Verbruggen, F and Bonin, L and Hennebel, T and Korneel, R}, title = {A sulfate reducing bioreactor controlled by an electrochemical system enables near-zero chemical treatment of metallurgical wastewater.}, journal = {Water research}, volume = {242}, number = {}, pages = {120215}, doi = {10.1016/j.watres.2023.120215}, pmid = {37327546}, issn = {1879-2448}, abstract = {Metallurgical wastewaters are characterized by a low pH (<4), high concentrations of sulfate (15 gSO4[2-] L[-1]), and metal(loid)s. Current treatment requires the consumption of chemicals such as alkali and high levels of waste sludge generation. In this study, we have shown that combining water electrolysis and sulfate reducing bioreactors enables the in-situ generation of base and H2, eliminating the need for base and electron donor addition, resulting in the near-zero treatment of metallurgical wastewater. By extracting cations from the effluent of the system to the bioreactor, the bioreactor pH could be maintained by the in-situ production of alkali. The current for pH control varied between 112-753 mol electrons per m[3] wastewater or 5-48 A m[-2] electrode area. High concentrations of sulfate in the influent and addition of CO2 increased the current required to maintain a steady bioreactor pH. On the other hand, a high sulfate reduction rate and increased influent pH lowered the current required for pH control. Moreover, the current efficiency varied from 14% to 91% and increased with higher pH and cation (Na[+], NH4[+], K[+], Mg[2+], Ca[2+]) concentrations in the middle compartment of the electrochemical cell. The salinity was lowered from 70-120 mS cm[-1] in the influent to 5-20 mS cm[-1] in the system effluent. The energy consumption of the electrochemical pH control varied between 10 and 100 kWh m[-3] and was affected by the conductivity of the wastewater. Industrial wastewater was treated successfully with an average energy consumption of 39 ± 7 kWh m[-3], removing sulfate from 15 g SO4[2-] L[-1] to 0.5 ± 0.5 g SO4[2-] L[-1] at a reduction rate of 20 ± 1 gSO4[2-] L[-1] d[-1]..Metal(loid)s such as As, Cd, Cu, Pb, Te, Tl, Ni and Zn were removed to levels of 1-50 µg L[-1].}, }
@article {pmid37326636, year = {2023}, author = {Dos Santos Ribeiro, P and Carvalho, NB and Aburjaile, F and Sousa, T and Veríssimo, G and Gomes, T and Neves, F and Blanco, L and Lima, JA and de Oliveira, D and Jaiswal, AK and Brenig, B and Soares, S and Ramos, R and Matiuzzi, M and Góes-Neto, A and Figueira, CP and Costa, F and Ristow, P and Azevedo, V}, title = {Environmental Biofilms from an Urban Community in Salvador, Brazil, Shelter Previously Uncharacterized Saprophytic Leptospira.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37326636}, issn = {1432-184X}, abstract = {Biofilms are complex microecosystems with valuable ecological roles that can shelter a variety of microorganisms. Spirochetes from the genus Leptospira have been observed to form biofilms in vitro, in rural environments, and in the kidneys of reservoir rats. The genus Leptospira is composed of pathogenic and non-pathogenic species, and the description of new species is ongoing due to the advent of whole genome sequencing. Leptospires have increasingly been isolated from water and soil samples. To investigate the presence of Leptospira in environmental biofilms, we collected three distinct samples of biofilms formed in an urban setting with poor sanitation: Pau da Lima, in Salvador, Bahia, Brazil. All biofilm samples were negative for the presence of pathogenic leptospires via conventional PCR, but cultures containing saprophytic Leptospira were identified. Whole genomes were generated and analyzed for twenty isolates obtained from these biofilms. For species identification, we used digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analysis. The obtained isolates were classified into seven presumptive species from the saprophytic S1 clade. ANI and dDDH analysis suggest that three of those seven species were new. Classical phenotypic tests confirmed the novel isolated bacteria as saprophytic Leptospira. The isolates presented typical morphology and ultrastructure according to scanning electron microscopy and formed biofilms under in vitro conditions. Our data indicate that a diversity of saprophytic Leptospira species survive in the Brazilian poorly sanitized urban environment, in a biofilm lifestyle. We believe our results contribute to a better understanding of Leptospira biology and ecology, considering biofilms as natural environmental reservoirs for leptospires.}, }
@article {pmid37325551, year = {2023}, author = {Cao, Y and Almeida-Silva, F and Zhang, WP and Ding, YM and Bai, D and Bai, WN and Zhang, BW and Van de Peer, Y and Zhang, DY}, title = {Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {msad121}, pmid = {37325551}, issn = {1537-1719}, abstract = {When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes, and its only congeneric species, P. strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics, and the driving forces underneath the incipient speciation of the two Platycarya lineages.}, }
@article {pmid37323900, year = {2023}, author = {Ho, PM and Nazeer, RR and Welch, M}, title = {Therapeutic interventions alter ecological interactions among cystic fibrosis airway microbiota.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1178131}, pmid = {37323900}, issn = {1664-302X}, abstract = {The airways of people with cystic fibrosis (CF) often harbor a diverse microbiota and in recent years, much effort has been invested in cataloguing these. In spite of providing a wealth of insight, this cataloguing tells us little about how the organisms interact with one another in the CF airways. However, such relationships can be inferred using the theoretical framework of the Lotka-Volterra (LV) model. In the current work, we use a generalized Lotka-Volterra model to interrogate the nationwide data collected and curated by the UK CF Registry. This longitudinal dataset (covering the period 2008-2020) contains annual depositions that record the presence/absence of microbial taxa in each patient, their medication, and their CF genotype. Specifically, we wanted to identify trends in ecological relationships between the CF microbiota at a nationwide level, and whether these are potentially affected by medication. Our results show that some medications have a distinct influence on the microbial interactome, especially those that potentially influence the "gut-lung axis" or mucus viscosity. In particular, we found that patients treated with a combination of antimicrobial agents (targeting the airway microbiota), digestive enzymes (assisting in the assimilation of dietary fats and carbohydrates), and DNase (to reduce mucus viscosity) displayed a distinctly different airway interactome compared with patients treated separately with these medications.}, }
@article {pmid37323646, year = {2023}, author = {Rodrigues-Filho, JL and Macêdo, RL and Sarmento, H and Pimenta, VRA and Alonso, C and Teixeira, CR and Pagliosa, PR and Netto, SA and Santos, NCL and Daura-Jorge, FG and Rocha, O and Horta, P and Branco, JO and Sartor, R and Muller, J and Cionek, VM}, title = {From ecological functions to ecosystem services: linking coastal lagoons biodiversity with human well-being.}, journal = {Hydrobiologia}, volume = {850}, number = {12-13}, pages = {2611-2653}, pmid = {37323646}, issn = {0018-8158}, abstract = {In this review we highlight the relevance of biodiversity that inhabit coastal lagoons, emphasizing how species functions foster processes and services associated with this ecosystem. We identified 26 ecosystem services underpinned by ecological functions performed by bacteria and other microbial organisms, zooplankton, polychaetae worms, mollusks, macro-crustaceans, fishes, birds, and aquatic mammals. These groups present high functional redundancy but perform complementary functions that result in distinct ecosystem processes. Because coastal lagoons are located in the interface between freshwater, marine and terrestrial ecosystems, the ecosystem services provided by the biodiversity surpass the lagoon itself and benefit society in a wider spatial and historical context. The species loss in coastal lagoons due to multiple human-driven impacts affects the ecosystem functioning, influencing negatively the provision of all categories of services (i.e., supporting, regulating, provisioning and cultural). Because animals' assemblages have unequal spatial and temporal distribution in coastal lagoons, it is necessary to adopt ecosystem-level management plans to protect habitat heterogeneity and its biodiversity, ensuring the provision of services for human well-being to multi-actors in the coastal zone.}, }
@article {pmid37318372, year = {2023}, author = {Rani, S and Sørensen, MT and Estellé, J and Noel, SJ and Nørskov, N and Krogh, U and Foldager, L and Højberg, O}, title = {Gastrointestinal Microbial Ecology of Weaned Piglets Fed Diets with Different Levels of Glyphosate.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0061523}, doi = {10.1128/spectrum.00615-23}, pmid = {37318372}, issn = {2165-0497}, abstract = {Glyphosate possesses antimicrobial properties, and the present study investigated potential effects of feed glyphosate on piglet gastrointestinal microbial ecology. Weaned piglets were allocated to four diets (glyphosate contents [mg/kg feed]: 0 mg/kg control [CON; i.e., basal diet with no glyphosate added], 20 mg/kg as Glyphomax commercial herbicide [GM20], and 20 mg/kg [IPA20] and 200 mg/kg [IPA200] as glyphosate isopropylamine [IPA] salt). Piglets were sacrificed after 9 and 35 days of treatment, and stomach, small intestine, cecum, and colon digesta were analyzed for glyphosate, aminomethylphosphonic acid (AMPA), organic acids, pH, dry matter content, and microbiota composition. Digesta glyphosate contents reflected dietary levels (on day 35, 0.17, 16.2, 20.5, and 207.5 mg/kg colon digesta, respectively). Overall, we observed no significant glyphosate-associated effects on digesta pH, dry matter content, and-with few exceptions-organic acid levels. On day 9, only minor gut microbiota changes were observed. On day 35, we observed a significant glyphosate-associated decrease in species richness (CON, 462; IPA200, 417) and in the relative abundance of certain Bacteroidetes genera: CF231 (CON, 3.71%; IPA20, 2.33%; IPA200, 2.07%) and g_0.24 (CON, 3.69%; IPA20, 2.07%; IPA200, 1.75%) in cecum. No significant changes were observed at the phylum level. In the colon, we observed a significant glyphosate-associated increase in the relative abundance of Firmicutes (CON, 57.7%; IPA20, 69.4%; IPA200, 66.1%) and a decrease in Bacteroidetes (CON, 32.6%; IPA20, 23.5%). Significant changes were only observed for few genera, e.g., g_0.24 (CON, 7.12%; IPA20, 4.59%; IPA200, 4.00%). In conclusion, exposing weaned piglets to glyphosate-amended feed did not affect gastrointestinal microbial ecology to a degree that was considered actual dysbiosis, e.g., no potential pathogen bloom was observed. IMPORTANCE Glyphosate residues can be found in feed made from genetically modified glyphosate-resistant crops treated with glyphosate or from conventional crops, desiccated with glyphosate before harvest. If these residues affect the gut microbiota to an extent that is unfavorable to livestock health and productivity, the widespread use of glyphosate on feed crops may need to be reconsidered. Few in vivo studies have been conducted to investigate potential impact of glyphosate on the gut microbial ecology and derived health issues of animals, in particular livestock, when exposed to dietary glyphosate residues. The aim of the present study was therefore to investigate potential effects on the gastrointestinal microbial ecology of newly weaned piglets fed glyphosate-amended diets. Piglets did not develop actual gut dysbiosis when fed diets, containing a commercial herbicide formulation or a glyphosate salt at the maximum residue level, defined by the European Union for common feed crops, or at a 10-fold-higher level.}, }
@article {pmid37318344, year = {2023}, author = {Diner, RE and Zimmer-Faust, A and Cooksey, E and Allard, S and Kodera, SM and Kunselman, E and Garodia, Y and Verhougstraete, MP and Allen, AE and Griffith, J and Gilbert, JA}, title = {Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0031823}, doi = {10.1128/aem.00318-23}, pmid = {37318344}, issn = {1098-5336}, abstract = {Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter-feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to the microbial ecology of pathogenic bacteria and their relationship with oyster hosts likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of Vibrio parahaemolyticus, Vibrio vulnificus, or fecal indicator bacteria. Site-specific environmental conditions significantly influenced microbial communities and potential pathogen concentrations in water. Oyster microbial communities, however, exhibited less variability in microbial community diversity and accumulation of target bacteria overall and were less impacted by environmental differences between sites. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated levels of potential pathogens. For example, increased levels of V. parahaemolyticus were associated with higher relative abundances of cyanobacteria, which could represent an environmental vector for Vibrio spp. transport, and with decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters. IMPORTANCE Bacteria in the marine environment cause thousands of human illnesses annually. Bivalves are a popular seafood source and are important in coastal ecology, but their ability to concentrate pathogens from the water can cause human illness, threatening seafood safety and security. To predict and prevent disease, it is critical to understand what causes pathogenic bacteria to accumulate in bivalves. In this study, we examined how environmental factors and host and water microbial communities were linked to potential human pathogen accumulation in oysters. Oyster microbial communities were more stable than water communities, and both contained the highest concentrations of Vibrio parahaemolyticus at sites with warmer temperatures and lower salinities. High oyster V. parahaemolyticus concentrations corresponded with abundant cyanobacteria, a potential vector for transmission, and a decrease in potentially beneficial oyster microbes. Our study suggests that poorly understood factors, including host and water microbiota, likely play a role in pathogen distribution and pathogen transmission.}, }
@article {pmid37317205, year = {2023}, author = {Maatouk, M and Rolain, JM and Bittar, F}, title = {Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/microorganisms11051231}, pmid = {37317205}, issn = {2076-2607}, abstract = {Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.}, }
@article {pmid37317127, year = {2023}, author = {Varliero, G and Lebre, PH and Frey, B and Fountain, AG and Anesio, AM and Cowan, DA}, title = {Glacial Water: A Dynamic Microbial Medium.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/microorganisms11051153}, pmid = {37317127}, issn = {2076-2607}, abstract = {Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.}, }
@article {pmid37317116, year = {2023}, author = {Malajacan, GT and Nacario, MAG and Obusan, MCM and Rivera, WL}, title = {Host-Associated Bacteroides 16S rDNA-Based Markers for Source Tracking of Fecal Pollution in Laguna Lake, Philippines.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/microorganisms11051142}, pmid = {37317116}, issn = {2076-2607}, abstract = {Sources of fecal contamination in Laguna Lake, Philippines, were identified using a library-independent microbial source tracking method targeting host-associated Bacteroides 16S rDNA-based markers. Water samples from nine lake stations were assessed for the presence of the fecal markers HF183 (human), BoBac (cattle), Pig-2-Bac (swine), and DuckBac (duck) from August 2019 to January 2020. HF183 (average concentration = 1.91 log10 copies/mL) was the most frequently detected, while Pig-2-Bac (average concentration = 2.47 log10 copies/mL) was the most abundant. The detected marker concentrations in different stations corresponded to the land use patterns around the lake. Generally, all marker concentrations were higher during the wet season (August-October), suggesting the effect of rainfall-associated factors on the movement and retention of markers from sources. There was a significant association (ρ = 0.45; p < 0.001) between phosphate and the concentration of HF183, suggesting domestic sewage-derived pollution. The markers had acceptable sensitivity and specificity, i.e., HF183 (S = 0.88; R = 0.99), Pig-2-Bac (S = 1.00; R = 1.00), and DuckBac (S = 0.94; R = 1.00), and therefore may be used for the continuous monitoring of fecal pollution in the lake and in designing interventions to improve the quality of the lake water.}, }
@article {pmid37317051, year = {2023}, author = {Wang, M and Sun, X and Cao, B and Chiariello, NR and Docherty, KM and Field, CB and Gao, Q and Gutknecht, JLM and Guo, X and He, G and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Shi, Z and Shu, W and Yuan, M and Zhou, J and Yang, Y}, title = {Long-term elevated precipitation induces grassland soil carbon loss via microbe-plant-soil interplay.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16811}, pmid = {37317051}, issn = {1365-2486}, abstract = {Global climate models predict that the frequency and intensity of precipitation events will increase in many regions across the world. However, the biosphere-climate feedback to elevated precipitation (eP) remains elusive. Here, we report a study on one of the longest field experiments assessing the effects of eP, alone or in combination with other climate change drivers such as elevated CO2 (eCO2), warming and nitrogen deposition. Soil total carbon (C) decreased after a decade of eP treatment, while plant root production decreased after 2 years. To explain this asynchrony, we found that the relative abundances of fungal genes associated with chitin and protein degradation increased and were positively correlated with bacteriophage genes, suggesting a potential viral shunt in C degradation. In addition, eP increased the relative abundances of microbial stress tolerance genes, which are essential for coping with environmental stressors. Microbial responses to eP were phylogenetically conserved. The effects of eP on soil total C, root production, and microbes were interactively affected by eCO2 . Collectively, we demonstrate that long-term eP induces soil C loss, owing to changes in microbial community composition, functional traits, root production, and soil moisture. Our study unveils an important, previously unknown biosphere-climate feedback in Mediterranean-type water-limited ecosystems, namely how eP induces soil C loss via microbe-plant-soil interplay.}, }
@article {pmid37316492, year = {2023}, author = {Cuypers, WL and Meysman, P and Weill, FX and Hendriksen, RS and Beyene, G and Wain, J and Nair, S and Chattaway, MA and Perez-Sepulveda, BM and Ceyssens, PJ and de Block, T and Lee, WWY and Pardos de la Gandara, M and Kornschober, C and Moran-Gilad, J and Veldman, KT and Cormican, M and Torpdahl, M and Fields, PI and Černý, T and Hardy, L and Tack, B and Mellor, KC and Thomson, N and Dougan, G and Deborggraeve, S and Jacobs, J and Laukens, K and Van Puyvelde, S}, title = {A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3517}, pmid = {37316492}, issn = {2041-1723}, support = {206194/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.}, }
@article {pmid37314477, year = {2023}, author = {An, Y and Braga, MP and Garcia, SL and Grudzinska-Sterno, M and Hambäck, PA}, title = {Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37314477}, issn = {1432-184X}, abstract = {Gut microbes play important roles for their hosts. Previous studies suggest that host-microbial systems can form long-term associations over evolutionary time and the dynamic changes of the intestinal system may represent major driving forces and contribute to insect dietary diversification and speciation. Our study system includes a set of six closely related leaf beetle species (Galerucella spp.) and our study aims to separate the roles of host phylogeny and ecology in determining the gut microbial community and to identify eventual relationship between host insects and gut bacteria. We collected adult beetles from their respective host plants and quantified their microbial community using 16S rRNA sequencing. The results showed that the gut bacteria community composition was structured by host beetle phylogeny, where more or less host-specific gut bacteria interact with the different Galerucella species. For example, the endosymbiotic bacteria Wolbachia was found almost exclusively in G. nymphaea and G. sagittariae. Diversity indicators also suggested that α- and β-diversities of gut bacteria communities varied among host beetle species. Overall, our results suggest a phylogenetically controlled co-occurrence pattern between the six closely related Galerucella beetles and their gut bacteria, indicating the potential of co-evolutionary processes occurring between hosts and their gut bacterial communities.}, }
@article {pmid37310275, year = {2023}, author = {Saati-Santamaría, Z}, title = {Global Map of Specialized Metabolites Encoded in Prokaryotic Plasmids.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0152323}, doi = {10.1128/spectrum.01523-23}, pmid = {37310275}, issn = {2165-0497}, abstract = {Plasmids are the main mobile elements responsible for horizontal gene transfer (HGT) in microorganisms. These replicons extend the metabolic spectrum of their host cells by carrying functional genes. However, it is still unknown to what extent plasmids carry biosynthetic gene clusters (BGCs) related to the production of secondary or specialized metabolites (SMs). Here, we analyzed 9,183 microbial plasmids to unveil their potential to produce SMs, finding a large diversity of cryptic BGCs in a few varieties of prokaryotic host taxa. Some of these plasmids harbored 15 or more BGCs, and many others were exclusively dedicated to mobilizing BGCs. We found an occurrence pattern of BGCs within groups of homologous plasmids shared by a common taxon, mainly in host-associated microbes (e.g., Rhizobiales, Enterobacteriaceae members). Our results add to the knowledge of the ecological functions and potential industrial uses of plasmids and shed light on the dynamics and evolution of SMs in prokaryotes. IMPORTANCE Plasmids are mobile DNA elements that can be shared among microbial cells, and they are useful for bringing to fruition some microbial ecological traits. However, it is not known to what extent plasmids harbor genes related to the production of specialized/secondary metabolites (SMs). In microbes, these metabolites are frequently useful for defense purposes, signaling, etc. In addition, these molecules usually have biotechnological and clinical applications. Here, we analyzed the content, dynamics, and evolution of genes related to the production of SMs in >9,000 microbial plasmids. Our results confirm that some plasmids act as a reservoir of SMs. We also found that some families of biosynthetic gene clusters are exclusively present in some groups of plasmids shared among closely related microbes. Host-associated bacteria (e.g., plant and human microbes) harbor the majority of specialized metabolites encoded in plasmids. These results provide new knowledge about microbial ecological traits and might enable the discovery of novel metabolites.}, }
@article {pmid37308155, year = {2023}, author = {Timmis, K and Verstraete, W and Regina, VR and Hallsworth, JE}, title = {The Pareto principle: To what extent does it apply to resource acquisition in stable microbial communities and thereby steer their geno-/ecotype compositions and interactions between their members?.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16438}, pmid = {37308155}, issn = {1462-2920}, abstract = {The Pareto principle, or 20:80 rule, describes resource distribution in stable communities whereby 20% of community members acquire 80% of a key resource. In this Burning Question, we ask to what extent the Pareto principle applies to the acquisition of limiting resources in stable microbial communities; how it may contribute to our understanding of microbial interactions, microbial community exploration of evolutionary space, and microbial community dysbiosis; and whether it can serve as a benchmark of microbial community stability and functional optimality?}, }
@article {pmid37307484, year = {2023}, author = {Chadwick, GL and Joiner, AMN and Ramesh, S and Mitchell, DA and Nayak, DD}, title = {McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {25}, pages = {e2302815120}, doi = {10.1073/pnas.2302815120}, pmid = {37307484}, issn = {1091-6490}, abstract = {Methyl-coenzyme M reductase (MCR) catalyzes the formation of methane, and its activity accounts for nearly all biologically produced methane released into the atmosphere. The assembly of MCR is an intricate process involving the installation of a complex set of posttranslational modifications and the unique Ni-containing tetrapyrrole called coenzyme F430. Despite decades of research, details of MCR assembly remain largely unresolved. Here, we report the structural characterization of MCR in two intermediate states of assembly. These intermediate states lack one or both F430 cofactors and form complexes with the previously uncharacterized McrD protein. McrD is found to bind asymmetrically to MCR, displacing large regions of the alpha subunit and increasing active-site accessibility for the installation of F430-shedding light on the assembly of MCR and the role of McrD therein. This work offers crucial information for the expression of MCR in a heterologous host and provides targets for the design of MCR inhibitors.}, }
@article {pmid37303746, year = {2023}, author = {Martinez-Rabert, E and Sloan, WT and Gonzalez-Cabaleiro, R}, title = {Multiscale models driving hypothesis and theory-based research in microbial ecology.}, journal = {Interface focus}, volume = {13}, number = {4}, pages = {20230008}, pmid = {37303746}, issn = {2042-8898}, abstract = {Hypothesis and theory-based studies in microbial ecology have been neglected in favour of those that are descriptive and aim for data-gathering of uncultured microbial species. This tendency limits our capacity to create new mechanistic explanations of microbial community dynamics, hampering the improvement of current environmental biotechnologies. We propose that a multiscale modelling bottom-up approach (piecing together sub-systems to give rise to more complex systems) can be used as a framework to generate mechanistic hypotheses and theories (in-silico bottom-up methodology). To accomplish this, formal comprehension of the mathematical model design is required together with a systematic procedure for the application of the in-silico bottom-up methodology. Ruling out the belief that experimentation before modelling is indispensable, we propose that mathematical modelling can be used as a tool to direct experimentation by validating theoretical principles of microbial ecology. Our goal is to develop methodologies that effectively integrate experimentation and modelling efforts to achieve superior levels of predictive capacity.}, }
@article {pmid37303745, year = {2023}, author = {Sloan, WT and Gómez-Borraz, TL}, title = {Engineering biology in the face of uncertainty.}, journal = {Interface focus}, volume = {13}, number = {4}, pages = {20230001}, pmid = {37303745}, issn = {2042-8898}, abstract = {Combining engineering and biology surely must be a route to delivering solutions to the world's most pressing problems in depleting resources, energy and the environment. Engineers and biologists have long recognized the power in coupling their disciplines and have evolved a healthy variety of approaches to realizing technologies. Yet recently, there has been a movement to narrow the remit of engineering biology. Its definition as 'the application of engineering principles to the design of biological systems' ought to encompass a broad church. However, the emphasis is firmly on construction '…of novel biological devices and systems from standardized artificial parts' within cells. Thus, engineering biology has become synonymous with synthetic biology, despite the many longstanding technologies that use natural microbial communities. The focus on the nuts and bolts of synthetic organisms may be deflecting attention from the significant challenge of delivering solutions at scale, which cuts across all engineering biology, synthetic and natural. Understanding, let alone controlling, every component of an engineered system is an unrealistic goal. To realize workable solutions in a timely manner we must develop systematic ways of engineering biology in the face of the uncertainties that are inherent in biological systems and that arise through lack of knowledge.}, }
@article {pmid37303743, year = {2023}, author = {Sierocinski, P and Stilwell, P and Padfield, D and Bayer, F and Buckling, A}, title = {The ecology of scale: impact of volume on coalescence and function in methanogenic communities.}, journal = {Interface focus}, volume = {13}, number = {4}, pages = {20220089}, pmid = {37303743}, issn = {2042-8898}, abstract = {Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.}, }
@article {pmid37302588, year = {2023}, author = {Rosinger, C and Rousk, J and Bonkowski, M and Rethemeyer, J and Jaeschke, A}, title = {Rewetting the hyper-arid Atacama Desert soil reactivates a carbon-starved microbial decomposer community and also triggers archaeal metabolism.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164785}, doi = {10.1016/j.scitotenv.2023.164785}, pmid = {37302588}, issn = {1879-1026}, abstract = {Extreme environmental conditions make soils of the hyper-arid Atacama Desert one of the most hostile habitats for life on the planet. During the short intervals of moisture availability that occur, it remains unresolved how soil microorganisms physiologically respond to such dramatic environmental changes. Therefore, we simulated a precipitation event - without (H2O) and with (H2O + C) labile carbon (C) supplementation - and investigated the responses in microbial communities (using phospholipid fatty acids (PLFAs) and archaeal glycerol dialkyl glycerol tetraether (GDGTs)) and physiology (by means of respiration, bacterial and fungal growth and C-use efficiency (CUE)) during a five-day incubation. We demonstrated that bacterial and fungal growth does occur in these extreme soils following rewetting, albeit at 100-10,000-fold lower rates compared to previously studied soil systems. C supplementation increased levels of bacterial growth and respiration responses by 5- and 50-fold, respectively, demonstrating a C-limited microbial decomposer community. While the microbial CUE following rewetting was c. 14 %, the addition of labile C during rewetting resulted in a substantial reduction (c. 1.6 %). Consistent with these interpretations, the PLFA composition clearly shifted from saturated towards more unsaturated and branched PLFAs, which could arise from (i) a physiological adaptation of the cell membrane to changing osmotic conditions or (ii) a community composition shift. Significant increases in total PLFA concentrations were solely found with H2O + C addition. Contrary to other recent studies, we found evidence for a metabolically active archaeal community in these hyper-arid soils upon rewetting. We conclude that (i) microorganisms in this extreme soil habitat can be activated and grow within days following rewetting, (ii) available C is the limiting factor for microbial growth and biomass gains, and (iii) that an optimization of tolerating the extreme conditions while maintaining a high CUE comes at the expense of very poor resource-use efficiency during high resource availability.}, }
@article {pmid37302271, year = {2023}, author = {Sakarika, M and Ganigué, R and Rabaey, K}, title = {Corrigendum to "Methylotrophs: from C1 compounds to food" [Curr Opin Biotechnol 75 (2022) 102685].}, journal = {Current opinion in biotechnology}, volume = {82}, number = {}, pages = {102964}, doi = {10.1016/j.copbio.2023.102964}, pmid = {37302271}, issn = {1879-0429}, }
@article {pmid37301781, year = {2023}, author = {Zhu, YL and Huang, YJ and Nuerhamanti, N and Bai, XY and Wang, HN and Zhu, XY and Zhang, W}, title = {Composition and Distribution Characteristics of Rhizosphere Bacterial Community of Ammodendron bifolium Growing in Takeermohuer Desert Are Different from Those in Non-rhizosphere.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37301781}, issn = {1432-184X}, abstract = {Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing and endangered plant in Takeermohuer Desert, and bacterial community associated with this plant rhizosphere is still unclear. In this study, we studied the composition and diversity of bacterial community from A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using traditional bacterial isolation and high-throughput sequencing approaches, and preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. Results showed that Takeermohuer Desert with high salinity has been an oligotrophic environment, while the rhizosphere exhibited eutrophication resulting from high content SOM (soil organic matter) and SAN (soil alkaline nitrogen) compared with bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phyla level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in eutrophic rhizosphere, and Firmicutes (9.8%) and Chloroflexi (6.9%) relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genus was Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD indexes in rhizosphere were significantly higher than those in bulk soil at the same soil depth, and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in Takeermohuer Desert were Actinobacteria, Acidobacteria, Proteobacteria, and Chlorofexi. Furthermore, the major environmental factors affecting rhizosphere bacterial community were EC (electrical conductivity), SOM, STN (soil total nitrogen), SAN, and SAK (soil available potassium), while bulk soil were distance and C/N (STC/STN). We concluded that A. bifolium rhizosphere bacterial community is different from non-rhizosphere in composition, distribution, and environmental influencing factors, which will have important significances for understanding their ecological functions and maintaining biodiversity.}, }
@article {pmid37300728, year = {2023}, author = {Wasmund, K and Trueba-Santiso, A and Vicent, T and Adrian, L and Vuilleumier, S and Marco-Urrea, E}, title = {Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37300728}, issn = {1614-7499}, abstract = {Dichloromethane (DCM, methylene chloride) is a toxic, high-volume industrial pollutant of long-standing. Anaerobic biodegradation is crucial for its removal from contaminated environments, yet prevailing mechanisms remain unresolved, especially concerning dehalogenation. In this study, we obtained an assembled genome of a novel DCM-degrading strain, Dehalobacterium formicoaceticum strain EZ94, from a stable DCM-degrading consortium, and we analyzed its proteome during degradation of DCM. A gene cluster recently predicted to play a major role in anaerobic DCM catabolism (the mec cassette) was found. Methyltransferases and other proteins encoded by the mec cassette were among the most abundant proteins produced, suggesting their involvement in DCM catabolism. Reductive dehalogenases were not detected. Genes and corresponding proteins for a complete Wood-Ljungdahl pathway, which could enable further metabolism of DCM carbon, were also found. Unlike for the anaerobic DCM degrader "Ca. F. warabiya," no genes for metabolism of the quaternary amines choline and glycine betaine were identified. This work provides independent and supporting evidence that mec-associated methyltransferases are key to anaerobic DCM metabolism.}, }
@article {pmid37296446, year = {2023}, author = {Peral-Aranega, E and Saati-Santamaría, Z and Ayuso-Calles, M and Kostovčík, M and Veselská, T and Švec, K and Rivas, R and Kolařik, M and García-Fraile, P}, title = {New insight into the bark beetle ips typographus bacteriome reveals unexplored diversity potentially beneficial to the host.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {53}, pmid = {37296446}, issn = {2524-6372}, abstract = {BACKGROUND: Ips typographus (European spruce bark beetle) is the most destructive pest of spruce forests in Europe. As for other animals, it has been proposed that the microbiome plays important roles in the biology of bark beetles. About the bacteriome, there still are many uncertainties regarding the taxonomical composition, insect-bacteriome interactions, and their potential roles in the beetle ecology. Here, we aim to deep into the ecological functions and taxonomical composition of I. typographus associated bacteria.<br><br>RESULTS: We assessed the metabolic potential of a collection of isolates obtained from different life stages of I. typographus beetles. All strains showed the capacity to hydrolyse one or more complex polysaccharides into simpler molecules, which may provide an additional carbon source to its host. Also, 83.9% of the strains isolated showed antagonistic effect against one or more entomopathogenic fungi, which could assist the beetle in its fight against this pathogenic threat. Using culture-dependent and -independent techniques, we present a taxonomical analysis of the bacteriome associated with the I. typographus beetle during its different life stages. We have observed an evolution of its bacteriome, which is diverse at the larval phase, substantially diminished in pupae, greater in the teneral adult phase, and similar to that of the larval stage in mature adults. Our results suggest that taxa belonging to the Erwiniaceae family, and the Pseudoxanthomonas and Pseudomonas genera, as well as an undescribed genus within the Enterobactereaceae family, are part of the core microbiome and may perform vital roles in maintaining beetle fitness.<br><br>CONCLUSION: Our results indicate that isolates within the bacteriome of I. typographus beetle have the metabolic potential to increase beetle fitness by proving additional and assimilable carbon sources for the beetle, and by antagonizing fungi entomopathogens. Furthermore, we observed that isolates from adult beetles are more likely to have these capacities but those obtained from larvae showed strongest antifungal activity. Our taxonomical analysis showed that Erwinia typographi, Pseudomonas bohemica, and Pseudomonas typographi species along with Pseudoxanthomonas genus, and putative new taxa belonging to the Erwiniaceae and Enterobacterales group are repeatedly present within the bacteriome of I. typographus beetles, indicating that these species might be part of the core microbiome. In addition to Pseudomonas and Erwinia group, Staphylococcus, Acinetobacter, Curtobacterium, Streptomyces, and Bacillus genera seem to also have interesting metabolic capacities but are present in a lower frequency. Future studies involving bacterial-insect interactions or analysing other potential roles would provide more insights into the bacteriome capacity to be beneficial to the beetle.}, }
@article {pmid37296336, year = {2023}, author = {Yu, T and Nie, J and Zang, H and Zeng, Z and Yang, Y}, title = {Peanut-based Rotation Stabilized Diazotrophic Communities and Increased Subsequent Wheat Yield.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37296336}, issn = {1432-184X}, abstract = {The introduction of legumes into rotations can improve nitrogen use efficiency and crop yield; however, its microbial mechanism involved remains unclear. This study aimed to explore the temporal impact of peanut introduction on microorganisms related to nitrogen metabolism in rotation systems. In this study, the dynamics of diazotrophic communities in two crop seasons and wheat yields of two rotation systems: winter wheat - summer maize (WM) and spring peanut → winter wheat - summer maize (PWM) in the North China Plain were investigated. Our results showed that peanut introduction increased wheat yield and biomass by 11.6% (p < 0.05) and 8.9%, respectively. Lower Chao1 and Shannon indexes of the diazotrophic communities were detected in soils that sampling in June compared with those sampling in September, although no difference was found between WM and PWM. Principal co-ordinates analysis (PCoA) showed that rotation system significantly changed the diazotrophic community structures (PERMANOVA; p < 0.05). Compared with WM, the genera of Azotobacter, Skermanella, Azohydromonas, Rhodomicrobium, Azospirillum, Unclassified_f_Opitutaceae, and Unclassified_f_Rhodospirillaceae were significantly enriched (p < 0.05) in PWM. Furthermore, rotation system and sampling time significantly influenced soil properties, which significantly correlated with the top 15 genera in relative abundance. Partial least squares path modeling (PLS-PM) analysis further showed that the diazotrophic community diversity (alpha- and beta-diversity) and soil properties (pH, SOC and TN) significantly affected wheat yield. In conclusion, legume inclusion has the potential to stabilize diazotrophic community structure at the temporal scales and increase subsequent crop yield.}, }
@article {pmid37294090, year = {2023}, author = {Upadhyay, V and Suryawanshi, RK and Tasoff, P and McCavitt-Malvido, M and Kumar, RG and Murray, VW and Noecker, C and Bisanz, JE and Hswen, Y and Ha, CWY and Sreekumar, B and Chen, IP and Lynch, SV and Ott, M and Lee, S and Turnbaugh, PJ}, title = {Mild SARS-CoV-2 infection results in long-lasting microbiota instability.}, journal = {mBio}, volume = {}, number = {}, pages = {e0088923}, doi = {10.1128/mbio.00889-23}, pmid = {37294090}, issn = {2150-7511}, abstract = {Viruses targeting mammalian cells can indirectly alter the gut microbiota, potentially compounding their phenotypic effects. Multiple studies have observed a disrupted gut microbiota in severe cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that require hospitalization. Yet, despite demographic shifts in disease severity resulting in a large and continuing burden of non-hospitalized infections, we still know very little about the impact of mild SARS-CoV-2 infection on the gut microbiota in the outpatient setting. To address this knowledge gap, we longitudinally sampled 14 SARS-CoV-2-positive subjects who remained outpatient and 4 household controls. SARS-CoV-2 cases exhibited a significantly less stable gut microbiota relative to controls. These results were confirmed and extended in the K18-humanized angiotensin-converting enzyme 2 mouse model, which is susceptible to SARS-CoV-2 infection. All of the tested SARS-CoV-2 variants significantly disrupted the mouse gut microbiota, including USA-WA1/2020 (the original variant detected in the USA), Delta, and Omicron. Surprisingly, despite the fact that the Omicron variant caused the least severe symptoms in mice, it destabilized the gut microbiota and led to a significant depletion in Akkermansia muciniphila. Furthermore, exposure of wild-type C57BL/6J mice to SARS-CoV-2 disrupted the gut microbiota in the absence of severe lung pathology.IMPORTANCETaken together, our results demonstrate that even mild cases of SARS-CoV-2 can disrupt gut microbial ecology. Our findings in non-hospitalized individuals are consistent with studies of hospitalized patients, in that reproducible shifts in gut microbial taxonomic abundance in response to SARS-CoV-2 have been difficult to identify. Instead, we report a long-lasting instability in the gut microbiota. Surprisingly, our mouse experiments revealed an impact of the Omicron variant, despite producing the least severe symptoms in genetically susceptible mice, suggesting that despite the continued evolution of SARS-CoV-2, it has retained its ability to perturb the intestinal mucosa. These results will hopefully renew efforts to study the mechanisms through which Omicron and future SARS-CoV-2 variants alter gastrointestinal physiology, while also considering the potentially broad consequences of SARS-CoV-2-induced microbiota instability for host health and disease.}, }
@article {pmid37293832, year = {2023}, author = {Mortier, C and Quintelier, K and De Craemer, AS and Renson, T and Deroo, L and Dumas, E and Verheugen, E and Coudenys, J and Decruy, T and Lukasik, Z and Van Gassen, S and Saeys, Y and Hoorens, A and Lobatón, T and Van den Bosch, F and Van de Wiele, T and Venken, K and Elewaut, D}, title = {Gut Inflammation in axial Spondyloarthritis patients is characterized by a marked Type 17 skewed mucosal Innate-like T cell signature.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/art.42627}, pmid = {37293832}, issn = {2326-5205}, abstract = {OBJECTIVE: SpA patients often present with microscopic signs of gut inflammation, a risk factor for progressive disease. We investigated whether mucosal innate-like T-cells are involved in dysregulated interleukin (IL)-23/IL-17 responses in the gut-joint axis in SpA.<br><br>METHODS: Ileal and colonic intraepithelial lymphocytes (IEL) and lamina propria lymphocytes (LPL), and paired peripheral blood mononuclear cells (PBMC), were isolated from treatment-naive non-radiographic axial (nr-ax)SpA patients with (n=11) and without (n=14) microscopic gut inflammation, and healthy controls (n=15), undergoing ileocolonoscopy. Presence of gut inflammation was assessed histopathologically. Immunophenotyping of innate-like T-cells and conventional T-cells was performed using intracellular flow cytometry. Unsupervised clustering analysis was done by FlowSOM technology. Serum IL-17A levels were measured via Luminex.<br><br>RESULTS: Microscopic gut inflammation in nr-axSpA was characterized by increased ileal intraepithelial &#x3b3;&#x3b4;-hi-T cells. &#x3b3;&#x3b4;-hi T cells were also increased in PBMC of nr-axSpA patients versus healthy controls, and were strongly associated with ASDAS. The abundance of mucosal associated invariant T (MAIT)-cells and invariant natural killer T (iNKT)-cells was unaltered. Innate-like T-cells in the inflamed gut showed increased ROR&#x3b3;t, IL-17A and IL-22 levels with loss of Tbet, a signature that was less pronounced in conventional T-cells. Presence of gut inflammation was associated with higher serum IL-17A levels. In patients treated with TNF blockade, the proportion of &#x3b3;&#x3b4;-hi cells and ROR&#x3b3;t expression in blood was completely restored.<br><br>CONCLUSION: Intestinal innate-like T-cells display marked type 17 skewing in the inflamed gut mucosa of nr-axSpA patients. &#x3b3;&#x3b4;-hi T cells are linked to intestinal inflammation and disease activity in SpA. This article is protected by copyright. All rights reserved.}, }
@article {pmid37291701, year = {2023}, author = {Suarez, C and Hackl, T and Wilen, BM and Persson, F and Hagelia, P and Jetten, M and Martins, PD}, title = {Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnad049}, pmid = {37291701}, issn = {1574-6968}, abstract = {The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.}, }
@article {pmid37286586, year = {2023}, author = {Leung, H and Xiong, L and Ni, Y and Busch, A and Bauer, M and Press, AT and Panagiotou, G}, title = {Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {35}, pmid = {37286586}, issn = {2055-5008}, abstract = {Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.}, }
@article {pmid37285121, year = {2023}, author = {Tran, PQ and Bachand, SC and Hotvedt, JC and Kieft, K and McDaniel, EA and McMahon, KD and Anantharaman, K}, title = {Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0020123}, doi = {10.1128/msystems.00201-23}, pmid = {37285121}, issn = {2379-5077}, abstract = {The sulfur-containing amino acid cysteine is abundant in the environment, including in freshwater lakes. Biological cysteine degradation can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments. Here, we investigated the ecological significance of cysteine in oxic freshwater, using isolated cultures, controlled experiments, and multiomics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. We identified 29 isolates (Bacteroidota, Proteobacteria, and Actinobacteria) that produced H2S. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized three isolates using whole-genome sequencing (using a combination of short-read and long-read sequencing) and tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophilia (Gammaproteobacteria), S. bentonitica (Gammaproteobacteria), and Chryseobacterium piscium (Bacteroidota). Cysteine decreased and H2S increased, and all three genomes had genes involved in cysteine degradation. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a 5-year time series of metagenomic data from the same isolation source (Lake Mendota, Madison, WI, USA) and identified their presence throughout the time series. Overall, our study shows that diverse isolated bacterial strains can use cysteine and produce H2S under oxic conditions, and we show evidence using metagenomic data that this process may occur more broadly in natural freshwater lakes. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from the degradation of organosulfur compounds.IMPORTANCEHydrogen sulfide (H2S), a naturally occurring gas with both biological and abiotic origins, can be toxic to living organisms. In aquatic environments, H2S production typically originates from anoxic (lacking oxygen) environments, such as sediments, or the bottom layers of thermally stratified lakes. However, the degradation of sulfur-containing amino acids such as cysteine, which all cells and life forms rely on, can be a source of ammonia and H2S in the environment. Unlike other approaches for biological H2S production such as dissimilatory sulfate reduction, cysteine degradation can occur in the presence of oxygen. Yet, little is known about how cysteine degradation influences sulfur availability and cycling in freshwater lakes. In our study, we identified diverse bacteria from a freshwater lake that can produce H2S in the presence of O2. Our study highlights the ecological importance of oxic H2S production in natural ecosystems and necessitates a change in our outlook on sulfur biogeochemistry.}, }
@article {pmid37283549, year = {2023}, author = {Oba, PM and Carroll, MQ and Sieja, KM and Yang, X and Epp, TY and Warzecha, CM and Varney, JL and Fowler, JW and Coon, CN and Swanson, KS}, title = {Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs undergoing transport stress.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skad191}, pmid = {37283549}, issn = {1525-3163}, abstract = {Previously, a Saccharomyces cerevisiae fermentation product (SCFP) positively altered fecal microbiota, fecal metabolites, and immune cell function of adult dogs. Our objective was to determine the fecal characteristics, microbiota, and metabolites of SCFP-supplemented dogs subjected to transport stress. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (18 male, 18 female; age: 7.1 ± 0.77 y; body weight: 28.97 ± 3.67 kg) were randomly assigned to be controls or receive SCFP supplementation (250 mg/dog/d) (n=18/group) for 11 wk. At that time, fresh fecal samples were collected before and after transport in a hunting dog trailer with individual kennels. The trailer was driven 40 miles round trip for about 45 min. Fecal microbiota data were evaluated using Quantitative Insights Into Microbial Ecology 2, while all other data were analyzed using the Mixed Models procedure of Statistical Analysis System. Effects of treatment, transport, and treatment*transport were tested, with P<0.05 being considered significant. Transport stress increased fecal indole concentrations and relative abundances of fecal Actinobacteria, Collinsella, Slackia, Ruminococcus, and Eubacterium. In contrast, relative abundances of fecal Fusobacteria, Streptococcus, and Fusobacterium were reduced by transport. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by diet alone. Several diet*transport interactions were significant, however. Following transport, relative abundance of fecal Turicibacter increased in SCFP-supplemented dogs, but decreased in controls. Following transport, relative abundances of fecal Proteobacteria, Bacteroidetes, Prevotella, and Sutterella increased in controls, but not in SCFP-supplemented dogs. In contrast, relative abundances of fecal Firmicutes, Clostridium, Faecalibacterium, and Allobaculum increased and fecal Parabacteroides and Phascolarctobacterium decreased after transport stress in SCFP-supplemented dogs, but not in controls. Our data demonstrate that both transport stress and SCFP alter fecal microbiota in dogs, with transport being the primary cause for shifts. SCFP supplementation may provide benefits to dogs undergoing transport stress, but more research is necessary to determine proper dosages. More research is also necessary to determine if and how transport stress impacts gastrointestinal microbiota and other indicators of health.}, }
@article {pmid37280438, year = {2023}, author = {Ndour, PMS and Bargaz, A and Rchiad, Z and Pawlett, M and Clark, IM and Mauchline, TH and Harris, J and Lyamlouli, K}, title = {Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37280438}, issn = {1432-184X}, abstract = {Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.}, }
@article {pmid37280212, year = {2023}, author = {Weyhenmeyer, GA and Obertegger, U and Rudebeck, H and Jakobsson, E and Jansen, J and Zdorovennova, G and Bansal, S and Block, BD and Carey, CC and Doubek, JP and Dugan, H and Erina, O and Fedorova, I and Fischer, JM and Grinberga, L and Grossart, HP and Kangur, K and Knoll, LB and Laas, A and Lepori, F and Meier, J and Palshin, N and Peternell, M and Pulkkanen, M and Rusak, JA and Sharma, S and Wain, D and Zdorovennov, R}, title = {Author Correction: Towards critical white ice conditions in lakes under global warming.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3283}, doi = {10.1038/s41467-023-39005-3}, pmid = {37280212}, issn = {2041-1723}, }
@article {pmid37280177, year = {2023}, author = {Gralka, M}, title = {Searching for principles of microbial ecology across levels of biological organization.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icad060}, pmid = {37280177}, issn = {1557-7023}, abstract = {Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.}, }
@article {pmid37279442, year = {2023}, author = {Suzzi, AL and Stat, M and Gaston, TF and Huggett, MJ}, title = {Spatial patterns in host-associated and free-living bacterial communities across six temperate estuaries.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad061}, pmid = {37279442}, issn = {1574-6941}, abstract = {A major goal of microbial ecology is to establish the importance of spatial and environmental factors in driving community variation. Their relative importance likely varies across spatial scales, but focus has primarily been on free-living communities within well-connected aquatic environments rather than less connected island-like habitats such as estuaries, and key host-associated communities within these systems. Here we sampled both free-living (seawater and sediment) and host-associated (estuarine fish hindgut microbiome, Pelates sexlineatus) communities across six temperate Australian estuaries spanning ∼500 km. We find that spatial and environmental factors have different influences on these communities, with seawater demonstrating strong distance-decay relationships (R = -0.69) and significant associations with a range of environmental variables. Distance-decay relationships were weak for sediment communities but became stronger over smaller spatial scales (within estuaries, R = -0.5) potentially reflecting environmental filtering across biogeochemical gradients or stochastic processes within estuary sediments. Finally, P. sexlineatus hindgut microbiome communities displayed weak distance-decay relationships (R = -0.36) and limited variation explained by environmental variables, indicating the significance of host-related factors in driving community variation. Our findings provide important ecological insights into the spatial distributions and driving forces of both free-living and host-associated bacterial patterns across temperate estuarine systems.}, }
@article {pmid37278908, year = {2023}, author = {Gao, H and Wu, M and Liu, H and Ou, Y and Zhang, T and Duan, X}, title = {Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37278908}, issn = {1432-184X}, abstract = {Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.}, }
@article {pmid37278524, year = {2023}, author = {Dedrick, S and Warrier, V and Lemon, KP and Momeni, B}, title = {When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0075722}, doi = {10.1128/msystems.00757-22}, pmid = {37278524}, issn = {2379-5077}, abstract = {To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities.IMPORTANCEAlthough mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.}, }
@article {pmid37278360, year = {2023}, author = {Zayed, N and Ghesquière, J and Kamarudin, NHN and Bernaerts, K and Boon, N and Braem, A and Van Holm, W and Teughels, W}, title = {Oral Biofilm Cryotherapy as a Novel Ecological Modulation Approach.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345231172688}, doi = {10.1177/00220345231172688}, pmid = {37278360}, issn = {1544-0591}, abstract = {Oral cryotherapy is used in dentistry as a safe, simple, and low-cost treatment for a variety of oral lesions. It is well known for its ability to aid in the healing process. However, its effect on oral biofilms is unknown. As a result, the purpose of this study was to assess the effects of cryotherapy on in vitro oral biofilms. In vitro multispecies oral biofilms were grown on the surface of hydroxyapatite discs in symbiotic or dysbiotic states. CryoPen X+ was used to treat the biofilms, whereas untreated biofilms served as control. One set of biofilms was collected for study immediately after cryotherapy, whereas another group was reincubated for 24 h to permit biofilm recovery. Changes in biofilm structure were analyzed with a confocal laser scanning microscope (CLSM) and a scanning electron microscope (SEM), while biofilm ecology and community compositional changes were analyzed with viability DNA extraction and quantitative polymerase chain reaction (v-qPCR) analysis. One cryo-cycle immediately reduced biofilm load by 0.2 to 0.4 log10 Geq/mL, which increased with additional treatment cycles. Although the bacterial load of the treated biofilms recovered to the same level as the control biofilms within 24 h, the CLSM detected structural alterations. Compositional alterations were also detected by SEM, corroborating the v-qPCR findings that showed ≈≤10% incidence of pathogenic species compared to nontreated biofilms that encompassed ≈45% and 13% pathogenic species in dysbiotic and symbiotic biofilms, respectively. Spray cryotherapy showed promising results in a novel conceptual approach to the control of oral biofilms. Acting selectively by targeting oral pathobionts and retaining commensals, spray cryotherapy could modify the ecology of in vitro oral biofilms to become more symbiotic and prevent the evolution of dysbiosis without the use of antiseptics/antimicrobials.}, }
@article {pmid37275175, year = {2023}, author = {Timmusk, S and Pall, T and Raz, S and Fetsiukh, A and Nevo, E}, title = {The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1141862}, doi = {10.3389/fmicb.2023.1141862}, pmid = {37275175}, issn = {1664-302X}, abstract = {Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.}, }
@article {pmid37272971, year = {2023}, author = {Zhang, Y and Wang, M and Cheng, W and Huang, C and Ren, J and Zhai, H and Niu, L}, title = {Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37272971}, issn = {1432-184X}, abstract = {Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.}, }
@article {pmid37272815, year = {2023}, author = {Tang, K and Tao, L and Wang, Y and Wang, Q and Fu, C and Chen, B and Zhang, Z and Fu, Y}, title = {Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0074723}, doi = {10.1128/aem.00747-23}, pmid = {37272815}, issn = {1098-5336}, abstract = {Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.}, }
@article {pmid37272792, year = {2023}, author = {Wu, X and Gushgari-Doyle, S and Lui, LM and Hendrickson, AJ and Liu, Y and Jagadamma, S and Nielsen, TN and Justice, NB and Simmons, T and Hess, NJ and Joyner, DC and Hazen, TC and Arkin, AP and Chakraborty, R}, title = {Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0050023}, doi = {10.1128/aem.00500-23}, pmid = {37272792}, issn = {1098-5336}, abstract = {Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.}, }
@article {pmid37272710, year = {2023}, author = {Miller, SE and Colman, AS and Waldbauer, JR}, title = {Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0123822}, doi = {10.1128/msystems.01238-22}, pmid = {37272710}, issn = {2379-5077}, abstract = {Microbial activity in Arctic soils controls the cycling of significant stores of organic carbon and nutrients. We studied in situ processes in Alaskan soils using original metaproteomic methods in order to relate important heterotrophic functions to microbial taxa and to understand the microbial response to Arctic greening. Major bacterial groups show strong metabolic specialization in organic topsoils. α-/β-/γ-Proteobacteria specialized in the acquisition of small, soluble compounds, whereas Acidobacteria, Actinobacteria, and other detritosphere groups specialized in the degradation of plant-derived polymers. α-/β-/γ-Proteobacteria dominated the expression of transporters for common root exudates and limiting nitrogenous compounds, supporting an ecological model of dependence upon plants for carbon and competition with plants for nitrogen. Detritosphere groups specialized in distinct substrates, with Acidobacteria producing the most enzymes for hemicellulose depolymerization. Acidobacteria was the most active group across the three plant ecotypes sampled-the largely nonvascular, lower biomass intertussock and the largely vascular, higher biomass tussock and shrub. Functional partitioning among bacterial groups was stable between plant ecotypes, but certain functions associated with α-/β-/γ-Proteobacteria were more strongly expressed in higher biomass ecotypes. We show that refined metaproteomic approaches can elucidate soil microbial ecology as well as biogeochemical trajectories of major carbon stocks.IMPORTANCEThe Arctic is warming twice as fast as the rest of the planet, and Arctic soils currently store twice as much carbon as the entire atmosphere-two facts that make understanding how Arctic soil microbial communities are responding to climate change particularly urgent. Greening of vegetation cover across the Arctic landscape is one of the most prominent climate-driven shifts in Arctic terrestrial ecology, with potentially profound effects on biogeochemical cycling by the soil microbiome. Here we use metaproteomics to document microbial metabolic functions that drive soil carbon and nutrient cycling processes in an Arctic tundra landscape. We identify functional roles among bacterial taxonomic groups that are largely stable across vegetation types, with certain functions strongly expressed by rhizosphere groups reflecting a community metabolic response to greening.}, }
@article {pmid37270320, year = {2023}, author = {M Venturini, A and B Gontijo, J and A Mandro, J and Berenguer, E and Peay, KG and M Tsai, S and Bohannan, BJM}, title = {Soil microbes under threat in the Amazon Rainforest.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2023.04.014}, pmid = {37270320}, issn = {1872-8383}, abstract = {Soil microorganisms are sensitive indicators of land-use and climate change in the Amazon, revealing shifts in important processes such as greenhouse gas (GHG) production, but they have been overlooked in conservation and management initiatives. Integrating soil biodiversity with other disciplines while expanding sampling efforts and targeted microbial groups is crucially needed.}, }
@article {pmid37268771, year = {2023}, author = {Listmann, L and Peters, C and Rahlff, J and Esser, SP and Schaum, CE}, title = {Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37268771}, issn = {1432-184X}, abstract = {Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.}, }
@article {pmid37268258, year = {2023}, author = {Yu, Y and Fu, D and Zhou, H and Su, J and Chen, S and Lv, G}, title = {Potential application of Atractylodes macrocephala Koidz. as a natural drug for bone mass regulation: A review.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {116718}, doi = {10.1016/j.jep.2023.116718}, pmid = {37268258}, issn = {1872-7573}, abstract = {The root of Atractylodes macrocephala Koidz. (AM) has been used for thousands of years in China, and it's extracts contain various constituents, such as volatile oils, polysaccharides, and lactones, with a myriad of pharmacological effects, including improves the healthy state of the gastrointestinal system and regulating immunity, hormone secretion, anti-inflammatory, antibacterial, antioxidation, anti-aging, and antitumor properties. Recently, researchers have focused on the effect of AM in regulating bone mass; therefore, its potential mechanism of action in regulating bone mass needs to be elucidated.<br><br>AIM OF REVIEW: This study reviewed the known and possible mechanisms of bone mass regulation by AM.<br><br>MATERIALS AND METHODS: Cochrane, Medline via PubMed, Embase, CENTRAL, CINAHL, Web of Science, Chinese biomedical literature database, Chinese Science and Technology Periodical Database, and Wanfang Database were used to search AM root extracts-related studies. The retrieval date was from the establishment of the database to January 1, 2023.<br><br>RESULTS: By summarizing 119 natural active substances that have been isolated from AM root to date, we explored its possible targets and pathways (such as Hedgehog, Wnt/&#x3b2;-catenin, and BMP/Smads pathways etc.) for bone growth and presented our position on possible future research/perspectives in the regulation of bone mass using this plant.<br><br>CONCLUSIONS: AM root extracts (incuding aqueous, ethanol etc.) promotes osteogenesis and inhibits osteoclastogenesis. These functions promote the absorption of nutrients, regulate gastrointestinal motility and intestinal microbial ecology, regulate endocrine function, strengthen bone immunity, and exert anti-inflammatory and antioxidant effects.}, }
@article {pmid37266990, year = {2023}, author = {Nikolaidis, M and Hesketh, A and Frangou, N and Mossialos, D and Van de Peer, Y and Oliver, SG and Amoutzias, GD}, title = {A panoramic view of the genomic landscape of the genus Streptomyces.}, journal = {Microbial genomics}, volume = {9}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001028}, pmid = {37266990}, issn = {2057-5858}, abstract = {We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species-level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon demonstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus-level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species-level fingerprints, smBGCs, CAZymes and TTA-codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.}, }
@article {pmid37263428, year = {2023}, author = {Van Peteghem, L and Matassa, S and Rabaey, K and Sakarika, M}, title = {Microbial protein from recovered nitrogen: Nutritional quality, safety, and feasibility assessment.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164525}, doi = {10.1016/j.scitotenv.2023.164525}, pmid = {37263428}, issn = {1879-1026}, abstract = {In contrast to traditional agriculture, microbial protein (MP) production is highly efficient in nitrogen (N) usage and can be employed to valorize a variety of recovered resources, thereby increasing the overall sustainability of food production. The present study aimed to establish the potential of seven recovered N sources originating from different waste streams for MP production using ethanol and acetate as growth substrates. The evaluation was based on specific growth rate, biomass yield, nutritional quality (i.e. macromolecular composition, amino acid (AA) and lipid profile) and food safety (i.e. concentration of heavy metals, polyaromatic hydrocarbons (PAH), pesticides and antibiotics) of the MP. The majority of the recovered N sources did not affect the kinetics and had a minor impact on the biomass yield, compared to their commercial equivalents. The nutritional content of the biomass was similar to soy flour and did not show major variations in AA and lipid profile for the different recovered N sources. Considering the heavy metal content, an average-weighing adult should not consume >53-213 g of the microbial biomass produced on recovered N per day due to its high copper content. A substantial amount of PAH were also found in the biomass. A daily consumption of 20 g/person/day would impose 2.0-2.8 times higher dietary exposure than the mean PAH exposure through nutrition in the EU, indicating a potential concern for human health. On the other hand, the biomass was free of antibiotics, and the traces of pesticides found did not raise any major concern for food applications. Based on the results of this work, no evidence was found to restrict the application of microbial biomass produced on recovered nitrogen as food.}, }
@article {pmid37264467, year = {2023}, author = {Wainwright, BJ and Millar, T and Bowen, L and Semon, L and Hickman, KJE and Lee, JN and Yeo, ZY and Zahn, G}, title = {The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {47}, pmid = {37264467}, issn = {2524-6372}, abstract = {BACKGROUND: Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.<br><br>CONCLUSION: The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.}, }
@article {pmid37264141, year = {2023}, author = {Zehnle, H and Laso-Pérez, R and Lipp, J and Riedel, D and Benito Merino, D and Teske, A and Wegener, G}, title = {Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {37264141}, issn = {2058-5276}, abstract = {Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.}, }
@article {pmid37260833, year = {2023}, author = {Myers, KS and Ingle, AT and Walters, KA and Fortney, NW and Scarborough, MJ and Donohue, TJ and Noguera, DR}, title = {Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1197175}, pmid = {37260833}, issn = {2296-4185}, abstract = {The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.}, }
@article {pmid37260392, year = {2023}, author = {Putman, LI and Schaerer, LG and Wu, R and Kulas, DG and Zolghadr, A and Ong, RG and Shonnard, DR and Techtmann, SM}, title = {Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0036223}, doi = {10.1128/spectrum.00362-23}, pmid = {37260392}, issn = {2165-0497}, abstract = {Over half of the world's plastic waste is landfilled, where it is estimated to take hundreds of years to degrade. Given the continued use and disposal of plastic products, it is vital that we develop fast and effective ways to utilize plastic waste. Here, we explore the potential of tandem chemical and biological processing to process various plastics quickly and effectively. Four samples of compost or sediment were used to set up enrichment cultures grown on mixtures of compounds, including disodium terephthalate and terephthalic acid (monomers of polyethylene terephthalate), compounds derived from the chemical deconstruction of polycarbonate, and pyrolysis oil derived from high-density polyethylene plastics. Established enrichment communities were also grown on individual substrates to investigate the substrate preferences of different taxa. Biomass harvested from the cultures was characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. These data reveal low-diversity microbial communities structured by differences in culture inoculum, culture substrate source plastic type, and time. Microbial populations from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteriae were significantly enriched when grown on substrates derived from high-density polyethylene and polycarbonate. The metagenomic data contain abundant aromatic and aliphatic hydrocarbon degradation genes relevant to the biodegradation of deconstructed plastic substrates used here. We show that microbial populations from diverse environments are capable of growth on substrates derived from the chemical deconstruction or pyrolysis of multiple plastic types and that paired chemical and biological processing of plastics should be further developed for industrial applications to manage plastic waste. IMPORTANCE The durability and impermeable nature of plastics have made them a popular material for numerous applications, but these same qualities make plastics difficult to dispose of, resulting in massive amounts of accumulated plastic waste in landfills and the natural environment. Since plastic use and disposal are projected to increase in the future, novel methods to effectively break down and dispose of current and future plastic waste are desperately needed. We show that the products of chemical deconstruction or pyrolysis of plastic can successfully sustain the growth of low-diversity microbial communities. These communities were enriched from multiple environmental sources and are capable of degrading complex xenobiotic carbon compounds. This study demonstrates that tandem chemical and biological processing can be used to degrade multiple types of plastics over a relatively short period of time and may be a future avenue for the mitigation of rapidly accumulating plastic waste.}, }
@article {pmid37259890, year = {2023}, author = {Geisen, S and Lara, E and Mitchell, E}, title = {Contemporary issues, current best practice and ways forward in soil protist ecology.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13819}, pmid = {37259890}, issn = {1755-0998}, abstract = {Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.}, }
@article {pmid37258870, year = {2023}, author = {Yung, PYM and Tan, SM}, title = {Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {303-315}, pmid = {37258870}, issn = {1940-6029}, abstract = {Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.}, }
@article {pmid37257612, year = {2023}, author = {Cheng, X and Zeng, Z and Liu, X and Li, L and Wang, H and Zhao, R and Bodelier, PLE and Wang, W and Wang, Y and Tuovinen, OH}, title = {Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164562}, doi = {10.1016/j.scitotenv.2023.164562}, pmid = {37257612}, issn = {1879-1026}, abstract = {Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogen community composition and their interaction with MOBs in the Heshang Cave to comprehensively understand methane cycling in subsurface biosphere. MOBs in karst cave were dominated by high-affinity MOB, upland soil cluster (USC), with USCγ pmoA gene abundance within the range of 1.34 × 10[4] to 1.8 × 10[7] copies·g[-1] DW. In contrast, methanogens were dominated by Methanoregula and cluster ZC-I. The mcrA numbers were 7.21 × 10[3] to 8.31 × 10[4] copies·g[-1] DW, 1-3 orders of magnitude lower than those of MOB. The inter-domain network analysis indicated that MOBs and methanogens cooperated more in the interior of the cave. Despite of the higher number of methanogenic nodes in the network, MOB dominated the keystone taxa, suggesting a leading functional role of MOB. MOB in caves showed a comparable with or higher potential methane oxidizing rate (PMOR, 0.63 ng CH4·g[-1] DW·h[-1] in sediment versus 11.02 ng CH4·g[-1] DW·h[-1] in weathered rock) than those in soils, whereas methane produced by methanogens was undetected. Collectively, high absolute abundances of MOB, high PMORs, the dominance of methanotrophic keystone taxa in the inter-domain network confirmed the superiority of MOB over methanogens in the oligotrophic karst cave, mounting new evidence on caves as important methane sink in terms of the interaction between methanogens and MOBs.}, }
@article {pmid37257501, year = {2023}, author = {Osorio-Doblado, AM and Feldmann, KP and Lourenco, JM and Stewart, RL and Smith, WB and Tedeschi, LO and Fluharty, FL and Callaway, TR}, title = {Forages and Pastures Symposium: Forage biodegradation: Advances in ruminal microbial ecology.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skad178}, pmid = {37257501}, issn = {1525-3163}, abstract = {The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography (LC) and mass spectrometry (MS) that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.}, }
@article {pmid37257378, year = {2023}, author = {Sun, W and Jing, Z}, title = {Migration of rare and abundant species, assembly mechanisms, and ecological networks of microbiomes in drinking water treatment plants: Effects of different treatment processes.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131726}, doi = {10.1016/j.jhazmat.2023.131726}, pmid = {37257378}, issn = {1873-3336}, abstract = {Microorganisms play an important role in the degradation of pollutants. However, they also cause problems in drinking water distribution systems, such as pipe corrosion and biofilm growth. The microbial assembly mechanisms and molecular ecological networks associated with different drinking water treatment processes have not yet been clearly analyzed. Therefore, this study investigated the microbiomes of three processes (coal filtration-activated carbon, ozone-activated carbon and UV, and ozone-activated carbon) during different seasons. The results showed that the microbial composition and diversity among the different processes and during different seasons. Water treatment processes had deterministic effects on the microbial assembly process and significantly changed the composition of rare and abundant species, altering the size and modules of molecular ecology networks. Rare species considered as keystone species play important roles in microbial ecology and microbial community construction. Ozone-activated carbon and UV/chlorination decreased the bacterial concentration, increased the deterministic process of microbial assembly, and significantly reduced the size of the network, which is of great significance to microbial control in drinking water. This research broadens our perspectives on the microbial assembly associated with drinking water treatment processes and contributes to ensuring the safe supply of drinking water.}, }
@article {pmid37253619, year = {2023}, author = {Takahashi, N and Terauchi, Y and Tanaka, T and Yoshimi, A and Yabu, H and Abe, K}, title = {Involvement of ionic interactions in self-assembly and resultant rodlet formation of class I hydrophobin RolA from Aspergillus oryzae.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbad066}, pmid = {37253619}, issn = {1347-6947}, abstract = {Hydrophobins are small amphiphilic proteins that are conserved in filamentous fungi. They localized on the conidial surface to make it hydrophobic, which contributes to conidial dispersal in air, and help fungi to infect plants and mammals and to degrade polymers. Hydrophobins self-assemble and undergo structural transition from the amorphous state to the rodlet (rod-like multimeric structure) state. However, it remains unclear whether the amorphous or rodlet state is biologically functional and what external factors regulate state transition. In this study, we analyzed the self-assembly of hydrophobin RolA of Aspergillus oryzae in detail and identified factors regulating this process. Using atomic force microscopy, we observed RolA rodlet formation over time, and determined "rodlet elongation rate" and "rodlet formation frequency." Changes in these kinetic parameters in response to pH and salt concentration suggest that RolA rodlet formation is regulated by the strength of ionic interactions between RolA molecules.}, }
@article {pmid37249591, year = {2023}, author = {Wu-Chuang, A and Hartmann, D and Maitre, A and Mateos-Hernández, L and Frantová, H and Urbanová, V and Obregon, D and Cabezas-Cruz, A and Perner, J}, title = {Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37249591}, issn = {1432-184X}, abstract = {Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.}, }
@article {pmid37247701, year = {2023}, author = {Garrido-Benavent, I and de Los Ríos, A and Núñez-Zapata, J and Ortiz-Álvarez, R and Schultz, M and Pérez-Ortega, S}, title = {Ocean crossers: a tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota).}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {107829}, doi = {10.1016/j.ympev.2023.107829}, pmid = {37247701}, issn = {1095-9513}, abstract = {Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.}, }
@article {pmid37247028, year = {2023}, author = {Gao, K and Li, W and Gan, E and Li, J and Jiang, L and Liu, Y}, title = {Impacts of 10 Years of Elevated CO2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37247028}, issn = {1432-184X}, abstract = {Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.}, }
@article {pmid37242886, year = {2023}, author = {Mattelin, V and Verfaille, L and Kundu, K and De Wildeman, S and Boon, N}, title = {A New Colorimetric Test for Accurate Determination of Plastic Biodegradation.}, journal = {Polymers}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/polym15102311}, pmid = {37242886}, issn = {2073-4360}, abstract = {As plastic waste is accumulating in both controlled waste management settings and natural settings, much research is devoted to search for solutions, also in the field of biodegradation. However, determining the biodegradability of plastics in natural environments remains a big challenge due to the often very low biodegradation rates. Many standardised test methods for biodegradation in natural environments exist. These are often based on mineralisation rates in controlled conditions and are thus indirect measurements of biodegradation. It is of interest for both researchers and companies to have tests that are more rapid, easier, and more reliable to screen different ecosystems and/or niches for their plastic biodegradation potential. In this study, the goal is to validate a colorimetric test, based on carbon nanodots, to screen biodegradation of different types of plastics in natural environments. After introducing carbon nanodots into the matrix of the target plastic, a fluorescent signal is released upon plastic biodegradation. The in-house-made carbon nanodots were first confirmed regarding their biocompatibility and chemical and photostability. Subsequently, the effectivity of the developed method was evaluated positively by an enzymatic degradation test with polycaprolactone with Candida antarctica lipase B. Finally, validation experiments were performed with enriched microorganisms and real environmental samples (freshwater and seawater), of which the results were compared with parallel, frequently used biodegradation measures such as O2 and CO2, dissolved organic carbon, growth and pH, to assess the reliability of the test. Our results indicate that this colorimetric test is a good alternative to other methods, but a combination of different methods gives the most information. In conclusion, this colorimetric test is a good fit to screen, in high throughput, the depolymerisation of plastics in natural environments and under different conditions in the lab.}, }
@article {pmid37236880, year = {2023}, author = {Malard, LA and Guisan, A}, title = {Into the microbial niche.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2023.04.015}, pmid = {37236880}, issn = {1872-8383}, abstract = {The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.}, }
@article {pmid37236039, year = {2023}, author = {Anderson, AG and Bedford, MR and Parsons, CM}, title = {Effects of adaptation diet and exogenous enzymes on true metabolizable energy and cecal microbial ecology, short-chain fatty acid profile, and enzyme activity in roosters fed barley and rye diets.}, journal = {Poultry science}, volume = {102}, number = {7}, pages = {102768}, doi = {10.1016/j.psj.2023.102768}, pmid = {37236039}, issn = {1525-3171}, abstract = {Three experiments evaluated effects of adaptation diet and exogenous β-glucanase and xylanase on TMEn of barley and rye. Single Comb White Leghorn roosters were fed adaptation diets based on corn/soybean meal (SBM), barley/SBM with and without β-glucanase, or rye/corn/SBM with and without xylanase for 4 wk. In Experiments 1 and 2, after the adaptation period, TMEn was determined using a 48 h precision-fed rooster assay for 100% barley or 100% rye diets with or without β-glucanase or xylanase, respectively. Experiment 3 consisted only of feeding adaptation diets for 4 wk. Cecal samples were collected at the end of experiments for microbial ecology, short-chain fatty acid (SCFA) profiles, and enzyme activity analyses. In Experiments 1 and 2, β-glucanase increased (P < 0.05) TMEn of barley, and there was no significant effect of adaptation diet on TMEn values. Total cecal Eubacteria and Ruminococcaceae were decreased (P < 0.05) and Escherichia coli were increased (P < 0.05) at the end of the TMEn assay compared with the end of the adaptation period (with no TMEn assay). There was a large decrease (P < 0.05) for most cecal SCFA at the end of the TMEn assay compared with the end of the adaptation period. Both cecal β-glucanase and xylanase activity were increased for birds fed adaptation diets containing the respective enzyme. In Experiment 3, there were no consistent effects of adaptation diet on cecal microbial profiles or SCFA but cecal β-glucanase activity was increased (P < 0.05) by exogenous β-glucanase for barley and cecal xylanase activity was increased (P < 0.05) by exogenous xylanase for rye. Overall, the results indicated that TMEn of barley was increased by exogenous β-glucanase, adaptation diet did not significantly influence the TMEn response to the dietary enzymes, and cecal fermentation (based on cecal SCFA) was greatly reduced by the TMEn assay. Cecal β-glucanase and xylanase activity, however, were often increased by feeding high barley and high rye diets containing exogenous enzymes.}, }
@article {pmid37235689, year = {2023}, author = {Esteves, SM and Jadoul, A and Iacono, F and Schloesser, M and Bosman, B and Carnol, M and Druet, T and Cardol, P and Hanikenne, M}, title = {Natural variation of nutrient homeostasis among laboratory and field strains in Chlamydomonas reinhardtii.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erad194}, pmid = {37235689}, issn = {1460-2431}, abstract = {Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macro-nutrients have a wide range of functions in photosynthetic organisms and mineral nutrition plays thus a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, twenty-four Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared to autotrophy and 9 deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, -S) and micronutrients (-Cu, -Fe, -Mn, -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.}, }
@article {pmid37235378, year = {2023}, author = {Gomes, TC and Conrado, R and Oliveira, RC and Selari, PJRG and Melo, IS and Araújo, WL and Maria, DA and De Souza, AO}, title = {Effect of Monocerin, a Fungal Secondary Metabolite, on Endothelial Cells.}, journal = {Toxins}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/toxins15050344}, pmid = {37235378}, issn = {2072-6651}, abstract = {This study reports the isolation and identification of the endophytic fungus Exserohilum rostratum through molecular and morphological analysis using optical and transmission electron microscopy (TEM), as well as the procurement of its secondary metabolite monocerin, an isocoumarin derivative. Considering the previously observed biological activities of monocerin, this study was performed on human umbilical vein endothelial cells (HUVECs) that are widely used as an in vitro model for several different purposes. Important parameters, such as cell viability, senescence-associated β-galactosidase, cellular proliferation by using 5(6)-carboxyfluorescein diacetate N-succinimidyl ester (CFSE), apoptosis analysis with annexin, cellular morphology through scanning electron microscopy (SEM), and laser confocal analysis were evaluated after exposing the cells to monocerin. After 24 h of exposure to monocerin at 1.25 mM, there was more than 80% of cell viability and a low percentage of cells in the early and late apoptosis and necrosis. Monocerin increased cell proliferation and did not induce cell senescence. Morphological analysis showed cellular integrity. The study demonstrates aspects of the mechanism of action of monocerin on endothelial cell proliferation, suggesting the possibility of its pharmaceutical application, such as in regenerative medicine.}, }
@article {pmid37234538, year = {2023}, author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB}, title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203870}, doi = {10.3389/fmicb.2023.1203870}, pmid = {37234538}, issn = {1664-302X}, }
@article {pmid37233803, year = {2023}, author = {Leonhardt, F and Keller, A and Arranz Aveces, C and Ernst, R}, title = {From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37233803}, issn = {1432-184X}, abstract = {Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions.}, }
@article {pmid37230675, year = {2022}, author = {Haskell-Ramsay, CF and Dodd, FL and Smith, D and Cuthbertson, L and Nelson, A and Lodge, JK and Jackson, PA}, title = {Mixed Tree Nuts, Cognition, and Gut Microbiota: A 4-Week, Placebo-Controlled, Randomized Crossover Trial in Healthy Nonelderly Adults.}, journal = {The Journal of nutrition}, volume = {152}, number = {12}, pages = {2778-2788}, doi = {10.1093/jn/nxac228}, pmid = {37230675}, issn = {1541-6100}, abstract = {BACKGROUND: Beneficial effects of nut supplementation on cognitive function have previously been demonstrated in young and older adults. Alterations to gut microbiota have also been shown following tree nut consumption. However, no data exists on the effects of nuts on cognition and intestinal microbial communities assessed within the same study.<br><br>OBJECTIVES: The study aimed to examine the effects of daily consumption of tree nuts for 4 wk on cognitive function (primary outcome), mood, metabolomics, and gut microbial species (secondary outcomes) in healthy, nonelderly adults.<br><br>METHODS: This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30 g/d mixed tree nuts versus placebo on cognition and mood in 79 healthy adults aged 18-49 y. Metabolic responses, gut bacterial community structure, and the potential for these to impact cognition were explored using a multi-omic approach. Bacterial community analysis was conducted in Quantitative Insights Into Microbial Ecology 2 (QIIME2).<br><br>RESULTS: Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M = 92.2% compared with NUTS M = 94.5%; P = 0.019) and speed of response (placebo M = 788 ms compared with NUTS M = 757 ms; P = 0.004) on a picture recognition task. No significant changes to bacterial community &#x3b1; or &#x3b2; diversity were observed when comparing nut consumption to the placebo arm. However, an unclassified Lachnospiraceae amplicon sequence variant (ASV) was significantly enriched in participants when supplemented with nuts (P = 0.015). No correlations were observed between the changes to picture recognition and the changes to the unclassified Lachnospiraceae ASV. There were no significant changes to the urinary metabolome.<br><br>CONCLUSIONS: These findings indicate a positive effect of nut on cognition following only 4 wk of consumption in a healthy nonelderly sample, as well as upregulation of a microbial taxa associated with gut health. The effects appear to be independent of one another, but further exploration is required in those experiencing cognitive decline and/or gut dysbiosis.}, }
@article {pmid37230351, year = {2023}, author = {Bossolani, JW and Leite, MFA and Momesso, L and Ten Berge, H and Bloem, J and Kuramae, EE}, title = {Nitrogen input on organic amendments alters the pattern of soil-microbe-plant co-dependence.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164347}, doi = {10.1016/j.scitotenv.2023.164347}, pmid = {37230351}, issn = {1879-1026}, abstract = {The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil- microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity on the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio.}, }
@article {pmid37229861, year = {2023}, author = {Zou, J and Cai, L and Lin, J and Wang, R and Li, J and Jia, M}, title = {Anaerobic fermentation of aerobic granular sludge: Insight into the effect of granule size and sludge structure on hydrolysis and acidification.}, journal = {Journal of environmental management}, volume = {343}, number = {}, pages = {118202}, doi = {10.1016/j.jenvman.2023.118202}, pmid = {37229861}, issn = {1095-8630}, abstract = {Aerobic granular sludge (AGS) has different physicochemical properties and microbial communities compared to conventional activated sludge (CAS), which may result in different behaviors during anaerobic fermentation and require further investigation. This study investigated the effect of granule size and sludge structure on the hydrolysis and acidification of AGS. Experimental results show that AGS exhibited significantly higher soluble chemical oxygen demand (SCOD) dissolution and total volatile fatty acids (TVFA) production (330.6-430.3 mg/gVSS and 231.0-312.5 mgCOD/gVSS) compared to conventional activated sludge (CAS) (167.0 mg/gVSS and 133.3 mgCOD/gVSS). This is because AGS (90.6-96.9 mg/gVSS) had higher extracellular polymeric substances (EPS) content than CAS (81.2 mg/gVSS). EPS can not only serve as substrates but also release the trapped hydrolases. Moreover, the relative abundances of hydrolytic/acidogenic bacteria and genes were higher in AGS (0.46%-3.60% and 3.01 × 10[-3]%-4.04 × 10[-3]%) than in CAS (0.30% and 1.23 × 10[-3]%). The optimal granule size for AGS fermentation was found to be 500-1600 μm. The crushing of granule structure promoted the dissolution of small amounts of EPS and the release of some trapped hydrolases, thereby potentially enhancing the enzyme-substrate contacts and bacteria-substrate interactions. Therefore, the highest SCOD dissolution (510.6 mg/gVSS) and TVFA production (352.1 mgCOD/gVSS) from crushed 500-1600 μm AGS were observed. Overall, the findings of this study provide valuable insights into the recovery of organic carbon from AGS via anaerobic fermentation.}, }
@article {pmid37227467, year = {2023}, author = {S Camargo, T and A Nickele, M and Reis Filho, W and do R C Penteado, S and C de Queiroz, E and G Auer, C}, title = {Correction to: Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: A Search for Potential Biocontrol Agents.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02247-1}, pmid = {37227467}, issn = {1432-184X}, }
@article {pmid37225998, year = {2023}, author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y}, title = {Microbial carbon use efficiency promotes global soil carbon storage.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37225998}, issn = {1476-4687}, abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.}, }
@article {pmid37225918, year = {2023}, author = {Elston, KM and Phillips, LE and Leonard, SP and Young, E and Holley, JC and Ahsanullah, T and McReynolds, B and Moran, NA and Barrick, JE}, title = {The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {49}, pmid = {37225918}, issn = {2730-6151}, abstract = {Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli, a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying microbial ecology and host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.}, }
@article {pmid37225767, year = {2023}, author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F}, title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {314}, pmid = {37225767}, issn = {2052-4463}, abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.}, }
@article {pmid37223788, year = {2023}, author = {Venbrux, M and Crauwels, S and Rediers, H}, title = {Current and emerging trends in techniques for plant pathogen detection.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1120968}, pmid = {37223788}, issn = {1664-462X}, abstract = {Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.}, }
@article {pmid37222807, year = {2023}, author = {Broman, E and Abdelgadir, M and Bonaglia, S and Forsberg, SC and Wikström, J and Gunnarsson, JS and Nascimento, FJA and Sjöling, S}, title = {Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37222807}, issn = {1432-184X}, abstract = {Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.}, }
@article {pmid37222806, year = {2023}, author = {Korpita, TM and Muths, EL and Watry, MK and McKenzie, VJ}, title = {Captivity, Reintroductions, and the Rewilding of Amphibian-associated Bacterial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37222806}, issn = {1432-184X}, abstract = {Many studies have noted differences in microbes associated with animals reared in captivity compared to their wild counterparts, but few studies have examined how microbes change when animals are reintroduced to the wild after captive rearing. As captive assurance populations and reintroduction programs increase, a better understanding of how microbial symbionts respond during animal translocations is critical. We examined changes in microbes associated with boreal toads (Anaxyrus boreas), a threatened amphibian, after reintroduction to the wild following captive rearing. Previous studies demonstrate that developmental life stage is an important factor in amphibian microbiomes. We collected 16S marker-gene sequencing datasets to investigate: (i) comparisons of the skin, mouth, and fecal bacteria of boreal toads across four developmental life stages in captivity and the wild, (ii) tadpole skin bacteria before and after reintroduction to the wild, and (iii) adult skin bacteria during reintroduction to the wild. We demonstrated that differences occur across skin, fecal, and mouth bacterial communities in captive versus wild boreal toads, and that the degree of difference depends on developmental stage. Skin bacterial communities from captive tadpoles were more similar to their wild counterparts than captive post-metamorphic individuals were to their wild counterparts. When captive-reared tadpoles were introduced to a wild site, their skin bacteria changed rapidly to resemble wild tadpoles. Similarly, the skin bacterial communities of reintroduced adult boreal toads also shifted to resemble those of wild toads. Our results indicate that a clear microbial signature of captivity in amphibians does not persist after release into natural habitat.}, }
@article {pmid37222805, year = {2023}, author = {Rodríguez, MF and Gomez, AP and Parra-Giraldo, CM and Ceballos-Garzon, A}, title = {Proteomics and Genetic Approaches Elucidate the Circulation of Low Variability Staphylococcus aureus Strains on Colombian Dairy Farms.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37222805}, issn = {1432-184X}, abstract = {Staphylococcus aureus is one of the most prevalent pathogens causing bovine mastitis in the world, in part because of its ease of adaptation to various hosts and the environment. This study aimed to determine the prevalence of S. aureus in Colombian dairy farms and its relationship with the causal network of subclinical mastitis. From thirteen dairy farms enrolled, 1288 quarter milk samples (QMS) and 330 teat samples were taken from cows with positive (70.1%) and negative California Mastitis Test (CMT). In addition, 126 samples from the milking parlor environment and 40 from workers (nasal) were collected. On each dairy farm, a survey was conducted, and the milking process was monitored on the day of sampling. S. aureus was identified in 176 samples, i.e., 138 QMS, 20 from teats, 8 from the milking parlor environment, and 10 from workers' nasal swabs. Isolates identified as S. aureus underwent proteomics (clustering of mass spectrum) and molecular (tuf, coa, spa Ig, clfA, and eno genes) analysis. Regarding proteomics results, isolates were distributed into three clusters, each with members from all sources and all farms. Concerning molecular analysis, the virulence-related genes clfA and eno were identified in 41.3% and 37.8% of S. aureus isolates, respectively. We provide evidence on the circulation of S. aureus strains with limited variability among animals, humans, and the environment. The parameters with the lowest compliance in the farms which may be implicated in the transmission of S. aureus are the lack of handwashing and abnormal milk handling.}, }
@article {pmid37222804, year = {2023}, author = {Liu, B and Wang, Y and Zhang, H and Zhou, Y and Zhang, C and Yang, N and Wang, W}, title = {The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37222804}, issn = {1432-184X}, abstract = {The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.}, }
@article {pmid37222803, year = {2023}, author = {Malesevic, M and Stanisavljevic, N and Matijasevic, D and Curcic, J and Tasic, V and Tasic, S and Kojic, M}, title = {Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37222803}, issn = {1432-184X}, abstract = {The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.}, }
@article {pmid37221307, year = {2023}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Correction to: Paired root-soil samples and metabarcoding reveal taxon-based colonization strategies in arbuscular mycorrhizal fungi communities in Japanese cedar and cypress stands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02246-2}, pmid = {37221307}, issn = {1432-184X}, }
@article {pmid37221014, year = {2023}, author = {Carr, EC and Barton, Q and Grambo, S and Sullivan, M and Renfro, CM and Kuo, A and Pangilinan, J and Lipzen, A and Keymanesh, K and Savage, E and Barry, K and Grigoriev, IV and Riekhof, WR and Harris, SD}, title = {Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkad110}, pmid = {37221014}, issn = {2160-1836}, abstract = {Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primarily yeast form. These fungi grow in xeric, nutrient deplete environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community is not well understood. We have isolated two novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e., E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin that can potentially provide UV resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.}, }
@article {pmid37216901, year = {2023}, author = {Cao, Y and Almeida-Silva, F and Zhang, WP and Ding, YM and Bai, D and Bai, WN and Zhang, BW and Van de Peer, Y and Zhang, DY}, title = {Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad121}, pmid = {37216901}, issn = {1537-1719}, abstract = {When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes, and its only congeneric species, P. strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics, and the driving forces underneath the incipient speciation of the two Platycarya lineages.}, }
@article {pmid37213502, year = {2023}, author = {Díaz, M and Monfort-Lanzas, P and Quiroz-Moreno, C and Rivadeneira, E and Castillejo, P and Arnau, V and Díaz, W and Agathos, SN and Sangari, FJ and Jarrín-V, P and Molina, CA}, title = {The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1154815}, pmid = {37213502}, issn = {1664-302X}, abstract = {A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.}, }
@article {pmid37212664, year = {2023}, author = {Wu, SY and Ou, CC and Lee, ML and Hsin, IL and Kang, YT and Jan, MS and Ko, JL}, title = {Polysaccharide of Ganoderma lucidum Ameliorates Cachectic Myopathy Induced by the Combination Cisplatin plus Docetaxel in Mice.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0313022}, doi = {10.1128/spectrum.03130-22}, pmid = {37212664}, issn = {2165-0497}, abstract = {Cachexia is a lethal muscle-wasting syndrome associated with cancer and chemotherapy use. Mounting evidence suggests a correlation between cachexia and intestinal microbiota, but there is presently no effective treatment for cachexia. Whether the Ganoderma lucidum polysaccharide Liz-H exerts protective effects on cachexia and gut microbiota dysbiosis induced by the combination cisplatin plus docetaxel (cisplatin + docetaxel) was investigated. C57BL/6J mice were intraperitoneally injected with cisplatin + docetaxel, with or without oral administration of Liz-H. Body weight, food consumption, complete blood count, blood biochemistry, and muscle atrophy were measured. Next-generation sequencing was also performed to investigate changes to gut microbial ecology. Liz-H administration alleviated the cisplatin + docetaxel-induced weight loss, muscle atrophy, and neutropenia. Furthermore, upregulation of muscle protein degradation-related genes (MuRF-1 and Atrogin-1) and decline of myogenic factors (MyoD and myogenin) after treatment of cisplatin and docetaxel were prevented by Liz-H. Cisplatin and docetaxel treatment resulted in reducing comparative abundances of Ruminococcaceae and Bacteroides, but Liz-H treatment restored these to normal levels. This study indicates that Liz-H is a good chemoprotective reagent for cisplatin + docetaxel-induced cachexia. IMPORTANCE Cachexia is a multifactorial syndrome driven by metabolic dysregulation, anorexia, systemic inflammation, and insulin resistance. Approximately 80% of patients with advanced cancer have cachexia, and cachexia is the cause of death in 30% of cancer patients. Nutritional supplementation has not been shown to reverse cachexia progression. Thus, developing strategies to prevent and/or reverse cachexia is urgent. Polysaccharide is a major biologically active compound in the fungus Ganoderma lucidum. This study is the first to report that G. lucidum polysaccharides could alleviate chemotherapy-induced cachexia via reducing expression of genes that are known to drive muscle wasting, such as MuRF-1 and Atrogin-1. These results suggest that Liz-H is an effective treatment for cisplatin + docetaxel-induced cachexia.}, }
@article {pmid37211183, year = {2023}, author = {Yokoyama, D and Kikuchia, J}, title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116202}, doi = {10.1016/j.envres.2023.116202}, pmid = {37211183}, issn = {1096-0953}, abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.}, }
@article {pmid37211607, year = {2023}, author = {Liu, Y and Wang, H and Qian, X and Gu, J and Chen, W and Shen, X and Tao, S and Jiao, S and Wei, G}, title = {Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {109}, pmid = {37211607}, issn = {2049-2618}, abstract = {BACKGROUND: Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.<br><br>RESULTS: Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.<br><br>CONCLUSIONS: Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.}, }
@article {pmid37209180, year = {2023}, author = {Kostešić, E and Mitrović, M and Kajan, K and Marković, T and Hausmann, B and Orlić, S and Pjevac, P}, title = {Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37209180}, issn = {1432-184X}, abstract = {Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.}, }
@article {pmid37207751, year = {2023}, author = {Jin, Z and Shen, M and Wang, L and Wang, C and Gao, M and Yu, G and Chang, Z and Zhang, X}, title = {Antibacterial and immunoregulatory activity of an antimicrobial peptide hepcidin in loach (Misgurnus anguillicaudatus).}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {124833}, doi = {10.1016/j.ijbiomac.2023.124833}, pmid = {37207751}, issn = {1879-0003}, abstract = {Antimicrobial peptides (AMPs) are members of humoral immunity and particpate in resisting microbial invasion. In this study, an AMP gene hepcidin was obtained from the oriental loach Misgurnus anguillicaudatus and named Ma-Hep. This Ma-Hep encodes a peptide of 90 amino acids, with a predicted active peptide segment (Ma-sHep) of 25 amino acids at C terminus. Stimulation by a bacterial pathogen Aeromonas hydrophila resulted in significant up-regulation of Ma-Hep transcripts in loach midgut, head kidney, and gill. Ma-Hep and Ma-sHep proteins were expressed in Pichia pastoris and their antibacterial activity was examined. Results showed that Ma-sHep possessed stronger antibacterial activity against various Gram-positive and Gram-negative bacteria, compared to Ma-Hep. Scanning electron microscopy showed that Ma-sHep might kill bacteria by destroying bacterial cell membranes. Moreover, we found that Ma-sHep had an inhibitory effect on blood cell apoptosis induced by A. hydrophila and facilitated the bacterial phagocytosis and clearance in loach. Histopathological analysis indicated Ma-sHep could protect liver and gut of loach from bacterial infection. Ma-sHep has high thermal stability and PH stability, which is conducive to further feed addition. Feed supplemented with Ma-sHep expressing yeast improved the intestinal flora of loach by increasing the dominant bacteria and decreasing the harmful bacteria. Feed supplemented with Ma-sHep expressing yeast also regulated the expression of inflammatory related factors in various tissues of loach and reduced the mortality of loach upon bacterial infection. These findings show that the antibacterial peptide Ma-sHep is involved in the antibacterial defense of loach and can be used as a candidate for new antimicrobial agents in aquaculture.}, }
@article {pmid37206339, year = {2023}, author = {Rasmussen, KL and Stamps, BW and Vanzin, GF and Ulrich, SM and Spear, JR}, title = {Spatial and temporal dynamics at an actively silicifying hydrothermal system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172798}, doi = {10.3389/fmicb.2023.1172798}, pmid = {37206339}, issn = {1664-302X}, abstract = {Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.}, }
@article {pmid37206314, year = {2023}, author = {Van de Walle, A and Kim, M and Alam, MK and Wang, X and Wu, D and Dash, SR and Rabaey, K and Kim, J}, title = {Greywater reuse as a key enabler for improving urban wastewater management.}, journal = {Environmental science and ecotechnology}, volume = {16}, number = {}, pages = {100277}, doi = {10.1016/j.ese.2023.100277}, pmid = {37206314}, issn = {2666-4984}, abstract = {Sustainable water management is essential to guaranteeing access to safe water and addressing the challenges posed by climate change, urbanization, and population growth. In a typical household, greywater, which includes everything but toilet waste, constitutes 50-80% of daily wastewater generation and is characterized by low organic strength and high volume. This can be an issue for large urban wastewater treatment plants designed for high-strength operations. Segregation of greywater at the source for decentralized wastewater treatment is therefore necessary for its proper management using separate treatment strategies. Greywater reuse may thus lead to increased resilience and adaptability of local water systems, reduction in transport costs, and achievement of fit-for-purpose reuse. After covering greywater characteristics, we present an overview of existing and upcoming technologies for greywater treatment. Biological treatment technologies, such as nature-based technologies, biofilm technologies, and membrane bioreactors (MBR), conjugate with physicochemical treatment methods, such as membrane filtration, sorption and ion exchange technologies, and ultraviolet (UV) disinfection, may be able to produce treated water within the allowable parameters for reuse. We also provide a novel way to tackle challenges like the demographic variance of greywater quality, lack of a legal framework for greywater management, monitoring and control systems, and the consumer perspective on greywater reuse. Finally, benefits, such as the potential water and energy savings and sustainable future of greywater reuse in an urban context, are discussed.}, }
@article {pmid37204848, year = {2023}, author = {Rattray, JB and Kramer, PJ and Gurney, J and Thomas, S and Brown, SP}, title = {The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {5}, pages = {}, doi = {10.1099/mic.0.001321}, pmid = {37204848}, issn = {1465-2080}, abstract = {Quorum sensing (QS) is a widespread mechanism of environment sensing and behavioural coordination in bacteria. At its core, QS is based on the production, sensing and response to small signalling molecules. Previous work with Pseudomonas aeruginosa shows that QS can be used to achieve quantitative resolution and deliver a dosed response to the bacteria's density environment, implying a sophisticated mechanism of control. To shed light on how the mechanistic signal components contribute to graded responses to density, we assess the impact of genetic (AHL signal synthase deletion) and/or signal supplementation (exogenous AHL addition) perturbations on lasB reaction-norms to changes in density. Our approach condenses data from 2000 timeseries (over 74 000 individual observations) into a comprehensive view of QS-controlled gene expression across variation in genetic, environmental and signal determinants of lasB expression. We first confirm that deleting either (∆lasI, ∆rhlI) or both (∆lasIrhlI) AHL signal synthase gene attenuates QS response to density. In the ∆rhlI background we show persistent yet attenuated density-dependent lasB expression due to native 3-oxo-C12-HSL signalling. We then test if density-independent quantities of AHL signal (3-oxo-C12-HSL, C4-HSL) added to the WT either flatten or increase responsiveness to density and find that the WT response is robust to all tested concentrations of signal, alone or in combination. We then move to progressively supplementing the genetic knockouts and find that cognate signal supplementation of a single AHL signal (∆lasI +3-oxo-C12-HSL, ∆rhlI +C4HSL) is sufficient to restore the ability to respond in a density-dependent manner to increasing density. We also find that dual signal supplementation of the double AHL synthase knockout restores the ability to produce a graded response to increasing density, despite adding a density-independent amount of signal. Only the addition of high concentrations of both AHLs and PQS can force maximal lasB expression and ablate responsiveness to density. Our results show that density-dependent control of lasB expression is robust to multiple combinations of QS gene deletion and density-independent signal supplementation. Our work develops a modular approach to query the robustness and mechanistic bases of the central environmental sensing phenotype of quorum sensing.}, }
@article {pmid37201636, year = {2023}, author = {He, Y and Xu, M and Lu, S and Zou, W and Wang, Y and Fakhar-E-Alam Kulyar, M and Iqbal, M and Li, K}, title = {Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106159}, doi = {10.1016/j.micpath.2023.106159}, pmid = {37201636}, issn = {1096-1208}, abstract = {Gastrointestinal (GI) disease is a common digestive tract disease effects health of millions of human globally each year, thus the role of intestinal microflora had been emphasized. Seaweed polysaccharides featured a wide range of pharmacological activities, such as antioxidant activity and pharmacological action, but whether they can alleviate the dysbiosis of gut microbial ecology caused by lipopolysaccharide (LPS) exposure has not been well conducted. In this study, we investigated the effects of different concentration of seaweed polysaccharides on LPS-induced intestinal disorder by using microscope and 16S rRNA high-throughput sequencing. Histopathological results indicated that the intestinal structure in the LPS-induced group was damaged. Furthermore, LPS exposure not only reduced the intestinal microbial diversity in mice but also induced momentous transformation in its composition, including a significantly increased in some pathogenic bacteria (Helicobacter, Citrobacter and Mucispirillum) and decreased in several beneficial bacteria (Firmicutes, Lactobacillus, Akkermansia and Parabacteroides). Nonetheless, seaweed polysaccharide administration could recover the gut microbial dysbiosis and the loss of gut microbial diversity induced by LPS exposure. In summary, seaweed polysaccharides were effective against LPS-induced intestinal damage in mice via the modulation of intestinal microecology.}, }
@article {pmid37200211, year = {2023}, author = {Pascual, J and Lepleux, C and Methner, A and Spröer, C and Bunk, B and Overmann, J}, title = {Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005895}, pmid = {37200211}, issn = {1466-5034}, abstract = {A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2[T], was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2[T] was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2[T] was closely related to Arcobacter lekithochrous LFT 1.7[T] and Arcobacter caeni RW17-10[T](95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2[T] was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2[T] represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2[T] as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2[T] (DSM 29169[T]=KCTC 52423[T]).}, }
@article {pmid37196970, year = {2023}, author = {Farrell, ML and Chueiri, A and O'Connor, L and Duane, S and Maguire, M and Miliotis, G and Cormican, M and Hooban, B and Leonard, A and Gaze, WH and Devane, G and Tuohy, A and Burke, LP and Morris, D}, title = {Assessing the impact of recreational water use on carriage of antimicrobial resistant organisms.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164201}, doi = {10.1016/j.scitotenv.2023.164201}, pmid = {37196970}, issn = {1879-1026}, abstract = {Understanding the role of exposure to natural recreational waters in the acquisition and transmission of antimicrobial resistance (AMR) is an area of increasing interest. A point prevalence study was carried out in the island of Ireland to determine the prevalence of colonisation with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) in recreational water users (WU) and matched controls. A total of 411 adult participants (199 WU, 212 controls) submitted at least one faecal sample between September 2020 - October 2021. In total, 80 Enterobacterales were isolated from 73 participants. ESBL-PE were detected in 29 (7.1 %) participants (7 WU, 22 controls), and CRE were detected in nine (2.2 %) participants (4 WU, 5 controls). No carbapenemase-producing Enterobacterales (CPE) were detected. WU were significantly less likely to harbour ESBL-PE than controls (risk ratio = 0.34, 95 % CI 0.148 to 0.776, χ[2] 7.37, p = 0.007). This study demonstrates the occurrence of ESBL-PE and CRE in healthy participants in Ireland. Recreational exposure to bathing water in Ireland was associated with a decreased prevalence of colonisation with ESBL-PE and CRE.}, }
@article {pmid37196741, year = {2023}, author = {Lin, B and Tan, B and Zhang, Q and Li, M and Peng, H and Su, J and He, J and Zhang, Y and Liu, X and Wu, N}, title = {Unraveling the nexus of Cr (Ⅵ), Aniline, and Microbial Ecology on aniline-degrading biosystem: Removal efficiency, sludge type, microbial ecology.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129185}, doi = {10.1016/j.biortech.2023.129185}, pmid = {37196741}, issn = {1873-2976}, abstract = {In order to explore the stress principle of Cr (Ⅵ) on aniline biodegradation system, a control group and experimental groups with the concentration of Cr (Ⅵ) at 2, 5, 8 mg/L were set up. The results demonstrated that Cr (Ⅵ) had minimal effects on the degradation efficiency of aniline but significantly inhibited nitrogen removal function. When Cr (Ⅵ) concentration was below 5 mg/L, the nitrification performance recovered spontaneously, while denitrification performance was severely impaired. Furthermore, the secretion of extracellular polymeric substances (EPS) and its fluorescence substance concentration were strongly inhibited with increasing Cr (Ⅵ) concentration. High-throughput sequencing revealed that the experimental groups were enriched with Leucobacter and Cr (Ⅵ)-reducing bacteria, but the abundance of nitrifiers and denitrifiers was significantly decreased compared to the control group. Overall, the effects of Cr (Ⅵ) stress at different concentrations on nitrogen removal performance were more significant than those on aniline degradation.}, }
@article {pmid37196568, year = {2023}, author = {Xu, Y and Teng, Y and Wang, X and Ren, W and Zhao, L and Luo, Y and Christie, P and Greening, C}, title = {Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107962}, doi = {10.1016/j.envint.2023.107962}, pmid = {37196568}, issn = {1873-6750}, abstract = {Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of [13]C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.}, }
@article {pmid37193669, year = {2023}, author = {Delbaere, K and Roegiers, I and Bron, A and Durif, C and Van de Wiele, T and Blanquet-Diot, S and Marinelli, L}, title = {The small intestine: dining table of host-microbiota meetings.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuad022}, pmid = {37193669}, issn = {1574-6976}, abstract = {Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host's nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo and in vitro models developed to simulate the small intestinal environment, some applied for (diet-)host-bacteria interaction studies. Lastly, we highlight recent technological, medical and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.}, }
@article {pmid37191674, year = {2023}, author = {Zhao, J and Fan, D and Guo, W and Wu, J and Zhang, X and Zhuang, X and Kong, W}, title = {Precipitation Drives Soil Protist Diversity and Community Structure in Dry Grasslands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37191674}, issn = {1432-184X}, abstract = {Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.}, }
@article {pmid37190986, year = {2023}, author = {Yang, Y and Suyamud, B and Liang, S and Liang, X and Wan, W and Zhang, W}, title = {Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16400}, pmid = {37190986}, issn = {1462-2920}, abstract = {The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.}, }
@article {pmid37188366, year = {2023}, author = {Harder, CB and Hesling, E and Botnen, SS and Lorberau, KE and Dima, B and von Bonsdorff-Salminen, T and Niskanen, T and Jarvis, SG and Ouimette, A and Hester, A and Hobbie, EA and Taylor, AFS and Kauserud, H}, title = {Mycena species can be opportunist-generalist plant root invaders.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16398}, pmid = {37188366}, issn = {1462-2920}, abstract = {Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of [13] C/[15] N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published [13] C/[15] N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.}, }
@article {pmid37187536, year = {2023}, author = {Liao, Q and Ye, Y and Li, Z and Chen, H and Zhuo, L}, title = {Prediction of miRNA-disease associations in microbes based on graph convolutional networks and autoencoders.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1170559}, doi = {10.3389/fmicb.2023.1170559}, pmid = {37187536}, issn = {1664-302X}, abstract = {MicroRNAs (miRNAs) are short RNA molecular fragments that regulate gene expression by targeting and inhibiting the expression of specific RNAs. Due to the fact that microRNAs affect many diseases in microbial ecology, it is necessary to predict microRNAs' association with diseases at the microbial level. To this end, we propose a novel model, termed as GCNA-MDA, where dual-autoencoder and graph convolutional network (GCN) are integrated to predict miRNA-disease association. The proposed method leverages autoencoders to extract robust representations of miRNAs and diseases and meantime exploits GCN to capture the topological information of miRNA-disease networks. To alleviate the impact of insufficient information for the original data, the association similarity and feature similarity data are combined to calculate a more complete initial basic vector of nodes. The experimental results on the benchmark datasets demonstrate that compared with the existing representative methods, the proposed method has achieved the superior performance and its precision reaches up to 0.8982. These results demonstrate that the proposed method can serve as a tool for exploring miRNA-disease associations in microbial environments.}, }
@article {pmid37188915, year = {2023}, author = {Moeller, FU and Herbold, CW and Schintlmeister, A and Mooshammer, M and Motti, C and Glasl, B and Kitzinger, K and Behnam, F and Watzka, M and Schweder, T and Albertsen, M and Richter, A and Webster, NS and Wagner, M}, title = {Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37188915}, issn = {1751-7370}, abstract = {Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.}, }
@article {pmid37186228, year = {2023}, author = {Woksepp, H and Camara, F and Bonnedahl, J}, title = {High prevalence of blaCTX-M-15 type extended-spectrum beta-lactamases in Gambian hooded vultures (Necrosyrtes monachus): A threatened species with substantial human interaction.}, journal = {MicrobiologyOpen}, volume = {12}, number = {2}, pages = {e1349}, doi = {10.1002/mbo3.1349}, pmid = {37186228}, issn = {2045-8827}, abstract = {One hundred fecal samples from hooded vultures in the Gambia (Banjul area) were investigated for the presence of bacteria with extended-spectrum cephalosporin- (ESBL/AmpC), carbapenemases, and colistin resistance. No Enterobacteriales carrying carbapenemases or resistance against colistin were detected. Fifty-four ESBL-producing Escherichia coli and five ESBL-producing Klebsiella pneumoniae isolates were identified in 52 of the samples, of which 52 E. coli and 4 K. pneumoniae yielded passed sequencing results. Fifty of the E. coli had ESBL phenotype and genotype harboring blaCTX-M genes, of which 88.5% (n = 46) were the blaCTX-M-15 gene, commonly found on the African continent. Furthermore, the genetic context around blaCTX-M-15 was similar between isolates, being colocalized with ISKpn19. In contrast, cgMLST analysis of the E. coli harboring ESBL genes revealed a genetic distribution over a large fraction of the currently known existing E. coli populations in the Gambia. Hooded vultures in the Gambia thus have a high ESBL E. coli-prevalence (>50%) with low diversity regarding key resistance genes. Furthermore, given the urban presence and frequent interactions between hooded vultures and humans, data from this study implies hooded vultures as potential vectors contributing to the further dissemination of antibiotic-resistance genes.}, }
@article {pmid37185621, year = {2023}, author = {Li, J and Liu, T and McIlroy, SJ and Tyson, GW and Guo, J}, title = {Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {39}, pmid = {37185621}, issn = {2730-6151}, abstract = {The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m[3]/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.}, }
@article {pmid37184385, year = {2023}, author = {Sänger, PA and Knüpfer, M and Kegel, M and Spanier, B and Liebler-Tenorio, EM and Fuchs, TM}, title = {Regulation and Functionality of a Holin/Endolysin Pair Involved in Killing of Galleria mellonella and Caenorhabditis elegans by Yersinia enterocolitica.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0003623}, doi = {10.1128/aem.00036-23}, pmid = {37184385}, issn = {1098-5336}, abstract = {The insecticidal toxin complex (Tc) proteins are produced by several insect-associated bacteria, including Yersinia enterocolitica strain W22703, which oscillates between two distinct pathogenicity phases in invertebrates and humans. The mechanism by which this high-molecular-weight toxin is released into the extracellular surrounding, however, has not been deciphered. In this study, we investigated the regulation and functionality of a phage-related holin/endolysin (HE) cassette located within the insecticidal pathogenicity island Tc-PAIYe of W22703. Using the Galleria mellonella infection model and luciferase reporter fusions, we revealed that quorum sensing contributes to the insecticidal activity of W22703 upon influencing the transcription of tcaR2, which encodes an activator of the tc and HE genes. In contrast, a lack of the Yersinia modulator, YmoA, stimulated HE gene transcription, and mutant W22703 ΔymoA exhibited a stronger toxicity toward insect larvae than did W22703. A luciferase reporter fusion demonstrated transcriptional activation of the HE cassette in vivo, and a significantly larger extracellular amount of subunit TcaA was found in W22703 ΔymoA relative to its ΔHE mutant. Using competitive growth assays, we demonstrated that at least in vitro, the TcaA release upon HE activity is not mediated by cell lysis of a significant part of the population. Oral infection of Caenorhabditis elegans with a HE deletion mutant attenuated the nematocidal activity of the wild type, similar to the case with a mutant lacking a Tc subunit. We conclude that the dual holin/endolysin cassette of yersiniae is a novel example of a phage-related function adapted for the release of a bacterial toxin. IMPORTANCE Members of the genus Yersinia cause gastroenteritis in humans but also exhibit toxicity toward invertebrates. A virulence factor required for this environmental life cycle stage is the multisubunit toxin complex (Tc), which is distinct from the insecticidal toxin of Bacillus thuringiensis and has the potential to be used in pest control. The mechanism by which this high-molecular-weight Tc is secreted from bacterial cells has not been uncovered. Here, we show that a highly conserved phage-related holin/endolysin pair, which is encoded by the genes holY and elyY located between the Tc subunit genes, is essential for the insecticidal activity of Y. enterocolitica and that its activation increases the amount of Tc subunits in the supernatant. Thus, the dual holY-elyY cassette of Y. enterocolitica constitutes a new example for a type 10 secretion system to release bacterial toxins.}, }
@article {pmid37182790, year = {2023}, author = {Refisch, A and Sen, ZD and Klassert, TE and Busch, A and Besteher, B and Danyeli, LV and Helbing, D and Schulze-Späte, U and Stallmach, A and Bauer, M and Panagiotou, G and Jacobsen, ID and Slevogt, H and Opel, N and Walter, M}, title = {Microbiome and immuno-metabolic dysregulation in patients with major depressive disorder with atypical clinical presentation.}, journal = {Neuropharmacology}, volume = {}, number = {}, pages = {109568}, doi = {10.1016/j.neuropharm.2023.109568}, pmid = {37182790}, issn = {1873-7064}, abstract = {Depression is highly prevalent (6% 1-year prevalence) and is the second leading cause of disability worldwide. Available treatment options for depression are far from optimal, with response rates only around 50%. This is most likely related to a heterogeneous clinical presentation of major depression disorder (MDD), suggesting different manifestations of underlying pathophysiological mechanisms. Poorer treatment outcomes to first-line antidepressants were reported in MDD patients endorsing an "atypical" symptom profile that is characterized by preserved reactivity in mood, increased appetite, hypersomnia, a heavy sensation in the limbs, and interpersonal rejection sensitivity. In recent years, evidence has emerged that immunometabolic biological dysregulation is an important underlying pathophysiological mechanism in depression, which maps more consistently to atypical features. In the last few years human microbial residents have emerged as a key influencing variable associated with immunometabolic dysregulations in depression. The microbiome plays a critical role in the training and development of key components of the host's innate and adaptive immune systems, while the immune system orchestrates the maintenance of key features of the host-microbe symbiosis. Moreover, by being a metabolically active ecosystem commensal microbes may have a huge impact on signaling pathways, involved in underlying mechanisms leading to atypical depressive symptoms. In this review, we discuss the interplay between the microbiome and immunometabolic imbalance in the context of atypical depressive symptoms. Although research in this field is in its infancy, targeting biological determinants in more homogeneous clinical presentations of MDD may offer new avenues for the development of novel therapeutic strategies for treatment-resistant depression.}, }
@article {pmid37180236, year = {2023}, author = {Huang, W and Li, S and Li, S and Laanbroek, HJ and Zhang, Q}, title = {Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1151768}, doi = {10.3389/fmicb.2023.1151768}, pmid = {37180236}, issn = {1664-302X}, abstract = {The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.}, }
@article {pmid37178239, year = {2023}, author = {Nandni,  and Rani, S and Chopra, G and Wati, L}, title = {Deciphering the Potential of Sulphur-Oxidizing Bacteria for Sulphate Production Correlating with pH Change.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37178239}, issn = {1432-184X}, abstract = {Sulphur, available in the form of sulphate, is one of the essential nutrients that is required by plants. Bacteria capable of oxidizing reduced forms of sulphur to sulphate play an important role in sulphur nutrition for plants. The present study was conducted to isolate, screen, and characterize sulphur-oxidizing bacteria from different soil samples collected from mustard rhizosphere and fly ash mixed soil. A total of 33 sulphur-oxidizing bacterial isolates (HMSOB1-33) were retrieved from soil and further screened for sulphur-oxidizing ability. Maximum solubilization index (3.76), pH reduction (3.93), and sulphate production (173.61 µg/ml) were observed for the isolate HMSOB2 which on the basis of 16S rDNA sequencing was identified as Pantoea dispersa with sequence similarity 98.22%. Four other selected bacterial isolates were identified as Bacillus megaterium, Bacillus tropicus, Bacillus velezensis, and Bacillus cereus. Sulphate solubilization index (SSI) correlated positively (r = 0.91) with sulphate production; however, pH showed negative correlation (r = - 0.82) with SSI as well as sulphate production after 120 h of incubation. These promising bacterial isolates could be further explored as bioinoculant after assessing plant growth traits.}, }
@article {pmid37177981, year = {2023}, author = {Bier, RL and Mosher, JJ and Kaplan, LA and Kan, J}, title = {Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16396}, pmid = {37177981}, issn = {1462-2920}, abstract = {A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.}, }
@article {pmid37173204, year = {2023}, author = {Pan, X and Raaijmakers, JM and Carrión, VJ}, title = {Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.03.018}, pmid = {37173204}, issn = {1878-4380}, abstract = {Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.}, }
@article {pmid37173060, year = {2023}, author = {Krebs, NF and Belfort, MB and Meier, PP and Mennella, JA and O'Connor, DL and Taylor, SN and Raiten, DJ}, title = {Infant factors that impact the ecology of human milk secretion and composition-a report from "Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)" Working Group 3.}, journal = {The American journal of clinical nutrition}, volume = {117 Suppl 1}, number = {}, pages = {S43-S60}, doi = {10.1016/j.ajcnut.2023.01.021}, pmid = {37173060}, issn = {1938-3207}, abstract = {Infants drive many lactation processes and contribute to the changing composition of human milk through multiple mechanisms. This review addresses the major topics of milk removal; chemosensory ecology for the parent-infant dyad; the infant's inputs into the composition of the human milk microbiome; and the impact of disruptions in gestation on the ecology of fetal and infant phenotypes, milk composition, and lactation. Milk removal, which is essential for adequate infant intake and continued milk synthesis through multiple hormonal and autocrine/paracrine mechanisms, should be effective, efficient, and comfortable for both the lactating parent and the infant. All 3 components should be included in the evaluation of milk removal. Breastmilk "bridges" flavor experiences in utero with postweaning foods, and the flavors become familiar and preferred. Infants can detect flavor changes in human milk resulting from parental lifestyle choices, including recreational drug use, and early experiences with the sensory properties of these recreational drugs impact subsequent behavioral responses. Interactions between the infant's own developing microbiome, that of the milk, and the multiple environmental factors that are drivers-both modifiable and nonmodifiable-in the microbial ecology of human milk are explored. Disruptions in gestation, especially preterm birth and fetal growth restriction or excess, impact the milk composition and lactation processes such as the timing of secretory activation, adequacy of milk volume and milk removal, and duration of lactation. Research gaps are identified in each of these areas. To assure a sustained and robust breastfeeding ecology, these myriad infant inputs must be systematically considered.}, }
@article {pmid37169795, year = {2023}, author = {Conners, R and León-Quezada, RI and McLaren, M and Bennett, NJ and Daum, B and Rakonjac, J and Gold, VAM}, title = {Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2724}, pmid = {37169795}, issn = {2041-1723}, abstract = {Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.}, }
@article {pmid37166501, year = {2023}, author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A}, title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37166501}, issn = {1432-184X}, abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.}, }
@article {pmid37166500, year = {2023}, author = {Zeng, Z and Yang, Z and Yang, A and Li, Y and Zhang, H}, title = {Genetic Evidence for Colletotrichum gloeosporioides Transmission Between the Invasive Plant Ageratina adenophora and Co-occurring Neighbor Plants.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37166500}, issn = {1432-184X}, abstract = {To understand the disease-mediated invasion of exotic plants and the potential risk of disease transmission in local ecosystems, it is necessary to characterize population genetic structure and spatio-temporal dynamics of fungal community associated with both invasive and co-occurring plants. In this study, multiple genes were used to characterize the genetic diversity of 165 strains of Colletotrichum gloeosporioides species complex (CGSC) isolated from healthy leaves and symptomatic leaves of invasive plant Ageratina adenophora, as well as symptomatic leaves of its neighbor plants from eleven geographic sites in China. The data showed that these CGSC strains had a high genetic diversity in each geographic site (all Hd > 0.67 and Pi > 0.01). Haplotype diversity and nucleotide diversity varied greatly in individual gene locus: gs had the highest haplotype diversity (Hd = 0.8972), gapdh had the highest nucleotide diversity (Pi = 0.0705), and ITS had the lowest nucleotide diversity (Pi = 0.0074). Haplotypes were not clustered by geographic site, invasive age, or isolation source. AMOVA revealed that the genetic variation was mainly from within-populations, regardless of geographic or isolation origin. Both AMOVA and neutrality tests indicated these CGSC strains occurred gene exchange among geographic populations but did not experience population expansion along with A. adenophora invasion progress. Our data indicated that A. adenophora primarily accumulated these CGSC fungi in the introduced range, suggesting a high frequency of CGSC transmission between A. adenophora and co-occurring neighbor plants. This study is valuable for understanding the disease-mediated plant invasion and the potential risk of disease transmission driven by exotic plants in local ecosystems.}, }
@article {pmid37163314, year = {2023}, author = {Cai, P and Zhang, W and Duan, X and Gong, S and Qiu, Z and Zhu 朱, M&#x58a8;}, title = {First Report of Powdery Mildew Caused by Golovinomyces bolayi on Veronica persica in Central China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-04-23-0641-PDN}, pmid = {37163314}, issn = {0191-2917}, abstract = {Veronica persica, Persian speedwell, is a flowering plant belonging to the family Plantaginaceae. Due to its showy flowers, this plant is widely planted in many home gardens, city parks and universities in China. From April to June 2021, signs and symptoms of powdery mildew were found on leaves of V. persica growing on the campus of Henan Normal University, Henan Province, China. Signs initially appeared as thin white colonies and subsequently white powdery masses were abundant on the adaxial and abaxial surfaces of leaves and covered up to 99 % of the leaf area. The infected leaves showed chlorotic, deformed or senescence features. About 150 V. persica plants were monitored and more than 90 % of the plants showed these signs and symptoms. Conidiophores (n = 20) were 108 to 220 × 10 to 13 μm and composed of foot cells, followed by short cells and conidia. Conidia were hyaline, doliiform-subcylindrical shaped, 21 to 37 × 15 to 22 μm, and showed distinct fibrosin bodies. Conidial germ tubes were produced at the perihilar position. No chasmothecia were observed. The observed morphological characteristics were consistent with those of previously documented Golovinomyces bolayi (Braun and Cook 2012). To further confirm the powdery mildew fungus, structures of the pathogen were harvested and total genomic DNA was isolated using the method previously described by Zhu et al. (2019, 2021). Using the primers ITS1/ITS4, the internal transcribed spacer (ITS) region of rDNA was amplified (White et al. 1990) and the amplicon was sequenced. The resulting sequence was deposited into GenBank under Accession No. MZ343575 and was 100 % identical (592/592 bp) to G. bolayi on Kalanchoe blossfeldiana (LC417096) (Braun et al. 2019). The additional phylogenetic analysis clearly illustrated that the identified fungus and G. bolayi were clustered in the same branch (Zhu et al. 2022a; Zhu et al. 2022b). To test pathogenicity, healthy V. persica plants were collected from the campus of Henan Normal University and leaf surfaces of three plants were inoculated by dusting fungal conidia from mildew-infested leaves using pressurized air. Three plants without inoculation served as a control. The spore-treated and non-treated plants were separately placed in two growth chambers (temperature, 18℃; humidity, 60%; light/dark, 16h/8h). Seven- to eight-days post-inoculation, pathogen signs were noticeable on inoculated plants, whereas control plants remained healthy. Similar results were obtained by conducting the pathogenicity assays twice. Therefore, based on the analysis, G. bolayi was identified and confirmed as the causal agent of the powdery mildew. This pathogen has been reported on V. persica in Iran (Golmohammadi et al. 2019). However, to our best knowledge, there is no report concerning the powdery mildew caused by G. bolayi on V. persica in China. Recently, G. bolayi was segregated from species clades of G. orontii complex (Braun et al. 2019). Our record of the molecular characterization of G. bolayi will support the further phylogeny and taxonomy analysis of the G. orontii complex. The sudden outbreak of powdery mildew caused by G. bolayi on V. persica may detract from plant health and ornamental value. The identification and confirmation of this disease expands the understanding of this causal agent and will offer support for future powdery mildew control.}, }
@article {pmid37162342, year = {2023}, author = {Cruz-Paredes, C and Tájmel, D and Rousk, J}, title = {Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0209022}, doi = {10.1128/aem.02090-22}, pmid = {37162342}, issn = {1098-5336}, abstract = {Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.}, }
@article {pmid37161621, year = {2023}, author = {Talukdar, D and Bandopadhyay, P and Ray, Y and Paul, SR and Sarif, J and D'Rozario, R and Lahiri, A and Das, S and Bhowmick, D and Chatterjee, S and Das, B and Ganguly, D}, title = {Association of gut microbial dysbiosis with disease severity, response to therapy and disease outcomes in Indian patients with COVID-19.}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {22}, pmid = {37161621}, issn = {1757-4749}, abstract = {BACKGROUND: Severe coronavirus disease 2019 (COVID-19) is associated with systemic hyper-inflammation. An adaptive interaction between gut microbiota and host immune systems is important for intestinal homeostasis and systemic immune regulation. The association of gut microbial composition and functions with COVID-19 disease severity is sparse, especially in India. We analysed faecal microbial diversity and abundances in a cohort of Indian COVID-19 patients to identify key signatures in the gut microbial ecology in patients with severe COVID-19 disease as well as in response to different therapies. The composition of the gut microbiome was characterized using 16Sr RNA gene sequences of genomic DNA extracted from faecal samples of 52 COVID-19 patients. Metabolic pathways across the groups were predicted using PICRUSt2. All statistical analyses were done using Vegan in the R environment. Plasma cytokine abundance at recruitment was measured in a multiplex assay.<br><br>RESULTS: The gut microbiome composition of mild and severe patients was found to be significantly different. Immunomodulatory commensals, viz. Lachnospiraceae family members and Bifidobacteria producing butyrate and short-chain fatty acids (SCFAs), were under represented in patients with severe COVID-19, with an increased abundance of opportunistic pathogens like Eggerthella. The higher abundance of Lachnoclostridium in severe disease was reduced in response to convalescent plasma therapy. Specific microbial genera showed distinctive trends in enriched metabolic pathways, strong correlations with blood plasma cytokine levels, and associative link to disease outcomes.<br><br>CONCLUSION: Our study indicates that, along with SARS-CoV-2, a dysbiotic gut microbial community may also play an important role in COVID-19 severity through modulation of host immune responses.}, }
@article {pmid37158858, year = {2023}, author = {Bi, S and Lai, H and Guo, D and Yi, H and Li, H and Liu, X and Chen, Q and Chen, J and Zhang, Z and Wei, X and Li, G and Xin, G}, title = {The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {16}, pmid = {37158858}, issn = {2730-7182}, abstract = {BACKGROUND: Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.<br><br>RESULTS: The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats.&#xa0;In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.<br><br>CONCLUSIONS: This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.}, }
@article {pmid37156959, year = {2023}, author = {Banaszkiewicz, S and Tabiś, A and Wałecki, B and Łyżwińska, K and Bystroń, J and Bania, J}, title = {spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37156959}, issn = {1432-184X}, abstract = {Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.}, }
@article {pmid37155494, year = {2023}, author = {Gomez-Alvarez, V and Siponen, S and Kauppinen, A and Hokajärvi, AM and Tiwari, A and Sarekoski, A and Miettinen, IT and Torvinen, E and Pitkänen, T}, title = {A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.}, journal = {Water research}, volume = {229}, number = {}, pages = {119495}, doi = {10.1016/j.watres.2022.119495}, pmid = {37155494}, issn = {1879-2448}, abstract = {The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.}, }
@article {pmid37154919, year = {2023}, author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW}, title = {Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37154919}, issn = {1432-184X}, abstract = {Insect-associated bacteria can mediate the intersection of insect and plant immunity. In this study, we aimed to evaluate the effects of single isolates or communities of gut-associated bacteria of Helicoverpa zea larvae on herbivore-induced defenses in tomato. We first identified bacterial isolates from the regurgitant of field-collected H. zea larvae by using a culture-dependent method and 16S rRNA gene sequencing. We identified 11 isolates belonging to the families Enterobacteriaceae, Streptococcaceae, Yersiniaceae, Erwiniaceae, and unclassified Enterobacterales. Seven different bacterial isolates, namely Enterobacteriaceae-1, Lactococcus sp., Klebsiella sp. 1, Klebsiella sp. 3, Enterobacterales, Enterobacteriaceae-2, and Pantoea sp., were selected based on their phylogenetic relationships to test their impacts on insect-induced plant defenses. We found that the laboratory population of H. zea larvae inoculated with individual isolates did not induce plant anti-herbivore defenses, whereas larvae inoculated with a bacterial community (combination of the 7 bacterial isolates) triggered increased polyphenol oxidase (PPO) activity in tomato, leading to retarded larval development. Additionally, field-collected H. zea larvae with an unaltered bacterial community in their gut stimulated higher plant defenses than the larvae with a reduced gut microbial community. In summary, our findings highlight the importance of the gut microbial community in mediating interactions between herbivores and their host plants.}, }
@article {pmid37150906, year = {2023}, author = {Rasmussen, TS and Mentzel, CMJ and Danielsen, MR and Jakobsen, RR and Zachariassen, LSF and Castro Mejia, JL and Brunse, A and Hansen, LH and Hansen, CHF and Hansen, AK and Nielsen, DS}, title = {Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2208504}, doi = {10.1080/19490976.2023.2208504}, pmid = {37150906}, issn = {1949-0984}, abstract = {Probiotics are intended to improve gastrointestinal health when consumed. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome. Here, we investigate the use of fecal virome transplantation (FVT, sterile filtrated feces) as a mean to alter the gut microbiome composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs from 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, LGG+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT donor material originated from mice with high relative abundance of A. muciniphila. All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly (p < 0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of propagating the existing commensal "probiotics" that have already permanently colonized the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly (p < 0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating interactions between the gut microbiome and fertility.}, }
@article {pmid37150044, year = {2023}, author = {Hu, D and Li, S and Liu, X and Liu, H and Liu, G}, title = {Kinetic model derivation for design, building and operation of solid waste treatment unit based on system dynamics and computer simulation.}, journal = {Waste management (New York, N.Y.)}, volume = {166}, number = {}, pages = {58-69}, doi = {10.1016/j.wasman.2023.04.037}, pmid = {37150044}, issn = {1879-2456}, abstract = {Solid waste disposal is significantly important to maintaining normal operation of both natural and artificial ecosystems. In this study, a kinetic model of solid waste treatment unit (SWTU) was upfront developed based on microbial ecology, system dynamics, cybernetics and digital simulation, which accurately described the relationships and interactions between solid waste decomposition (SWD) processes and biotic/abiotic factors. Then a specific SWTU prototype was designed and built from this kinetic model. A 370-day experiment demonstrated that SWTU maintained normal operation with robust stability and desired dynamic behaviors, and effectively disposed the solid waste. Therefore, this kinetic model was highly valid due to its high structural and behavioral similarity with the prototype. This research could lay a strong theoretical foundation for further closed-loop control as well as optimization of SWTU, and provide scientific guidance to environmental management as well as sustainable development.}, }
@article {pmid37149807, year = {2023}, author = {Pjevac, P and Bartosik, T and Schneider, S and Eckl-Dorna, J}, title = {Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2023.04.001}, pmid = {37149807}, issn = {1097-6825}, }
@article {pmid37149500, year = {2023}, author = {Kharshandi, F and Kayang, H}, title = {Antagonistic potential of rhizobacterial isolates against fungal pathogens causing rhizome rot in turmeric.}, journal = {Archives of microbiology}, volume = {205}, number = {6}, pages = {221}, pmid = {37149500}, issn = {1432-072X}, abstract = {The study aims to select potent bacterial antagonists to be used as biocontrol agents against rhizome rot disease in turmeric (Curcuma longa L.). A total of 48 bacterial isolates were isolated from the rhizosphere of turmeric. These isolates were screened for their in vitro antagonism against Fusarium solani FS-01 and Pythium aphanidermatum (ITCC 7908). Production of volatile organic compounds and chitinase activity were also performed. Among the tested isolates, two bacterial isolates (IJ2 and IJ10) showed the highest inhibitory activity against these fungal pathogens. GC/MS analysis of the crude extract produced by Pseudomonas sp. IJ2 and B. subtilis IJ10 was found to contain many bioactive compounds with antifungal and antimicrobial activities. The rhizome treatment with these isolates exhibited the lowest percent disease severity with high biocontrol efficacy against the tested pathogens. These isolates with promising antagonistic potential, therefore, can be used as biocontrol agents against rhizome rot in turmeric.}, }
@article {pmid37149269, year = {2023}, author = {Li, Y and Kuramae, EE and Nasir, F and Wang, E and Zhang, Z and Li, J and Yao, Z and Tian, L and Sun, Y and Luo, S and Guo, L and Ren, G and Tian, C}, title = {Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting: Construction the complex co-degradation system.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129132}, doi = {10.1016/j.biortech.2023.129132}, pmid = {37149269}, issn = {1873-2976}, abstract = {To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully colonized, which improve cellulose degrading ability. Continuous colonization of cellulose-degrading bacteria can promote the fungi to produce more precursors for humus and promote the negative correlation with Ascomycota. In the current study, the addition of cellulose-degrading bacteria has resulted in the rapid development of Mycothermus and Remersonia in the phylum Ascomycota as keystone fungal genera which constitute the foundation of the co-degradation system. Network analysis reveals the complex co-degradation system of efficient cellulose bacteria and mature fungi to treat cellulose in the process of straw aerobic composting mainly related to the influence of total carbon (TC) /total nitrogen (TN) and humic acid (HA)/fulvic acid (FA). This research offers a complex co-degradation system more efficiently to decompose cellulose aiming to maintain the long-term sustainability of agriculture.}, }
@article {pmid37148310, year = {2023}, author = {Burgess, WL and Bishop, CD}, title = {Bacterial Diversity in Egg Capsular Fluid of the Spotted Salamander Ambystoma maculatum Decreases with Embryonic Development.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37148310}, issn = {1432-184X}, abstract = {Egg capsules within egg masses of the spotted salamander Ambystoma maculatum host a symbiosis with the unicellular green alga Oophila amblystomatis. However, this alga is not the only microbe to inhabit those capsules, and the significance of these additional taxa for the symbiosis is unknown. Spatial and temporal patterns of bacterial diversity in egg capsules of A. maculatum have recently begun to be characterized, but patterns of bacterial diversity as a function of embryonic development are unknown. We sampled fluid from individual capsules in egg masses over a large range of host embryonic development in 2019 and 2020. We used 16S rRNA gene amplicon sequencing to examine how diversity and relative abundance of bacteria changed with embryonic development. In general, bacterial diversity decreased as embryos developed; significant differences were observed (depending on the metric) by embryonic development, pond, and year, and there were interaction effects. The function of bacteria in what is thought of as a bipartite symbiosis calls for further research.}, }
@article {pmid37148309, year = {2023}, author = {Gazulla, CR and Cabello, AM and Sánchez, P and Gasol, JM and Sánchez, O and Ferrera, I}, title = {A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37148309}, issn = {1432-184X}, abstract = {Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.}, }
@article {pmid37146562, year = {2023}, author = {Todorović, I and Abrouk, D and Kyselková, M and Lavire, C and Rey, M and Raičević, V and Jovičić-Petrović, J and Moënne-Loccoz, Y and Muller, D}, title = {Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {4}, pages = {126425}, doi = {10.1016/j.syapm.2023.126425}, pmid = {37146562}, issn = {1618-0984}, abstract = {Pseudomonas strains IT-194P, IT-215P, IT-P366[T] and IT-P374[T] were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366[T] and IT-194P and clustering (whole genome analysis) next to P. umsongensis DSM16611[T], and another species containing strains IT-P374[T] and IT-215P and clustering next to P. koreensis LMG21318[T]. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366[T] (compared with P. umsongensis DSM16611[T]) and IT-P374[T] (compared with P. koreensis LMG21318[T]). Unlike P. umsongensis DSM16611[T], strains of P. serbica can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to P. koreensis LMG21318[T], strains of P. serboccidentalis can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names Pseudomonas serbica sp. nov., with the type strain IT-P366[T] (=CFBP 9060 [T] = LMG 32732 [T] = EML 1791 [T]) and Pseudomonas serboccidentalis sp. nov., with the type strain IT-P374[T] (=CFBP 9061 [T] = LMG 32734 [T] = EML 1792 [T]). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).}, }
@article {pmid37145936, year = {2023}, author = {Fiskal, A and Shuster, J and Fischer, S and Joshi, P and Raghunatha Reddy, L and Wulf, SE and Kappler, A and Fischer, H and Herrig, I and Meier, J}, title = {Microbially influenced corrosion and rust tubercle formation on sheet piles in freshwater systems.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16393}, pmid = {37145936}, issn = {1462-2920}, abstract = {The extent of how complex natural microbial communities contribute to metal corrosion is still not fully resolved, especially not for freshwater environments. In order to elucidate the key processes, we investigated rust tubercles forming massively on sheet piles along the river Havel (Germany) applying a complementary set of techniques. In-situ microsensor profiling revealed steep gradients of O2 , redox potential and pH within the tubercle. Micro-computed tomography and scanning electron microscopy showed a multi-layered inner structure with chambers and channels and various organisms embedded in the mineral matrix. Using Mössbauer spectroscopy we identified typical corrosion products including electrically conductive iron (Fe) minerals. Determination of bacterial gene copy numbers and sequencing of 16S rRNA and 18S rRNA amplicons supported a densely populated tubercle matrix with a phylogenetically and metabolically diverse microbial community. Based on our results and previous models of physic(electro)chemical reactions, we propose here a comprehensive concept of tubercle formation highlighting the crucial reactions and microorganisms involved (such as phototrophs, fermenting bacteria, dissimilatory sulphate and Fe(III) reducers) in metal corrosion in freshwaters.}, }
@article {pmid37142893, year = {2023}, author = {Paul, P and Sarkar, S and Dastidar, DG and Shukla, A and Das, S and Chatterjee, S and Chakraborty, P and Tribedi, P}, title = {1, 4-naphthoquinone efficiently facilitates the disintegration of pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {37142893}, issn = {1874-9356}, abstract = {1, 4-naphthoquinone, a plant-based quinone derivative, has gained much attention for its effectiveness against several biofilm-linked diseases. The biofilm inhibitory effect of 1, 4-naphthoquinone against Staphylococcus aureus has already been reported in our previous study. We observed that the extracellular DNA (eDNA) could play an important role in holding the structural integrity of the biofilm. Hence, in this study, efforts have been directed to examine the possible interactions between 1, 4-naphthoquinone and DNA. An in silico analysis indicated that 1, 4-naphthoquinone could interact with DNA through intercalation. To validate the same, UV-Vis spectrophotometric analysis was performed in which a hypochromic shift was observed when the said molecule was titrated with calf-thymus DNA (CT-DNA). Thermal denaturation studies revealed a change of 8℃ in the melting temperature (Tm) of CT-DNA when complexed with 1, 4-naphthoquinone. The isothermal calorimetric titration (ITC) assay revealed a spontaneous intercalation between CT-DNA and 1, 4-naphthoquinone with a binding constant of 0.95 ± 0.12 × 10[8]. Furthermore, DNA was run through an agarose gel electrophoresis with a fixed concentration of ethidium bromide and increasing concentrations of 1, 4-naphthoquinone. The result showed that the intensity of ethidium bromide-stained DNA got reduced concomitantly with the gradual increase of 1, 4-naphthoquinone suggesting its intercalating nature. To gain further confidence, the pre-existing biofilm was challenged with ethidium bromide wherein we observed that it could also show biofilm disintegration. Therefore, the results suggested that 1, 4-naphthoquinone could exhibit disintegration of the pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.}, }
@article {pmid37142736, year = {2023}, author = {Mukorako, P and St-Pierre, DH and Flamand, N and Biertho, L and Lebel, S and Lemoine, N and Plamondon, J and Roy, MC and Tchernof, A and Varin, TV and Marette, A and Silvestri, C and Di Marzo, V and Richard, D}, title = {Hypoabsorptive surgeries cause limb-dependent changes in the gut endocannabinoidome and microbiome in association with beneficial metabolic effects.}, journal = {International journal of obesity (2005)}, volume = {}, number = {}, pages = {}, pmid = {37142736}, issn = {1476-5497}, abstract = {OBJECTIVE: To determine whether the metabolic benefits of hypoabsorptive surgeries are associated with changes in the gut endocannabinoidome (eCBome) and microbiome.<br><br>METHODS: Biliopancreatic diversion with duodenal switch (BPD-DS) and single anastomosis duodeno-ileal bypass with sleeve gastrectomy (SADI-S) were performed in diet-induced obese (DIO) male Wistar rats. Control groups fed a high-fat diet (HF) included sham-operated (SHAM HF) and SHAM HF-pair-weighed to BPD-DS (SHAM HF-PW). Body weight, fat mass gain, fecal energy loss, HOMA-IR, and gut-secreted hormone levels were measured. The levels of eCBome lipid mediators and prostaglandins were quantified in different intestinal segments by LC-MS/MS, while expression levels of genes encoding eCBome metabolic enzymes and receptors were determined by RT-qPCR. Metataxonomic (16S rRNA) analysis was performed on residual distal jejunum, proximal jejunum, and ileum contents.<br><br>RESULTS: BPD-DS and SADI-S reduced fat gain and HOMA-IR, while increasing glucagon-like peptide-1 (GLP-1) and peptide tyrosine tyrosine (PYY) levels in HF-fed rats. Both surgeries induced potent limb-dependent alterations in eCBome mediators and in gut microbial ecology. In response to BPD-DS and SADI-S, changes in gut microbiota were significantly correlated with those of eCBome mediators. Principal component analyses revealed connections between PYY, N-oleoylethanolamine (OEA), N-linoleoylethanolamine (LEA), Clostridium, and Enterobacteriaceae_g_2 in the proximal and distal jejunum and in the ileum.<br><br>CONCLUSIONS: BPD-DS and SADI-S caused limb-dependent changes in the gut eCBome and microbiome. The present results indicate that these variables could significantly influence the beneficial metabolic outcome of hypoabsorptive bariatric surgeries.}, }
@article {pmid37138640, year = {2023}, author = {Sorouri, B and Rodriguez, CI and Gaut, BS and Allison, SD}, title = {Variation in Sphingomonas traits across habitats and phylogenetic clades.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1146165}, pmid = {37138640}, issn = {1664-302X}, abstract = {Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.}, }
@article {pmid37138619, year = {2023}, author = {Yin, H and Zhao, M and Pan, G and Zhang, H and Yang, R and Sun, J and Yu, Z and Bai, C and Xue, Y}, title = {Effects of Bacillus subtilis or Lentilactobacillus buchneri on aerobic stability, and the microbial community in aerobic exposure of whole plant corn silage.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177031}, pmid = {37138619}, issn = {1664-302X}, abstract = {This study aimed to evaluate the effects of Bacillus subtilis or Lentilactobacillus buchneri on the fermentation quality, aerobic stability, and bacterial and fungal communities of whole plant corn silage during aerobic exposure. Whole plant corn was harvested at the wax maturity stage, which chopped to a length of approximately 1 cm, and treated with the following: distilled sterile water control, 2.0 × 10[5] CFU/g of Lentilactobacillus buchneri (LB) or 2.0 × 10[5] CFU/g of Bacillus subtilis (BS) for 42 days silage. Then, the samples were exposed to air (23-28[°]C) after opening and sampled at 0, 18 and 60 h, to investigate fermentation quality, bacterial and fungal communities, and aerobic stability. Inoculation with LB or BS increased the pH value, acetic acid, and ammonia nitrogen content of silage (P < 0.05), but it was still far below the threshold of inferior silage, the yield of ethanol was reduced (P < 0.05), and satisfactory fermentation quality was achieved. With the extension of the aerobic exposure time, inoculation with LB or BS prolonged the aerobic stabilization time of silage, attenuated the trend of pH increase during aerobic exposure, and increased the residues of lactic acid and acetic acid. The bacterial and fungal alpha diversity indices gradually declined, and the relative abundance of Basidiomycota and Kazachstania gradually increased. The relative abundance of Weissella and unclassified_f_Enterobacteria was higher and the relative abundance of Kazachstania was lower after inoculation with BS compared to the CK group. According to the correlation analysis, Bacillus and Kazachstania are bacteria and fungi that are more closely related to aerobic spoilage and inoculation with LB or BS could inhibit spoilage. The FUNGuild predictive analysis indicated that the higher relative abundance of fungal parasite-undefined saprotroph in the LB or BS groups at AS2, may account for its good aerobic stability. In conclusion, silage inoculated with LB or BS had better fermentation quality and improved aerobic stability by effectively inhibiting the microorganisms that induce aerobic spoilage.}, }
@article {pmid37133496, year = {2023}, author = {Donohue, ME and Hert, ZL and Karrick, CE and Rowe, AK and Wright, PC and Randriamanandaza, LJ and Zakamanana, F and Nomenjanahary, ES and Everson, KM and Weisrock, DW}, title = {Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37133496}, issn = {1432-184X}, abstract = {Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.}, }
@article {pmid37133495, year = {2023}, author = {Saikrishna, K and Talukdar, D and Das, S and Bakshi, S and Chakravarti, P and Jana, P and Karmakar, S and Wig, N and Das, B and Ray, A}, title = {Study on Effects of Probiotics on Gut Microbiome and Clinical Course in Patients with Critical Care Illnesses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37133495}, issn = {1432-184X}, abstract = {Ventilator-associated pneumonia (VAP) is a nosocomial infection contracted by ventilator patients in which bacteria colonize the upper digestive tract and contaminated secretions are released into the lower airway. This nosocomial infection increases the morbidity and mortality of the patients as well as the cost of treatment. Probiotic formulations have recently been proposed to prevent the colonization of these pathogenic bacteria. In this prospective observational study, we aimed to investigate the effects of probiotics on gut microbiota and their relation to clinical outcomes in mechanically ventilated patients. For this study, 35 patients were recruited (22 probiotic-treated and 13 without probiotic treatment) from a cohort of 169 patients. Patients in the probiotic group were given a dose of 6 capsules of a commercially available probiotic (VSL#3®:112.5 billion CFU/cap) in three divided doses for 10 days. Sampling was carried out after each dose to monitor the temporal change in the gut microbiota composition. To profile the microbiota, we used a 16S rRNA metagenomic approach, and differences among the groups were computed using multivariate statistical analyses. Differences in gut microbial diversity (Bray Curtis and Jaccard distance, p-value > 0.05) between the probiotic-treated group and the control group were not observed. Furthermore, treatment with probiotics resulted in the enrichment of Lactobacillus and Streptococcus in the gut microbiota of the probiotic-treated groups. Our results demonstrated that probiotics might lead to favorable alterations in gut microbiome characteristics. Future studies should focus on the appropriate dosages and frequency of probiotics, which can lead to improved clinical outcomes.}, }
@article {pmid37131715, year = {2023}, author = {Wu, L and Wang, XW and Tao, Z and Wang, T and Zuo, W and Zeng, Y and Liu, YY and Dai, L}, title = {Data-driven prediction of colonization outcomes for complex microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.04.19.537502}, pmid = {37131715}, abstract = {Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. Here, we proposed a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validated this approach using synthetic data, finding that machine learning models (including Random Forest and neural ODE) can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conducted colonization experiments for two commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approach can successfully predict the colonization outcomes. Furthermore, we found that while most resident species were predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., the presence of Enterococcus faecalis inhibits the invasion of E. faecium . The presented results suggest that the data-driven approach is a powerful tool to inform the ecology and management of complex microbial communities.}, }
@article {pmid37130890, year = {2023}, author = {Onyango, LA and Ngonga, FA and Karanja, EN and Kuja, JO and Boga, HI and Cowan, DA and Mwangi, KW and Maghenda, MW and Marinho Lebre, PBN and Kambura, AK}, title = {The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {7156}, pmid = {37130890}, issn = {2045-2322}, abstract = {Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.}, }
@article {pmid37129484, year = {2023}, author = {Farr, AD and Pesce, D and Das, SG and Zwart, MP and de Visser, JAGM}, title = {The Fitness of Beta-Lactamase Mutants Depends Nonlinearly on Resistance Level at Sublethal Antibiotic Concentrations.}, journal = {mBio}, volume = {}, number = {}, pages = {e0009823}, doi = {10.1128/mbio.00098-23}, pmid = {37129484}, issn = {2150-7511}, abstract = {Adaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit and together make up the fitness landscape, which maps genotype space onto fitness under specified conditions. Experimentally derived fitness landscapes have demonstrated a predictability to evolution by identifying limited "mutational routes" that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilize indirect measures to determine fitness. We estimated the competitive fitness of mutants relative to all single-mutation neighbors to describe the fitness landscape of three mutations in a β-lactamase enzyme. Fitness assays were performed at sublethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. In the unstructured environment, the antibiotic selected for higher-resistance types-but with an equivalent fitness for a subset of mutants, despite substantial variation in resistance-resulting in a stratified fitness landscape. In contrast, in a structured environment with a low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with subinhibitory concentrations of antibiotics and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes. IMPORTANCE The evolution of antibiotic-resistant bacterial populations underpins the ongoing antibiotic resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained, and whether it can be predictable. To this end, competition experiments were performed with a combinatorially complete set of mutants of a β-lactamase gene subject to subinhibitory concentrations of the antibiotic cefotaxime. While some mutations confer on their hosts high resistance to cefotaxime, in competition these mutations do not always confer a selective advantage. Specifically, high-resistance mutants had equivalent fitnesses despite different resistance levels and even had selective disadvantages under conditions involving spatial structure. Together, our findings suggest that the relationship between resistance level and fitness at subinhibitory concentrations is complex; predicting the evolution of antibiotic resistance requires knowledge of the conditions that select for resistant genotypes and the selective advantage evolved types have over their predecessors.}, }
@article {pmid37128070, year = {2020}, author = {Vandeweyer, D and Lievens, B and Van Campenhout, L}, title = {Identification of bacterial endospores and targeted detection of foodborne viruses in industrially reared insects for food.}, journal = {Nature food}, volume = {1}, number = {8}, pages = {511-516}, pmid = {37128070}, issn = {2662-1355}, abstract = {With edible insects being increasingly produced, food safety authorities have called for the determination of microbiological challenges posed to human health. Here, we find that the bacterial endospore fraction in industrially reared mealworm and cricket samples is largely comprised of Bacillus cereus group members that can pose insect or human health risks. Hepatitis A virus, hepatitis E virus and norovirus genogroup II were not detected in the sample collection, indicating a low food safety risk from these viral pathogens.}, }
@article {pmid37127168, year = {2023}, author = {Liu, YC and Ramiro-Garcia, J and Paulo, LM and Maria Braguglia, C and Cristina Gagliano, M and O'Flaherty, V}, title = {Psychrophilic and mesophilic anaerobic treatment of synthetic dairy wastewater with long chain fatty acids: Process performances and microbial community dynamics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {129124}, doi = {10.1016/j.biortech.2023.129124}, pmid = {37127168}, issn = {1873-2976}, abstract = {Facilitating the anaerobic degradation of long chain fatty acids (LCFA) is the key to unlock the energy potential of lipids-rich wastewater. In this study, the feasibility of psychrophilic anaerobic treatment of LCFA-containing dairy wastewater was assessed and compared to mesophilic anaerobic treatment. The results showed that psychrophilic treatment at 15 ℃ was feasible for LCFA-containing dairy wastewater, with high removal rates of soluble COD (>90%) and LCFA (∼100%). However, efficient long-term treatment required prior acclimation of the biomass to psychrophilic temperatures. The microbial community analysis revealed that putative syntrophic fatty acid bacteria and Methanocorpusculum played a crucial role in LCFA degradation during both mesophilic and psychrophilic treatments. Additionally, a fungal-bacterial biofilm was found to be important during the psychrophilic treatment. Overall, these findings demonstrate the potential of psychrophilic anaerobic treatment for industrial wastewaters and highlight the importance of understanding the microbial communities involved in the process.}, }
@article {pmid37127597, year = {2023}, author = {Mosquera, KD and Nilsson, LKJ and de Oliveira, MR and Rocha, EM and Marinotti, O and Håkansson, S and Tadei, WP and de Souza, AQL and Terenius, O}, title = {Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {156}, pmid = {37127597}, issn = {1756-3305}, abstract = {BACKGROUND: The neotropical anopheline mosquito Anopheles darlingi is a major malaria vector in the Americas. Studies on mosquito-associated microbiota have shown that symbiotic bacteria play a major role in host biology. Mosquitoes acquire and transmit microorganisms over their life cycle. Specifically, the microbiota of immature forms is largely acquired from their aquatic environment. Therefore, our study aimed to describe the microbial communities associated with An. darlingi immature forms and their breeding sites in the Coari municipality, Brazilian Amazon.<br><br>METHODS: Larvae, pupae, and breeding water were collected in two different geographical locations. Samples were submitted for DNA extraction and high-throughput 16S rRNA gene sequencing was conducted. Microbial ecology analyses were performed to explore and compare the bacterial profiles of An. darlingi and their aquatic habitats.<br><br>RESULTS: We found lower richness and diversity in An. darlingi microbiota than in water samples, which suggests that larvae are colonized by a subset of the bacterial community present in their breeding sites. Moreover, the bacterial community composition of the immature mosquitoes and their breeding water differed according to their collection sites, i.e., the microbiota associated with An. darlingi reflected that in the aquatic habitats where they developed. The three most abundant bacterial classes across the An. darlingi samples were Betaproteobacteria, Clostridia, and Gammaproteobacteria, while across the water samples they were Gammaproteobacteria, Bacilli, and Alphaproteobacteria.<br><br>CONCLUSIONS: Our findings reinforce the current evidence that the environment strongly shapes the composition and diversity of mosquito microbiota. A better understanding of mosquito-microbe interactions will contribute to identifying microbial candidates impacting host fitness and disease transmission.}, }
@article {pmid37126126, year = {2023}, author = {Kearns, PJ and Winter, AS and Woodhams, DC and Northup, DE}, title = {The Mycobiome of Bats in the American Southwest Is Structured by Geography, Bat Species, and Behavior.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37126126}, issn = {1432-184X}, abstract = {Bats are widespread mammals that play key roles in ecosystems as pollinators and insectivores. However, there is a paucity of information about bat-associated microbes, in particular their fungal communities, despite the important role microbes play in host health and overall host function. The emerging fungal disease, white-nose syndrome, presents a potential challenge to the bat microbiome and understanding healthy bat-associated taxa will provide valuable information about potential microbiome-pathogen interactions. To address this knowledge gap, we collected 174 bat fur/skin swabs from 14 species of bats captured in five locations in New Mexico and Arizona and used high-throughput sequencing of the fungal internal transcribed (ITS) region to characterize bat-associated fungal communities. Our results revealed a highly heterogeneous bat mycobiome that was structured by geography and bat species. Furthermore, our data suggest that bat-associated fungal communities are affected by bat foraging, indicating the bat skin microbiota is dynamic on short time scales. Finally, despite the strong effects of site and species, we found widespread and abundant taxa from several taxonomic groups including the genera Alternaria and Metschnikowia that have the potential to be inhibitory towards fungal and bacterial pathogens.}, }
@article {pmid37125162, year = {2023}, author = {Miao, Y and Colosimo, F and Mouser, PJ and De Long, S and Hanson Rhoades, A}, title = {Editorial: Emerging microbiological processes and tools that shine in pilot- and field-scale environmental engineering applications.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1194772}, doi = {10.3389/fmicb.2023.1194772}, pmid = {37125162}, issn = {1664-302X}, }
@article {pmid37124757, year = {2023}, author = {Esquivel-Hernández, DA and Martínez-López, YE and Sánchez-Castañeda, JP and Neri-Rosario, D and Padrón-Manrique, C and Giron-Villalobos, D and Mendoza-Ortíz, C and Resendis-Antonio, O}, title = {A network perspective on the ecology of gut microbiota and progression of type 2 diabetes: Linkages to keystone taxa in a Mexican cohort.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1128767}, pmid = {37124757}, issn = {1664-2392}, abstract = {INTRODUCTION: The human gut microbiota (GM) is a dynamic system which ecological interactions among the community members affect the host metabolism. Understanding the principles that rule the bidirectional communication between GM and its host, is one of the most valuable enterprise for uncovering how bacterial ecology influences the clinical variables in the host.<br><br>METHODS: Here, we used SparCC to infer association networks in 16S rRNA gene amplicon data from the GM of a cohort of Mexican patients with type 2 diabetes (T2D) in different stages: NG (normoglycemic), IFG (impaired fasting glucose), IGT (impaired glucose tolerance), IFG + IGT (impaired fasting glucose plus impaired glucose tolerance), T2D and T2D treated (T2D with a 5-year ongoing treatment).<br><br>RESULTS: By exploring the network topology from the different stages of T2D, we observed that, as the disease progress, the networks lose the association between bacteria. It suggests that the microbial community becomes highly sensitive to perturbations in individuals with T2D. With the purpose to identify those genera that guide this transition, we computationally found keystone taxa (driver nodes) and core genera for a Mexican T2D cohort. Altogether, we suggest a set of genera driving the progress of the T2D in a Mexican cohort, among them Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005, Alistipes, Anaerostipes, and Terrisporobacter.<br><br>DISCUSSION: Based on a network approach, this study suggests a set of genera that can serve as a potential biomarker to distinguish the distinct degree of advances in T2D for a Mexican cohort of patients. Beyond limiting our conclusion to one population, we present a computational pipeline to link ecological networks and clinical stages in T2D, and desirable aim to advance in the field of precision medicine.}, }
@article {pmid37120943, year = {2023}, author = {Gounari, Z and Bonatsou, S and Ferrocino, I and Cocolin, L and Papadopoulou, OS and Panagou, EZ}, title = {Exploring yeast diversity of dry-salted naturally black olives from Greek retail outlets with culture dependent and independent molecular methods.}, journal = {International journal of food microbiology}, volume = {398}, number = {}, pages = {110226}, doi = {10.1016/j.ijfoodmicro.2023.110226}, pmid = {37120943}, issn = {1879-3460}, abstract = {In the present study, the physicochemical (pH, water activity, moisture content, salt concentration) classical plate counts (total viable counts, yeasts, lactic acid bacteria, Staphylococcus aureus, Pseudomonas spp., Enterobacteriaceae) and amplicon sequencing of naturally black dry-salted olives obtained from different retail outlets of the Greek market were investigated. According to the results, the values of the physicochemical characteristics presented great variability among the samples. Specifically, pH and water activity (aw) values ranged between 4.0 and 5.0, as well as between 0.58 and 0.91, respectively. Moisture content varied between 17.3 and 56.7 % (g Η2Ο/100 g of olive pulp), whereas salt concentration ranged from 5.26 to 9.15 % (g NaCl/100 g of olive pulp). No lactic acid bacteria, S. aureus, Pseudomonas spp. and Enterobacteriaceae were detected. The mycobiota consisted of yeasts that were further characterized and identified by culture-dependent (rep-PCR, ITS-PCR, and RFLP) and amplicon target sequencing (ATS). Pichia membranifaciens, Candida sorbosivorans, Citeromyces nyonsensis, Candida etchelsii, Wickerhamomyces subpelliculosus, Candida apicola, Wickerhamomyces anomalus, Torulaspora delbrueckii and Candida versatilis were the dominant species according to ITS sequencing (culture-dependent), while ATS revealed the dominance of C. etchelsii, Pichia triangularis, P. membranifaciens, and C. versatilis among samples. The results of this study demonstrated considerable variability in quality attributes among the different commercial samples of dry-salted olives, reflecting a lack of standardization in the processing of this commercial style. However, the majority of the samples were characterized by satisfactory microbiological and hygienic quality and complied with the requirements of the trade standard for table olives of the International Olive Council (IOC) for this processing style in terms of salt concentration. In addition, the diversity of yeast species was elucidated for the first time in commercially available products, increasing our knowledge on the microbial ecology of this traditional food. Further investigation into the technological and multifunctional traits of the dominant yeast species may result in better control during dry-salting and enhance the quality and shelf-life of the final product.}, }
@article {pmid37120676, year = {2023}, author = {Ha, AD and Moniruzzaman, M and Aylward, FO}, title = {Assessing the biogeography of marine giant viruses in four oceanic transects.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {43}, pmid = {37120676}, issn = {2730-6151}, abstract = {Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation genes that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.}, }
@article {pmid37119999, year = {2023}, author = {Goswami, V and Deepika, S and Diwakar, S and Kothamasi, D}, title = {Arbuscular mycorrhizas amplify the risk of heavy metal transfer to human food chain from fly ash ameliorated agricultural soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121733}, doi = {10.1016/j.envpol.2023.121733}, pmid = {37119999}, issn = {1873-6424}, abstract = {Soil contaminants threaten global food security by posing threats to food safety through food chain pollution. Fly ash is a potential agent of soil contamination that contains heavy metals and hazardous pollutants. However, being rich in macro- and micronutrients that have direct beneficial effects on plant growth, fly ash has been recommended as a low-cost soil ameliorant in agriculture in countries of the Global South. Arbuscular mycorrhizal fungi (AMF), ubiquitous in agricultural soils, enhance efficiency of plant nutrient uptake from soils but can equally increase uptake of toxic pollutants from fly ash ameliorated soils to edible crop tissues. We investigated AMF-mediated amplification of nutrient and heavy metal uptake from fly ash amended soils to shoots, roots and grains of barley. We used a microcosm-based experiment to analyse the impacts of fly ash amendments to soil in concentrations of 0 (control), 15, 30 or 50% respectively, on root colonization by AMF Rhizophagus irregularis and AMF-mediated transfer of N, P and heavy metals: Ni, Co, Pb and Cr to barley tissues. These concentrations of fly ash are equivalent to 0, 137, 275 and 458 t ha[-1] respectively, in soil. Root AMF colonization correlated negatively with fly ash concentration and was not detected at 50% fly ash amendment. Shoots, roots and grains of mycorrhizal barley grown with 15, 30 and 50% fly ash amendments had significantly higher concentrations of Ni, Co, Pb and Cr compared to the control and their respective non-mycorrhizal counterparts. Presence of heavy metals in barley plants grown with fly ash amended soil and their increased AMF-mediated translocation to edible grains may significantly enhance the volume of heavy metals entering the human food chain. We recommend careful assessment of manipulation of agricultural soils with fly ash as heavy metal accumulation in agricultural soils and human tissues may cause irreversible damage.}, }
@article {pmid37117817, year = {2023}, author = {Woo, AYM and Aguilar Ramos, MA and Narayan, R and Richards-Corke, KC and Wang, ML and Sandoval-Espinola, WJ and Balskus, EP}, title = {Targeting the human gut microbiome with small-molecule inhibitors.}, journal = {Nature reviews. Chemistry}, volume = {}, number = {}, pages = {}, pmid = {37117817}, issn = {2397-3358}, abstract = {The human gut microbiome is a complex microbial community that is strongly linked to both host health and disease. However, the detailed molecular mechanisms underlying the effects of these microorganisms on host biology remain largely uncharacterized. The development of non-lethal, small-molecule inhibitors that target specific gut microbial activities enables a powerful but underutilized approach to studying the gut microbiome and a promising therapeutic strategy. In this Review, we will discuss the challenges of studying this microbial community, the historic use of small-molecule inhibitors in microbial ecology, and recent applications of this strategy. We also discuss the evidence suggesting that host-targeted drugs can affect the growth and metabolism of gut microbes. Finally, we address the issues of developing and implementing microbiome-targeted small-molecule inhibitors and define important future directions for this research.}, }
@article {pmid37115262, year = {2023}, author = {Camargo, TS and Nickele, MA and Filho, WR and do Rocio Chiarello Penteado, S and de Queiroz, EC and Auer, CG}, title = {Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: a Search for Potential Biocontrol Agents.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37115262}, issn = {1432-184X}, abstract = {The leaf-cutting ant Acromyrmex crassispinus is considered an important pest in forest plantations in southern Brazil. This work aimed to study the fungal community associated with A. crassispinus colonies, subjected to treatments with subdoses of granulated baits (sulfluramid), which might reduce the ability of the ants to care for their symbiotic fungus and other fungi (maybe biocontrol fungi) would take over, to prospect for potential biological control agents. Samplings of fungus gardens and dead ants allowed the identification of 195 fungal isolates, distributed in 29 families, 36 genera, and 53 species. The most frequent genera were Trichoderma (49.2%), Penicillium (13.8%), Chaetomium (6.2%), and Fusarium (3.6%). This is the first study that conducted a survey of antagonistic and entomopathogenic fungi to A. crassispinus and its symbiotic fungus, reporting for the first time the occurrence of potential biological control agents. Escovopsis weberi, Fusarium oxysporum, Rhizomucor variabilis, Trichoderma atroviride, Trichoderma harzianum, Trichoderma koningiopsis, and Trichoderma spirale are considered some of the potential biocontrol organisms.}, }
@article {pmid37115261, year = {2023}, author = {Djotan, AKG and Matsushita, N and Fukuda, K}, title = {Paired Root-Soil Samples and Metabarcoding Reveal Taxon-Based Colonization Strategies in Arbuscular Mycorrhizal Fungi Communities in Japanese Cedar and Cypress Stands.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37115261}, issn = {1432-184X}, abstract = {Arbuscular mycorrhizal fungi (AMF) in the roots and soil surrounding their hosts are typically independently investigated and little is known of the relationships between the communities of the two compartments. We simultaneously collected root and surrounding soil samples from Cryptomeria japonica (Cj) and Chamaecyparis obtusa (Co) at three environmentally different sites. Based on molecular and morphological analyses, we characterized their associated AMF communities. Cj was more densely colonized than Co and that root colonization intensity was significantly correlated with soil AMF diversity. The communities comprised 15 AMF genera dominated by Glomus and Paraglomus and 1443 operational taxonomic units (OTUs) of which 1067 and 1170 were in roots and soil, respectively. AMF communities were significantly different among sites, and the root AMF communities were significantly different from those of soil at each site. The root and soil AMF communities responded differently to soil pH. At the genus level, Glomus and Acaulospora were abundant in roots while Paraglomus and Redeckera were abundant in soil. Our findings suggest that AMF colonizing roots are protected from environmental stresses in soil. However, the root-soil-abundant taxa have adapted to both environments and represent a model AMF symbiont. This evidence of strategic exploitation of the rhizosphere by AMF supports prior hypotheses and provides insights into community ecology.}, }
@article {pmid37114064, year = {2023}, author = {Berman, TS and Weinberg, M and Moreno, KR and Czirják, G&#xc1; and Yovel, Y}, title = {In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1152107}, pmid = {37114064}, issn = {1664-3224}, abstract = {INTRODUCTION: Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown.<br><br>METHODS: Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge.<br><br>RESULTS: We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities.<br><br>CONCLUSION: Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.}, }
@article {pmid37113665, year = {2023}, author = {Crognale, S and Massimi, A and Sbicego, M and Braguglia, CM and Gallipoli, A and Gazzola, G and Gianico, A and Tonanzi, B and Di Pippo, F and Rossetti, S}, title = {Ecology of food waste chain-elongating microbiome.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1157243}, pmid = {37113665}, issn = {2296-4185}, abstract = {Microbial chain elongation has emerged as a valuable bioprocess for obtaining marketable products, such as medium chain fatty acids usable in several industrial applications, from organic waste. The understanding of the microbiology and microbial ecology in these systems is crucial to apply these microbiomes in reliable production processes controlling microbial pathways to promote favourable metabolic processes, which will in turn increase product specificity and yields. In this research, the dynamics, cooperation/competition and potentialities of bacterial communities involved in the long-term lactate-based chain elongation process from food waste extract were evaluated under different operating conditions by DNA/RNA amplicon sequencing and functional profile prediction. The feeding strategies and the applied organic loading rates strongly affected the microbial community composition. The use of food waste extract promoted the selection of primary fermenters (i.e., Olsenella, Lactobacillus) responsible for the in situ production of electron donors (i.e., lactate). The discontinuous feeding and the organic loading rate 15 gCOD L[-1] d[-1] selected the best performing microbiome in which microbes coexist and cooperate to complete the chain elongation process. Both at DNA and RNA level, this microbiome was composed by the lactate producer Olsenella, the short chain fatty acids producers Anaerostipes, Clostridium sensu stricto 7, C. sensu stricto 12, Corynebacterium, Erysipelotrichaceae UCG-004, F0332, Leuconostoc, and the chain elongator Caproiciproducens. This microbiome also showed the highest predicted abundance of short-chain acyl-CoA dehydrogenase, the functional enzyme responsible for the chain elongation process. The combined approach herein used allowed to study the microbial ecology of chain elongation process from food waste by identifying the main functional groups, establishing the presence of potential biotic interactions within the microbiomes, and predicting metabolic potentialities. This study provided pivotal indications for the selection of high-performance microbiome involved in caproate production from food waste that can serve as a basis for further improving system performance and engineering the process scale-up.}, }
@article {pmid37112890, year = {2023}, author = {Turzynski, V and Griesdorn, L and Moraru, C and Soares, AR and Simon, SA and Stach, TL and Rahlff, J and Esser, SP and Probst, AJ}, title = {Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/v15040910}, pmid = {37112890}, issn = {1999-4915}, abstract = {Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.}, }
@article {pmid37111201, year = {2023}, author = {Wong, MCS and Zhang, L and Ching, JYL and Mak, JWY and Huang, J and Wang, S and Mok, CKP and Wong, A and Chiu, OL and Fung, YT and Cheong, PK and Tun, HM and Ng, SC and Chan, FKL}, title = {Effects of Gut Microbiome Modulation on Reducing Adverse Health Outcomes among Elderly and Diabetes Patients during the COVID-19 Pandemic: A Randomised, Double-Blind, Placebo-Controlled Trial (IMPACT Study).}, journal = {Nutrients}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/nu15081982}, pmid = {37111201}, issn = {2072-6643}, abstract = {Gut microbiota is believed to be a major determinant of health outcomes. We hypothesised that a novel oral microbiome formula (SIM01) can reduce the risk of adverse health outcomes in at-risk subjects during the coronavirus disease 2019 (COVID-19) pandemic. In this single-centre, double-blind, randomised, placebo-controlled trial, we recruited subjects aged ≥65 years or with type two diabetes mellitus. Eligible subjects were randomised in a 1:1 ratio to receive three months of SIM01 or placebo (vitamin C) within one week of the first COVID-19 vaccine dose. Both the researchers and participants were blinded to the groups allocated. The rate of adverse health outcomes was significantly lower in the SIM01 group than the placebo at one month (6 [2.9%] vs. 25 [12.6], p < 0.001) and three months (0 vs. 5 [3.1%], p = 0.025). At three months, more subjects who received SIM01 than the placebo reported better sleep quality (53 [41.4%] vs. 22 [19.3%], p < 0.001), improved skin condition (18 [14.1%] vs. 8 [7.0%], p = 0.043), and better mood (27 [21.2%] vs. 13 [11.4%], p = 0.043). Subjects who received SIM01 showed a significant increase in beneficial Bifidobacteria and butyrate-producing bacteria in faecal samples and strengthened the microbial ecology network. SIM01 reduced adverse health outcomes and restored gut dysbiosis in elderly and diabetes patients during the COVID-19 pandemic.}, }
@article {pmid37110442, year = {2023}, author = {Maimone, G and Azzaro, M and Placenti, F and Paranhos, R and Cabral, AS and Decembrini, F and Zaccone, R and Cosenza, A and Rappazzo, AC and Patti, B and Basilone, G and Cuttitta, A and Ferreri, R and Aronica, S and Ferla, R}, title = {A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11041019}, pmid = {37110442}, issn = {2076-2607}, abstract = {A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.}, }
@article {pmid37110372, year = {2023}, author = {Zhou, T and Zhao, F and Xu, K}, title = {Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040949}, pmid = {37110372}, issn = {2076-2607}, abstract = {The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.}, }
@article {pmid37110315, year = {2023}, author = {Lashani, E and Amoozegar, MA and Turner, RJ and Moghimi, H}, title = {Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040891}, pmid = {37110315}, issn = {2076-2607}, abstract = {Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.}, }
@article {pmid37110258, year = {2023}, author = {Thomas, P and Knox, OGG and Powell, JR and Sindel, B and Winter, G}, title = {The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised?.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/microorganisms11040835}, pmid = {37110258}, issn = {2076-2607}, abstract = {Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe-plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host-microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.}, }
@article {pmid37108739, year = {2023}, author = {Codoñer-Franch, P and Gombert, M and Martínez-Raga, J and Cenit, MC}, title = {Circadian Disruption and Mental Health: The Chronotherapeutic Potential of Microbiome-Based and Dietary Strategies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {8}, pages = {}, doi = {10.3390/ijms24087579}, pmid = {37108739}, issn = {1422-0067}, abstract = {Mental illness is alarmingly on the rise, and circadian disruptions linked to a modern lifestyle may largely explain this trend. Impaired circadian rhythms are associated with mental disorders. The evening chronotype, which is linked to circadian misalignment, is a risk factor for severe psychiatric symptoms and psychiatric metabolic comorbidities. Resynchronization of circadian rhythms commonly improves psychiatric symptoms. Furthermore, evidence indicates that preventing circadian misalignment may help reduce the risk of psychiatric disorders and the impact of neuro-immuno-metabolic disturbances in psychiatry. The gut microbiota exhibits diurnal rhythmicity, as largely governed by meal timing, which regulates the host's circadian rhythms. Temporal circadian regulation of feeding has emerged as a promising chronotherapeutic strategy to prevent and/or help with the treatment of mental illnesses, largely through the modulation of gut microbiota. Here, we provide an overview of the link between circadian disruption and mental illness. We summarize the connection between gut microbiota and circadian rhythms, supporting the idea that gut microbiota modulation may aid in preventing circadian misalignment and in the resynchronization of disrupted circadian rhythms. We describe diurnal microbiome rhythmicity and its related factors, highlighting the role of meal timing. Lastly, we emphasize the necessity and rationale for further research to develop effective and safe microbiome and dietary strategies based on chrononutrition to combat mental illness.}, }
@article {pmid37106747, year = {2023}, author = {Ghouili, E and Abid, G and Hogue, R and Jeanne, T and D'Astous-Pagé, J and Sassi, K and Hidri, Y and M'Hamed, HC and Somenahally, A and Xue, Q and Jebara, M and Nefissi Ouertani, R and Riahi, J and de Oliveira, AC and Muhovski, Y}, title = {Date Palm Waste Compost Application Increases Soil Microbial Community Diversity in a Cropping Barley (Hordeum vulgare L.) Field.}, journal = {Biology}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/biology12040546}, pmid = {37106747}, issn = {2079-7737}, abstract = {Application of date palm waste compost is quite beneficial in improving soil properties and crop growth. However, the effect of its application on soil microbial communities is less understood. High-throughput sequencing and quantitative real-time PCR (qPCR) were used to evaluate the effect of compost application on the soil microbial composition in a barley field during the tillering, booting and ripening stages. The results showed that compost treatment had the highest bacterial and fungal abundance, and its application significantly altered the richness (Chao1 index) and α-diversity (Shannon index) of fungal and bacterial communities. The dominant bacterial phyla found in the samples were Proteobacteria and Actinobacteria while the dominant fungal orders were Ascomycota and Mortierellomycota. Interestingly, compost enriched the relative abundance of beneficial microorganisms such as Chaetomium, Actinobacteriota, Talaromyces and Mortierella and reduced those of harmful microorganisms such as Alternaria, Aspergillus and Neocosmospora. Functional prediction based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) showed that amplicon sequence variant (ASV) sequences related to energy metabolism, amino acid metabolism and carbohydrate metabolism were associated with compost-treated soil. Based on Fungi Functional Guild (FUNGuild), identified fungi community metabolic functions such as wood saprotroph, pathotroph, symbiotroph and endophyte were associated with compost-treated soil. Overall, compost addition could be considered as a sustainable practice for establishing a healthy soil microbiome and subsequently improving the soil quality and barley crop production.}, }
@article {pmid37103739, year = {2023}, author = {Balakrishnan, K and Krishnaa, D and Balakrishnan, G and Manickam, M and Abdulkader, AM and Dharumadurai, D}, title = {Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37103739}, issn = {1559-0291}, abstract = {Microbial communities' resident in the mushroom fruiting body and the soil around it play critical roles in the growth and propagation of the mushroom. Among the microbial communities associated with psychedelic mushrooms and the rhizosphere soil, bacterial communities are considered vital since their presence greatly influences the health of the mushrooms. The present study aimed at finding the microbiota present in the psychedelic mushroom Psilocybe cubensis and the soil the mushroom inhabits. The study was conducted at two different locations in Kodaikanal, Tamil Nadu, India. The composition and structure of microbial communities in the mushroom fruiting body and the soil were deciphered. The genomes of the microbial communities were directly assessed. High-throughput amplicon sequencing revealed distinct microbial diversity in the mushroom and the related soil. The interaction of environmental and anthropogenic factors appeared to have a significant impact on the mushroom and soil microbiome. The most abundant bacterial genera were Ochrobactrum, Stenotrophomonas, Achromobacter, and Brevundimonas. Thus, the study advances the knowledge of the composition of the microbiome and microbial ecology of a psychedelic mushroom, and paves the way for in-depth investigation of the influence of microbiota on the mushroom, with special emphasis on the impact of bacterial communities on mushroom growth. Further studies are required for a deeper understanding of the microbial communities that influence the growth of P. cubensis mushroom.}, }
@article {pmid37103495, year = {2023}, author = {Towett-Kirui, S and Morrow, JL and Close, S and Royer, JE and Riegler, M}, title = {Bacterial Communities Are Less Diverse in a Strepsipteran Endoparasitoid than in Its Fruit Fly Hosts and Dominated by Wolbachia.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37103495}, issn = {1432-184X}, abstract = {Microbiomes play vital roles in insect fitness and health and can be influenced by interactions between insects and their parasites. Many studies investigate the microbiome of free-living insects, whereas microbiomes of endoparasitoids and their interactions with parasitised insects are less explored. Due to their development in the constrained environment within a host, endoparasitoids are expected to have less diverse yet distinct microbiomes. We used high-throughput 16S rRNA gene amplicon sequencing to characterise the bacterial communities of Dipterophagus daci (Strepsiptera) and seven of its tephritid fruit fly host species. Bacterial communities of D. daci were less diverse and contained fewer taxa relative to the bacterial communities of the tephritid hosts. The strepsipteran's microbiome was dominated by Pseudomonadota (formerly Proteobacteria) (> 96%), mainly attributed to the presence of Wolbachia, with few other bacterial community members, indicative of an overall less diverse microbiome in D. daci. In contrast, a dominance of Wolbachia was not found in flies parasitised by early stages of D. daci nor unparasitised flies. Yet, early stages of D. daci parasitisation resulted in structural changes in the bacterial communities of parasitised flies. Furthermore, parasitisation with early stages of D. daci with Wolbachia was associated with a change in the relative abundance of some bacterial taxa relative to parasitisation with early stages of D. daci lacking Wolbachia. Our study is a first comprehensive characterisation of bacterial communities in a Strepsiptera species together with the more diverse bacterial communities of its hosts and reveals effects of concealed stages of parasitisation on host bacterial communities.}, }
@article {pmid37101565, year = {2023}, author = {Mosquera-Romero, S and Ntagia, E and Rousseau, DPL and Esteve-Núñez, A and Prévoteau, A}, title = {Water treatment and reclamation by implementing electrochemical systems with constructed wetlands.}, journal = {Environmental science and ecotechnology}, volume = {16}, number = {}, pages = {100265}, pmid = {37101565}, issn = {2666-4984}, abstract = {Seasonal or permanent water scarcity in off-grid communities can be alleviated by recycling water in decentralized wastewater treatment systems. Nature-based solutions, such as constructed wetlands (CWs), have become popular solutions for sanitation in remote locations. Although typical CWs can efficiently remove solids and organics to meet water reuse standards, polishing remains necessary for other parameters, such as pathogens, nutrients, and recalcitrant pollutants. Different CW designs and CWs coupled with electrochemical technologies have been proposed to improve treatment efficiency. Electrochemical systems (ECs) have been either implemented within the CW bed (ECin-CW) or as a stage in a sequential treatment (CW + EC). A large body of literature has focused on ECin-CW, and multiple scaled-up systems have recently been successfully implemented, primarily to remove recalcitrant organics. Conversely, only a few reports have explored the opportunity to polish CW effluents in a downstream electrochemical module for the electro-oxidation of micropollutants or electro-disinfection of pathogens to meet more stringent water reuse standards. This paper aims to critically review the opportunities, challenges, and future research directions of the different couplings of CW with EC as a decentralized technology for water treatment and recovery.}, }
@article {pmid37101495, year = {2023}, author = {Nakato, GV and Wicker, E and Coutinho, TA and Mahuku, G and Studholme, DJ}, title = {Corrigendum to "A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences" [Heliyon 4 (12) (December 2018) Article e01080].}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14606}, doi = {10.1016/j.heliyon.2023.e14606}, pmid = {37101495}, issn = {2405-8440}, abstract = {[This corrects the article DOI: 10.1016/j.heliyon.2018.e01080.].}, }
@article {pmid37100151, year = {2023}, author = {Wang, B and Zhu, C and Hu, Y and Zhang, B and Wang, J}, title = {Dynamics of microbial community composition during degradation of silks in burial environment.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163694}, doi = {10.1016/j.scitotenv.2023.163694}, pmid = {37100151}, issn = {1879-1026}, abstract = {The silk residues in the soil formed the unique niche, termed "silksphere." Here, we proposed a hypothesis that silksphere microbiota have great potential as a biomarker for unraveling the degradation of the ancient silk textiles with great archaeological and conservation values. To test our hypothesis, in this study, we monitored the dynamics of microbial community composition during silk degradation via both indoor soil microcosmos model and outdoor environment with amplicon sequencing against 16S and ITS gene. Microbial community divergence was evaluated with Welch two sample t-test, PCoA, negative binomial generalized log-linear model and clustering, etc. Community assembly mechanisms differences between silksphere and bulk soil microbiota were compared with dissimilarity-overlap curve (DOC) model, Neutral model and Null model. A well-established machine learning algorithm, random forest, was also applied to the screening of potential biomarkers of silk degradation. The results illustrated the ecological and microbial variability during the microbial degradation of silk. Vast majority of microbes populating the silksphere microbiota strongly diverged from those in bulk soil. Certain microbial flora can serve as an indicator of silk degradation, which would lead to a novel perspective to perform identification of archaeological silk residues in the field. To sum up, this study provides a new perspective to perform the identification of archaeological silk residue through the dynamics of microbial communities.}, }
@article {pmid37101136, year = {2023}, author = {Mosquera, KD and Martínez Villegas, LE and Rocha Fernandes, G and Rocha David, M and Maciel-de-Freitas, R and A Moreira, L and Lorenzo, MG}, title = {Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {97}, pmid = {37101136}, issn = {1741-7007}, abstract = {BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.<br><br>RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.<br><br>CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.}, }
@article {pmid37099394, year = {2023}, author = {McCartney, AL and Hoyles, L}, title = {The role of Klebsiella populations in preterm infants.}, journal = {Biochemical Society transactions}, volume = {51}, number = {2}, pages = {887-896}, doi = {10.1042/BST20200325}, pmid = {37099394}, issn = {1470-8752}, abstract = {The preterm infant microbiota is dominated by Enterobacteriaceae (Escherichia, Klebsiella or Enterobacter spp.), Enterococcus and Staphylococcus spp. Recent work has demonstrated the development of this microbiota is predictable and driven by simple microbe-microbe interactions. Because of their systemic immaturity, including an underdeveloped immune system, preterm infants are susceptible to a range of infections. Numerous retrospective studies have examined the association of the preterm gut microbiota with diseases such as necrotizing enterocolitis (NEC), early-onset sepsis and late-onset sepsis. To date, no single bacterium has been associated with infection in these infants, but a Klebsiella/Enterococcus-dominated faecal microbiota is associated with an increased risk of developing NEC. Staphylococci aid and enterococci inhibit establishment/maintenance of gastrointestinal Klebsiella populations in preterm infants, though the mechanisms underlying these interactions are poorly understood. Klebsiella spp. recovered from healthy and sick preterm infants display similar antimicrobial resistance and virulence profiles, giving no clues as to why some infants develop potentially life-threatening diseases while others do not. The identification of cytotoxin-producing Klebsiella oxytoca sensu lato in the gut microbiota of some preterm infants has led to the suggestion that these bacteria may contribute to NEC in a subset of neonates. This mini review highlights current knowledge on Klebsiella spp. contributing to the preterm gut microbiota and provides insights into areas of research that warrant further attention.}, }
@article {pmid37099156, year = {2023}, author = {Nguyen, PN and Rehan, SM}, title = {Environmental Effects on Bee Microbiota.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37099156}, issn = {1432-184X}, abstract = {Anthropogenic activities and increased land use, which include industrialization, agriculture and urbanization, directly affect pollinators by changing habitats and floral availability, and indirectly by influencing their microbial composition and diversity. Bees form vital symbioses with their microbiota, relying on microorganisms to perform physiological functions and aid in immunity. As altered environments and climate threaten bees and their microbiota, characterizing the microbiome and its complex relationships with its host offers insights into understanding bee health. This review summarizes the role of sociality in microbiota establishment, as well as examines if such factors result in increased susceptibility to altered microbiota due to environmental changes. We characterize the role of geographic distribution, temperature, precipitation, floral resources, agriculture, and urbanization on bee microbiota. Bee microbiota are affected by altered surroundings regardless of sociality. Solitary bees that predominantly acquire their microbiota through the environment are particularly sensitive to such effects. However, the microbiota of obligately eusocial bees are also impacted by environmental changes despite typically well conserved and socially inherited microbiota. We provide an overview of the role of microbiota in plant-pollinator relationships and how bee microbiota play a larger role in urban ecology, offering microbial connections between animals, humans, and the environment. Understanding bee microbiota presents opportunities for sustainable land use restoration and aiding in wildlife conservation.}, }
@article {pmid37099155, year = {2023}, author = {Wang, B and Qi, M and Ma, Y and Zhang, B and Hu, Y}, title = {Microbiome Diversity and Cellulose Decomposition Processes by Microorganisms on the Ancient Wooden Seawall of Qiantang River of Hangzhou, China.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37099155}, issn = {1432-184X}, abstract = {Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage.}, }
@article {pmid37098915, year = {2023}, author = {Kim, N and Vargas, P and Fortuna, K and Wagemans, J and Rediers, H}, title = {Draft Genome Sequences of 27 Rhizogenic Agrobacterium Biovar 1 Strains, the Causative Agent of Hairy Root Disease.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0012423}, doi = {10.1128/mra.00124-23}, pmid = {37098915}, issn = {2576-098X}, abstract = {Rhizogenic Agrobacterium biovar 1 strains are important plant pathogens that cause hairy root disease in Cucurbitaceae and Solanaceae crops cultivated under hydroponic conditions. In contrast to tumorigenic agrobacteria, only a few genome sequences of rhizogenic agrobacteria are currently available. Here, we report the draft genome sequences of 27 rhizogenic Agrobacterium strains.}, }
@article {pmid37097879, year = {2023}, author = {Stewart, CJ}, title = {2022 Fleming Prize Lecture: diet-microbe-host interaction in early life.}, journal = {Journal of medical microbiology}, volume = {72}, number = {4}, pages = {}, doi = {10.1099/jmm.0.001662}, pmid = {37097879}, issn = {1473-5644}, abstract = {The last decade has witnessed a meteoric rise in research focused on characterizing the human microbiome and identifying associations with disease risk. The advent of sequencing technology has all but eradicated gel-based fingerprinting approaches for studying microbial ecology, while at the same time traditional microbiological culture is undergoing a renaissance. Although multiplexed high-throughput sequencing is relatively new, the discoveries leading to this are nearly 50 years old, coinciding with the inaugural Microbiology Society Fleming Prize lecture. It was an honour to give the 2022 Fleming Prize lecture and this review will cover the topics from that lecture. The focus will be on the bacterial community in early life, beginning with term infants before moving on to infants delivered prematurely. The review will discuss recent work showing how human milk oligosaccharides (HMOs), an abundant but non-nutritious component of breast milk, can modulate infant microbiome and promote the growth of Bifidobacterium spp. This has important connotations for preterm infants at risk of necrotizing enterocolitis, a devastating intestinal disease representing the leading cause of death and long-term morbidity in this population. With appropriate mechanistic studies, it may be possible to harness the power of breast milk bioactive factors and infant gut microbiome to improve short- and long-term health in infants.}, }
@article {pmid37097592, year = {2023}, author = {Paul, P and Roy, R and Das, S and Sarkar, S and Chatterjee, S and Mallik, M and Shukla, A and Chakraborty, P and Tribedi, P}, title = {The combinatorial applications of 1,4-naphthoquinone and tryptophan inhibit the biofilm formation of Staphylococcus aureus.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {37097592}, issn = {1874-9356}, abstract = {Microorganisms embedded within an extracellular polymeric matrix are known as biofilm. The extensive use of antibiotics to overcome the biofilm-linked challenges has led to the emergence of multidrug-resistant strains. Staphylococcus aureus is one such nosocomial pathogen that is known to cause biofilm-linked infections. Thus, novel strategies have been adopted in this study to inhibit the biofilm formation of S. aureus. Two natural compounds, namely, 1,4-naphthoquinone (a quinone derivative) and tryptophan (aromatic amino acid), have been chosen as they could independently show efficient antibiofilm activity. To enhance the antibiofilm potential, the two compounds were combined and tested against the same organism. Several experiments like crystal violet (CV) assay, protein estimation, extracellular polymeric substance (EPS) extraction, and estimation of metabolic activity confirmed that the combination of the two compounds could significantly inhibit the biofilm formation of S. aureus. To comprehend the underlying mechanism, efforts were further directed to understand whether the two compounds could inhibit biofilm formation by compromising the cell surface hydrophobicity of the bacteria. The results revealed that the cell surface hydrophobicity got reduced by ~ 49% when the compounds were applied together. Thus, the combinations could show enhanced antibiofilm activity by attenuating cell surface hydrophobicity. Further studies revealed that the selected concentrations of the compounds could disintegrate (~ 70%) the pre-existing biofilm of the test bacteria without showing any antimicrobial activity. Hence, the combined application of tryptophan and 1,4-naphthoquinone could be used to inhibit the biofilm threats of S. aureus.}, }
@article {pmid37097162, year = {2023}, author = {Masasa, M and Kushmaro, A and Nguyen, D and Chernova, H and Shashar, N and Guttman, L}, title = {Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0051423}, doi = {10.1128/spectrum.00514-23}, pmid = {37097162}, issn = {2165-0497}, abstract = {Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.}, }
@article {pmid37093231, year = {2023}, author = {Ichige, R and Urabe, J}, title = {Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37093231}, issn = {1432-184X}, abstract = {The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.}, }
@article {pmid37093057, year = {2023}, author = {Chen, Q and Fan, Y and Zhang, B and Yan, C and Zhang, Q and Ke, Y and Chen, Z and Wang, L and Shi, H and Hu, Y and Huang, Q and Su, J and Xie, C and Zhang, X and Zhou, L and Ren, J and Xu, H}, title = {Capsulized Fecal Microbiota Transplantation Induces Remission in Patients with Ulcerative Colitis by Gut Microbial Colonization and Metabolite Regulation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0415222}, doi = {10.1128/spectrum.04152-22}, pmid = {37093057}, issn = {2165-0497}, abstract = {Fecal microbiota transplantation (FMT) can induce clinical remission in ulcerative colitis (UC) patients. Enemas, nasoduodenal tubes, and colonoscopies are the most common routes for FMT administration. However, there is a lack of definitive evidence regarding the effectiveness of capsulized FMT treatment in UC patients. In this study, we administered capsulized FMT to 22 patients with active UC to assess the efficiency of capsulized FMT and determine the specific bacteria and metabolite factors associated with the response to clinical remission. Our results showed that the use of capsulized FMT was successful in the treatment of UC patients. Capsulized FMT induced clinical remission and clinical response in 57.1% (12 of 21) and 76.2% (16 of 21) of UC patients, respectively. Gut bacterial richness was increased after FMT in patients who achieved remission. Patients in remission after FMT exhibited enrichment of Alistipes sp. and Odoribacter splanchnicus, along with increased levels of indolelactic acid. Patients who did not achieve remission exhibited enrichment of Escherichia coli and Klebsiella and increased levels of biosynthesis of 12,13-DiHOME (12,13-dihydroxy-9Z-octadecenoic acid) and lipopolysaccharides. Furthermore, we identified a relationship between specific bacteria and metabolites and the induction of remission in patients. These findings may provide new insights into FMT in UC treatment and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects. (This study has been registered at ClinicalTrails.gov under registration no. NCT03426683). IMPORTANCE Fecal microbiota transplantation has been successfully used in patients. Recently, capsulized FMT was reported to induce a response in patients with UC. However, limited patients were enrolled in such studies, and the functional factors of capsulized FMT have not been reported in the remission of patients with UC. In this study, we prospectively recruited patients with UC to receive capsulized FMT. First, we found that capsulized FMT could induce clinical remission in 57.1% of patients and clinical response in 76.2% after 12 weeks, which was more acceptable. Second, we found a relationship between the decrease of opportunistic pathogen and lipopolysaccharide synthesis in patients in remission after capsulized FMT. We also identified an association between specific bacteria and metabolites and remission induction in patients after capsulized FMT. These findings put forward a possibility for patients to receive FMT at home and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects.}, }
@article {pmid37090461, year = {2023}, author = {Al-Rshaidat, MMD and Al-Sharif, S and Refaei, AA and Shewaikani, N and Alsayed, AR and Rayyan, YM}, title = {Evaluating the clinical application of the immune cells' ratios and inflammatory markers in the diagnosis of inflammatory bowel disease.}, journal = {Pharmacy practice}, volume = {21}, number = {1}, pages = {2755}, pmid = {37090461}, issn = {1885-642X}, abstract = {OBJECTIVE: Inflammatory Bowel Diseases (IBDs) are chronic inflammatory conditions of the gastrointestinal tract, including Crohn's disease (CD) and ulcerative colitis (UC). Developing methods for effective screening and diagnosis is extremely needed. Accordingly, this study aims to evaluate the potential of immune cells ratios in the diagnosis of IBD.<br><br>METHODS: This case-control study includes data from Jordan University Hospital (JUH) medical records for IBD patients with age- and gender-matched healthy controls.<br><br>RESULTS: This study included 46 participants, of which 56.52% had IBD, 54.35% were males, with insignificant differences in sex, age, and body mass index (BMI) between IBD patients and controls (p>0.05). In the CD group, the variables with the highest sensitivity and specificity (HSS) were neutrophil-to-lymphocyte (NLR) (75%, 80%) and platelet-to-lymphocytes (PLR) (75%, 90%), in UC group; mean corpuscular hemoglobin (MCH) (80%, 80%). In CD group, the combinations giving the HSS were PLR+NLR (76%, 90.9%), C-reactive protein (CRP)+PLR (76%, 90.9%), and CRP+NLR (73.07%, 90%). In UC group, the combinations giving the HSS were erythrocyte sedimentation rate (ESR)+PLR (76.9%, 100%), PLR+MCH (74.07%, 100%), PLR+CRP (71.42%, 100%), and PLR+NLR (71.42%, 100%). Regression analysis identified five different combinations of significance in the diagnosis of CD and UC. Higher Youden's index was used and defined the most beneficial clinical combinations as NLR+PLR and CRP+PLR for CD, whereas ESR+PLR for UC.<br><br>CONCLUSION: Implications to our study include the clinical application of immune cell ratios, inflammatory markers, and their different combinations along with patients' history and physical examination findings for easier, faster, and more cost-effective diagnosis of IBDs.}, }
@article {pmid37091220, year = {2022}, author = {Obase, K}, title = {Morphological characteristics of ectomycorrhizas formed by in vitro synthesis between conifer seedlings and Tuber mycelial strains of the Puberulum clade isolated in Japan.}, journal = {Mycoscience}, volume = {63}, number = {1}, pages = {39-44}, pmid = {37091220}, issn = {1340-3540}, abstract = {Seedlings of Pinus densiflora and Abies sachalinensis were inoculated with Tuber mycelial strains of the Puberulum clade in vitro to examine the morphological characteristics of their ectomycorrhizas. Axenically germinated seedlings were inoculated with the mycelia of five taxa from the Puberulum clade and grown in glass jars for 4 mo in an illuminated incubator. The seedlings were successfully colonized by the inoculated Tuber strains, as confirmed by the nuclear ribosomal internal transcribed spacer barcoding of the synthesized ectomycorrhizas. The ectomycorrhizas were characterized by a pale yellow to brown color, short needle-shaped cystidia, and net-like hyphal arrangement, and epidermoid cells on the mantle surface; notably, these features are similar to the ectomycorrhizas of various Puberulum clade members. As the ectomycorrhizas of different Tuber species are indistinguishable by morphological characters, molecular techniques are necessary to identify ectomycorrhizas formed by Tuber species within the Puberulum clade.}, }
@article {pmid37089255, year = {2021}, author = {Obase, K and Yamanaka, S and Kinoshita, A and Tamai, Y and Yamanaka, T}, title = {Phylogenetic placements and cultural characteristics of Tuber species isolated from ectomycorrhizas.}, journal = {Mycoscience}, volume = {62}, number = {2}, pages = {124-131}, pmid = {37089255}, issn = {1340-3540}, abstract = {Pure cultures of Tuber were isolated from ectomycorrhizal root tips in Abies sachalinensis plantations in Hokkaido, Japan. Their phylogenetic relationships as well as vegetative hyphal characteristics on culture media were reported. Phylogenetic analysis based on the internal transcribed spacer within ribosomal DNA settled well-supported eight lineages within Puberulum, Latisporum, and Maculatum clades in Tuber. Three and one lineages were grouped with undescribed species of Puberulum clade in Japan and that of the Latisporum group in China, respectively. Two lineages were closely associated to but distinct from an undescribed species of Puberulum clade in Japan. One lineage did not group with any sequences in the International Nucleotide Sequence Database (INSD), proposing a new taxon in the Latisporum group. One lineage was grouped with T. foetidum in Maculatum clade. All strains in each lineage displayed yellowish white, thin, filamentous colonies on Melin-Norkrans agar medium. Various differences in morphological characteristics of hyphae on pure cultures of various strains were noted, but they were frequently uncommon among strains of the same taxa. Isolation from ectomycorrhizal root tips can be among the effective ways to acquire pure cultures of Tuber strains.}, }
@article {pmid37088849, year = {2023}, author = {Mills, TJT and Nelson, TM and Pearson, LA and Neilan, BA}, title = {Hive Transplantation Has Minimal Impact on the Core Gut Microbiome of the Australian Stingless Bee, Tetragonula carbonaria.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37088849}, issn = {1432-184X}, abstract = {Bacteria residing in the guts of pollinating insects play a key role in nutrient acquisition, digestion, and resistance to pests and diseases. Imbalances in microbial flora in response to environmental change and stress can therefore impact insect health and resilience. This study is aimed at defining the core gut microbiome of the Australian native stingless bee, Tetragonula carbonaria, and exploring the impact of colony transplantation on gut health. The gut microbiomes of nine forager bees from natural (log) and manufactured (box) hives were examined via 16S rRNA gene amplicon sequencing. Some differences were observed at the ASV level between the microbiomes of log and box hive bees. However, a core microbiome, dominated by Lactobacillus spp., unclassified Acetobacteraceae spp., and Bombella spp., was maintained. Further, the inferred functional potential of the microbiomes was consistent across all individuals. This study highlights that although hive transplantation has an impact on the overall diversity of stingless bee gut microbiomes, it is unlikely to have a significant negative impact on the overall health and resilience of the colony.}, }
@article {pmid37088357, year = {2023}, author = {Philippe, S and Sebastian, L and Gytis, D and Sam, P and Pascal, L and Freddy, K and Kadrie, R and Isabel, M and Steve, AM and Veerle, V and Marjan, VE and Kevin, AK}, title = {Phylogeographic analysis of dengue virus serotype 1 and Cosmopolitan serotype 2 in Africa.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2023.04.391}, pmid = {37088357}, issn = {1878-3511}, abstract = {BACKGROUND: The origin and spread of dengue virus (DENV) circulating in Africa remain poorly characterized, with African sequences representing <1% of global sequence data.<br><br>METHODS: Whole genome sequencing was performed on serum samples (n=29) from an undifferentiated fever study in 2016 in the Democratic Republic of Congo (DRC), and from febrile travelers returning from Africa. The evolutionary history of the newly acquired African DENV-1 (n=1) and Cosmopolitan genotype DENV-2 (n=18) genomes, was reconstructed using a phylogeographic, time-scaled Bayesian analysis on a curated DENV panel including all known African sequences.<br><br>RESULTS: A minimum of 10 and 8 introductions could be identified into Africa for respectively DENV-1 and Cosmopolitan DENV-2, almost all originating from Asia. Three introductions were previously unknown. The currently circulating virus comprises mainly recently introduced clades and one long-established, African clade. Robust geographical clustering suggests limited spread of DENV after each introduction. Our data identified the DRC as the source of the 2018 Angolan DENV-2 epidemic, and similarly, the 2013 Angolan DENV-1 outbreak as the origin of our DRC study.<br><br>CONCLUSION: Active genomic surveillance of DENV in Africa at the portals of entry might help early outbreak response, and limit sero- and genotype spread and human disease burden.}, }
@article {pmid37086855, year = {2023}, author = {Buivydaitė, &#x17d; and Aryal, L and Corrêa, FB and Chen, T and Langlois, V and Elberg, CL and Netherway, T and Wang, R and Zhao, T and Acharya, B and Emerson, JB and Hillary, L and Khadka, RB and Mason-Jones, K and Sapkota, R and Sutela, S and Trubl, G and White, RA and Winding, A and Carreira, C}, title = {Meeting Report: The First Soil Viral Workshop 2022.}, journal = {Virus research}, volume = {}, number = {}, pages = {199121}, doi = {10.1016/j.virusres.2023.199121}, pmid = {37086855}, issn = {1872-7492}, abstract = {Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15-17[th] of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarised in this report.}, }
@article {pmid37086668, year = {2023}, author = {Wu, K and Atasoy, M and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV}, title = {Impact of wastewater characteristics on the removal of organic micropollutants by Chlorella sorokiniana.}, journal = {Journal of hazardous materials}, volume = {453}, number = {}, pages = {131451}, doi = {10.1016/j.jhazmat.2023.131451}, pmid = {37086668}, issn = {1873-3336}, abstract = {Microalgae-based technologies can be used for the removal of organic micropollutants (OMPs) from different types of wastewater. However, the effect of wastewater characteristics on the removal is still poorly understood. In this study, the removal of sixteen OMPs by Chlorella sorokiniana, cultivated in three types of wastewater (anaerobically digested black water (AnBW), municipal wastewater (MW), and secondary clarified effluent (SCE)), were assessed. During batch operational mode, eleven OMPs were removed from AnBW and MW. When switching from batch to continuous mode (0.8 d HRT), the removal of most OMPs from AnBW and MW decreased, suggesting that a longer retention time enhances the removal of some OMPs. Most OMPs were not removed from SCE since poor nutrient availability limited C. sorokiniana growth. Further correlation analyses between wastewater characteristics, biomass and OMPs removal indicated that the wastewater soluble COD and biomass concentration predominantly affected the removal of OMPs. Lastly, carbon uptake rate had a higher effect on the removal of OMPs than nitrogen and phosphate uptake rate. These data will give an insight on the implementation of microalgae-based technologies for the removal of OMPs in wastewater with varying strengths and nutrient availability.}, }
@article {pmid37084659, year = {2023}, author = {Zeng, Z and Yue, W and Kined, C and Wang, P and Liu, R and Liu, J and Chen, X}, title = {Bacillus licheniformis reverses the environmental ceftriaxone sodium-induced gut microbial dysbiosis and intestinal inflammation in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {257}, number = {}, pages = {114890}, doi = {10.1016/j.ecoenv.2023.114890}, pmid = {37084659}, issn = {1090-2414}, abstract = {Antibiotics used as a common clinical treatment have saved many lives. Widespread use of antibiotic therapy has been known to disrupt the balance of pathogenic bacteria, host-associated microorganisms and environment. However, our understanding of Bacillus licheniformis for health benefits and ability to restore the ceftriaxone sodium-induced gut microbial dysbiosis is severely limited. We used Caco-2 cell, H&amp;E (hematoxylin-eosin staining), RT-PCR and 16S rRNA sequencing techniques to investigate the influence of Bacillus licheniformis on gut microbial dysbiosis and inflammation following ceftriaxone sodium treatment. The results showed that treatment of ceftriaxone sodium in 7 days suppressed the expression of Nf-κB pathway mRNA levels, which caused cytoplasmic vacuolization in intestinal tissues, afterward, the administration of Bacillus licheniformis could effectively restore intestinal morphology and inflammation levels. Moreover, the ceftriaxone sodium treatment entirely affected the intestinal microbial ecology, leading to a decrease in microbial abundance. Firmicutes, Proteobacteria, and Epsilonbacteraeota were the most predominant phyla in each of the four groups. Specifically, the MA group (ceftriaxone sodium treatment) resulted in a significant decrease in the relative abundance of 2 bacterial phyla and 20 bacterial genera compared to the administration of Bacillus licheniformis after ceftriaxone sodium treatment. The supplementation of Bacillus licheniformis could increase the growth of Firmicutes and Lactobacillus and encourage the construction of a more mature and stable microbiome. Furthermore, Bacillus licheniformis could restore the intestinal microbiome disorders and inflammation levels following ceftriaxone sodium treatment.}, }
@article {pmid37082712, year = {2023}, author = {Song, W and Zhang, S and Li, X and Gao, C and Cai, J and Li, Y}, title = {Editorial: Relationship between intestinal microbiome and vasculitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1165730}, pmid = {37082712}, issn = {2235-2988}, }
@article {pmid37082182, year = {2023}, author = {Zhang, J and Wang, J and Labes, A and Zeng, R}, title = {Editorial: Marine microbial-derived molecules and their potential medical and cosmetic applications, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1188008}, doi = {10.3389/fmicb.2023.1188008}, pmid = {37082182}, issn = {1664-302X}, }
@article {pmid37081077, year = {2023}, author = {Zorz, J and Li, C and Chakraborty, A and Gittins, DA and Surcon, T and Morrison, N and Bennett, R and MacDonald, A and Hubert, CRJ}, title = {SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {33}, pmid = {37081077}, issn = {2730-6151}, abstract = {Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.}, }
@article {pmid37075990, year = {2023}, author = {Svigruha, R and Prikler, B and Farkas, A and Ács, A and Fodor, I and Tapolczai, K and Schmidt, J and Bordós, G and Háhn, J and Harkai, P and Kaszab, E and Szoboszlay, S and Pirger, Z}, title = {Presence, variation, and potential ecological impact of microplastics in the largest shallow lake of Central Europe.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163537}, doi = {10.1016/j.scitotenv.2023.163537}, pmid = {37075990}, issn = {1879-1026}, abstract = {The presence of microplastics (MPs) in the global ecosystem has generated a rapidly growing concern worldwide. Although their presence in the marine environment has been well-studied, much less data are available on their abundance in freshwaters. MPs alone and in combination with different chemicals has been shown to cause acute and chronic effects on algae and aquatic invertebrate and vertebrate species at different biological levels. However, the combined ecotoxicological effects of MPs with different chemicals on aquatic organisms are still understudied in many species and the reported data are often controversial. In the present study, we investigated, for the first time, the presence of MPs in Lake Balaton, which is the largest shallow lake of Central Europe and an important summer holiday destination. Moreover, we exposed neonates of the well-established ecotoxicological model organism Daphnia magna to different MPs (polystyrene [3 μm] or polyethylene [≤ 100 μm]) alone and in combination with three progestogen compounds (progesterone, drospirenone, levonorgestrel) at an environmentally relevant concentration (10 ng L[-1]) for 21 days. The presence of 7 polymer types of MPs in the size range of 50-100 μm was detected in Lake Balaton. Similarly to the global trends, polypropylene and polyethylene MPs were the most common types of polymer. The calculated polymer-independent average particle number was 5.5 particles m[-3] (size range: 50 μm - 100 μm) which represents the values detected in other European lakes. Our ecotoxicological experiments confirmed that MPs and progestogens can affect D. magna at the behavioral (body size and reproduction) and biochemical (detoxification-related enzyme activity) levels. The joint effects were negligible. The presence of MPs may lead to reduced fitness in the aquatic biota in freshwaters such as Lake Balaton, however, the potential threat of MPs as vectors for progestogens may be limited.}, }
@article {pmid37076812, year = {2023}, author = {De Wolfe, TJ and Wright, ES}, title = {Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {107}, pmid = {37076812}, issn = {1471-2180}, abstract = {BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.<br><br>RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an&#xa0;increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).<br><br>CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.}, }
@article {pmid37071646, year = {2023}, author = {Poudel, SK and Padmanabhan, R and Dave, H and Guinta, K and Stevens, T and Sanaka, MR and Chahal, P and Sohal, DPS and Khorana, AA and Eng, C}, title = {Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0283021}, doi = {10.1371/journal.pone.0283021}, pmid = {37071646}, issn = {1932-6203}, abstract = {BACKGROUND: The prognostic and pathophysiologic significance of the biliary microbiota in pancreaticobiliary malignancies is little understood. Our goal was to find malignancy-related microbiomic fingerprints in bile samples taken from patients with benign and malignant pancreaticobiliary diseases.<br><br>METHODS: Bile specimens were collected from consenting patients during routine endoscopic retrograde cholangiopancreatography. We used PowerViral RNA/DNA Isolation kit to extract DNA from bile specimens. The Illumina 16S Metagenomic Sequencing Library Preparation guide was used to amplify the bacterial 16S rRNA gene and create libraries. QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq, and mixMC packages were used for post-sequencing analysis.<br><br>RESULTS: Of 46 enrolled patients, 32 patients had pancreatic cancers, 6 had cholangiocarcinoma and 1 had gallbladder cancer. Rest of the patients had benign diseases including gallstones, and acute and chronic pancreatitis. We used multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs). Doing this, we found a predominance of genera Dickeya (p = 0.00008), [Eubacterium] hallii group (p = 0.0004), Bacteroides (p = 0.0006), Faecalibacterium (p = 0.006), Escherichia-Shigella (p = 0.008), and Ruminococcus 1 (p = 0.008) in bile samples from pancreaticobiliary cancers as compared to benign diseases. Additionally, bile samples from patients with pancreatic cancer exhibited a predominance of genus Rothia (p = 0.008) as compared to those with cholangiocarcinoma, whereas bile samples from patients with cholangiocarcinoma exhibited a predominance of genera Akkermansia (p = 0.031) and Achromobacter (p = 0.031) as compared to those with pancreatic cancers.<br><br>CONCLUSIONS: Both benign and malignant pancreaticobiliary diseases have distinct microbiomic fingerprints. The relative abundance of OTUs in bile samples varies between patients with benign and malignant pancreaticobiliary diseases, as well as between cholangiocarcinoma and pancreatic cancer. Our data suggest that either these OTUs play a role in carcinogenesis or that benign disease-specific microenvironmental changes differ from cancer-specific microenvironmental changes, resulting to a clear separation of OTU clusters. We need more research to confirm and expand on our findings.}, }
@article {pmid37070710, year = {2023}, author = {García Mendez, DF and Sanabria, J and Wist, J and Holmes, E}, title = {Effect of Operational Parameters on the Cultivation of the Gut Microbiome in Continuous Bioreactors Inoculated with Feces: A Systematic Review.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.2c08146}, pmid = {37070710}, issn = {1520-5118}, abstract = {Since the early 1980s, multiple researchers have contributed to the development of in vitro models of the human gastrointestinal system for the mechanistic interrogation of the gut microbiome ecology. Using a bioreactor for simulating all the features and conditions of the gastrointestinal system is a massive challenge. Some conditions, such as temperature and pH, are readily controlled, but a more challenging feature to simulate is that both may vary in different regions of the gastrointestinal tract. Promising solutions have been developed for simulating other functionalities, such as dialysis capabilities, peristaltic movements, and biofilm growth. This research field is under constant development, and further efforts are needed to drive these models closer to in vivo conditions, thereby increasing their usefulness for studying the gut microbiome impact on human health. Therefore, understanding the influence of key operational parameters is fundamental for the refinement of the current bioreactors and for guiding the development of more complex models. In this review, we performed a systematic search for operational parameters in 229 papers that used continuous bioreactors seeded with human feces. Despite the reporting of operational parameters for the various bioreactor models being variable, as a result of a lack of standardization, the impact of specific operational parameters on gut microbial ecology is discussed, highlighting the advantages and limitations of the current bioreactor systems.}, }
@article {pmid37069235, year = {2023}, author = {Zhang, Y and Liu, T and Li, MM and Hua, ZS and Evans, P and Qu, Y and Tan, S and Zheng, M and Lu, H and Jiao, JY and Lücker, S and Daims, H and Li, WJ and Guo, J}, title = {Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37069235}, issn = {1751-7370}, abstract = {The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.}, }
@article {pmid37065146, year = {2023}, author = {Vannier, P and Farrant, GK and Klonowski, A and Gaidos, E and Thorsteinsson, T and Marteinsson, V&#xde;}, title = {Metagenomic analyses of a microbial assemblage in a subglacial lake beneath the Vatnajökull ice cap, Iceland.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1122184}, pmid = {37065146}, issn = {1664-302X}, abstract = {Skaftárkatlar are two subglacial lakes located beneath the Vatnajökull ice cap in Iceland associated with geothermal and volcanic activity. Previous studies of these lakes with ribosomal gene (16S rDNA) tag sequencing revealed a limited diversity of bacteria adapted to cold, dark, and nutrient-poor waters. In this study, we present analyses of metagenomes from the lake which give new insights into its microbial ecology. Analyses of the 16S rDNA genes in the metagenomes confirmed the existence of a low-diversity core microbial assemblage in the lake and insights into the potential metabolisms of the dominant members. Seven taxonomic genera, Sulfuricurvum, Sulfurospirillum, Acetobacterium, Pelobacter/Geobacter, Saccharibacteria, Caldisericum, and an unclassified member of Prolixibacteraceae, comprised more than 98% of the rDNA reads in the library. Functional characterisation of the lake metagenomes revealed complete metabolic pathways for sulphur cycling, nitrogen metabolism, carbon fixation via the reverse Krebs cycle, and acetogenesis. These results show that chemolithoautotrophy constitutes the main metabolism in this subglacial ecosystem. This assemblage and its metabolisms are not reflected in enrichment cultures, demonstrating the importance of in situ investigations of this environment.}, }
@article {pmid37060391, year = {2023}, author = {Adhikari, NP and Adhikari, S}, title = {First report on the bacterial community composition, diversity, and functions in Ramsar site of Central Himalayas, Nepal.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {5}, pages = {573}, pmid = {37060391}, issn = {1573-2959}, abstract = {Wetland bacterial communities are highly sensitive to altered hydrology and the associated change in water physicochemical and biological properties leading to shifts in community composition and diversity, hence affecting the ecological roles. However, relevant studies are lacking in the wetlands of central Himalayas Nepal. Thus, we aimed to explore the variation of bacterial communities, diversity, and ecologic functions in the wet and dry periods of a wetland (designed as Ramsar site, Ramsar no 2257) by using 16S rRNA gene-based Illumina MiSeq sequencing. We reported a pronounced variation in water physicochemical and biological properties (temperature, pH, Chla, DOC, and TN), bacterial diversity, and community composition. Bacterial communities in the dry season harbored significantly higher alpha diversity, while significantly higher richness and abundance were reflected in the wet season. Our results uncovered the effect of nutrients on bacterial abundance, richness, and community composition. Fourteen percent of the total OTUs were shared in two hydrological periods, and the largest portion of unique OTUs (58%) was observed in the dry season. Planctomycetes and Bacteroidetes dominated the wet season exclusive OTUs; meanwhile, Actinobacteria dominated the dry season exclusive OTUs. Bacteria in these wetlands exhibited divergent ecological functions during the dry and wet seasons. By disclosing the variation of water bacterial communities in different hydrologic periods and their relationship with environmental factors, this first-hand work in the Ramsar site of Nepal will develop a baseline dataset for the scientific community that will assist in understanding the wetland's microbial ecology and biogeography.}, }
@article {pmid37056166, year = {2023}, author = {Lindsay, RJ and Holder, PJ and Talbot, NJ and Gudelj, I}, title = {Metabolic efficiency reshapes the seminal relationship between pathogen growth rate and virulence.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.14218}, pmid = {37056166}, issn = {1461-0248}, support = {BB/T015985/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {A cornerstone of classical virulence evolution theories is the assumption that pathogen growth rate is positively correlated with virulence, the amount of damage pathogens inflict on their hosts. Such theories are key for incorporating evolutionary principles into sustainable disease management strategies. Yet, empirical evidence raises doubts over this central assumption underpinning classical theories, thus undermining their generality and predictive power. In this paper, we identify a key component missing from current theories which redefines the growth-virulence relationship in a way that is consistent with data. By modifying the activity of a single metabolic gene, we engineered strains of Magnaporthe oryzae with different nutrient acquisition and growth rates. We conducted in planta infection studies and uncovered an unexpected non-monotonic relationship between growth rate and virulence that is jointly shaped by how growth rate and metabolic efficiency interact. This novel mechanistic framework paves the way for a much-needed new suite of virulence evolution theories.}, }
@article {pmid37055390, year = {2023}, author = {Dudek, NK and Galaz-Montoya, JG and Shi, H and Mayer, M and Danita, C and Celis, AI and Viehboeck, T and Wu, GH and Behr, B and Bulgheresi, S and Huang, KC and Chiu, W and Relman, DA}, title = {Previously uncharacterized rectangular bacterial structures in the dolphin mouth.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2098}, pmid = {37055390}, issn = {2041-1723}, abstract = {Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.}, }
@article {pmid37049481, year = {2023}, author = {Pham, VT and Steinert, RE and Duysburgh, C and Ghyselinck, J and Marzorati, M and Dekker, PJT}, title = {In Vitro Effect of Enzymes and Human Milk Oligosaccharides on FODMAP Digestion and Fecal Microbiota Composition.}, journal = {Nutrients}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/nu15071637}, pmid = {37049481}, issn = {2072-6643}, abstract = {Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) cause intestinal discomfort in patients with irritable bowel syndrome (IBS). An enzyme mix (2500 SU invertase, 2400 GalU α-galactosidase, 10,000 ALU β-galactosidase) optimized for FODMAP digestion, and/or human milk oligosaccharides (HMO) (2'-FL, DFL, and LNnT), were evaluated for effects on microbial community activity and composition in short-term colonic incubations using the fecal microbiota of four patients with IBS-D symptoms under the following test conditions: (i) FODMAP, (ii) pre-digested (with enzyme mix) FODMAP, (iii) FODMAP + HMO, and (iv) pre-digested FODMAP + HMO. Pre-digested FODMAP reduced short-chain fatty acid (SCFA) production versus FODMAP; HMO restored this. A 10-day experiment with the simulator of the human intestinal microbial ecosystem (SHIME[®]), using fecal samples from two patients with IBS-D, further evaluated these findings. FODMAP resulted in decreased microbial diversity versus blank. Pre-digestion with the enzyme mix restored microbial diversity, improved FODMAP digestibility, and reduced gas pressure versus undigested FODMAP; however, SCFA production decreased. HMO restored SCFA production along with an increase in gas pressure and increased abundance of Lachnospiraceae. When used in combination, the FODMAP enzyme mix and HMO may resolve FODMAP-related IBS symptoms while maintaining a healthy gut microbiome via prebiotic activity.}, }
@article {pmid37044393, year = {2022}, author = {Datta, R and Maity, P and Bhadury, P and Rizvi, AN and Raghunathan, C}, title = {An Updated Checklist of Free-living Marine Nematodes from Coastal India.}, journal = {Zootaxa}, volume = {5196}, number = {2}, pages = {151-196}, doi = {10.11646/zootaxa.5196.2.1}, pmid = {37044393}, issn = {1175-5334}, abstract = {The present study provides an updated species list of free-living marine nematodes reported from coastal India (Coasts and Islands) based on the thorough consultation of literature published from 1956 to 2022. This exercise resulted in a total of 617 valid species belonging to 266 genera, 48 families, 21 superfamilies and 9 orders. Class Chromadorea comprises 487 species represented by 205 genera, while class Enoplea includes 130 species belonging to 61 genera. The most common family was Xyalidae, with 76 species and the least common families having a single species each were represented by Aegialoalaimidae, Rhadinematidae, Aphanolaimidae, Rhabditidae, Pandolaimidae and Rhabdodemaniidae. The checklist provides a robust framework for the distribution and biogeography of free-living marine nematodes from the Indian waters and could be used to relate with marine ecosystems of other countries.}, }
@article {pmid37044259, year = {2023}, author = {Kim, HS and Keum, HL and Chung, IY and Nattkemper, L and Head, C and Koh, A and Sul, WJ and Pastar, I and Yosipovitch, G}, title = {Characterization of a Perturbed Skin Microbiome in Prurigo Nodularis and Lichen Simplex Chronicus.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2023.03.1669}, pmid = {37044259}, issn = {1523-1747}, }
@article {pmid37042985, year = {2023}, author = {Zhang, Y and Xia, X and Wan, L and Han, BP and Liu, H and Jing, H}, title = {Microbial Communities Are Shaped by Different Ecological Processes in Subtropical Reservoirs of Different Trophic States.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37042985}, issn = {1432-184X}, abstract = {Understanding microbial community structure and the underlying control mechanisms are fundamental purposes of aquatic ecology. However, little is known about the seasonality and how trophic conditions regulate plankton community in subtropical reservoirs. In this study, we study the prokaryotic and picoeukaryotic communities and their interactions during wet and dry seasons in two subtropical reservoirs: one at oligotrophic state and another at mesotrophic state. Distinct microbial community compositions (prokaryotes and picoeukaryotes) and seasonal variation pattern were detected in the oligotrophic and mesotrophic reservoirs. The interactions between prokaryotic and picoeukaryotic communities were more prevalent in the oligotrophic reservoir, suggesting enhanced top-down control of small eukaryotic grazers on the prokaryotic communities. On the other hand, the microbial community in the mesotrophic reservoir was more influenced by physico-chemical parameters and showed a stronger seasonal variation, which may be the result of distinct nutrient levels in wet and dry seasons, indicating the importance of bottom-up control. Our study contributes to new understandings of the environmental and biological processes that shape the structure and dynamics of the planktonic microbial communities in reservoirs of different trophic states.}, }
@article {pmid37039841, year = {2023}, author = {Del Campo, EM and Gasulla, F and Hell, AF and González-Hourcade, M and Casano, LM}, title = {Comparative Transcriptomic and Proteomic Analyses Provide New Insights into the Tolerance to Cyclic Dehydration in a Lichen Phycobiont.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37039841}, issn = {1432-184X}, abstract = {Desiccation tolerance (DT) is relatively frequent in non-vascular plants and green algae. However, it is poorly understood how successive dehydration/rehydration (D/R) cycles shape their transcriptomes and proteomes. Here, we report a comprehensive analysis of adjustments on both transcript and protein profiles in response to successive D/R cycles in Coccomyxa simplex (Csol), isolated from the lichen Solorina saccata. A total of 1833 transcripts and 2332 proteins were differentially abundant as a consequence of D/R; however, only 315 of these transcripts/proteins showed similar trends. Variations in both transcriptomes and proteomes along D/R cycles together with functional analyses revealed an extensive decrease in transcript and protein levels during dehydration, most of them involved in gene expression, metabolism, substance transport, signalling and folding catalysis, among other cellular functions. At the same time, a series of protective transcripts/proteins, such as those related to antioxidant defence, polyol metabolism and autophagy, was upregulated during dehydration. Overall, our results show a transient decrease in most cellular functions as a result of drying and a gradual reactivation of specific cell processes to accommodate the hydration status along successive D/R cycles. This study provides new insights into key mechanisms involved in the DT of Csol and probably other dehydration-tolerant microalgae. In addition, functionally characterising the high number of genes/proteins of unknown functions found in this study may lead to the discovery of new DT mechanisms.}, }
@article {pmid37037922, year = {2023}, author = {Lemke, M and DeSalle, R}, title = {The Role of Microbial Ecology in Restoration Ecology in the Age of Genomics: A Summary of the Microbial Ecology Special Issue.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37037922}, issn = {1432-184X}, }
@article {pmid37037808, year = {2023}, author = {Song, A and Su, J and Wang, H and Zhang, Z and Zhang, X and Van de Peer, Y and Chen, F and Fang, W and Guan, Z and Zhang, F and Wang, Z and Wang, L and Ding, B and Zhao, S and Ding, L and Liu, Y and Zhou, L and He, J and Jia, D and Zhang, J and Chen, C and Yu, Z and Sun, D and Jiang, J and Chen, S and Chen, F}, title = {Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2021}, pmid = {37037808}, issn = {2041-1723}, abstract = {Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement.}, }
@article {pmid37032887, year = {2023}, author = {Prendergast, DM and Slowey, R and Burgess, CM and Murphy, D and Johnston, D and Morris, D and O' Doherty, &#xc1; and Moriarty, J and Gutierrez, M}, title = {Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1118264}, doi = {10.3389/fmicb.2023.1118264}, pmid = {37032887}, issn = {1664-302X}, abstract = {BACKGROUND: The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.<br><br>METHODS: To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n&#x2009;=&#x2009;72) and after (n&#x2009;=&#x2009;10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.<br><br>RESULTS: A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n&#x2009;=&#x2009;24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.<br><br>CONCLUSION: Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.}, }
@article {pmid37030359, year = {2023}, author = {Yang, X and Duan, P and Hicks, L and Wang, K and Li, D}, title = {Mechanisms underlying the responses of microbial carbon and nitrogen use efficiencies to nitrogen addition are mediated by topography in a subtropical forest.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163236}, doi = {10.1016/j.scitotenv.2023.163236}, pmid = {37030359}, issn = {1879-1026}, abstract = {Microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are key parameters determining the fate of C and N in soils. Atmospheric N deposition has been found to heavily impact multiple soil C and N transformations, but we lack understanding of the responses of CUE and NUE to N deposition, and it remains uncertain whether responses may be mediated by topography. Here, a N addition experiment with three treatment levels (0, 50 and 100 kg N ha[-1] yr[-1]) was conducted in the valley and on the slope of a subtropical karst forest. Nitrogen addition increased microbial CUE and NUE at both topographic positions, but the underlying mechanisms differed. In the valley, the increase in CUE was associated with an increase in soil fungal richness:biomass and lower litter C:N, whereas on the slope, the response was linked with a reduced ratio of dissolved soil organic C (DOC) to available phosphorus (AVP) which reduced respiration, and increased root N:P stoichiometry. In the valley, the increase in NUE was explained by stimulated microbial N growth relative to gross N mineralization, which was associated with increased ratios of soil total dissolved N:AVP and fungal richness:biomass. In contrast, on the slope, the increase in NUE was attributed to reduced gross N mineralization, linked to increased DOC:AVP. Overall, our results highlight how topography-driven soil substrate availability and microbial properties can regulate microbial CUE and NUE.}, }
@article {pmid37030231, year = {2023}, author = {Liu, H and Jiao, Q and Fan, L and Jiang, Y and Alyemeni, MN and Ahmad, P and Chen, Y and Zhu, M and Liu, H and Zhao, Y and Liu, F and Liu, S and Li, G}, title = {Integrated physio-biochemical and transcriptomic analysis revealed mechanism underlying of Si-mediated alleviation to cadmium toxicity in wheat.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131366}, doi = {10.1016/j.jhazmat.2023.131366}, pmid = {37030231}, issn = {1873-3336}, abstract = {Cadmium (Cd) contamination has resulted in serious reduction of crop yields. Silicon (Si), as a beneficial element, regulates plant growth to heavy metal toxicity mainly through reducing metal uptake and protecting plants from oxidative injury. However, the molecular mechanism underlying Si-mediated Cd toxicity in wheat has not been well understood. This study aimed to reveal the beneficial role of Si (1 mM) in alleviating Cd-induced toxicity in wheat (Triticum aestivum) seedlings. The results showed that exogenous supply of Si decreased Cd concentration by 67.45% (root) and 70.34% (shoot), and maintained ionic homeostasis through the function of important transporters, such as Lsi, ZIP, Nramp5 and HIPP. Si ameliorated Cd-induced photosynthetic performance inhibition through up-regulating photosynthesis-related genes and light harvesting-related genes. Si minimized Cd-induced oxidative stress by decreasing MDA contents by 46.62% (leaf) and 75.09% (root), and helped re-establish redox homeostasis by regulating antioxidant enzymes activities, AsA-GSH cycle and expression of relevant genes through signal transduction pathway. The results revealed molecular mechanism of Si-mediated wheat tolerance to Cd toxicity. Si fertilizer is suggested to be applied in Cd contaminated soil for food safety production as a beneficial and eco-friendly element.}, }
@article {pmid37026303, year = {2023}, author = {Pal, S and Vani, G and Donthineni, PR and Basu, S and Arunasri, K}, title = {Tear film microbiome in Sjogren's and non-Sjogren's aqueous deficiency dry eye.}, journal = {Indian journal of ophthalmology}, volume = {71}, number = {4}, pages = {1566-1573}, doi = {10.4103/IJO.IJO_2821_22}, pmid = {37026303}, issn = {1998-3689}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Dry Eye Syndromes ; *Sjogren's Syndrome/diagnosis/complications ; Tears ; *Microbiota ; Bacteria/genetics ; }, abstract = {PURPOSE: To understand the bacterial microbiome changes associated with Sjogren's syndrome (SS) and non-Sjogren's syndrome (NSS) aqueous-deficient dry eyes compared to healthy eyes.<br><br>METHODS: Bacterial microbiome was generated from the deoxyribonucleic acid of tear film samples in healthy (n = 33), SS (n = 17), and NSS (n = 28) individuals. Sequencing of the V3-V4 region of the 16S rRNA gene was performed on the Illumina HiSeq2500 platform. Quantitative Insights Into Microbial Ecology (QIIME) pipeline was used to assign taxa to sequences. Statistical analysis was performed in R to assess the alpha diversity and beta diversity indices. Significant changes between the healthy, SS, and NSS cohorts were depicted by principal coordinate analysis (PCoA), differential abundance, and network analysis.<br><br>RESULTS: Tear microbiome was generated in healthy, SS, and NSS samples. Phyla Actinobacteria, Firmicutes, and Bacteroidetes showed significant changes in SS and NSS compared to healthy. Genera Lactobacillus and Bacillus were predominantly present in all samples. PCoA and heat map analysis showed distinct clusters for SS and NSS from the healthy cohort. Genera Prevotella, Coriobacteriaceae UCG-003, Enterococcus, Streptomyces, Rhodobacter, Ezakiella, and Microbacterium significantly increased in abundance in SS and NSS compared to a healthy cohort. Bacteria-bacteria interaction in SS, NSS, and healthy cohorts was predicted by CoNet network analysis. This analysis predicted a major hub of interaction for the pro-inflammatory bacterium Prevotella in the SS and NSS cohorts.<br><br>CONCLUSION: The results of the study indicate significant changes in the phyla and genera in SS and NSS compared to healthy. Both discriminative analysis and network analysis indicated a possible association of predominant pro-inflammatory bacteria with SS and NSS.}, }
@article {pmid37024470, year = {2023}, author = {Young, E and Melaugh, G and Allen, RJ}, title = {Active layer dynamics drives a transition to biofilm fingering.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {17}, pmid = {37024470}, issn = {2055-5008}, mesh = {*Biofilms ; }, abstract = {The emergence of spatial organisation in biofilm growth is one of the most fundamental topics in biofilm biophysics and microbiology. It has long been known that growing biofilms can adopt smooth or rough interface morphologies, depending on the balance between nutrient supply and microbial growth; this 'fingering' transition has been linked with the average width of the 'active layer' of growing cells at the biofilm interface. Here we use long-time individual-based simulations of growing biofilms to investigate in detail the driving factors behind the biofilm-fingering transition. We show that the transition is associated with dynamical changes in the active layer. Fingering happens when gaps form in the active layer, which can cause local parts of the biofilm interface to pin, or become stationary relative to the moving front. Pinning can be transient or permanent, leading to different biofilm morphologies. By constructing a phase diagram for the transition, we show that the controlling factor is the magnitude of the relative fluctuations in the active layer thickness, rather than the active layer thickness per se. Taken together, our work suggests a central role for active layer dynamics in controlling the pinning of the biofilm interface and hence biofilm morphology.}, }
@article {pmid37024159, year = {2023}, author = {Vikram, S and Ramond, JB and Ortiz, M and Maggs-Kölling, G and Pelser, K and Cowan, DA}, title = {Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert.}, journal = {Fungal biology}, volume = {127}, number = {4}, pages = {997-1003}, doi = {10.1016/j.funbio.2023.03.001}, pmid = {37024159}, issn = {1878-6146}, mesh = {*Soil/chemistry ; Bacteria ; Soil Microbiology ; Desert Climate ; *Ascomycota ; }, abstract = {The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.}, }
@article {pmid37020129, year = {2023}, author = {Berman, TS and Izraeli, Y and Lalzar, M and Mozes-Daube, N and Lepetit, D and Tabic, A and Varaldi, J and Zchori-Fein, E}, title = {RNA Viruses Are Prevalent and Active Tenants of the Predatory Mite Phytoseiulus persimilis (Acari: Phytoseiidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37020129}, issn = {1432-184X}, abstract = {Many arthropod species harbor a diverse range of viruses. While much is known about pathogenic viruses of some economically important insects and arthropods involved in disease transmission, viruses associated with mites have rarely been studied. The main objective of this study was to characterize the virome of Phytoseiulus persimilis (Phytoseiidae), a predatory mite commercially used worldwide for the biological control of the key pest Tetranychus urticae (Tetranichidae). A combination of de novo transcriptome assembly and virion sequencing, revealed that RNA viruses are highly prevalent and active tenants of commercial populations of P. persimilis, comprising on average 9% of the mite's total mRNA. Seventeen RNA viruses dominated the mite's virome (i.e., were highly transcribed) with over half (n = 10) belonging to the order Picornavirales, + ssRNA viruses that infect a large range of hosts, including arthropods. Screening of the 17 dominant virus sequences in P. persimilis and T. urticae revealed that three viruses (two Picornavirales of the families Iflaviridae and Dicistroviridae, and one unclassified Riboviria) are unique to P. persimilis and three others (two unclassified Picornavirales and one unclassified Riboviria) are present in both mite species. Most of the sequences were related to viruses previously documented in economically important arthropods, while others have rarely been documented before in arthropods. These findings demonstrate that P. persimilis, like many other arthropods, harbors a diverse RNA virome, which might affect the mite's physiology and consequently its efficiency as a biological control agent.}, }
@article {pmid37017718, year = {2023}, author = {Thompson, CC and Tschoeke, D and Coutinho, FH and Leomil, L and Garcia, GD and Otsuki, K and Turcq, BJ and Moreira, LS and Turcq, PFM and Cordeiro, RC and Asp, NE and Thompson, FL}, title = {Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37017718}, issn = {1432-184X}, abstract = {The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.}, }
@article {pmid37010970, year = {2023}, author = {May, AK}, title = {Host Microbiome Threats in the Intensive Care Unit.}, journal = {Surgical infections}, volume = {24}, number = {3}, pages = {276-283}, doi = {10.1089/sur.2023.029}, pmid = {37010970}, issn = {1557-8674}, mesh = {Humans ; *Microbiota ; Anti-Bacterial Agents/therapeutic use ; Intensive Care Units ; Dysbiosis/therapy ; }, abstract = {Human microbiota demonstrate diversity and balance that is adaptive for the host and supports maintaining homeostasis. Although acute illness or injury may derange microbiota diversity and the proportion of potentially pathogenic microbes, that derangement may be further exacerbated by commonly deployed intensive care unit (ICU) therapeutic and practices. These include antibiotic administration, delayed luminal nutrition, acid suppression, and vasopressor infusion. Furthermore, the local ICU microbial ecology, regardless of disinfection practices, shapes the patient's microbiota, especially with the acquisition of multi-drug-resistant pathogens. Current approaches to protect a normal microbiome, or restore a deranged one, are part of a multifaceted approach that may include antibiotic stewardship and infection control practices as microbiome-directed therapeutics emerge.}, }
@article {pmid37010558, year = {2023}, author = {Khatri, S and Chaudhary, P and Shivay, YS and Sharma, S}, title = {Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37010558}, issn = {1432-184X}, abstract = {Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.}, }
@article {pmid37010433, year = {2023}, author = {Fortuna, KJ and Holtappels, D and Venneman, J and Baeyen, S and Vallino, M and Verwilt, P and Rediers, H and De Coninck, B and Maes, M and Van Vaerenbergh, J and Lavigne, R and Wagemans, J}, title = {Back to the Roots: Agrobacterium-Specific Phages Show Potential to Disinfect Nutrient Solution from Hydroponic Greenhouses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0021523}, doi = {10.1128/aem.00215-23}, pmid = {37010433}, issn = {1098-5336}, abstract = {Agrobacterium biovar 1 is a soilborne plant pathogen with the ability to colonize the irrigation system of greenhouses, causing hairy root disease (HRD). Currently, management focuses on using hydrogen peroxide to disinfect the nutrient solution, but due to the emergence of resistant strains, its efficacy and sustainability are questioned. Using a relevant collection of pathogenic Agrobacterium biovar 1 strains, OLIVR1 to 6, six phages specific to this pathogen and belonging to three different genera were isolated from Agrobacterium biovar 1-infected greenhouses. All phages were named OLIVR, referring to their location of isolation, Onze-Lieve-Vrouwe-Waver, and were characterized by whole-genome analysis, confirming their strictly lytic lifestyle. They remained stable under greenhouse-relevant conditions. To assess the efficacy of the phages, their ability to disinfect greenhouse nutrient solution inoculated with agrobacteria was tested. Each of the phages infected their host, but their ability to decrease the bacterial concentration differed. For instance, OLIVR1 reduced the bacterial concentration with 4 log units without phage resistance emerging. While OLIVR4 and OLIVR5 were also infectious in nutrient solution, they did not always decrease the bacterial load below the limit of detection, and phage resistance emerged. Finally, the mutations causing phage resistance by receptor modification were identified. For OLIVR4-resistant Agrobacterium isolates, but not for OLIVR5-resistant isolates, motility decreased. Together, these data show the potential of some of these phages as disinfectant of nutrient solution, and they might be a valuable tool to tackle HRD. IMPORTANCE Hairy root disease, caused by rhizogenic Agrobacterium biovar 1 is a rapidly emerging bacterial disease worldwide. It affects tomatoes, cucumbers, eggplant, and bell pepper, causing high yield losses in hydroponic greenhouses. Recent findings suggest that the current management practices, mainly focusing on UV-C and hydrogen peroxide to disinfect contaminated water, have a questionable efficacy. Hence, we investigate the potential of phages as a biological means of preventing this disease. Using a diverse collection of Agrobacterium biovar 1, we isolated three different phage species that together infect 75% of the collection. Since these phages are strictly lytic, while remaining both stable and infectious under greenhouse-relevant conditions, they might be suitable candidates for biological control.}, }
@article {pmid37009161, year = {2023}, author = {Cummings, S and Ardor Bellucci, LM and Seabrook, S and Raineault, NA and McPhail, KL and Thurber, AR}, title = {Variations and gradients between methane seep and off-seep microbial communities in a submarine canyon system in the Northeast Pacific.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15119}, pmid = {37009161}, issn = {2167-8359}, mesh = {*Seawater ; Methane/chemistry ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Microbiota/genetics ; }, abstract = {Methane seeps are highly abundant marine habitats that contribute sources of chemosynthetic primary production to marine ecosystems. Seeps also factor into the global budget of methane, a potent greenhouse gas. Because of these factors, methane seeps influence not only local ocean ecology, but also biogeochemical cycles on a greater scale. Methane seeps host specialized microbial communities that vary significantly based on geography, seep gross morphology, biogeochemistry, and a diversity of other ecological factors including cross-domain species interactions. In this study, we collected sediment cores from six seep and non-seep locations from Grays and Quinault Canyons (46-47°N) off Washington State, USA, as well as one non-seep site off the coast of Oregon, USA (45°N) to quantify the scale of seep influence on biodiversity within marine habitats. These samples were profiled using 16S rRNA gene sequencing. Predicted gene functions were generated using the program PICRUSt2, and the community composition and predicted functions were compared among samples. The microbial communities at seeps varied by seep morphology and habitat, whereas the microbial communities at non-seep sites varied by water depth. Microbial community composition and predicted gene function clearly transitioned from on-seep to off-seep in samples collected from transects moving away from seeps, with a clear ecotone and high diversity where methane-fueled habitats transition into the non-seep deep sea. Our work demonstrates the microbial and metabolic sphere of influence that extends outwards from methane seep habitats.}, }
@article {pmid37008301, year = {2022}, author = {Deyaert, S and Moens, F and Pirovano, W and van den Bogert, B and Klaassens, ES and Marzorati, M and Van de Wiele, T and Kleerebezem, M and Van den Abbeele, P}, title = {Development of a reproducible small intestinal microbiota model and its integration into the SHIME[®]-system, a dynamic in vitro gut model.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1054061}, pmid = {37008301}, issn = {1664-302X}, abstract = {The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME[®]-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology.}, }
@article {pmid37002423, year = {2023}, author = {Pushpakumara, BLDU and Tandon, K and Willis, A and Verbruggen, H}, title = {The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37002423}, issn = {1432-184X}, abstract = {Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.}, }
@article {pmid37001600, year = {2023}, author = {Gilles, S and Meinzer, M and Landgraf, M and Kolek, F and von Bargen, S and Pack, K and Charalampopoulos, A and Ranpal, S and Luschkova, D and Traidl-Hoffmann, C and Jochner-Oette, S and Damialis, A and Büttner, C}, title = {Betula pendula trees infected by birch idaeovirus and cherry leaf roll virus: Impacts of urbanisation and NO2 levels.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {327}, number = {}, pages = {121526}, doi = {10.1016/j.envpol.2023.121526}, pmid = {37001600}, issn = {1873-6424}, abstract = {Viruses are frequently a microbial biocontaminant of healthy plants. The occurrence of the infection can be also due to environmental stress, like urbanisation, air pollution and increased air temperature, especially under the ongoing climate change. The aim of the present study was to investigate the hypothesis that worsened air quality and fewer green areas may favour the higher frequency of common viral infections, particularly in a common tree in temperate and continental climates, Betula pendula ROTH. We examined 18 trees, during the years 2015-2017, the same always for each year, in the region of Augsburg, Germany. By specific PCR, the frequency of two viruses, Cherry leaf roll virus (CLRV, genus Nepovirus, family Secoviridae), which is frequent in birch trees, and a novel virus tentatively named birch idaeovirus (BIV), which has been only recently described, were determined in pollen samples. The occurrence of the viruses was examined against the variables of urban index, air pollution (O3 and NO2), air temperature, and tree morphometrics (trunk perimeter, tree height, crown height and diameter). Generalized Non-linear models (binomial logit with backward stepwise removal of independent variables) were employed. During the study period, both CLRV and BIV were distributed widely throughout the investigated birch individuals. CLRV seemed to be rather cosmopolitan and was present independent of any abiotic factor. BIV's occurrence was mostly determined by higher values of the urban index and of NO2. Urban birch trees, located next to high-traffic roads with higher NO2 levels, are more likely to be infected by BIV. Increased environmental stress may lead to more plant viral infections. Here we suggest that this is particularly true for urban spaces, near high-traffic roads, where plants may be more stressed, and we recommend taking mitigation measures for controlling negative human interventions.}, }
@article {pmid37001406, year = {2023}, author = {Vaezzadeh, V and Yi, X and Rais, FR and Bong, CW and Thomes, MW and Lee, CW and Zakaria, MP and Wang, AJ and Zhong, G and Zhang, G}, title = {Corrigendum to "Distribution of black carbon and PAHs in sediments of Peninsular Malaysia" [Mar. Pollut. Bull.172 (2021) 112871].}, journal = {Marine pollution bulletin}, volume = {190}, number = {}, pages = {114797}, doi = {10.1016/j.marpolbul.2023.114797}, pmid = {37001406}, issn = {1879-3363}, }
@article {pmid37001405, year = {2023}, author = {Kundu, K and Van Landuyt, J and Mattelin, V and Martin, B and Neyts, M and Parmentier, K and Boon, N}, title = {Enhanced removal of warfare agent tri-nitro-toluene by a Methylophaga-dominated microbiome.}, journal = {Marine pollution bulletin}, volume = {190}, number = {}, pages = {114866}, doi = {10.1016/j.marpolbul.2023.114866}, pmid = {37001405}, issn = {1879-3363}, abstract = {Historical exposure of the marine environment to 2,4,6-trinitrotoluene (TNT) happened due to the dumping of left-over munitions. Despite significant research on TNT decontamination, the potential of marine microbiome for TNT degradation remains only little explored. In this study, TNT degradation experiments were conducted with sediment located near the World War I munition dumpsite - Paardenmarkt in the Belgian part of North Sea. A slow removal was observed using TNT as sole source of C and N, which could be enhanced by adding methanol. Degradation was reflected in nitro-reduced metabolites and microbial growth. 16S Illumina sequencing analysis revealed several enriched genera that used TNT as a sole source of C and N - Colwellia, Thalossospira, and Methylophaga. Addition of methanol resulted in increased abundance of Methylophaga, which corresponded to the rapid removal of TNT. Methanol enhanced the degradation by providing additional energy and establishing syntrophic association between methanol-utilizing and TNT-utilizing bacteria.}, }
@article {pmid37000232, year = {2023}, author = {Stupar, M and Savković, &#x17d; and Popović, S and Simić, GS and Grbić, ML}, title = {Speleomycology of Air in Stopića Cave (Serbia).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {1-11}, pmid = {37000232}, issn = {1432-184X}, abstract = {Fungi can colonize organic matter present in subterranean sites and have a significant role as dwellers in different microniches of cave habitats. In order to analyze the content of airborne fungal propagules in different parts of "Stopića Cave," a touristic site in Serbia, air sampling was carried out in three seasons during 2020, prior to and during the onset of COVID-19 pandemic. Culturable mycobiota was identified using both microscopic techniques and ITS region/BenA gene barcoding, while multivariate analyses were employed to establish the link between fungal taxa and different environmental factors. The maximal measured fungal propagule concentrations were recorded during spring sampling which were based on fungal propagule concentration categories; the cave environment matches the category V. A total of 29 fungal isolates were identified, while Aspergillus, Cladosporium, Fusarium, Lecanicillium, Mucor, and Penicillium were the most diverse genera. According to the trophic mode, most of the isolated fungal species were pathotrophs (75.86%), but when regarding ecological guilds, the most dominant were undefined saprobes and animal pathogens (41.38% for each). Show caves are especially vulnerable to human impacts, and the fungal propagules' concentration within the caves could be good indices for the level of ecological disturbance.}, }
@article {pmid37000231, year = {2023}, author = {Kurm, V and Visser, J and Schilder, M and Nijhuis, E and Postma, J and Korthals, G}, title = {Soil Suppressiveness Against Pythium ultimum and Rhizoctonia solani in Two Land Management Systems and Eleven Soil Health Treatments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37000231}, issn = {1432-184X}, abstract = {The soil microbiome is known to be crucial for the control of soil-borne plant diseases. However, there is still little knowledge on how to modify the soil microbiome to induce or increase disease suppressiveness. In the present study, we applied eleven soil health treatments combined with conventional and organic agricultural management in a long-term field experiment. Suppressiveness against Pythium ultimum and Rhizoctonia solani was assessed in bioassays for 2 years. In addition, the microbiome community composition and microbial abundance were determined. We found that while several treatments changed the microbial community composition compared to the control, only a combination treatment of anaerobic soil disinfestation, hair meal, and compost addition resulted in suppressiveness against P. ultimum. Pythium suppressiveness is likely to have been caused by an increased microbial abundance and activity. Moreover, the increased abundance of several bacterial taxa, such as Pseudomonas sp., Chryseobacterium sp., members of the family Chitinophagaceae, and the fungal genus Mortierella sp. and family Trichosporonaceae, was measured. There was no overall difference in suppressiveness between conventional and organic land management. Also, no suppressiveness against R. solani could be detected. Our results indicate that a treatment combining the reduction of microorganisms followed by a recovery phase with high amounts of organic amendments may be more effective in inducing suppressiveness than treatments consisting of only one of these measures.}, }
@article {pmid37000121, year = {2023}, author = {Lopes, LD and Futrell, SL and Wright, EE and Danalatos, GJ and Castellano, MJ and Vyn, TJ and Archontoulis, SV and Schachtman, DP}, title = {Soil depth and geographic distance modulate bacterial β-diversity in deep soil profiles throughout the U.S. Corn Belt.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16945}, pmid = {37000121}, issn = {1365-294X}, abstract = {Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyze the factors underlying the bacterial β-diversity along vertical (0-240 cm of soil depth) and horizontal spatial dimensions (~500,000 Km[2]) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray-Curtis) and phylogenetic (Weighted Unifrac) β-diversity. Additionally, we assessed whether the distance-decay (horizontal dimension) was greater in the topsoil (0-30 cm) or subsoil (in each 30 cm layer from 30-240 cm) using Mantel tests. The influence of geographic distance versus edaphic variables on the bacterial communities from the different soil layers was also compared. Results indicated that the phylogenetic β-diversity was impacted more by soil depth, while the taxonomic β-diversity changed more between geographic locations. The distance-decay was lower in the topsoil than in all subsoil layers analyzed. Moreover, some subsoil layers were influenced more by geographic distance than any edaphic variable, including pH. Although different factors affected the topsoil and subsoil biogeography, niche-based models explained the community assembly of all soil layers. This comprehensive study contributed to elucidating important aspects of soil bacterial biogeography including the major impact of soil depth on the phylogenetic β-diversity, and the greater influence of geographic distance on subsoil than on topsoil bacterial communities in agroecosystems.}, }
@article {pmid36999338, year = {2023}, author = {Garbeva, P and Avalos, M and Ulanova, D and van Wezel, GP and Dickschat, JS}, title = {Volatile sensation: The chemical ecology of the earthy odorant geosmin.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16381}, pmid = {36999338}, issn = {1462-2920}, abstract = {Geosmin may be the most familiar volatile compound, as it lends the earthy smell to soil. The compound is a member of the largest family of natural products, the terpenoids. The broad distribution of geosmin among bacteria in both terrestrial and aquatic environments suggests that this compound has an important ecological function, for example, as a signal (attractant or repellent) or as a protective specialized metabolite against biotic and abiotic stresses. While geosmin is part of our everyday life, scientists still do not understand the exact biological function of this omnipresent natural product. This minireview summarizes the current general observations regarding geosmin in prokaryotes and introduces new insights into its biosynthesis and regulation, as well as its biological roles in terrestrial and aquatic environments.}, }
@article {pmid36998391, year = {2023}, author = {Rajala, P and Bomberg, M}, title = {Editorial: Geomicrobes: Life in terrestrial deep subsurface, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1169127}, pmid = {36998391}, issn = {1664-302X}, }
@article {pmid36996916, year = {2023}, author = {Hidalgo, J and Epelde, L and Anza, M and Becerril, JM and Garbisu, C}, title = {Mycoremediation with Agaricus bisporus and Pleurotus ostreatus growth substrates versus phytoremediation with Festuca rubra and Brassica sp. for the recovery of a Pb and γ-HCH contaminated soil.}, journal = {Chemosphere}, volume = {327}, number = {}, pages = {138538}, doi = {10.1016/j.chemosphere.2023.138538}, pmid = {36996916}, issn = {1879-1298}, abstract = {Mycoremediation with mushroom growth substrates can be used for the recovery of mixed contaminated soils due to the benefits derived from the physicochemical characteristics of the substrates, the activity of extracellular enzymes secreted by the fungi, and the presence of the fungal mycelia. The objective of this work was to assess the potential of Agaricus bisporus and Pleurotus ostreatus growth substrates (inoculated mushroom substrates vs. spent mushroom substrates) for the mycoremediation of soils co-contaminated with lead and lindane (γ-HCH). We compared the efficiency of these mycoremediation strategies with the phytoremediation with Brassica spp. Or Festuca rubra plants, in terms of both reduction in contaminant levels and enhancement of soil health. An enhanced soil health was achieved as a result of the application of mycoremediation treatments, compared to phytoremediation and control (untreated) treatments. The application of P. ostreatus inoculated substrate led to the most significant reduction in γ-HCH concentration (up to 88.9% compared to corresponding controls). In the presence of inoculated mushroom substrate, P. ostreatus fruiting bodies extracted more Pb than Brassica spp. Or F. rubra plants. Mycoremediation with P. ostreatus growth substrates appears a promising strategy for the recovery of the health of soils co-contaminated with Pb and γ-HCH.}, }
@article {pmid36991472, year = {2023}, author = {Wang, Y and Jiménez, DJ and Zhang, Z and van Elsas, JD}, title = {Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: a metatranscriptomic study.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {16}, number = {1}, pages = {54}, pmid = {36991472}, issn = {2731-3654}, abstract = {BACKGROUND: In a previous study, shaking speed was found to be an important factor affecting the population dynamics and lignocellulose-degrading activities of a synthetic lignocellulolytic microbial consortium composed of the bacteria Sphingobacterium paramultivorum w15, Citrobacter freundii so4, and the fungus Coniochaeta sp. 2T2.1. Here, the gene expression profiles of each strain in this consortium were examined after growth at two shaking speeds (180 and 60 rpm) at three time points (1, 5 and 13 days).<br><br>RESULTS: The results indicated that, at 60&#xa0;rpm, C. freundii so4 switched, to a large extent, from aerobic to flexible&#xa0;(aerobic/microaerophilic/anaerobic) metabolism, resulting in continued slow growth till late stage. In addition, Coniochaeta sp. 2T2.1 tended to occur to a larger extent in the hyphal form, with genes encoding adhesion proteins being highly expressed. Much like at 180&#xa0;rpm, at 60&#xa0;rpm, S. paramultivorum w15 and Coniochaeta sp. 2T2.1 were key players in hemicellulose degradation processes, as evidenced from the respective CAZy-specific transcripts. Coniochaeta sp. 2T2.1 exhibited expression of genes encoding arabinoxylan-degrading enzymes (i.e., of CAZy groups GH10, GH11, CE1, CE5 and GH43), whereas, at 180&#xa0;rpm, some of these genes were suppressed at early stages of growth. Moreover, C. freundii so4 stably expressed genes that were predicted to encode proteins with (1) &#x3b2;-xylosidase/&#x3b2;-glucosidase and (2) peptidoglycan/chitinase activities, (3) stress response- and detoxification-related proteins. Finally, S. paramultivorum w15 showed involvement in vitamin B2 generation in the early stages across the two shaking speeds, while this role was taken over by C. freundii so4 at late stage at 60&#xa0;rpm.<br><br>CONCLUSIONS: We provide evidence that S. paramultivorum w15 is involved in the degradation of mainly hemicellulose and in vitamin B2 production, and C. freundii so4 in the degradation of oligosaccharides or sugar dimers, next to detoxification processes. Coniochaeta sp. 2T2.1 was held to be strongly involved in cellulose and xylan (at early stages), next to lignin modification processes (at later stages). The synergism and alternative functional roles presented in this study enhance the eco-enzymological understanding of the degradation of lignocellulose in this tripartite microbial consortium.}, }
@article {pmid36989794, year = {2023}, author = {Goswami, V and Deepika, S and Chandra, R and Babu, CR and Kothamasi, D}, title = {Arbuscular mycorrhizas accelerate the degradation of colour containing organic pollutants present in distillery spent wash leachates.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131291}, doi = {10.1016/j.jhazmat.2023.131291}, pmid = {36989794}, issn = {1873-3336}, abstract = {Distillery spent wash (DSW) from molasses-based distilleries is being used as a low-cost alternative to chemical fertilizers in countries like India and Brazil. However, using DSW as a fertilizer substitute causes organic pollutant leaching, including melanoidins and caramel colourants that turn bodies of water dark brown. This study investigated the arbuscular mycorrhiza (AM) mediated degradation of organic pollutants in DSW. Mycorrhizal and non-mycorrhizal Sorghum bicolor were grown in microcosms for 16 weeks. The plants were fertilized with either raw DSW or Hoagland solution. Leachates draining from the microcosms after fertilization were collected three times in 30-day intervals. Each 30-day collection was preceded by two fertilizations. A gas chromatography-mass spectrometry comparative analyses of raw DSW with leachates of the third collection from mycorrhizal and non-mycorrhizal microcosms was made. Sixty-five and 42 complex organic compounds were detected in raw DSW and leachate collected from the non-mycorrhizal pots respectively. Only 26 compounds were detected in leachate collected from mycorrhizal pots. Absent from leachate of the mycorrhizal pots were: colour-containing organic compounds diacetone alcohol; 3-amino-2-cyano-6-methyl-6,7-dihydrothieno[2,3-b]pyrazine S-oxide; cyclohexane; 1,2-benzenedicarboxylic acid, butyl 8-methylnonyl ester; 2-pyrrolidinone; and acetic acid, dodecyl ester present in raw DSW. The results indicate that AM fungi can degrade organic pollutants in DSW.}, }
@article {pmid36988842, year = {2023}, author = {Messaoudi, Y and Smichi, N and Allaf, T and Besombes, C and Allaf, K and Gargouri, M}, title = {Instant Controlled Pressure-Drop (DIC) for Volatile Compound Extraction and Bioethanol Production from Empty Aleppo Pinecones and Eucalyptus Chips: Process Optimization and Statistical Modeling.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {36988842}, issn = {1559-0291}, abstract = {Several plant species contain volatile compounds extracted as "essential oils" through different technologies. After essential oil extraction, the residual solid is a lignocellulosic solid waste. This work proposes the instant controlled pressure-drop (DIC) technology to autovaporize volatile compounds and modify the lignocellulosic matrix. Indeed, DIC technology is a thermomechanical process based on short-time/high-temperature and pressure pretreatment. It enhances the saccharification and fermentation process (SSF) for bioethanol production. A 3-variable design of experiments optimized the DIC processing parameters to reach 100% efficiency (EE) of volatile compound extraction using response surface methodology (RSM). Eucalyptus chips presented 50 volatile identified compounds after 7 min of DIC treatment. 1,8-Cineole, β-phellandrene, aromadendrene, eudesmol, and spathulenol are the most important volatile compounds. The empty Aleppo pinecones delivered 32 volatile compounds in 5 min of DIC treatment, the most important of which were caryophyllene, nortricyclene, verbenol, and camphor. After the autovaporization extraction stage, solid fraction residues were hydrolyzed and fermented in the same stirred bioreactor, using SSF strategy for 72 h at 37 °C. The highest bioethanol yields reached 73.9% and 54.82% (g per 100 g DM) from eucalyptus chip and empty Aleppo pinecone, respectively.}, }
@article {pmid36987547, year = {2023}, author = {Coats, ER and Appel, FJ and Guho, N and Brinkman, CK and Mellin, J}, title = {Interrogating the Performance and Microbial Ecology of an EBPR/Post-Anoxic Denitrification Process at Bench and Pilot Scales.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {}, number = {}, pages = {e10852}, doi = {10.1002/wer.10852}, pmid = {36987547}, issn = {1554-7531}, abstract = {Research focused on interrogating post-anoxic enhanced biological phosphorus removal (EBPR) at bench and pilot scale. Average bench-scale effluent ranged from 0.33-1.4 mgP/L, 0.35-3.7 mgNH3 -N/L, and 1.1-3.9 mgNOx -N/L. Comparatively, the pilot achieved effluent (50[th] percentile/average) of 0.13/0.2 mgP/L, 9.7/8.2 mgNH3 -N/L, and 0.38/3.3 mgNOx -N/L under dynamic influent and environmental conditions. For EBPR process monitoring, P:C ratio data indicated 0.2-0.4 molP/molC will result in stable EBPR; related, a target design influent volatile fatty acid (VFA):P ratio would exceed 15 mgCOD/mgP. Post-anoxic EBPR enriched for Nitrobacter spp. at 1.70-20.27%, with Parcubacteria also dominating; the former is putatively associated with nitritation and the latter is a putative fermenting heterotrophic organism. Post-anoxic specific denitrification rates (20°C) ranged from 0.70-3.10 mgN/gVSS-hr; there was a strong correlation (R[2] =0.94) between the SDNR and %Parcubacteria for systems operated at a 20 d SRT. These results suggest carbon substrate potentially generated by this putative fermenter may enhance post-anoxic EBPR.}, }
@article {pmid36985355, year = {2023}, author = {Masigol, H and Grossart, HP and Taheri, SR and Mostowfizadeh-Ghalamfarsa, R and Pourmoghaddam, MJ and Bouket, AC and Khodaparast, SA}, title = {Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985355}, issn = {2076-2607}, abstract = {Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.}, }
@article {pmid36985156, year = {2023}, author = {Nayduch, D and Neupane, S and Pickens, V and Purvis, T and Olds, C}, title = {House Flies Are Underappreciated Yet Important Reservoirs and Vectors of Microbial Threats to Animal and Human Health.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985156}, issn = {2076-2607}, abstract = {House flies are well recognized as filth-associated organisms and public nuisances. House flies create sanitation issues when they bridge the gap between microbe-rich breeding environments and animal/human habitations. Numerous scientific surveys have demonstrated that house flies harbor bacterial pathogens that pose a threat to humans and animals. More extensive and informative surveys incorporating next-generation sequencing technologies have shown that house fly carriage of pathogens and harmful genetic elements, such as antimicrobial resistance genes, is more widespread and dangerous than previously thought. Further, there is a strong body of research confirming that flies not only harbor but also transmit viable, and presumably infectious, bacterial pathogens. Some pathogens replicate and persist in the fly, permitting prolonged shedding and dissemination. Finally, although the drivers still have yet to be firmly determined, the potential range of dissemination of flies and their associated pathogens can be extensive. Despite this evidence, the house flies' role as reservoirs, disseminators, and true, yet facultative, vectors for pathogens have been greatly underestimated and underappreciated. In this review, we present key studies that bolster the house fly's role both an important player in microbial ecology and population biology and as transmitters of microbial threats to animal and human health.}, }
@article {pmid36983540, year = {2023}, author = {Veas-Mattheos, K and Almendras, K and Pezoa, M and Muster, C and Orlando, J}, title = {High Andean Steppes of Southern Chile Contain Little-Explored Peltigera Lichen Symbionts.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {36983540}, issn = {2309-608X}, abstract = {Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high Andean steppes of southern Chile using LSU, β-tubulin, COR3 and ITS loci for mycobionts, and SSU and rbcLX loci for cyanobionts. We obtained 240 sequences for the different mycobiont markers and 118 for the cyanobiont markers, including the first report of β-tubulin sequences of P. patagonica through modifying a previously designed primer. Phylogenetic analyses, ITS scrutiny and variability of haplotypes were used to compare the sequences with those previously reported. We found seven mycobiont species and eleven cyanobiont haplotypes, including considerable novel symbionts. This was reflected by ~30% of mycobionts and ~20% of cyanobionts haplotypes that yielded less than 99% BLASTn sequence identity, 15 new sequences of the ITS1-HR, and a putative new Peltigera species associated with 3 Nostoc haplotypes not previously reported. Our results suggest that high Andean steppe ecosystems are habitats of unknown or little-explored lichen species and thus valuable environments to enhance our understanding of global Peltigera biodiversity.}, }
@article {pmid36983467, year = {2023}, author = {Hkiri, N and Olicón-Hernández, DR and Pozo, C and Chouchani, C and Asses, N and Aranda, E}, title = {Simultaneous Heavy Metal-Polycyclic Aromatic Hydrocarbon Removal by Native Tunisian Fungal Species.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, pmid = {36983467}, issn = {2309-608X}, abstract = {Multi-contamination by organic pollutants and toxic metals is common in anthropogenic and industrial environments. In this study, the five fungal strains Chaetomium jodhpurense (MH667651.1), Chaetomium maderasense (MH665977.1), Paraconiothyrium variabile (MH667653.1), Emmia lacerata, and Phoma betae (MH667655.1), previously isolated in Tunisia, were investigated for the simultaneous removal and detoxification of phenanthrene (PHE) and benzo[a]anthracene (BAA), as well as heavy metals (HMs) (Cu, Zn, Pb and Ag) in Kirk's media. The removal was analysed using HPLC, ultra-high performance liquid chromatography (UHPLC) coupled to a QToF mass spectrometer, transmission electron microscopy, and toxicology was assessed using phytotoxicity (Lepidium sativum seeds) and Microtox[®] (Allivibrio fisherii) assays. The PHE and BAA degradation rates, in free HMs cultures, reached 78.8% and 70.7%, respectively. However, the addition of HMs considerably affected the BAA degradation rate. The highest degradation rates were associated with the significant production of manganese-peroxidase, lignin peroxidase, and unspecific peroxygenase. The Zn and Cu removal efficacy was considerably higher with live cells than dead cells. Transmission electron microscopy confirmed the involvement of both bioaccumulation and biosorption processes in fungal HM removal. The environmental toxicological assays proved that simultaneous PAH and HM removal was accompanied by detoxification. The metabolites produced during co-treatment were not toxic for plant tissues, and the acute toxicity was reduced. The obtained results indicate that the tested fungi can be applied in the remediation of sites simultaneously contaminated with PAHs and HMs.}, }
@article {pmid36979988, year = {2023}, author = {Lindner, C and Looijesteijn, E and Dijck, HV and Bovee-Oudenhoven, I and Heerikhuisen, M and Broek, TJVD and Marzorati, M and Triantis, V and Nauta, A}, title = {Infant Fecal Fermentations with Galacto-Oligosaccharides and 2'-Fucosyllactose Show Differential Bifidobacterium longum Stimulation at Subspecies Level.}, journal = {Children (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {36979988}, issn = {2227-9067}, abstract = {The objective of the current study was to evaluate the potential of 2'-FL and GOS, individually and combined, in beneficially modulating the microbial composition of infant and toddler (12-18 months) feces using the micro-Matrix bioreactor. In addition, the impacts of GOS and 2'-FL, individually and combined, on the outgrowth of fecal bifidobacteria at (sub)species level was investigated using the baby M-SHIME[®] model. For young toddlers, significant increases in the genera Bifidobacterium, Veillonella, and Streptococcus, and decreases in Enterobacteriaceae, Clostridium XIVa, and Roseburia were observed in all supplemented fermentations. In addition, GOS, and combinations of GOS and 2'-FL, increased Collinsella and decreased Salmonella, whereas 2'-FL, and combined GOS and 2'-FL, decreased Dorea. Alpha diversity increased significantly in infants with GOS and/or 2'-FL, as well as the relative abundances of the genera Veillonella and Akkermansia with 2'-FL, and Lactobacillus with GOS. Combinations of GOS and 2'-FL significantly stimulated Veillonella, Lactobacillus, Bifidobacterium, and Streptococcus. In all supplemented fermentations, Proteobacteria decreased, with the most profound decreases accomplished by the combination of GOS and 2'-FL. When zooming in on the different (sub)species of Bifidobacterium, GOS and 2'-FL were shown to be complementary in stimulating breast-fed infant-associated subspecies of Bifidobacterium longum in a dose-dependent manner: GOS stimulated Bifidobacterium longum subsp. longum, whereas 2'-FL supported outgrowth of Bifidobacterium longum subsp. infantis.}, }
@article {pmid36978500, year = {2023}, author = {Peruzzo, A and Vascellari, M and Massaro, A and Mancin, M and Stefani, A and Orsini, M and Danesi, P and Petrin, S and Carminato, A and Santoro, MM and Speranza, R and Losasso, C and Capelli, G}, title = {Giardia duodenalis Colonization Slightly Affects Gut Microbiota and Hematological Parameters in Clinically Healthy Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {6}, pages = {}, pmid = {36978500}, issn = {2076-2615}, abstract = {Giardia duodenalis (Giardia) is a worldwide cause of acute diarrheal disease both in humans and animals. The primary aim of this study was to investigate possible variations in gut microbiota in a population of asymptomatic dogs (n = 31), naturally infected or not by Giardia. Gut microbiota and the hematological, biochemical, and fecal parameters related to intestinal function were investigated. Giardia infection was associated with a significant shift of beta diversity, showing a relevant reduction of Gammaproteobacteria and an increase of Fusobacteria in male-positive dogs if compared with negatives. A significant imbalance of different bacterial taxa, with particular reference to the Erysipelotrichales, Lactobacillales, Clostridiales, and Burkholderiales orders, was observed, with the first two being higher in Giardia-positive dogs. Giardia-positive males displayed significantly higher values of cCRP than negative males as well as positive females, supporting the presence of a pro-inflammatory state. Taken together, these results indicate that the presence of Giardia does not substantially modify the microbial ecology of the intestine nor the hematological markers of disease. Thus treatments against Giardia should be considered with caution in asymptomatic subjects.}, }
@article {pmid36978419, year = {2023}, author = {Perestrelo, S and Amaro, A and Brouwer, MSM and Clemente, L and Ribeiro Duarte, AS and Kaesbohrer, A and Karpíšková, R and Lopez-Chavarrias, V and Morris, D and Prendergast, D and Pista, A and Silveira, L and Skarżyńska, M and Slowey, R and Veldman, KT and Zając, M and Burgess, C and Alvarez, J}, title = {Building an International One Health Strain Level Database to Characterise the Epidemiology of AMR Threats: ESBL-AmpC Producing E. coli as An Example-Challenges and Perspectives.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36978419}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) is one of the top public health threats nowadays. Among the most important AMR pathogens, Escherichia coli resistant to extended spectrum cephalosporins (ESC-EC) is a perfect example of the One Health problem due to its global distribution in animal, human, and environmental sources and its resistant phenotype, derived from the carriage of plasmid-borne extended-spectrum and AmpC β-lactamases, which limits the choice of effective antimicrobial therapies. The epidemiology of ESC-EC infection is complex as a result of the multiple possible sources involved in its transmission, and its study would require databases ideally comprising information from animal (livestock, companion, wildlife), human, and environmental sources. Here, we present the steps taken to assemble a database with phenotypic and genetic information on 10,763 ESC-EC isolates retrieved from multiple sources provided by 13 partners located in eight European countries, in the frame of the DiSCoVeR Joint Research project funded by the One Health European Joint Programme (OH-EJP), along with its strengths and limitations. This database represents a first step to help in the assessment of different geographical and temporal trends and transmission dynamics in animals and humans. The work performed highlights aspects that should be considered in future international efforts, such as the one presented here.}, }
@article {pmid36978279, year = {2023}, author = {Horsch, CCA and Antunes, PM and Fahey, C and Grandy, AS and Kallenbach, CM}, title = {Trait-based assembly of arbuscular mycorrhizal fungal communities determines soil carbon formation and retention.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18914}, pmid = {36978279}, issn = {1469-8137}, abstract = {Fungi are crucial for soil organic carbon (SOC) formation, especially for the more persistent mineral-associated organic C (MAOC) pool. Yet, evidence for this often overlooks arbuscular mycorrhizal fungi (AMF) communities and how their composition and traits impact SOC accumulation. We grew sudangrass with AMF communities representing different traits conserved at the family-level: 1) competitors, from the Gigasporaceae family; 2) ruderals, from the Glomeraceae family; or 3) both families combined. We labeled sudangrass with [13] C-CO2 to assess AMF contributions to SOC, impacts on SOC priming, and fungal biomass persistence in MAOC. Single-family AMF communities decreased total SOC by 13.8%, likely due to fungal priming. Despite net SOC losses, all AMF communities contributed fungal C to soil but only the Glomeraceae community initially contributed to MAOC. After a month of decomposition, both the Glomeraceae and mixed-family communities contributed to MAOC formation. Plant phosphorus uptake, but not hyphal chemistry, was positively related to AMF soil C and MAOC accumulation. AMF contribution to MAOC is dependent on the specific traits of the AMF community and related to phosphorus uptake. These findings provide insight into how variations in AMF community composition and traits, and thus processes like environmental filtering of AMF, may impact SOC accumulation.}, }
@article {pmid36975801, year = {2023}, author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S}, title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0100322}, doi = {10.1128/msystems.01003-22}, pmid = {36975801}, issn = {2379-5077}, support = {T32 AI007140/AI/NIAID NIH HHS/United States ; }, abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.}, }
@article {pmid36973438, year = {2023}, author = {Xu, Z and Chen, J and Li, Y and Shekarriz, E and Wu, W and Chen, B and Liu, H}, title = {High Microeukaryotic Diversity in the Cold-Seep Sediment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36973438}, issn = {1432-184X}, abstract = {Microeukaryotic diversity, community structure, and their regulating mechanisms remain largely unclear in chemosynthetic ecosystems. Here, using high-throughput sequencing data of 18S rRNA genes, we explored microeukaryotic communities from the Haima cold seep in the northern South China Sea. We compared three distinct habitats: active, less active, and non-seep regions, with vertical layers (0-25 cm) from sediment cores. The results showed that seep regions harbored more abundant and diverse parasitic microeukaryotes (e.g., Apicomplexa and Syndiniales) as indicator species, compared to nearby non-seep region. Microeukaryotic community heterogeneity was larger between habitats than within habitat, and greatly increased when considering molecular phylogeny, suggesting the local diversification in cold-seep sediments. Microeukaryotic α-diversity at cold seeps was positively increased by metazoan richness and dispersal rate of microeukaryotes, while its β-diversity was promoted by heterogeneous selection mainly from metazoan communities (as potential hosts). Their combined effects led to the significant higher γ-diversity (i.e., total diversity in a region) at cold seeps than non-seep regions, suggesting cold-seep sediment as a hotspot for microeukaryotic diversity. Our study highlights the importance of microeukaryotic parasitism in cold-seep sediment and has implications for the roles of cold seep in maintaining and promoting marine biodiversity.}, }
@article {pmid36971795, year = {2023}, author = {Lemke, M and DeSalle, R}, title = {The Role of Microbial Genomics in Restoration Ecology: An Introduction.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02207-9}, pmid = {36971795}, issn = {1432-184X}, }
@article {pmid36970136, year = {2023}, author = {Munley, JA and Nagpal, R and Hanson, NC and Mirzaie, A and Laquian, L and Mohr, AM and Efron, PA and Arnaoutakis, DJ and Cooper, MA}, title = {Chronic mesenteric ischemia-induced intestinal dysbiosis resolved after revascularization.}, journal = {Journal of vascular surgery cases and innovative techniques}, volume = {9}, number = {2}, pages = {101084}, pmid = {36970136}, issn = {2468-4287}, abstract = {OBJECTIVE: Chronic mesenteric ischemia (CMI) is a debilitating condition arising from intestinal malperfusion from mesenteric artery stenosis or occlusion. Mesenteric revascularization has been the standard of care but can result in substantial morbidity and mortality. Most of the perioperative morbidity has been secondary to postoperative multiple organ dysfunction, potentially from ischemia-reperfusion injury. The intestinal microbiome is a dense community of microorganisms in the gastrointestinal tract that help regulate pathways ranging from nutritional metabolism to the immune response. We hypothesized that patients with CMI will have microbiome perturbations that contribute to this inflammatory response and could potentially normalize in the postoperative period.<br><br>METHODS: We performed a prospective study of patients with CMI who had undergone mesenteric bypass and/or stenting from 2019 to 2020. Stool samples were collected at three time points: preoperatively at the clinic, perioperatively within 14&#xa0;days after surgery, and postoperatively at the clinic at >30&#xa0;days after revascularization. Stool samples from healthy controls were used for comparison. The microbiome was measured using 16S rRNA sequencing on an Illumina-MiSeq sequence platform and analyzed using the QIIME2 (quantitative insights into microbial ecology 2)-DADA2 bioinformatics pipeline with the Silva database. Beta-diversity was analyzed using a principal coordinates analysis and permutational analysis of variance. Alpha-diversity (microbial richness and evenness) was compared using the nonparametric Mann-Whitney U test. Microbial taxa unique to CMI patients vs controls were identified using linear discriminatory analysis effect size analysis. P&#xa0;< .05 was considered statistically significant.<br><br>RESULTS: Eight patients with CMI had undergone mesenteric revascularization (25% men; average age, 71&#xa0;years). Nine healthy controls were also analyzed (78% men; average age, 55&#xa0;years). Bacterial alpha-diversity (number of operational taxonomic units) was dramatically reduced preoperatively compared with that of the controls (P&#xa0;= .03). However, revascularization partially restored the species richness and evenness in the perioperative and postoperative phases. Beta-diversity was only different between the perioperative and postoperative groups (P&#xa0;= .03). Further analyses revealed increased abundance of Bacteroidetes and Clostridia taxa preoperatively and perioperatively compared with the controls, which was reduced during the postoperative period.<br><br>CONCLUSIONS: The results from the present study have shown that patients with CMI have intestinal dysbiosis that resolves after revascularization. The intestinal dysbiosis is characterized by the loss of alpha-diversity, which is restored perioperatively and maintained postoperatively. This microbiome restoration demonstrates the importance of intestinal perfusion to sustain gut homeostasis and suggests that microbiome modulation could be a possible intervention to ameliorate acute and subacute postoperative outcomes in these patients.}, }
@article {pmid36964230, year = {2023}, author = {Abdullahi, IN and Juárez-Fernández, G and Höfle, U and Latorre-Fernández, J and Cardona-Cabrera, T and Mínguez-Romero, D and Zarazaga, M and Lozano, C and Torres, C}, title = {Staphylococcus aureus Carriage in the Nasotracheal Cavities of White Stork Nestlings (Ciconia ciconia) in Spain: Genetic Diversity, Resistomes and Virulence Factors.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36964230}, issn = {1432-184X}, abstract = {The molecular ecology of Staphylococcus aureus in migratory birds (such as white storks) is necessary to understand their relevance in the "One Health" ecosystems. This study determined the nasotracheal carriage rates of S. aureus from white storks in Southern Spain and genetically characterized the within-host diversity. A collection of 67 S. aureus strains, previously obtained from 87 white stork nestlings (52 nasal and 85 tracheal samples) fed by their parents with food foraged in natural and landfill habitats, were tested for their antimicrobial resistance (AMR) phenotypes. Moreover, the AMR genotypes, immune evasion cluster (IEC), virulence genes and the detection of CC398 lineage were studied by PCR. The spa types and multilocus-sequencing-typing (MLST) were also determined by PCR and sequencing. Staphylococcus aureus carriage was found in 31% of storks (36.5%/11.9% in nasal/tracheal samples). All isolates were methicillin-susceptible (MSSA) and 8.8% of them were also susceptible to all tested antibiotics. The AMR phenotype/percentage/genes detected were as follows: penicillin/79.1%/blaZ; erythromycin-clindamycin-inducible/19.1%/ermA, ermT; tetracycline/11.9%/tetK; clindamycin/4.5%/lnuA and ciprofloxacin/4.5%. Twenty-one different spa types, including 2 new ones (t7778-ST15-CC15 and t18009-ST26-CC25), were detected and ascribed to 11 clonal complexes (CCs). MSSA-CC398 (8.2%), MSSA-CC15 (7.1%) and MSSA-ST291 (5.9%) were the most prevalent lineages in storks. Moreover, tst-positive (MSSA-CC22-t223 and MSSA-CC30-t1654), eta-positive (MSSA-CC9-t209) and etb-positive strains (MSSA-CC45-t015) were detected in four storks. The 18.5% of storks harboured distinct MSSA strains (with different lineages and/or AMR genes). Nestlings of storks foraging in landfills (10 CCs) had more diverse S. aureus strains than those of parents foraging in natural habitats (3 CCs). Low level of AMR was demonstrated among S. aureus strains. The predominance of MSSA-CC398 (an emergent clade) and toxigenic MSSA strains in stork nestlings highlight the need for continuous surveillance of S. aureus in wild birds.}, }
@article {pmid36964199, year = {2023}, author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M}, title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36964199}, issn = {1751-7370}, abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.}, }
@article {pmid36963636, year = {2023}, author = {Campos, EVR and Pereira, ADES and Aleksieienko, I and do Carmo, GC and Gohari, G and Santaella, C and Fraceto, LF and Oliveira, HC}, title = {Encapsulated plant growth regulators and associative microorganisms: Nature-based solutions to mitigate the effects of climate change on plants.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {331}, number = {}, pages = {111688}, doi = {10.1016/j.plantsci.2023.111688}, pmid = {36963636}, issn = {1873-2259}, abstract = {Over the past decades, the atmospheric CO2 concentration and global average temperature have been increasing, and this trend is projected to soon become more severe. This scenario of climate change intensifies abiotic stress factors (such as drought, flooding, salinity, and ultraviolet radiation) that threaten forest and associated ecosystems as well as crop production. These factors can negatively affect plant growth and development with a consequent reduction in plant biomass accumulation and yield, in addition to increasing plant susceptibility to biotic stresses. Recently, biostimulants have become a hotspot as an effective and sustainable alternative to alleviate the negative effects of stresses on plants. However, the majority of biostimulants have poor stability under environmental conditions, which leads to premature degradation, shortening their biological activity. To solve these bottlenecks, micro- and nano-based formulations containing biostimulant molecules and/or microorganisms are gaining attention, as they demonstrate several advantages over their conventional formulations. In this review, we focus on the encapsulation of plant growth regulators and plant associative microorganisms as a strategy to boost their application for plant protection against abiotic stresses. We also address the potential limitations and challenges faced for the implementation of this technology, as well as possibilities regarding future research.}, }
@article {pmid36963187, year = {2023}, author = {Wang, B and Xiao, L and Xu, A and Mao, W and Wu, Z and Hicks, LC and Jiang, Y and Xu, J}, title = {Silicon fertilization enhances the resistance of tobacco plants to combined Cd and Pb contamination: Physiological and microbial mechanisms.}, journal = {Ecotoxicology and environmental safety}, volume = {255}, number = {}, pages = {114816}, doi = {10.1016/j.ecoenv.2023.114816}, pmid = {36963187}, issn = {1090-2414}, mesh = {Cadmium/analysis ; Silicon/pharmacology ; Tobacco/metabolism ; Lead/toxicity ; Fertilizers/analysis ; *Metals, Heavy/metabolism ; Soil/chemistry ; Fertilization ; *Soil Pollutants/analysis ; }, abstract = {Remediation of soil contaminated with cadmium (Cd) and lead (Pb) is critical for tobacco production. Silicon (Si) fertilizer can relieve heavy metal stress and promote plant growth, however, it remains unknown whether fertilization with Si can mitigate the effects of Cd and Pb on tobacco growth and alter microbial community composition in polluted soils. Here we assessed the effect of two organic (OSiFA, OSiFB) and one mineral Si fertilizer (MSiF) on Cd and Pb accumulation in tobacco plants, together with responses in plant biomass, physiological parameters and soil bacterial communities in pot experiments. Results showed that Si fertilizer relieved Cd and Pb stress on tobacco, thereby promoting plant growth: Si fertilizer reduced available Cd and Pb in the soil by 37.3 % and 28.6 %, respectively, and decreased Cd and Pb contents in the plant tissue by 42.0-55.5 % and 17.2-25.6 %, resulting in increased plant biomass by 13.0-30.5 %. Fertilization with Si alleviated oxidative damage by decreasing malondialdehyde content and increasing peroxidase and ascorbate peroxidase content. In addition, Si fertilization increased photosynthesis, chlorophyll and carotenoid content. Microbial community structure was also affected by Si fertilization. Proteobacteria and Actinobacteria were the dominant phylum in the Cd and Pb contaminated soils, but Si fertilization reduced the abundance of Actinobacteria. Si fertilization also altered microbial metabolic pathways associated with heavy metal resistance. Together, our results suggest that both organic and mineral Si fertilizers can promote tobacco growth by relieving plant physiological stress and favoring a heavy metal tolerant soil microbial community.}, }
@article {pmid36960281, year = {2023}, author = {Kapinusova, G and Lopez Marin, MA and Uhlik, O}, title = {Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1089630}, pmid = {36960281}, issn = {1664-302X}, abstract = {In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.}, }
@article {pmid36959175, year = {2023}, author = {Bjerg, JJ and Lustermans, JJM and Marshall, IPG and Mueller, AJ and Brokjær, S and Thorup, CA and Tataru, P and Schmid, M and Wagner, M and Nielsen, LP and Schramm, A}, title = {Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1614}, pmid = {36959175}, issn = {2041-1723}, mesh = {Oxidation-Reduction ; *Oxygen ; Geologic Sediments/microbiology ; *Deltaproteobacteria ; Bacteria/genetics ; Sulfides ; }, abstract = {Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.}, }
@article {pmid36958555, year = {2023}, author = {Zhang, X and Chen, L and Wang, Y and Jiang, P and Hu, Y and Ouyang, S and Wu, H and Lei, P and Kuzyakov, Y and Xiang, W}, title = {Plantations thinning: A meta-analysis of consequences for soil properties and microbial functions.}, journal = {The Science of the total environment}, volume = {877}, number = {}, pages = {162894}, doi = {10.1016/j.scitotenv.2023.162894}, pmid = {36958555}, issn = {1879-1026}, abstract = {Thinning is a widely-used management practice to reduce tree competition and improve wood production and quality in forest plantations. Thinning affects the soil ecosystem by changing the microclimate and plant growth, as well as litter inputs above and belowground, with all the resulting consequences for microbial communities and functions. Although many case studies have been carried out, a comprehensive understanding of the thinning effects on soil properties and microbial communities and functions in plantations remains to be explored. In this study, a meta-analysis was performed on 533 paired observations based on 90 peer-reviewed articles to evaluate the general responses of soil (mainly 0-20 cm depth) physicochemical properties, microbial biomass and community structure, and enzyme activities to thinning. Results showed that thinning increased soil temperature (13 %), moisture (8.0 %), electric conductivity (13 %), and the contents of total nitrogen (TN, 4.1 %), dissolved organic carbon (DOC, 9.7 %), nitrate N (NO3[-]-N, 27 %) and available phosphorous (22 %). For microbial properties, thinning decreased the fungi to bacteria ratio (F:B, -28 %) and the gram-positive bacteria to gram-negative bacteria ratio (G+:G-, -12 %), while increased microbial biomass C (7.1 %), microbial respiration (13 %), and nutrient-cycle related enzyme activities, including phenol oxidase (14 %), cellobiohydrolase (21 %), urease (10 %), and acid phosphatase (9 %). In particular, moderate thinning (30-60 % intensity) has higher conservation benefits for soil C and nutrients than light and heavy intensity, thus being recommended as the optimal thinning activity. This meta-analysis suggests that thinning consistently altered soil properties, shifted microbial community compositions from K- to-r strategist dominance, and stimulated microbial activities. These results are essential for optimizing plantation thinning management and provide evidence for applying the macro-ecology theory to ecosystem disturbance in soil microbial ecology.}, }
@article {pmid36948064, year = {2023}, author = {Goswami, P and Bhadury, P}, title = {First record of an Anthropocene marker plastiglomerate in Andaman Island, India.}, journal = {Marine pollution bulletin}, volume = {190}, number = {}, pages = {114802}, doi = {10.1016/j.marpolbul.2023.114802}, pmid = {36948064}, issn = {1879-3363}, abstract = {One of the most significant environmental issues confronting our world is plastic trash, which is of particular concern to the marine environment. The sedimentary record of the planet may likely one day contain a horizon of plastic that can be potentially identified as an Anthropocene marker. Here we report the presence of 'plastiglomerate' from coastal habitats located in the Aves Island, Andaman Sea, India. This novel form of plastic pollution forms with the incineration of plastic litter in the environment and then mixing of organic/inorganic composite materials in the molten plastic matrix. The plastic pollutants were collected from the Aves Island beach during marine litter surveys. Micro-Raman (μ-Raman) spectroscopy was used to evaluate and confirm all putative plastic forms. Plastiglomerates were made of a polyethylene (PE) and polyvinyl chloride (PVC) matrix with inclusions of rock and sand. Therefore, our research offers new insight into the intricate process of plastiglomerates formation.}, }
@article {pmid36947551, year = {2023}, author = {Bourne, ME and Gloder, G and Weldegergis, BT and Slingerland, M and Ceribelli, A and Crauwels, S and Lievens, B and Jacquemyn, H and Dicke, M and Poelman, EH}, title = {Parasitism causes changes in caterpillar odours and associated bacterial communities with consequences for host-location by a hyperparasitoid.}, journal = {PLoS pathogens}, volume = {19}, number = {3}, pages = {e1011262}, pmid = {36947551}, issn = {1553-7374}, mesh = {Animals ; Odorants ; Larva ; *Butterflies/parasitology ; *Wasps/parasitology ; Host-Parasite Interactions ; }, abstract = {Microorganisms living in and on macroorganisms may produce microbial volatile compounds (mVOCs) that characterise organismal odours. The mVOCs might thereby provide a reliable cue to carnivorous enemies in locating their host or prey. Parasitism by parasitoid wasps might alter the microbiome of their caterpillar host, affecting organismal odours and interactions with insects of higher trophic levels such as hyperparasitoids. Hyperparasitoids parasitise larvae or pupae of parasitoids, which are often concealed or inconspicuous. Odours of parasitised caterpillars aid them to locate their host, but the origin of these odours and its relationship to the caterpillar microbiome are unknown. Here, we analysed the odours and microbiome of the large cabbage white caterpillar Pieris brassicae in relation to parasitism by its endoparasitoid Cotesia glomerata. We identified how bacterial presence in and on the caterpillars is correlated with caterpillar odours and tested the attractiveness of parasitised and unparasitised caterpillars to the hyperparasitoid Baryscapus galactopus. We manipulated the presence of the external microbiome and the transient internal microbiome of caterpillars to identify the microbial origin of odours. We found that parasitism by C. glomerata led to the production of five characteristic volatile products and significantly affected the internal and external microbiome of the caterpillar, which were both found to have a significant correlation with caterpillar odours. The preference of the hyperparasitoid was correlated with the presence of the external microbiome. Likely, the changes in external microbiome and body odour after parasitism were driven by the resident internal microbiome of caterpillars, where the bacterium Wolbachia sp. was only present after parasitism. Micro-injection of Wolbachia in unparasitised caterpillars increased hyperparasitoid attraction to the caterpillars compared to untreated caterpillars, while no differences were found compared to parasitised caterpillars. In conclusion, our results indicate that host-parasite interactions can affect multi-trophic interactions and hyperparasitoid olfaction through alterations of the microbiome.}, }
@article {pmid36947169, year = {2023}, author = {Hammerle, F and Quirós-Guerrero, L and Wolfender, JL and Peintner, U and Siewert, B}, title = {Highlighting the Phototherapeutical Potential of Fungal Pigments in Various Fruiting Body Extracts with Informed Feature-Based Molecular Networking.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36947169}, issn = {1432-184X}, abstract = {Fungal pigments are characterized by a diverse set of chemical backbones, some of which present photosensitizer-like structures. From the genus Cortinarius, for example, several biologically active photosensitizers have been identified leading to the hypothesis that photoactivity might be a more general phenomenon in the kingdom Fungi. This paper aims at testing the hypothesis. Forty-eight fruiting body-forming species producing pigments from all four major biosynthetic pathways (i.e., shikimate-chorismate, acetate-malonate, mevalonate, and nitrogen heterocycles) were selected and submitted to a workflow combining in vitro chemical and biological experiments with state-of-the-art metabolomics. Fungal extracts were profiled by high-resolution mass spectrometry and subsequently explored by spectral organization through feature-based molecular networking (FBMN), including advanced metabolite dereplication techniques. Additionally, the photochemical properties (i.e., light-dependent production of singlet oxygen), the phenolic content, and the (photo)cytotoxic activity of the extracts were studied. Different levels of photoactivity were found in species from all four metabolic groups, indicating that light-dependent effects are common among fungal pigments. In particular, extracts containing pigments from the acetate-malonate pathway, e.g., extracts from Bulgaria inquinans, Daldinia concentrica, and Cortinarius spp., were not only efficient producers of singlet oxygen but also exhibited photocytotoxicity against three different cancer cell lines. This study explores the distribution of photobiological traits in fruiting body forming fungi and highlights new sources for phototherapeutics.}, }
@article {pmid36946113, year = {2023}, author = {Kauai, F and Mortier, F and Milosavljevic, S and Van de Peer, Y and Bonte, D}, title = {Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1995}, pages = {20222456}, pmid = {36946113}, issn = {1471-2954}, mesh = {Humans ; *Ploidies ; *Diploidy ; Polyploidy ; Chromosomes ; Reproduction ; }, abstract = {Polyploidy, i.e. the occurrence of multiple sets of chromosomes, is regarded as an important phenomenon in plant ecology and evolution, with all flowering plants likely having a polyploid ancestry. Owing to genome shock, minority cytotype exclusion and reduced fertility, polyploids emerging in diploid populations are expected to face significant challenges to successful establishment. Their establishment and persistence are often explained by possible fitness or niche differences that would relieve the competitive pressure with diploid progenitors. Experimental evidence for such advantages is, however, not unambiguous, and considerable niche overlap exists among most polyploid species and their diploid counterparts. Here, we develop a neutral spatially explicit eco-evolutionary model to understand whether neutral processes can explain the eco-evolutionary patterns of polyploids. We present a general mechanism for polyploid establishment by showing that sexually reproducing organisms assemble in space in an iterative manner, reducing frequency-dependent mating disadvantages and overcoming potential reduced fertility issues. Moreover, we construct a mechanistic theoretical framework that allows us to understand the long-term evolution of mixed-ploidy populations and show that our model is remarkably consistent with recent phylogenomic estimates of species extinctions in the Brassicaceae family.}, }
@article {pmid36946107, year = {2023}, author = {Jones, KR and Hughey, MC and Belden, LK}, title = {Colonization order of bacterial isolates on treefrog embryos impacts microbiome structure in tadpoles.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1995}, pages = {20230308}, pmid = {36946107}, issn = {1471-2954}, mesh = {Animals ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anura/genetics ; Biota ; Bacteria ; }, abstract = {Priority effects, or impacts of colonization order, may have lasting influence on ecological community composition. The embryonic microbiome is subject to stochasticity in colonization order of bacteria. Stochasticity may be especially impactful for embryos developing in bacteria-rich environments, such as the embryos of many amphibians. To determine if priority effects experienced as embryos impacted bacterial community composition in newly hatched tadpoles, we selectively inoculated the embryos of laboratory-raised hourglass treefrogs, Dendropsophus ebraccatus, with bacteria initially isolated from the skin of wild D. ebraccatus adults over 2 days. First, embryos were inoculated with two bacteria in alternating sequences. Next, we evaluated the outcomes of priority effects in an in vitro co-culture assay absent of host factors. We then performed a second embryo experiment, inoculating embryos with one of three bacteria on the first day and a community of five target bacteria on the second. Through 16S rRNA gene amplicon sequencing, we observed relative abundance shifts in tadpole bacteria communities due to priority effects. Our results suggest that the initial bacterial source pools of embryos shape bacterial communities at later life stages; however, the magnitude of those changes is dependent on the host environment and the identity of bacterial colonists.}, }
@article {pmid36945867, year = {2023}, author = {Snyder, GM and Passaretti, CL and Stevens, MP}, title = {Ho