@article {pmid39431865,
year = {2024},
author = {Daly, SE and Feng, J and Daeschel, D and Kovac, J and Snyder, AB},
title = {The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0062024},
doi = {10.1128/msystems.00620-24},
pmid = {39431865},
issn = {2379-5077},
abstract = {Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm[2]) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.},
}

@article {pmid39430784,
year = {2024},
author = {Li, X and Wang, Q and Wu, F and Ye, Z and Li, Y},
title = {Association between advanced lung cancer inflammation index and chronic kidney disease: a cross-sectional study.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1430471},
pmid = {39430784},
issn = {2296-861X},
abstract = {BACKGROUND: Chronic kidney disease (CKD) is one of the common chronic diseases, and malnutrition and inflammation play a key role in the development of CKD. The advanced lung cancer inflammation index (ALI) is a novel index of nutrition and inflammation, and its association with CKD has not yet been clarified. The aim of this study was to explore the potential association between ALI and CKD.

METHODS: We conducted a cross-sectional survey using data extracted from the National Health and Nutrition Examination Survey (NHANES, 2003-2018). Weighted multivariate logistic regression was used to assess the association between ALI and CKD, and smoothed curve fitting and threshold effect analyses were used to describe the nonlinear association between ALI and CKD. Subgroup analyses were performed to further assess the influence of other covariates on the relationship between ALI and CKD.

RESULTS: A total of 39,469 adult participants were included in the study, of whom 7,204 (18.25%) were diagnosed with CKD. After adjusting for multiple confounders, we found a significant negative correlation between ALI and CKD (OR = 0.93; 95%CI, 0.91-0.95; p < 0.0001). The risk of CKD tended to decrease with increasing quartiles of ALI. Smoothed curve fitting showed an L-shaped negative correlation between ALI and CKD. Threshold analysis showed a saturation effect of ALI at the inflection point of 55.09. Subgroup analyses and interaction tests showed that this negative association was maintained across age, sex, race, BMI, diabetes, hypertension, cardiovascular disease, and cancer subgroups (P for interaction >0.05).

CONCLUSION: Our findings suggest a significant correlation between ALI and CKD in the US adult population. However, more large-scale prospective studies are still needed to further confirm our findings.},
}

@article {pmid39430052,
year = {2025},
author = {Qin, K and Wang, Q and Qing, J and Li, Y and Gong, H and Zha, Z and Zhou, B and Li, Y},
title = {Analysis of mutations in Chinese patients with polycystic kidney disease by targeted exome sequencing.},
journal = {Genes & diseases},
volume = {12},
number = {1},
pages = {101246},
pmid = {39430052},
issn = {2352-3042},
}

@article {pmid39425011,
year = {2024},
author = {Sánchez, V and Baumann, A and Kromm, F and Yergaliyev, T and Brandt, A and Scholda, J and Kopp, F and Camarinha-Silva, A and Bergheim, I},
title = {Oral supplementation of choline attenuates the development of alcohol-related liver disease (ALD).},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {30},
number = {1},
pages = {181},
pmid = {39425011},
issn = {1528-3658},
mesh = {Animals ; *Choline/administration & dosage/metabolism ; *Liver Diseases, Alcoholic/metabolism/etiology/prevention & control/pathology/drug therapy ; *Dietary Supplements ; Mice ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects/pathology ; Administration, Oral ; Permeability ; Ethanol/adverse effects ; Disease Models, Animal ; },
abstract = {BACKGROUND: Chronic alcohol intake is associated with alterations of choline metabolism in various tissues. Here, we assessed if an oral choline supplementation attenuated the development of alcohol-related liver disease (ALD) in mice.

METHODS: Female C57BL/6 J mice (n = 8/group) were either pair-fed a liquid control diet, or a Lieber DeCarli liquid diet (5% ethanol) ± 2.7 g choline/kg diet for 29 days. Liver damage, markers of intestinal permeability and intestinal microbiota composition were determined. Moreover, the effects of choline on ethanol-induced intestinal permeability were assessed in an ex vivo model.

RESULTS: ALD development as determined by liver histology and assessing markers of inflammation (e.g., nitric oxide, interleukin 6 and 4-hydroxynonenal protein adducts) was attenuated by the supplementation of choline. Intestinal permeability in small intestine being significantly higher in ethanol-fed mice was at the level of controls in ethanol-fed mice receiving choline. In contrast, no effects of the choline supplementation were found on intestinal microbiota composition. Choline also significantly attenuated the ethanol-induced intestinal barrier dysfunction in small intestinal tissue ex vivo, an effect almost entirely abolished by the choline oxidase inhibitor dimbunol.

CONCLUSION: Our results suggest that an oral choline supplementation attenuates the development of ALD in mice and is related to a protection from intestinal barrier dysfunction.},
}

Animals
*Choline/administration & dosage/metabolism
*Liver Diseases, Alcoholic/metabolism/etiology/prevention & control/pathology/drug therapy
*Dietary Supplements
Mice
Female
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Liver/metabolism/drug effects/pathology
Administration, Oral
Permeability
Ethanol/adverse effects
Disease Models, Animal

@article {pmid39423562,
year = {2024},
author = {Dal Bello, M and Abreu, CI},
title = {Temperature structuring of microbial communities on a global scale.},
journal = {Current opinion in microbiology},
volume = {82},
number = {},
pages = {102558},
doi = {10.1016/j.mib.2024.102558},
pmid = {39423562},
issn = {1879-0364},
abstract = {Temperature is a fundamental physical constraint regulating key aspects of microbial life. Protein binding, membrane fluidity, central dogma processes, and metabolism are all tightly controlled by temperature, such that growth rate profiles across taxa and environments follow the same general curve. An open question in microbial ecology is how the effects of temperature on individual traits scale up to determine community structure and function at planetary scales. Here, we review recent theoretical and experimental efforts to connect physiological responses to the outcome of species interactions, the assembly of microbial communities, and their function as temperature changes. We identify open questions in the field and define a roadmap for future studies.},
}

@article {pmid39423289,
year = {2024},
author = {Steensen, K and Séneca, J and Bartlau, N and Yu, XA and Hussain, FA and Polz, MF},
title = {Prophages in Vibrio.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae202},
pmid = {39423289},
issn = {1751-7370},
abstract = {Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1,158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.},
}

@article {pmid39419992,
year = {2024},
author = {Mei, S and Wang, M and Salles, JF and Hackl, T},
title = {Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1140},
pmid = {39419992},
issn = {2052-4463},
support = {[2020]596//China Scholarship Council (CSC)/ ; },
mesh = {*Rhizosphere ; *Pseudomonas/genetics ; *Soil Microbiology ; *Wetlands ; *Genome, Bacterial ; Artemisia/genetics/microbiology ; Biodiversity ; },
abstract = {Soil microbes are key drivers of ecosystem processes promoting nutrient cycling, system productivity, and resilience. While much is known about the roles of microbes in established systems, their impact on soil development and the successional transformation over time remains poorly understood. Here, we provide 67 diverse, rhizosphere-associated Pseudomonas draft genomes from an undisturbed salt march primary succession spanning >100 years of soil development. Pseudomonas are cosmopolitan bacteria with a significant role in plant establishment and growth. We obtained isolates associated with Limonium vulgare and Artemisia maritima, two typical salt marsh perennial plants with roles in soil stabilization, salinity regulation, and biodiversity support. We anticipate that our data, in combination with the provided physiochemical measurements, will help identify genomic signatures associated with the different selective regimes along the successional stages, such as varying soil complexity, texture, and nutrient availability. Such findings would advance our understanding of Pseudomonas' role in natural soil ecosystems and provide the basis for a better understanding of the roles of microbes throughout ecosystem transformations.},
}

*Rhizosphere
*Pseudomonas/genetics
*Soil Microbiology
*Wetlands
*Genome, Bacterial
Artemisia/genetics/microbiology
Biodiversity

@article {pmid39419884,
year = {2024},
author = {Mohammed, FA and Abu-Hussien, SH and Dougdoug, NKE and Koutb, N and Korayem, AS},
title = {Streptomyces fradiae Mitigates the Impact of Potato Virus Y by Inducing Systemic Resistance in Two Egyptian Potato (Solanum tuberosum L.) Cultivars.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {131},
pmid = {39419884},
issn = {1432-184X},
mesh = {*Solanum tuberosum/virology/microbiology ; *Streptomyces/isolation & purification/physiology/genetics ; *Potyvirus/physiology ; *Plant Diseases/virology/microbiology ; *Disease Resistance ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95-98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection.},
}

*Solanum tuberosum/virology/microbiology
*Streptomyces/isolation & purification/physiology/genetics
*Potyvirus/physiology
*Plant Diseases/virology/microbiology
*Disease Resistance
RNA, Ribosomal, 16S/genetics

@article {pmid39419230,
year = {2024},
author = {Siebert, C and Ionescu, D and Mallast, U and Merchel, S and Merkel, B and Möller, P and Pavetich, S and Pohl, T and Rödiger, T and Yechieli, Y},
title = {A new type of submarine chimneys built of halite.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176752},
doi = {10.1016/j.scitotenv.2024.176752},
pmid = {39419230},
issn = {1879-1026},
abstract = {In contrast to the subaquatic sulphide and carbonate chimneys, which are known from Mid Ocean Ridges and abyssal submarine volcanoes, chimneys built of salts have not been described yet. Here we present such halite chimneys as a new form of cold-water smokers in hypersaline environments. The here described structures rise up from the bottom of the Dead Sea and result from the submarine discharge of saturated halite-dissolution brines into the salt lake, which is at halite saturation and holds remarkable chloride excess. At the interface with the lake brine, halite precipitates instantaneously, forming chimneys up to several meters in height. The brines leading to the formation of these chimneys vary in composition, while their generation processes are similar. Fresh groundwater from surrounding aquifers enters the saline lake sediments and considerably leaches halite in the adjacencies of the lake. Simultaneously, it mixes with ancient brines before it emerges from the lake floor. The distinct differences in composition between the Dead Sea and the emerging chimney brines lead to the instantaneous crystallisation of halite and few other mineral phases. The chimney structure result from the buoyancy flow of the chimney brines, which are less dense then the ambient Dead Sea. The chimneys indicate intense cavitation of massive halite bodies in the subsurface of the Dead Sea environment, a process that leads to increasing formation of hazardous sinkholes. Since chimneys are proven in shallow water but may be expected in deeper parts too, they are comfortably mappable by echo-sounding or aerial imaging. They thus provide in the Dead Sea as in any likewise setting a potent predictive tool to locate dangerous subsurface cavitation and hence areas that are at risk of collapse in the near future.},
}

@article {pmid39419211,
year = {2024},
author = {Santos-Silva, L and Roque, WF and de Moura, JM and Mello, IS and de Carvalho, LAL and Pinheiro, DG and Bouzan, RS and Brescovit, AD and de Andrade, RLT and da Silva, GF and Battirola, LD and Soares, MA},
title = {Toxic metals in Amazonian soil modify the bacterial community associated with Diplopoda.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176915},
doi = {10.1016/j.scitotenv.2024.176915},
pmid = {39419211},
issn = {1879-1026},
abstract = {Toxic metal pollution in the Amazon is a serious problem that reduces the quality of water, soil, air, and consequently alters communities of fauna, flora, and microbiota, harming human health and well-being. Our aim was to determine the impact of toxic metals on the structure of the bacterial community associated with Diplopoda in the Amazon rainforest. Animals were kept in microcosms contaminated with cadmium (50 mg.kg[-1]), mercury (35 mg.kg[-1]) and no toxic metal (control). The intestinal and molting chamber microbiota were accessed by culture-dependent and culture-independent methods (16S metabarcoding). The cultivated strains were identified, and their functional traits evaluated: secretion of enzymes, growth at different pH, resistance to metals and antibiotics, and ability to reduce toxic effects of metals on plants. Our research described Brachyurodesmus albus, a new species of Diplopoda. We obtained 177 isolates distributed in 35 genera and 61 species of bacteria (Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota) associated with the gut and molting chamber of B. albus. Metabarcoding data provided a more robust access to the bacterial community, resulting in 24 phyla, 561 genera and 6792 ASVs. The presence of metal Cd and Hg alters the composition and abundance of bacteria associated with B. albus (PERMANOVA p < 0.05). The microhabitat (gut and molting chamber) harbours bacterial communities that differ in composition and abundance (PERMANOVA p < 0.05). The presence of Cd and Hg alters important metabolic pathways related to the prokaryotic defense system; antimicrobial resistance genes, endocytosis and secretion system, estimated by PICRUSt. Bacteria selected with high resistance to Cd and Hg buffer the toxic effect of metals on tomato seedlings. This work describes B. albus and concludes that its diverse bacterial microbiota is altered by soil contamination by toxic metals, as well as being an important repository for prospecting strains to be applied in bioremediation programs.},
}

@article {pmid39419002,
year = {2024},
author = {Meroz, N and Livny, T and Toledano, G and Sorokin, Y and Tovi, N and Friedman, J},
title = {Evolution in microbial microcosms is highly parallel, regardless of the presence of interacting species.},
journal = {Cell systems},
volume = {15},
number = {10},
pages = {930-940.e5},
doi = {10.1016/j.cels.2024.09.007},
pmid = {39419002},
issn = {2405-4720},
mesh = {*Biological Evolution ; Microbial Interactions/physiology ; Adaptation, Physiological ; Mutation ; Bacteria/genetics/metabolism ; Evolution, Molecular ; },
abstract = {Evolution often follows similar trajectories in replicate populations, suggesting that it may be predictable. However, populations are naturally embedded in multispecies communities, and the extent to which evolution is contingent on the specific species interacting with the focal population is still largely unexplored. Here, we study adaptations in strains of 11 different species, experimentally evolved both in isolation and in various pairwise co-cultures. Although partner-specific effects are detectable, evolution was mostly shared between strains evolved with different partners; similar changes occurred in strains' growth abilities, in community properties, and in about half of the repeatedly mutated genes. This pattern persisted even in species pre-adapted to the abiotic conditions. These findings indicate that evolution may not always depend strongly on the biotic environment, making predictions regarding coevolutionary dynamics less challenging than previously thought. A record of this paper's transparent peer review process is included in the supplemental information.},
}

*Biological Evolution
Microbial Interactions/physiology
Adaptation, Physiological
Mutation
Bacteria/genetics/metabolism
Evolution, Molecular

@article {pmid39418776,
year = {2024},
author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M},
title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.},
journal = {Multiple sclerosis and related disorders},
volume = {92},
number = {},
pages = {105936},
doi = {10.1016/j.msard.2024.105936},
pmid = {39418776},
issn = {2211-0356},
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.

METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.

RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the α-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.

CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.},
}

@article {pmid39418385,
year = {2024},
author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M},
title = {Mechanism of bacterial predation via ixotrophy.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6719},
pages = {eadp0614},
doi = {10.1126/science.adp0614},
pmid = {39418385},
issn = {1095-9203},
mesh = {*Cryoelectron Microscopy ; Type VI Secretion Systems/metabolism/genetics ; Single-Cell Analysis ; Bacteria/metabolism/genetics ; },
abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.},
}

*Cryoelectron Microscopy
Type VI Secretion Systems/metabolism/genetics
Single-Cell Analysis
Bacteria/metabolism/genetics

@article {pmid39417884,
year = {2024},
author = {Mircea, C and Rusu, I and Levei, EA and Cristea, A and Gridan, IM and Zety, AV and Banciu, HL},
title = {The Fungal Side of the Story: Saprotrophic- vs. Symbiotrophic-Predicted Ecological Roles of Fungal Communities in Two Meromictic Hypersaline Lakes from Romania.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {130},
pmid = {39417884},
issn = {1432-184X},
support = {PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-PD-2021-0634//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; PN-III-P4-ID-PCE-2020-1559//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; },
mesh = {*Lakes/microbiology ; Romania ; *Fungi/genetics/classification/isolation & purification/physiology ; *Salinity ; *Mycobiome ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Geologic Sediments/microbiology ; Soil Microbiology ; DNA, Fungal/genetics ; Phylogeny ; },
abstract = {Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments.},
}

*Lakes/microbiology
Romania
*Fungi/genetics/classification/isolation & purification/physiology
*Salinity
*Mycobiome
RNA, Ribosomal, 18S/genetics
Biodiversity
Geologic Sediments/microbiology
Soil Microbiology
DNA, Fungal/genetics
Phylogeny

@article {pmid39415203,
year = {2024},
author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH},
title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {198},
pmid = {39415203},
issn = {2049-2618},
support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; },
mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; },
abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.

RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.

CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.},
}

Humans
Hong Kong
*Microbiota
*Built Environment
*Metagenome
*Phylogeny
*Bacteria/classification/genetics/metabolism/isolation & purification
Skin/microbiology
Micrococcus luteus/genetics/metabolism
Genome, Bacterial

@article {pmid39414684,
year = {2024},
author = {Siqueira, JS and de Carvalho, LAL and Santos, CHB and Frezarin, ET and Pinheiro, DG and Nicodemo, D and Desoignies, N and Rigobelo, EC},
title = {Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {129},
pmid = {39414684},
issn = {1432-184X},
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; Fungi/classification/genetics/isolation & purification/physiology ; Biodiversity ; Trees/microbiology ; Soil Microbiology ; },
abstract = {Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization.},
}

*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Plant Roots/microbiology
*Plant Leaves/microbiology
Fungi/classification/genetics/isolation & purification/physiology
Biodiversity
Trees/microbiology
Soil Microbiology

@article {pmid39411441,
year = {2024},
author = {Pardo-Esté, C and Cortés, J and Castro-Severyn, J and Pérez, V and Henriquez-Aedo, K and Cuadros, F and Yañez, C and Cuadros-Orellana, S and Dorador, C and Molina, V and Eissler, Y and Paquis, P and Jeffrey, WH and Pozo, P and Pérez, PA and Hengst, MB},
title = {Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1477458},
pmid = {39411441},
issn = {1664-302X},
abstract = {Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.},
}

@article {pmid39411429,
year = {2024},
author = {Xiao, P and Wu, Y and Zuo, J and Grossart, HP and Sun, R and Li, G and Jiang, H and Cheng, Y and Wang, Z and Geng, R and Zhang, H and Ma, Z and Yan, A and Li, R},
title = {Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479158},
pmid = {39411429},
issn = {1664-302X},
abstract = {INTRODUCTION: In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.

METHODS: Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.

RESULTS AND DISCUSSION: This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.},
}

@article {pmid39409485,
year = {2024},
author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F},
title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.},
journal = {Sensors (Basel, Switzerland)},
volume = {24},
number = {19},
pages = {},
doi = {10.3390/s24196445},
pmid = {39409485},
issn = {1424-8220},
support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; },
abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.},
}

@article {pmid39406893,
year = {2024},
author = {Ioannou, A and Berkhout, MD and Geerlings, SY and Belzer, C},
title = {Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39406893},
issn = {1740-1534},
abstract = {Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.},
}

@article {pmid39406702,
year = {2024},
author = {Wegner, H and Roitman, S and Kupczok, A and Braun, V and Woodhouse, JN and Grossart, HP and Zehner, S and Béjà, O and Frankenberg-Dinkel, N},
title = {Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8783},
pmid = {39406702},
issn = {2041-1723},
support = {FR1487/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 143/18//Israel Science Foundation (ISF)/ ; },
mesh = {*Tetrapyrroles/biosynthesis/metabolism ; *Bacteriophages/genetics/metabolism ; Escherichia coli/genetics/virology/metabolism ; 5-Aminolevulinate Synthetase/genetics/metabolism ; Amino Acid Sequence ; Heme/metabolism/biosynthesis ; Aminolevulinic Acid/metabolism ; Phylogeny ; Fresh Water/virology ; Biosynthetic Pathways/genetics ; },
abstract = {Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.},
}

*Tetrapyrroles/biosynthesis/metabolism
*Bacteriophages/genetics/metabolism
Escherichia coli/genetics/virology/metabolism
5-Aminolevulinate Synthetase/genetics/metabolism
Amino Acid Sequence
Heme/metabolism/biosynthesis
Aminolevulinic Acid/metabolism
Phylogeny
Fresh Water/virology
Biosynthetic Pathways/genetics

@article {pmid39404095,
year = {2024},
author = {Leleiwi, I and Kokkinias, K and Kim, Y and Baniasad, M and Shaffer, M and Sabag-Daigle, A and Daly, RA and Flynn, RM and Wysocki, VH and Ahmer, BMM and Borton, MA and Wrighton, KC},
title = {Gut microbiota carbon and sulfur metabolisms support Salmonella infections.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae187},
pmid = {39404095},
issn = {1751-7370},
abstract = {Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, we performed multi-omics on fecal microbial communities from untreated and Salmonella-infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. These data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella-induced inflammation significantly reduced the diversity of genomes that recruited transcripts in the gut microbiome, yet increased transcript mapping was observed for 7 members, among which Luxibacter and Ligilactobacillus transcript read recruitment was most prevalent. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst members with detected transcript recruitment. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. This research advances physiological microbiome insights beyond prior amplicon-based approaches, with the transcriptionally active organismal and metabolic pathways outlined here offering intriguing intervention targets in the Salmonella-infected intestine.},
}

@article {pmid39404077,
year = {2024},
author = {Ellington, AJ and Walters, K and Christner, BC and Fox, S and Bonfantine, K and Walker, C and Lampman, P and Vuono, DC and Strickland, M and Lambert, K and Kobziar, LN},
title = {Dispersal of microbes from grassland fire smoke to soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae203},
pmid = {39404077},
issn = {1751-7370},
support = {P20GM103408//National Institute of General Medical Sciences of the National Institutes of Health/ ; 2039531//National Science Foundation/ ; },
abstract = {Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of fields including agriculture, restoration, plant disease, and biodiversity.},
}

@article {pmid39402079,
year = {2024},
author = {Ashraf, H and Dikarlo, P and Masia, A and Zarbo, IR and Solla, P and Ijaz, UZ and Sechi, LA},
title = {Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with multiple sclerosis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24027},
pmid = {39402079},
issn = {2045-2322},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobacterium avium subsp. paratuberculosis/isolation & purification ; *Paratuberculosis/microbiology ; *Multiple Sclerosis/microbiology ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Middle Aged ; },
abstract = {The microbial ecology of Mycobacterium avium subspecies paratuberculosis infections (MAP) within the context of Multiple Sclerosis (MS) is largely an unexplored topic in the literature. Thus, we have characterized the compositional and predicted functional differences of the gut microbiome between MS patients with MAP (MAP+) and without (MAP-) infection. This was done in the context of exposome differences (through self-reported filled questionnaires), principally in anthropometric and sociodemographic patterns to gain an understanding of the gut microbiome dynamics. 16S rRNA microbiome profiling of faecal samples (n = 69) was performed for four groups, which differed by disease and MAP infection: healthy cohort (HC) MAP-; HC MAP+ ; MS MAP-; and MS MAP+ . Using a dynamic strategy, with MAP infection and time of sampling as occupancy models, we have recovered the core microbiome for both HC and MS individuals. Additional application of neutral modeling suggests key genera that are under selection pressure by the hosts. These include members of the phyla Actinobacteriota, Bacteroidota, and Firmicutes. As several subjects provided multiple samples, a Quasi Conditional Association Test that incorporates paired-nature of samples found major differences in Archaea. To consolidate treatment groups, confounders, microbiome, and the disease outcome parameters, a mediation analysis is performed for MS cohort. This highlighted certain genera i.e., Sutterella, Akkermansia, Bacteriodes, Gastranaerophilales, Alistipes, Balutia, Faecalibacterium, Lachnospiraceae, Anaerostipes, Ruminococcaceae, Eggerthellaceae and Clostridia-UCG-014 having mediatory effect using disease duration as an outcome and MAP infection as a treatment group. Our analyses indicate that the gut microbiome may be an important target for dietary and lifestyle intervention in MS patients with and without MAP infection.},
}

Humans
*Gastrointestinal Microbiome
*Mycobacterium avium subsp. paratuberculosis/isolation & purification
*Paratuberculosis/microbiology
*Multiple Sclerosis/microbiology
Female
Male
*RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology
Middle Aged

@article {pmid39401449,
year = {2024},
author = {Ahmerkamp, S and Pacherres, CO and Mosshammer, M and Godefroid, M and Wind-Hansen, M and Kuypers, M and Behrendt, L and Koren, K and Kühl, M},
title = {Novel Approach for Lifetime-Proportional Luminescence Imaging Using Frame Straddling.},
journal = {ACS sensors},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssensors.4c01828},
pmid = {39401449},
issn = {2379-3694},
abstract = {Optode-based chemical imaging is a rapidly evolving field that has substantially enhanced our understanding of the role of microenvironments and chemical gradients in biogeochemistry, microbial ecology, and biomedical sciences. Progress in sensor chemistry has resulted in a broadened spectrum of analytes, alongside enhancements in sensor performance (e.g., sensitivity, brightness, and photostability). However, existing imaging techniques are often costly, challenging to implement, and limited in their recording speed. Here we use the "frame-straddling" technique, originally developed for particle image velocimetry for imaging the O2-dependent, integrated luminescence decay of optical O2 sensor materials. The method synchronizes short excitation pulses and camera exposures to capture two frames at varying brightness, where the first excitation pulse occurs at the end of the exposure of the first frame and the second excitation pulse at the beginning of the second frame. Here the first frame truncates the luminescence decay, whereas the second frame fully captures it. The difference between the frames quantifies the integral of the luminescence decay curve, which is proportional to the luminescence lifetime, at time scales below one millisecond. Short excitation pulses avoid depopulation of the ground state of luminophores, resulting in a linear Stern-Volmer response with increasing concentrations of the quencher (O2), which can be predicted through a simple model. This methodology is compatible with a wide range of camera systems, making it a versatile tool for various optode based chemical imaging applications. We showcase the utility of frame straddling in measuring O2 dynamics around algae and by observing O2 scavenging sodium dithionite particles sinking through oxygenated water.},
}

@article {pmid39399973,
year = {2024},
author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC},
title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
doi = {10.1093/gigascience/giae071},
pmid = {39399973},
issn = {2047-217X},
support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; },
mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; },
abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.},
}

*Isotope Labeling/methods
Reproducibility of Results
Microbiota/genetics
Metadata
Metagenomics/methods
Sequence Analysis, DNA/methods
Metagenome

@article {pmid39398475,
year = {2024},
author = {Kumar, G and Bhadury, P},
title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110961},
pmid = {39398475},
issn = {2352-3409},
abstract = {The data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained from genomic DNA extracted from frozen fecal samples collected from a healthy individual on Day 3, Day 5, Day 9, Day 12, and Day 30, in addition to Day 1 (unfrozen). The metagenomic sequence data have been deposited at NCBI SRA as BioProject PRJNA827663. The taxonomic annotation undertaken using MG-RAST showed relative abundance of bacteria represented by different taxonomic levels varied significantly based on two sequencing chemistries. There was distinct temporal variation in the relative abundance of bacteria at different taxonomic levels based on the day of extraction of genomic DNA. This dataset can be used to study differences in functional profiles of human gut microbiome using different sequencing technologies. Moreover, generated data can aid in selection of most appropriate sequencing chemistry to study future human gut microbiome studies based on the appropriate preservation method of fecal samples.},
}

@article {pmid39397203,
year = {2024},
author = {Liu, K and Yan, Q and Guo, X and Wang, W and Zhang, Z and Ji, M and Wang, F and Liu, Y},
title = {Glacier Retreat Induces Contrasting Shifts in Bacterial Biodiversity Patterns in Glacial Lake Water and Sediment : Bacterial Communities in Glacial Lakes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {128},
pmid = {39397203},
issn = {1432-184X},
support = {ANSO-CR-KP-2021-04//the Key Collaborative Research Program of the Alliance of International Science Organizations/ ; 42330410//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; },
mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; *Ice Cover/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Microbiota ; Ecosystem ; Tibet ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; },
abstract = {Glacial lake ecosystems are experiencing rapid changes due to accelerated glacier retreat. As glaciers recede, their influence on downstream habitats diminishes, potentially affecting the biodiversity of glacial lake microbial communities. However, there remains a knowledge gap regarding how bacterial biodiversity patterns in glacial lakes are altered by diminishing glacial influence. Here, we investigated shifts in bacterial communities in paired water and sediment samples collected from seven glacial lakes on the Tibetan Plateau, using a space-for-time substitution approach to understand the consequences of glacier retreat. Our findings reveal that bacterial diversity in lake water increases significantly with a higher glacier index (GI), whereas sediment bacterial diversity exhibits a negative correlation with GI. Both the water and sediment bacterial communities display significant structural shifts along the GI gradient. Notably, reduced glacial influence decreases the complexity of bacterial co-occurrence networks in lake water but enhances the network complexity in sediment. This divergence in diversity and co-occurrence patterns highlights that water and sediment bacterial communities respond differently to changes in glacial influence in these lake ecosystems. This study provides insights into how diminishing glacial influence impacts the bacterial biodiversity in glacial lake water and sediments, revealing contrasting patterns between the two habitats. These findings emphasize the need for comprehensive monitoring to understand the implications of glacier retreat on these fragile ecosystems.},
}

*Lakes/microbiology
*Geologic Sediments/microbiology
*Ice Cover/microbiology
*Bacteria/classification/genetics/isolation & purification
*Biodiversity
Microbiota
Ecosystem
Tibet
RNA, Ribosomal, 16S/genetics
Water Microbiology

@article {pmid39392836,
year = {2024},
author = {Daisley, BA and Allen-Vercoe, E},
title = {Microbes as medicine.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.15237},
pmid = {39392836},
issn = {1749-6632},
support = {950-232131//Canada Research Chairs/ ; PDF-402947//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; 2023//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Over the last two decades, advancements in sequencing technologies have significantly deepened our understanding of the human microbiome's complexity, leading to increased concerns about the detrimental effects of antibiotics on these intricate microbial ecosystems. Concurrently, the rise in antimicrobial resistance has intensified the focus on how beneficial microbes can be harnessed to treat diseases and improve health and offer potentially promising alternatives to traditional antibiotic treatments. Here, we provide a comprehensive overview of both established and emerging microbe-centric therapies, from probiotics to advanced microbial ecosystem therapeutics, examine the sophisticated ways in which microbes are used medicinally, and consider their impacts on microbiome homeostasis and health outcomes through a microbial ecology lens. In addition, we explore the concept of rewilding the human microbiome by reintroducing "missing microbes" from nonindustrialized societies and personalizing microbiome modulation to fit individual microbial profiles-highlighting several promising directions for future research. Ultimately, the advancements in sequencing technologies combined with innovative microbial therapies and personalized approaches herald a new era in medicine poised to address antibiotic resistance and improve health outcomes through targeted microbiome management.},
}

@article {pmid39387587,
year = {2024},
author = {Akob, DM and Oates, AE and Girguis, PR and Badgley, BD and Cooper, VS and Poretsky, RS and Tierney, BT and Litchman, E and Whitaker, RJ and Whiteson, KL and Metcalf, CJE and , },
title = {Perspectives on the future of ecology, evolution, and biodiversity from the Council on Microbial Sciences of the American Society for Microbiology.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0030724},
doi = {10.1128/msphere.00307-24},
pmid = {39387587},
issn = {2379-5042},
abstract = {The field of microbial ecology, evolution, and biodiversity (EEB) is at the leading edge of understanding how microbes shape our biosphere and influence the well-being of humankind and Earth. To that end, EEB is developing new transdisciplinary tools to analyze these ecologically critical, complex microbial communities. The American Society for Microbiology's Council on Microbial Sciences hosted a virtual retreat in 2023 to discuss the trajectory of EEB both within the Society and microbiology writ large. The retreat emphasized the interconnectedness of microbes and their outsized global influence on environmental and host health. The maximal potential impact of EEB will not be achieved without contributions from disparate fields that unite diverse technologies and data sets. In turn, this level of transdisciplinary efforts requires actively encouraging "broad" research, spanning inclusive global collaborations that incorporate both scientists and the public. Together, the American Society for Microbiology and EEB are poised to lead a paradigm shift that will result in a new era of collaboration, innovation, and societal relevance for microbiology.},
}

@article {pmid39387577,
year = {2024},
author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E},
title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084024},
doi = {10.1128/msystems.00840-24},
pmid = {39387577},
issn = {2379-5077},
abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.

IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.},
}

@article {pmid39387551,
year = {2024},
author = {Halbrook, S and Wilber, W and Barrow, ME and Farrer, EC},
title = {Bacterial community response to novel and repeated disturbances.},
journal = {Environmental microbiology reports},
volume = {16},
number = {5},
pages = {e70022},
doi = {10.1111/1758-2229.70022},
pmid = {39387551},
issn = {1758-2229},
support = {LEQSF(2017-20)-RD-A-14//Louisiana Board of Regents/ ; //Tulane University/ ; DEB-2141922//National Science Foundation/ ; },
mesh = {*Bacteria/genetics/classification/isolation & purification ; Salinity ; Microbiota ; Ecosystem ; Biodiversity ; },
abstract = {Disturbance response and recovery are increasingly important in microbial ecology, as microbes may recover from disturbances differently than macro communities. Past disturbances can alter microbial community structure and their response to subsequent disturbance events, but it remains unclear if the same recovery patterns persist after long-term exposure to stress. Here, we compare bacterial community composition in a community that experienced 2 years of monthly salinity addition disturbances with a community that has not experienced salinity additions. We then track the response and recovery to an additional salinity addition based on past disturbance exposure. We tested the following hypotheses: first, communities with a repeated disturbance history will have a different community composition than communities without a disturbance history; second, communities exposed to repeated disturbances will undergo a different recovery trajectory than communities experiencing a novel disturbance. We find that repeated disturbances alter community composition and affect community response and recovery to a subsequent disturbance after 2 years, primarily through increased resistance. This work enhances our understanding of microbial temporal dynamics and suggests that novel disturbances may pose a threat to microbial community structure and function.},
}

*Bacteria/genetics/classification/isolation & purification
Salinity
Microbiota
Ecosystem
Biodiversity

@article {pmid39392487,
year = {2024},
author = {Legeay, J and Basiru, S and Ziami, A and Errafii, K and Hijri, M},
title = {Response of Alternaria and Fusarium Species to Low Precipitation in a Drought-Tolerant Plant in Morocco.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {127},
pmid = {39392487},
issn = {1432-184X},
support = {Project AS-85//OPC Africa and OCP Innovation/ ; },
mesh = {Morocco ; *Fusarium/physiology/isolation & purification/classification ; *Droughts ; *Alternaria/physiology/classification ; *Plant Roots/microbiology ; *Rain ; Soil Microbiology ; Mycobiome ; Rhizosphere ; },
abstract = {The plant mycobiome plays a crucial role in the host life cycle, influencing both healthy and diseased states, and is essential for plant tolerance to drought. In this study, we used ITS metabarcoding to investigate the fungal community of the drought-resistant plant Malva sylvestris L. in Morocco along a gradient of precipitation, encompassing subhumid and semi-arid environments. We sampled three biotopes: rhizosphere, bulk soil, and root endosphere. Our findings revealed an absence of beta-diversity differences between bulk soil and rhizosphere, indicating that the plant does not selectively influence its rhizosphere mycobiome. Additionally, ASVs belonging to the genus Alternaria represented up to 30% of reads in the plant's roots and correlated with drought (p = 0.006), indicating a potential role for this fungal genus in mitigating drought, possibly as part of the dark septate endophyte group. Root staining and microscopic observation revealed extensive colonization by fungal hyphae and microsclerotia-like structures. Furthermore, ASVs identified as Fusarium equiseti were also correlated with low precipitation and recognized as a hub taxon in the roots. However, it remains uncertain whether this species is pathogenic or beneficial to the plant. These insights contribute to our understanding of the plant mycobiome's role in drought tolerance and highlight the importance of specific fungal taxa in supporting plant health under varying environmental conditions. Future research should focus on characterizing these taxa's functional roles and their interactions with the host plant to further elucidate their contributions to drought resistance.},
}

Morocco
*Fusarium/physiology/isolation & purification/classification
*Droughts
*Alternaria/physiology/classification
*Plant Roots/microbiology
*Rain
Soil Microbiology
Mycobiome
Rhizosphere

@article {pmid39390291,
year = {2024},
author = {Delzenne, NM and Bindels, LB and Neyrinck, AM and Walter, J},
title = {The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39390291},
issn = {1740-1534},
abstract = {Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.},
}

@article {pmid39389280,
year = {2024},
author = {Lima, M and Muddana, C and Xiao, Z and Bandyopadhyay, A and Wangikar, PP and Pakrasi, HB and Tang, YJ},
title = {The new chassis in the flask: Advances in Vibrio natriegens biotechnology research.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108464},
doi = {10.1016/j.biotechadv.2024.108464},
pmid = {39389280},
issn = {1873-1899},
abstract = {Biotechnology has been built on the foundation of a small handful of well characterized and well-engineered organisms. Recent years have seen a breakout performer gain attention as a new entrant into the bioengineering toolbox: Vibrio natriegens. This review covers recent research efforts into making V. natriegens a biotechnology platform, using a large language model (LLM) and knowledge graph to expedite the literature survey process. Scientists have made advancements in research pertaining to the fundamental metabolic characteristics of V. natriegens, development and characterization of synthetic biology tools, systems biology analysis and metabolic modeling, bioproduction and metabolic engineering, and microbial ecology. Each of these subcategories has relevance to the future of V. natriegens for bioengineering applications. In this review, we cover these recent advancements and offer context for the impact they may have on the field, highlighting benefits and drawbacks of using this organism. From examining the recent bioengineering research, it appears that V. natriegens is on the precipice of becoming a platform bacterium for the future of biotechnology.},
}

@article {pmid39386005,
year = {2024},
author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM},
title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.},
journal = {PNAS nexus},
volume = {3},
number = {10},
pages = {pgae411},
pmid = {39386005},
issn = {2752-6542},
abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.},
}

@article {pmid39383960,
year = {2024},
author = {Goswami, V and Deepika, S and Sharma, P and Kothamasi, D},
title = {Recycling steel slag as fertiliser proxy in agriculture is good circular economy but disrupts plant microbial symbioses in the soil.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176750},
doi = {10.1016/j.scitotenv.2024.176750},
pmid = {39383960},
issn = {1879-1026},
abstract = {Modern agriculture depends on synthetic fertilisers to ensure food security but their manufacture and use accounts for ~5 % of the global greenhouse gas emissions. Achieving climate change targets therefore requires alternatives, that while maintaining crop productivity, reduce emissions across the lifecycle of fertiliser utilisation. Steel slag, a nutrient-rich by-product of steel manufacture, offers a viable alternative. Being substantially cheaper than fertilisers, it is economically attractive for farmers, particularly in low-middle income countries of the Global South. However, slag application in agriculture poses risk of pollutant transfer to the human food chain and disruption of key plant-microbe symbioses like the arbuscular mycorrhizal fungi (AMF). Here, using barley as a model crop, we tested the suitability of slag as a fertiliser proxy. Mycorrhizal and non-mycorrhizal barley were grown in soils ameliorated with slag in concentrations of 0, 2, 5 and 10 t ha[-1]. We analysed slag-mycorrhiza interaction and their combined effects on crop yield and risks to human nourishment. Slag increased grain yield by respective 32 and 21 % in mycorrhizal and non-mycorrhizal barley. Grain concentration of metal pollutants in mycorrhizal and non-mycorrhizal barley fertilised with slag were within the WHO recommended limits. But slag reduced mycorrhizal colonisation in barley roots and extraradical hyphal spread in the soil. The consequent decline in symbiont function lowered AMF-mediated plant nutrient uptake and increased mineral losses in leachates. AMF are keystone species of the soil microbiome. Loss of AMF function presents long-term ecological consequences for agriculture and necessitates a careful evaluation of slag application to soil.},
}

@article {pmid39382725,
year = {2024},
author = {Wang, L and Liu, Z and Bres, C and Jin, G and Fanin, N},
title = {Coniferous Tree Species Identity and Leaf Aging Alter the Composition of Phyllosphere Communities Through Changes in Leaf Traits.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {126},
pmid = {39382725},
issn = {1432-184X},
support = {2572021AW30//Fundamental Research Funds for the Central Universities/ ; 2022YFD2201100//National Key R & D Program of China/ ; 2572022DS13//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Trees/microbiology/growth & development ; Fungi/classification/genetics/physiology/isolation & purification ; Pinus/microbiology/growth & development ; Abies/microbiology ; Picea/microbiology/growth & development ; Biodiversity ; Tracheophyta/microbiology ; },
abstract = {Phyllosphere microorganisms are essential for plant growth and health. Although there are an increasing number of studies showing that the composition of phyllosphere communities varies among different plant species, it remains unclear whether and how their bacterial and fungal community composition predictably varies with plant traits and leaf age. In this study, we used high-throughput sequencing to explore the diversity and composition of phyllosphere communities in needles of different ages (originating from different cohorts) for three evergreen coniferous species (Pinus koraiensis, Picea koraiensis, and Abies nephrolepis). Our results indicated that Gammaproteobacteria (bacteria) and Dothideomycetes (fungi) were dominant in newly formed needles, whereas Actinobacteria (bacteria) and Eurotiomycetes (fungi) were dominant in perennial needles. Tree species identity and needle age were the main factors explaining the variations of the α diversity (species richness of phyllosphere communities) and β diversity (dissimilarity among phyllosphere communities). In particular, we found that leaf dry matter content, leaf mass per area, and total phosphorus content emerged as key predictors of composition and diversity of phyllosphere microbial communities, underscoring the major influence of tree species identity and needle age on phyllosphere communities through changes in plant functional traits. Finally, we found that the interaction between tree species identity and needle age also contributed significantly to explaining the diversity and composition of phyllosphere communities, probably because differences in plant functional traits or environmental conditions between new and perennial needles depend on tree growth rates and resource acquisition strategies. These findings provide new insights into the mechanisms of community assembly among different evergreen tree species and offer a better understanding of the interactions between plant traits and phyllosphere microorganisms during needle aging.},
}

*Plant Leaves/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Trees/microbiology/growth & development
Fungi/classification/genetics/physiology/isolation & purification
Pinus/microbiology/growth & development
Abies/microbiology
Picea/microbiology/growth & development
Biodiversity
Tracheophyta/microbiology

@article {pmid39382674,
year = {2024},
author = {Murray, MLH and Dopheide, A and Leonard, J and Padamsee, M and Schwendenmann, L},
title = {Phyllosphere of Agathis australis Leaves and the Impact of the Soil-Borne Pathogen Phytophthora agathidicida.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {125},
pmid = {39382674},
issn = {1432-184X},
mesh = {*Plant Leaves/microbiology ; *Phytophthora/isolation & purification/genetics ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; New Zealand ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Combretaceae/microbiology ; },
abstract = {Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand's endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.},
}

*Plant Leaves/microbiology
*Phytophthora/isolation & purification/genetics
*Soil Microbiology
*Plant Diseases/microbiology
*Microbiota
New Zealand
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Soil/chemistry
Combretaceae/microbiology

@article {pmid39382297,
year = {2024},
author = {Eigemann, F and Hoffmann, J and Schampera, C and Liu, S and Bolaños, LM and Heemeyer, M and Carlson, CA and Giovannoni, S and Hellweger, FL},
title = {Emergent ecology in a microscale model of the surface ocean.},
journal = {mBio},
volume = {},
number = {},
pages = {e0237224},
doi = {10.1128/mbio.02372-24},
pmid = {39382297},
issn = {2150-7511},
abstract = {Microbial processes operate at the microscale, which is not resolved by existing ecosystem models. Here, we present a novel model that simulates a 1 mL three-dimensional cube using a hybrid Lagrangian-Eulerian approach, at ecologically relevant timescales. The model simulates individual microbes, including three phytoplankton size classes with healthy, senescent, and dead lifecycle stages; copiotrophic and oligotrophic heterotrophic bacteria; and dissolved organic matter at 50 µm resolution. Diffusion, shear, sedimentation, chemotaxis, and attachment processes are explicitly resolved. The emerging quantitative representation of the ecosystem shows that (1) copiotrophs grow mostly attached to eukaryotic phytoplankters and get almost all of their carbon from them vs. oligotrophs that grow on exudates and lysates of cyanobacteria; (2) contrasting diel patterns in substrate appearance in the phycosphere vs. ambient water and growth of particle-associated copiotrophs vs. free-living oligotrophs; (3) attached bacteria reduce carbon flux from the phycosphere, lowering chemotactic efficiency toward eukaryotes below that toward cyanobacteria; (4) shear reduces chemotactic efficiency and fitness of the copiotroph; and (5) the main benefit of chemotaxis is to locate attachment partners. These patterns are consistent with available observations. Our study provides insights into the microscale ecology of marine bacteria, and the open-source code is a tool for further research in this area.IMPORTANCEA large amount of global CO2 fixation is performed by marine phytoplankton, and a substantial fraction of that is released as dissolved organic carbon and further processed by heterotrophic bacteria. The interaction between phytoplankton and bacteria, i.e., the carbon flux between them, is therefore an important process in the global carbon and climate system. Some bacteria have developed specialized behavioral traits, like swimming and attachment, to increase their carbon acquisition. These interactions occur at the micrometer scale, for example, the immediate vicinity of phytoplankters (the phycosphere), but existing biogeochemical models typically only simulate down to the 1 meter vertical or ~100 kilometer horizontal scale. We present a new microscale model and use it to predict fluxes and other features in the surface ocean. The model makes important predictions about the fluxes between various types of phytoplankton and bacteria and the role of behavioral traits, and it provides a basis and tool for further research in this area.},
}

@article {pmid39381885,
year = {2024},
author = {Witzgall, K and Hesse, BD and Pacay-Barrientos, NL and Jansa, J and Seguel, O and Oses, R and Buegger, F and Guigue, J and Rojas, C and Rousk, K and Grams, TEE and Pietrasiak, N and Mueller, CW},
title = {Soil carbon and nitrogen cycling at the atmosphere-soil interface: Quantifying the responses of biocrust-soil interactions to global change.},
journal = {Global change biology},
volume = {30},
number = {10},
pages = {e17519},
doi = {10.1111/gcb.17519},
pmid = {39381885},
issn = {1365-2486},
support = {MU3021/6-2//Deutsche Forschungsgemeinschaft/ ; EAR-2012475//National Science Foundation (NSF)/ ; },
mesh = {*Soil/chemistry ; *Climate Change ; *Nitrogen Cycle ; *Soil Microbiology ; *Carbon Cycle ; *Droughts ; *Atmosphere/chemistry ; Carbon/metabolism/analysis ; Carbon Dioxide/metabolism/analysis ; Nitrogen/metabolism/analysis ; Ecosystem ; },
abstract = {In drylands, where water scarcity limits vascular plant growth, much of the primary production occurs at the soil surface. This is where complex macro- and microbial communities, in an intricate bond with soil particles, form biological soil crusts (biocrusts). Despite their critical role in regulating C and N cycling in dryland ecosystems, there is limited understanding of the fate of biologically fixed C and N from biocrusts into the mineral soil, or how climate change will affect C and N fluxes between the atmosphere, biocrusts, and subsurface soils. To address these gaps, we subjected biocrust-soil systems to experimental warming and drought under controlled laboratory conditions, monitored CO2 fluxes, and applied dual isotopic labeling pulses ([13]CO2 and [15]N2). This allowed detailed quantification of elemental pathways into specific organic matter (OM) pools and microbial biomass via density fractionation and phospholipid fatty acid analyses. While biocrusts modulated CO2 fluxes regardless of the temperature regime, drought severely limited their photosynthetic C uptake to the extent that the systems no longer sustained net C uptake. Furthermore, the effect of biocrusts extended into the underlying 1 cm of mineral soil, where C and N accumulated as mineral-associated OM (MAOM<63μm). This was strongly associated with increased relative dominance of fungi, suggesting that fungal hyphae facilitate the downward C and N translocation and subsequent MAOM formation. Most strikingly, however, these pathways were disrupted in systems exposed to warming, where no effects of biocrusts on the elemental composition of the underlying soil nor on MAOM were determined. This was further associated with reduced net biological N fixation under combined warming and drought, highlighting how changing climatic conditions diminish some of the most fundamental ecosystem functions of biocrusts, with detrimental repercussions for C and N cycling and the persistence of soil organic matter pools in dryland ecosystems.},
}

*Soil/chemistry
*Climate Change
*Nitrogen Cycle
*Soil Microbiology
*Carbon Cycle
*Droughts
*Atmosphere/chemistry
Carbon/metabolism/analysis
Carbon Dioxide/metabolism/analysis
Nitrogen/metabolism/analysis
Ecosystem

@article {pmid39380680,
year = {2024},
author = {Karavaeva, V and Sousa, FL},
title = {Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1433224},
pmid = {39380680},
issn = {1664-302X},
abstract = {Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.},
}

@article {pmid39379763,
year = {2024},
author = {Peng, Z and Xu, Z and Tong, H and Xing, Y and Luo, Z and Wu, Y and Yu, Z},
title = {Leaf Rust Pathogens on Hypericum pseudohenryi: Describing Melampsora danbaensis sp. nov. and M. hyperici-pseudohenryi sp. nov. from China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {122},
pmid = {39379763},
issn = {1432-184X},
support = {2023YFC2604800-03//National Key Research and Development Program of China/ ; },
mesh = {China ; *Hypericum/microbiology/classification ; *Phylogeny ; *Plant Diseases/microbiology ; *Plant Leaves/microbiology ; *Basidiomycota/classification/genetics/isolation & purification ; DNA, Fungal/genetics ; Spores, Fungal ; },
abstract = {Based on morphological and phylogenetic evidence, two novel species of Melampsora were discovered on Hypericum pseudohenryi in China and have been thoroughly characterized. One of these species, designated as M. danbaensis, exhibits distinct features such as aecia of Uredo-type, typically appearing in gregarious or grouped arrangements, and presenting a shallowly pulvinate structure. Aeciospores exhibit tremendous variations in size, ranging in shape from globose to ellipsoidal and bearing pronounced verrucose texture. Telia resemble crusts one-spore deep, covering nearly the entire abaxial leaf surface, with sessile teliospores reaching sizes of up to 65.8 µm, and exhibiting a clavate to cylindrical shape. Another species, designated as M. hyperici-pseudohenryi, is distinguished by Uredo-type uredinia, which are hypophyllous, scattered or grouped, and interspersed with numerous paraphyses. Its urediniospores tend to be globose, ellipsoidal or obovoid, echinulate, and are accompanied by clavate to capitate paraphyses reaching lengths up to 77.6 µm. Phylogenetically, both species form a novel monophyletic clade within the Melampsora genus, with robust support demonstrated by a high Maximum likelihood bootstrap support (MLBS) value of 100% and a Bayesian posterior probability (BPP) of 1. This study enriches our understanding of the diversity and geographical distribution of Melampsora species that infect Hypericum plants in China.},
}

China
*Hypericum/microbiology/classification
*Phylogeny
*Plant Diseases/microbiology
*Plant Leaves/microbiology
*Basidiomycota/classification/genetics/isolation & purification
DNA, Fungal/genetics
Spores, Fungal

@article {pmid39379709,
year = {2024},
author = {Larrouy, JL and Ridgway, HJ and Dhami, MK and Jones, EE},
title = {Improvement in Microbiota Recovery Using Cas-9 Digestion of Mānuka Plastid and Mitochondrial DNA.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {124},
pmid = {39379709},
issn = {1432-184X},
support = {C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; C11X1803//Ministry of Business, Innovation and Employment/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Plastids/genetics ; *DNA, Mitochondrial/genetics ; *Bacteria/genetics/classification/isolation & purification ; Lamiales/microbiology/genetics ; CRISPR-Cas Systems ; DNA, Bacterial/genetics ; RNA, Guide, CRISPR-Cas Systems/genetics ; Sequence Analysis, DNA ; },
abstract = {Understanding host-microbe interactions in planta is an expanding area of research. Amplicon sequencing of the 16S rRNA gene is a powerful and common method to study bacterial communities associated with plants. However, the co-amplification of mitochondrial and plastid 16S rRNA genes by universal primers impairs the sensitivity and performance of 16S rRNA sequencing. In 2020, a new method, Cas-16S-seq, was reported in the literature to remove host contamination for profiling the microbiota in rice, a well-studied domestic plant, by engineering RNA-programmable Cas9 nuclease in 16S rRNA sequencing. For the first time, we tested the efficiency and applicability of the Cas-16S-seq method on foliage, flowers, and seed of a non-domesticated wild plant for which there is limited genomic information, Leptospermum scoparium (mānuka). Our study demonstrated the efficiency of the Cas-16S-seq method for L. scoparium in removing host contamination in V4-16S amplicons. An increase of 46% in bacterial sequences was found using six guide RNAs (gRNAs), three gRNAs targeting the mitochondrial sequence, and three gRNAs targeting the chloroplast sequence of L. scoparium in the same reaction. An increase of 72% in bacterial sequences was obtained by targeting the mitochondrial and chloroplast sequences of L. scoparium in the same sample at two different steps of the library preparation (DNA and 1st step PCR). The number of OTUs (operational taxonomic units) retrieved from soil samples was consistent when using the different methods (Cas-16S-seq and 16S-seq) indicating that the Cas-16S-seq implemented for L. scoparium did not introduce bias to microbiota profiling. Our findings provide a valuable tool for future studies investigating the bacterial microbiota of L. scoparium in addition to evaluating an important tool in the plant microbiota research on other non-domesticated wild species.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota
*Plastids/genetics
*DNA, Mitochondrial/genetics
*Bacteria/genetics/classification/isolation & purification
Lamiales/microbiology/genetics
CRISPR-Cas Systems
DNA, Bacterial/genetics
RNA, Guide, CRISPR-Cas Systems/genetics
Sequence Analysis, DNA

@article {pmid39379544,
year = {2024},
author = {Bastidas Navarro, M and Balseiro, E and Modenutti, B},
title = {Lake Bacterial Communities in North Patagonian Andes: The Effect of the Nothofagus pumilio Treeline.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {123},
pmid = {39379544},
issn = {1432-184X},
support = {PICT 2015-2138//Fondo para la Investigación Científica y Tecnológica/ ; PICT 2017-1940//Fondo para la Investigación Científica y Tecnológica/ ; PICT 2018-1563//Fondo para la Investigación Científica y Tecnológica/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Bacteria/classification/genetics/isolation & purification ; *Phylogeny ; Cyanobacteria/genetics/classification ; Microbiota ; Nitrogen/analysis ; Carbon/analysis/metabolism ; Phosphorus/analysis ; Biodiversity ; Altitude ; Trees/microbiology ; Argentina ; },
abstract = {One of the most noticeable environmental discontinuities in mountains is the transition that exists in vegetation below and above the treeline. In the North Patagonian Andean lakes (between 900 and 1950 m a.s.l.), we analyzed the bacterial community composition of lakes in relation to surrounding vegetation (erected trees, krummholz belt, and bare rocks), dissolved organic carbon (DOC), and total dissolved nutrients (nitrogen, TDN and phosphorus, TDP). We observed a decrease in DOC, TDP, and TDN concentrations with altitude, reflecting shifts in the source inputs entering the lakes by runoff. Cluster analysis based on bacterial community composition showed a segregation of the lakes below treeline, from those located above. This first cluster was characterized by the cyanobacteria Cyanobium PCC-6307, while in the krummholz belt and bare rocks, bacterial communities were dominated by Actinobacteria hgcl-clade and Proteobacteria (Sandarakinorhabdus and Rhodovarius), with the presence of pigments such as actinorhodopsin, carotenoids, and bacteriochlorophyll a. The net relatedness index (NRI), which considers the community phylogenetic dispersion, showed that lakes located on bare rocks were structured by environmental filtering, while communities of lakes below treeline were structured by species interactions such as competition. Beta-diversity was higher among lakes below than among lakes located above the treeline. The contribution of species turnover was more important than nestedness. Our study brings light on how bacterial communities may respond to changes in the surrounding vegetation, highlighting the importance of evaluating different aspects of community structure to understand metacommunity organization.},
}

*Lakes/microbiology/chemistry
*Bacteria/classification/genetics/isolation & purification
*Phylogeny
Cyanobacteria/genetics/classification
Microbiota
Nitrogen/analysis
Carbon/analysis/metabolism
Phosphorus/analysis
Biodiversity
Altitude
Trees/microbiology
Argentina

@article {pmid39378744,
year = {2024},
author = {Zhu, T and Li, S and Tao, C and Chen, W and Chen, M and Zong, Z and Wang, Y and Li, Y and Yan, B},
title = {Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122570},
doi = {10.1016/j.watres.2024.122570},
pmid = {39378744},
issn = {1879-2448},
abstract = {The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R[2]tra = 0.882, R[2]test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives.},
}

@article {pmid39377576,
year = {2024},
author = {Woldetsadik, YA and Lazinski, DW and Camilli, A},
title = {A Vibrio cholerae anti-phage system depletes nicotinamide adenine dinucleotide to restrict virulent bacteriophages.},
journal = {mBio},
volume = {},
number = {},
pages = {e0245724},
doi = {10.1128/mbio.02457-24},
pmid = {39377576},
issn = {2150-7511},
abstract = {Bacteria and their predatory viruses (bacteriophages or phages) are in a perpetual molecular arms race. This has led to the evolution of numerous phage defensive systems in bacteria that are still being discovered, as well as numerous ways of interference or circumvention on the part of phages. Here, we identify a unique molecular battle between the classical biotype of Vibrio cholerae and virulent phages ICP1, ICP2, and ICP3. We show that classical biotype strains resist almost all isolates of these phages due to a 25-kb genomic island harboring several putative anti-phage systems. We observed that one of these systems, Nezha, encoding SIR2-like and helicase proteins, inhibited the replication of all three phages. Bacterial SIR2-like enzymes degrade the essential metabolic coenzyme nicotinamide adenine dinucleotide (NAD[+]), thereby preventing replication of the invading phage. In support of this mechanism, we identified one phage isolate, ICP1_2001, which circumvents Nezha by encoding two putative NAD[+] regeneration enzymes. By restoring the NAD[+] pool, we hypothesize that this system antagonizes Nezha without directly interacting with its proteins and should be able to antagonize other anti-phage systems that deplete NAD[+].IMPORTANCEBacteria and phages are in a perpetual molecular arms race, with bacteria evolving an extensive arsenal of anti-phage systems and phages evolving mechanisms to overcome these systems. This study identifies a previously uncharacterized facet of the arms race between Vibrio cholerae and its phages. We identify an NAD[+]-depleting anti-phage defensive system called Nezha, potent against three virulent phages. Remarkably, one phage encodes proteins that regenerate NAD[+] to counter the effects of Nezha. Without Nezha, the NAD[+] regeneration genes are detrimental to the phage. Our study provides new insight into the co-evolutionary dynamics between bacteria and phages and informs the microbial ecology and phage therapy fields.},
}

@article {pmid39376571,
year = {2024},
author = {Qian, C and Hui, J and Peng, Z and Sun, X and Zhang, J},
title = {Mucosal microbiota characterization in gastric cancer identifies immune-activated-related transcripts relevant gastric microbiome signatures.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1435334},
pmid = {39376571},
issn = {1664-3224},
mesh = {Humans ; *Stomach Neoplasms/immunology/microbiology/genetics/mortality ; *Gastric Mucosa/microbiology/immunology/metabolism ; Female ; *Tumor Microenvironment/immunology ; Male ; Middle Aged ; *Gastrointestinal Microbiome/immunology/genetics ; Aged ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/immunology/genetics ; Adult ; },
abstract = {Tumor microenvironment (TME) immune cells and gastric mucosal microbiome constitute two vital elements of tumor tissue. Increasing evidence has elucidated their clinicopathological significance in predicting outcomes and therapeutic efficacy. However, comprehensive characterization of immune cell-associated microbiome signatures in the TME is still in the early stages of development. Here, we characterized the gastric mucosa microbiome and its associations with immune-activated related transcripts (IATs) in 170 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and quantitative reverse transcription-PCR. Microbial diversity and richness were significantly higher in GC tumor tissues than in non-tumor tissues. Differences in microbial composition between the groups were evident, with Firmicutes, Proteobacteria, Bacteroidota, Campilobacterota, Actinobacteria, Fusobacteriota, Verrucomicrobiota, Acidobacteriota, and Cyanobacteria being the dominant phyla in the gastric mucosal microbiota. Microbial interaction network analysis revealed distinctive centralities of oral bacteria (such as Fusobacterium, Porphyromonas, Prevotella, etc.) in both tumor and normal mucosae networks, suggesting their significant influence on GC microbial ecology. Furthermore, we analyzed the expression of IATs (CXCL9, CXCL10, GZMA, GZMB, PRF1, CD8A, IFNG, TBX2, and TNF) and characterized IAT-relevant gastric microbiome signatures in GC patients. Our results showed that the expression of CXCL9, CXCL10, GZMA, GZMB, PRF1 and IFNG was significantly higher in tumor tissues than in adjacent normal tissues in GC patients. Notably, high expression of IATs in tumor tissues was associated with improved survival in GC patients and could serve as a powerful predictor for disease-free survival. Additionally, analysis of IAT levels and mucosal microbiota diversity revealed a correlation between higher IAT expression and increased microbiota richness and evenness in the IATs [high] group, suggesting potential interactions between mucosal microbiota and tumor immunopathology. Spearman correlation analysis showed positive associations between IAT expression and specific mucosal bacterial species. Notably, Akkermansia muciniphila demonstrated potential involvement in modulating GZMB expression in the GC mucosal microenvironment. These findings underscore the importance of mucosal microbiota alterations in GC and suggest potential therapeutic targets focusing on modulating the tumor microbiota for improved clinical outcomes. The detailed characterization of these elements has profound implications for both treatment and survival prediction in GC. We observed that microbial diversity and richness were significantly higher in GC tumor tissues compared to non-tumor tissues. These differences highlight the unique microbial landscape of GC tumors and suggest that the microbiome could influence tumor development and progression. Importantly, our study demonstrated that high expression levels of IATs in GC tumor tissues were associated with improved patient survival. This suggests that IATs not only reflect immune activation but also serve as valuable biomarkers for predicting disease-free survival. The potential of IATs as predictive markers underscores their utility in guiding therapeutic strategies and personalizing treatment approaches. Moreover, the correlation between higher IAT expression and increased microbiota richness and evenness suggests that a diverse and balanced microbiome may enhance immune responses and contribute to better clinical outcomes. These findings highlight the critical need to consider mucosal microbiota alterations in GC management. Targeting the tumor microbiota could emerge as a promising therapeutic strategy, potentially leading to more effective treatments and improved patient outcomes. Understanding and modulating the microbiome's role in GC opens new avenues for innovative therapeutic interventions and personalized medicine.},
}

Humans
*Stomach Neoplasms/immunology/microbiology/genetics/mortality
*Gastric Mucosa/microbiology/immunology/metabolism
Female
*Tumor Microenvironment/immunology
Male
Middle Aged
*Gastrointestinal Microbiome/immunology/genetics
Aged
RNA, Ribosomal, 16S/genetics
Bacteria/classification/immunology/genetics
Adult

@article {pmid39375832,
year = {2024},
author = {Obiol, A and Del Campo, J and de Vargas, C and Mahé, F and Massana, R},
title = {How marine are Marine Stramenopiles (MAST)? A cross-system evaluation.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae130},
pmid = {39375832},
issn = {1574-6941},
abstract = {Marine Stramenopiles (MAST) were first described two decades ago through ribosomal RNA gene (rRNA gene) sequences from marine surveys of microbial eukaryotes. MAST comprise several independent lineages at the base of the Stramenopiles. Despite their prevalence in the ocean, the majority of MAST diversity remains uncultured. Previous studies, mainly in marine environments, have explored MAST's cell morphology, distribution, trophic strategies, and genomics using culturing-independent methods. In comparison, less is known about their presence outside marine habitats. Here, we analyze the extensive EukBank dataset to assess the extent to which MAST can be considered marine protists. Additionally, by incorporating newly available rRNA gene sequences, we update Stramenopiles phylogeny, identifying three novel MAST lineages. Our results indicate that MAST are primarily marine with notable exceptions within MAST-2 and MAST-12, where certain subclades are prevalent in freshwater and soil habitats. In the marine water column, only a few MAST species, particularly within clades -1, -3, -4 and -7, dominate and exhibit clear latitudinal distribution patterns. Overall, the massive sequencing dataset analyzed in our study confirms and partially expands the previously described diversity of MASTs groups and underscores the predominantly marine nature of most of these uncultured lineages.},
}

@article {pmid39366327,
year = {2024},
author = {Xu, J and Li, X and Xi, C and Weir, MH},
title = {Development of a machine learning model to support low cost real-time Legionella monitoring in premise plumbing systems.},
journal = {Water research},
volume = {267},
number = {},
pages = {122510},
doi = {10.1016/j.watres.2024.122510},
pmid = {39366327},
issn = {1879-2448},
abstract = {Legionella pneumophila (L. pneumophila) is a pathogenic bacterium primarily known for causing Legionnaires' Disease which is known for high mortality rates, particularly in the elderly. With caseloads continuing to increase, further research is needed to improve our understanding of optimized sampling schema and safe limits of L. pneumophila, in part to target improved treatment options and realistic population-level risk modeling. Particularly in healthcare and other high-risk locations these become crucial and time sensitive needs. Therefore, we conceptualized this research as a means of incorporating easily measured physiochemical water quality parameters and generalization of the unique ecology of building water systems to build a computational model that can allow for more rapid and accurate decision making. This research uses the specific machine learning (ML) method called statistical learning theory to incorporate concentration of host cells, such as native amoeba, and physiochemical water quality parameters to estimate the probability of observing ranges of Legionella gene copy concentrations. Using data from previously published research on Legionella prevalence in a large building, our ML method trains the model on the relative impacts of physiochemical parameters on likely amoeba host cell occurrences. The model is expanded to estimate host cell concentrations using correlations and regressions operated through LASSO algorithms. After categorization variables from these results are then used to inform a logistic regression to provide an estimate of the probability of Legionella gene copy concentration ranges. In summary, conventional results generated by logistic regression and multiple linear regression quantified the associations among ecological conditions in the water and ability to predict a likely range of Legionella concentration in a management focused way. Further, two ML methods, PCA and LASSO, demonstrated feasibility in accurate real-time monitoring of Legionella through physiochemical indicators as evidenced with good accuracy of predictions based for validation results. Furthermore results demonstrate the vital need to account for the impact of water quality on building on host cells, and via their quantified water microbial ecology, not just Legionella concentrations.},
}

@article {pmid39365014,
year = {2024},
author = {Arnold, ND and Paper, M and Fuchs, T and Ahmad, N and Jung, P and Lakatos, M and Rodewald, K and Rieger, B and Qoura, F and Kandawa-Schulz, M and Mehlmer, N and Brück, TB},
title = {High-quality genome of a novel Thermosynechococcaceae species from Namibia and characterization of its protein expression patterns at elevated temperatures.},
journal = {MicrobiologyOpen},
volume = {13},
number = {5},
pages = {e70000},
pmid = {39365014},
issn = {2045-8827},
support = {031B0838B//Bundesministerium für Bildung und Forschung/ ; 031A305A//Bundesministerium für Wirtschaft und Energie/ ; //Bayerisches Staatsministerium für Umwelt und Verbraucherschutz/ ; },
mesh = {Namibia ; *Cyanobacteria/genetics/classification/metabolism ; *Genome, Bacterial ; *Phylogeny ; *Hot Springs/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Hot Temperature ; Sequence Analysis, DNA ; Proteome/analysis ; DNA, Bacterial/genetics ; },
abstract = {Thermophilic cyanobacteria thrive in extreme environments, making their thermoresistant enzymes valuable for industrial applications. Common habitats include hot springs, which act as evolutionary accelerators for speciation due to geographical isolation. The family Thermosynechococcaceae comprises thermophilic cyanobacteria known for their ability to thrive in high-temperature environments. These bacteria are notable for their photosynthetic capabilities, significantly contributing to primary production in extreme habitats. Members of Thermosynechococcaceae exhibit unique adaptations that allow them to perform photosynthesis efficiently at elevated temperatures, making them subjects of interest for studies on microbial ecology, evolution, and potential biotechnological applications. In this study, the genome of a thermophilic cyanobacterium, isolated from a hot spring near Okahandja in Namibia, was sequenced using a PacBio Sequel IIe long-read platform. Cultivations were performed at elevated temperatures of 40, 50, and 55°C, followed by proteome analyses based on the annotated genome. Phylogenetic investigations, informed by the 16S rRNA gene and aligned nucleotide identity (ANI), suggest that the novel cyanobacterium is a member of the family Thermosynechococcaceae. Furthermore, the new species was assigned to a separate branch, potentially representing a novel genus. Whole-genome alignments supported this finding, revealing few conserved regions and multiple genetic rearrangement events. Additionally, 129 proteins were identified as differentially expressed in a temperature-dependent manner. The results of this study broaden our understanding of cyanobacterial adaptation to extreme environments, providing a novel high-quality genome of Thermosynechococcaceae cyanobacterium sp. Okahandja and several promising candidate proteins for expression and characterization studies.},
}

Namibia
*Cyanobacteria/genetics/classification/metabolism
*Genome, Bacterial
*Phylogeny
*Hot Springs/microbiology
*RNA, Ribosomal, 16S/genetics
Bacterial Proteins/genetics/metabolism
Hot Temperature
Sequence Analysis, DNA
Proteome/analysis
DNA, Bacterial/genetics

@article {pmid39364584,
year = {2024},
author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F},
title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14023},
doi = {10.1111/1755-0998.14023},
pmid = {39364584},
issn = {1755-0998},
support = {//Hessisches Landesamt für Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz of the German federal State of Hesse/ ; },
abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.},
}

@article {pmid39361898,
year = {2024},
author = {Ramoneda, J and Hoffert, M and Stallard-Olivera, E and Casamayor, EO and Fierer, N},
title = {Leveraging genomic information to predict environmental preferences of bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae195},
pmid = {39361898},
issn = {1751-7370},
abstract = {Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.},
}

@article {pmid39360821,
year = {2024},
author = {Han, S and Kim, S and Sedlacek, CJ and Farooq, A and Song, C and Lee, S and Liu, S and Brüggemann, N and Rohe, L and Kwon, M and Rhee, S-K and Jung, M-Y},
title = {Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0216924},
doi = {10.1128/mbio.02169-24},
pmid = {39360821},
issn = {2150-7511},
abstract = {UNLABELLED: Nitrification is a core process in the global nitrogen (N) cycle mediated by ammonia-oxidizing microorganisms, including ammonia-oxidizing archaea (AOA) as a key player. Although much is known about AOA abundance and diversity across environments, the genetic drivers of the ecophysiological adaptations of the AOA are often less clearly defined. This is especially true for AOA within the genus Nitrosocosmicus, which have several unique physiological traits (e.g., high substrate tolerance, low substrate affinity, and large cell size). To better understand what separates the physiology of Nitrosocosmicus AOA, we performed comparative genomics with genomes from 39 cultured AOA, including five Nitrosocosmicus AOA. The absence of a canonical high-affinity type ammonium transporter and typical S-layer structural genes was found to be conserved across all Nitrosocosmicus AOA. In agreement, cryo-electron tomography confirmed the absence of a visible outermost S-layer structure, which has been observed in other AOA. In contrast to other AOA, the cryo-electron tomography highlighted the possibility that Nitrosocosmicus AOA may possess a glycoprotein or glycolipid-based glycocalyx cell covering outer layer. Together, the genomic, physiological, and metabolic properties revealed in this study provide insight into niche adaptation mechanisms and the overall ecophysiology of members of the Nitrosocosmicus clade in various terrestrial ecosystems.

IMPORTANCE: Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.},
}

@article {pmid39360459,
year = {2024},
author = {Li, X and Leizeaga, A and Rousk, J and Zhou, S and Hugelius, G and Manzoni, S},
title = {Recovery of Soil Microbial Metabolism After Rewetting Depends on Interacting Environmental Conditions and Changes in Functional Groups and Life History Strategies.},
journal = {Global change biology},
volume = {30},
number = {10},
pages = {e17522},
doi = {10.1111/gcb.17522},
pmid = {39360459},
issn = {1365-2486},
support = {101001608//H2020 European Research Council/ ; KAW 2017.0171//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; //Schmidt Sciences, LLC/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Fungi/physiology/metabolism ; *Climate Change ; Bacteria/metabolism/growth & development ; Microbiota ; Hydrogen-Ion Concentration ; },
abstract = {Climate change is causing an intensification of soil drying and rewetting events, altering microbial functioning and potentially destabilizing soil organic carbon. After rewetting, changes in microbial community carbon use efficiency (CUE), investment in life history strategies, and fungal to bacterial dominance co-occur. Still, we have yet to generalize what drives these dynamic responses. Here, we collated 123 time series of microbial community growth (G, sum of fungal and bacterial growth, evaluated by leucine and acetate incorporation, respectively) and respiration (R) after rewetting and calculated CUE = G/(G + R). First, we characterized CUE recovery by two metrics: maximum CUE and time to maximum CUE. Second, we translated microbial growth and respiration data into microbial investments in life history strategies (high yield (Y), resource acquisition (A), and stress tolerance (S)). Third, we characterized the temporal change in fungal to bacterial dominance. Finally, the metrics describing the CUE recovery, investment in life history strategies, and fungal to bacterial dominance after rewetting were explained by environmental factors and microbial properties. CUE increased after rewetting as fungal dominance declined, but the maximum CUE was explained by the CUE under moist conditions, rather than specific environmental factors. In contrast, higher soil pH and carbon availability accelerated the decline of microbial investment in stress tolerance and fungal dominance. We conclude that microbial CUE recovery is mostly driven by the shifting microbial community composition and the metabolic capacity of the community, whereas changes in microbial investment in life history strategies and fungal versus bacterial dominance depend on soil pH and carbon availability.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism
*Fungi/physiology/metabolism
*Climate Change
Bacteria/metabolism/growth & development
Microbiota
Hydrogen-Ion Concentration

@article {pmid39360321,
year = {2024},
author = {MacGregor, H and Fukai, I and Ash, K and Arkin, AP and Hazen, TC},
title = {Potential applications of microbial genomics in nuclear non-proliferation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1410820},
pmid = {39360321},
issn = {1664-302X},
abstract = {As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.},
}

@article {pmid39359935,
year = {2024},
author = {Li, Y and Li, Z and Zheng, S and Xu, X},
title = {Probiotics in the management of radiation-induced oral mucositis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1477143},
pmid = {39359935},
issn = {2235-2988},
mesh = {*Probiotics/therapeutic use ; Humans ; *Stomatitis/etiology/microbiology/therapy/prevention & control ; *Radiation Injuries/therapy ; *Dysbiosis ; Microbiota ; Head and Neck Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Mouth/microbiology ; Quality of Life ; },
abstract = {Oral mucositis is a common and debilitating oral complication in head and neck cancer patients undergoing radiotherapy, resulting in diminished quality of life and potential treatment disruptions. Oral microbiota has long been recognized as a contributing factor in the initiation and progression of radiation-induced oral mucositis (RIOM). Numerous studies have indicated that the radiation-induced oral microbial dysbiosis promotes the occurrence and severity of oral mucositis. Therefore, approaches that modulate oral microbial ecology are promising for the management of RIOM. Probiotics as a relatively predicable and safe measure that modulates microecology have garnered significant interest. In this review, we discussed the correlation between RIOM and oral microbiota, with a particular focus on the efficacy of probiotics in the control of RIOM, in order to provide novel paradigm for the management of this disease.},
}

*Probiotics/therapeutic use
Humans
*Stomatitis/etiology/microbiology/therapy/prevention & control
*Radiation Injuries/therapy
*Dysbiosis
Microbiota
Head and Neck Neoplasms/radiotherapy
Radiotherapy/adverse effects
Mouth/microbiology
Quality of Life

@article {pmid39358950,
year = {2024},
author = {Zhang, J and Qin, L and Chang, Y and He, Y and Zhao, W and Zhao, Y and Ding, Y and Gao, J and Zhao, X},
title = {One-Pot Assay for Rapid Detection of Stenotrophomonas maltophilia by RPA-CRISPR/Cas12a.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00481},
pmid = {39358950},
issn = {2161-5063},
abstract = {Stenotrophomonas maltophilia (S. maltophilia, SMA) is a common opportunistic pathogen that poses a serious threat to the food industry and human health. Traditional detection methods for SMA are time-consuming, have low detection rates, require complex and expensive equipment and professional technical personnel for operation, and are unsuitable for on-site detection. Therefore, establishing an efficient on-site detection method has great significance in formulating appropriate treatment strategies and ensuring food safety. In the present study, a rapid one-pot detection method was established for SMA using a combination of Recombinase Polymerase Amplification (RPA) and CRISPR/Cas12a, referred to as ORCas12a-SMA (one-pot RPA-CRISPR/Cas12a platform). In the ORCas12a-SMA detection method, all components were added into a single tube simultaneously to achieve one-pot detection and address the problems of nucleic acid cross-contamination and reduced sensitivity caused by frequent cap opening during stepwise detection. The ORCas12a-SMA method could detect at least 3 × 10° copies·μL[-1] of SMA genomic DNA within 30 min at 37 °C. Additionally, this method exhibited sensitivity compared to the typical two-step RPA-CRISPR/Cas12a method. Overall, the ORCas12a-SMA detection offered the advantages of rapidity, simplicity, high sensitivity and specificity, and decreased need for complex large-scale instrumentation. This assay is the first application of the one-pot platform based on the combination of RPA and CRISPR/Cas12a in SMA detection and is highly suitable for point-of-care testing. It helps reduce losses in the food industry and provides assistance in formulating timely and appropriate antimicrobial treatment plans.},
}

@article {pmid39358586,
year = {2024},
author = {de Lorenzo, V and Baquero, F and Aguilar, A},
title = {Carlos Asensio and the dawn of molecular microbial ecology.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39358586},
issn = {1618-1905},
support = {CL6-2021-UE 101060625//Horizon 2020 Framework Programme/ ; Y2020/TCS- 6555//Comunidad de Madrid/ ; },
abstract = {At near 50 years of the discovery of microcins, this article highlights the pivotal-but under-recognised-influence of Spanish biochemist Carlos Asensio (1925-1982) in contemporary microbiology, featuring the epistemological, sociological, and cultural impact of his scientific achievements. At a time when the intestinal microbiome is central to current biomedical research, it is due to emphasise his role in the establishment of new scientific fields that are now considered fundamental. Despite his premature death at the peak of his conceptual and experimental creativity, many of his ideas about microbial communication in complex communities inspired a generation of researchers and opened new topics reach to this day. Asensio was also a trailblazer in Spain, advocating for fundamental research within the socio-economic context of his time. He foresaw the shift towards what is now termed the knowledge-based bioeconomy, recognised the need for multidisciplinary research teams, and advocated integration science into societal and political agendas. These facets became evident during his research on microcins, low molecular weight bioactive compounds produced by enterobacteria. These molecules were hypothesised as mediators of microbial interactions in the human gut and were considered potential new antibiotics and even antitumoral agents. His research mobilised young talent and attracted unprecedented resources in Spain during the late 1970s-early 1980s. It underscored the medical value of microbial ecology and exemplified the benefits of collaboration between academia and industry. Asensio played a pivotal role in the emergence of molecular microbial ecology as a research discipline and its foundational and applied significance in biotechnology.},
}

@article {pmid39358432,
year = {2024},
author = {Zhi, W and Li, A and Wang, Q and Yuan, X and Qing, J and Zhang, C and Wang, Y and Li, Y},
title = {Safety and efficacy assessment of fecal microbiota transplantation as an adjunctive treatment for IgA nephropathy: an exploratory clinical trial.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22935},
pmid = {39358432},
issn = {2045-2322},
support = {82170716//National Science Foundation of China/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/therapy ; Male ; Female ; Adult ; *Fecal Microbiota Transplantation/methods/adverse effects ; *Gastrointestinal Microbiome ; Middle Aged ; Treatment Outcome ; Cytokines/blood/metabolism ; },
abstract = {To assess the safety and efficacy of fecal microbiota transplantation (FMT) as an adjunctive therapeutic intervention for IgA nephropathy (IgAN). Fifteen patients with IgA nephropathy were recruited based on inclusion and exclusion criteria and underwent FMT using enteric microbial capsules. Clinical indicators, intestinal microbiota and metabolomic profiles, as well as changes in serum immune cells and cytokines, were monitored before and after FMT. No severe adverse reactions were observed in the subjects. After FMT, there was a reduction in the 24-h urinary protein quantification in subjects. The relative abundances of Phocaeicola_vulgatus, Bacteroides_uniformis, Prevotella_copri, Phocaeicola_dorei, Bacteroides_ovatus, Bacteroides_xylanisolvens, Parabacteroides _distasonis, Bifidobacterium_pseudocatenulatum, Bacteroides_sp._HF-162, and Bifidobacterium_longum changed after FMT. In terms of intestinal metabolites, the levels of acylcarnitine18:0 (ACar.18:0), cotinine, N-arachidonoyl-L-serine, phosphatidylcholine (PC. (18:3e/22:6)), serotonin, and fumagillin showed significant changes. Flow cytometry analysis showed the absolute count of plasma B cells decreased in subjects, and this change correlated with alterations in the intestinal microbiota and metabolites. This study preliminarily evaluates the safety and efficacy of FMT in patients with IgAN. No significant adverse reactions were observed, and the administration of FMT alongside ACEI/ARB therapy was effective in reducing urinary protein levels in patients with IgAN, a process that may be associated with B-cell immunity.},
}

Humans
*Glomerulonephritis, IGA/therapy
Male
Female
Adult
*Fecal Microbiota Transplantation/methods/adverse effects
*Gastrointestinal Microbiome
Middle Aged
Treatment Outcome
Cytokines/blood/metabolism

@article {pmid39353102,
year = {2024},
author = {He, J and Castilla-Alcantara, JC and Ortega-Calvo, JJ and Harms, H and Wick, LY},
title = {DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02924},
pmid = {39353102},
issn = {1520-5851},
abstract = {Biofiltration is a simple and low-cost method for the cleanup of contaminated water. However, the reduced availability of dissolved chemicals to surface-attached degrader bacteria may limit its efficient use at certain hydraulic loadings. When a direct current (DC) electric field is applied to an immersed packed bed, it invokes electrokinetic processes, such as electroosmotic water flow (EOF). EOF is a surface-charge-induced plug-flow-shaped movement of pore fluids. It acts at a nanometer distance above surfaces and allows the change of microscale pressure-driven flow profiles and, hence, the availability of dissolved contaminants to microbial degraders. In laboratory percolation columns, we assessed the effects of a weak DC electric field (E = 0.5 V·cm[-1]) on the biodegradation of waterborne naphthalene (NAH) by surface-attached Pseudomonas fluorescens LP6a. To vary NAH bioavailability, we used different NAH concentrations (C0 = 2.7, 5.1, or 7.8 × 10[-5] mol·L[-1]) and Darcy velocities typical for biofiltration (U¯ = 0.2-1.2 × 10[-4] m·s[-1]). In DC-free controls, we observed higher specific degradation rates (qc) at higher NAH concentrations. The qc depended on U¯, suggesting bioavailability restrictions depending on the hydraulic residence times. DC fields consistently increased qc and resulted in linearly increasing benefits up to 55% with rising hydraulic loadings relative to controls. We explain these biodegradation benefits by EOF-altered microscale flow profiles allowing for better NAH provision to bacteria attached to the collectors even though the EOF was calculated to be 100-800 times smaller than bulk water flow. Our data suggest that electrokinetic approaches may give rise to future technical applications that allow regulating biodegradation, for example, in response to fluctuating hydraulic loadings.},
}

@article {pmid39357457,
year = {2024},
author = {Olavarria, K and Sousa, DZ},
title = {Thermodynamic tools for more efficient biotechnological processes: an example in poly-(3-hydroxybutyrate) production from carbon monoxide.},
journal = {Current opinion in biotechnology},
volume = {90},
number = {},
pages = {103212},
doi = {10.1016/j.copbio.2024.103212},
pmid = {39357457},
issn = {1879-0429},
abstract = {Modern biotechnology requires the integration of several disciplines, with thermodynamics being a crucial one. Experimental approaches frequently used in biotechnology, such as rewiring of metabolic networks or culturing of micro-organisms in engineered environments, can benefit from the application of thermodynamic tools. In this paper, we provide an overview of several thermodynamic tools that are useful for the design and optimization of biotechnological processes, and we demonstrate their potential application in the production of poly-(3-hydroxybutyrate) (PHB) from carbon monoxide (CO). We discuss how these tools can aid in the design of metabolic engineering strategies, the calculation of expected yields, the assessment of the thermodynamic feasibility of the targeted conversions, the identification of potential thermodynamic bottlenecks, and the selection of genetic engineering targets. Although we illustrate these tools using the specific example of PHB production from CO, they can be applied to other substrates and products.},
}

@article {pmid39357161,
year = {2024},
author = {Wan, W and Grossart, HP and Zhang, W and Xiong, X and Yuan, W and Liu, W and Yang, Y},
title = {Lake ecological restoration of vegetation removal mitigates algal blooms and alters landscape patterns of water and sediment bacteria.},
journal = {Water research},
volume = {267},
number = {},
pages = {122516},
doi = {10.1016/j.watres.2024.122516},
pmid = {39357161},
issn = {1879-2448},
abstract = {Elucidating the influences of ecological restoration measure of lakeshore vegetation removal on water quality and biological community is an important but underestimated subject. We adopted molecular and statistical tools to estimate ecological restoration performance in a plateau lake receiving vegetation removal and simultaneously investigated variabilities of bacterial communities in water and sediment. Significant decreases in lake trophic level and algal bloom degree followed notable decreases in water total nitrogen and total phosphorus after vegetation removal. Non-significant changes in sediment nutrients accompanied remarkable variabilities of abundance and composition of nutrient-cycling functional genes (NCFGs) of sediment bacteria. Taxonomic and phylogenetic α-diversities, functional redundancies, and dispersal potentials of bacteria in water and sediment decreased after vegetation removal, and community successions of water and sediment bacteria were separately significant and non-significant. There were opposite changes in ecological attributes of bacteria in water and sediment in response to vegetation removal, including niche breadth, species replacement, richness difference, community complexity, and community stability. Species replacement rather than richness difference affected more on taxonomic β-diversities of bacteria in water and sediment before and after vegetation removal, and determinism rather than stochasticity dominated bacterial community assemblage. Our results highlighted vegetation removal mitigated algal bloom and affected differently on landscapes of water and sediment bacteria. These findings point to dominant ecological mechanisms underlying landscape shifts in water and sediment bacteria in a disturbed lake receiving vegetation removal and have the potential to guide lake ecological restoration.},
}

@article {pmid39354222,
year = {2024},
author = {Suzuki, Y and Webb, SJ and Kouduka, M and Kobayashi, H and Castillo, J and Kallmeyer, J and Moganedi, K and Allwright, AJ and Klemd, R and Roelofse, F and Mapiloko, M and Hill, SJ and Ashwal, LD and Trumbull, RB},
title = {Subsurface Microbial Colonization at Mineral-Filled Veins in 2-Billion-Year-Old Mafic Rock from the Bushveld Igneous Complex, South Africa.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {116},
pmid = {39354222},
issn = {1432-184X},
support = {AB0502//Astrobiology Center Program of National Institutes of Natural Sciences (NINS)/ ; },
mesh = {South Africa ; *Bacteria/isolation & purification/classification ; Geologic Sediments/microbiology ; Minerals/analysis/metabolism ; Clay/chemistry ; Soil Microbiology ; },
abstract = {Recent advances in subsurface microbiology have demonstrated the habitability of multi-million-year-old igneous rocks, despite the scarce energy supply from rock-water interactions. Given the minimal evolution coupled with exceedingly slow metabolic rates in subsurface ecosystems, spatiotemporally stable igneous rocks can sustain microbes over geological time scales. This study investigated a 2-billion-year-old mafic rock in the Bushveld Igneous Complex, South Africa, where ultradeep drilling is being executed by the International Continental Scientific Drilling Program (ICDP). New procedures were successfully developed to simultaneously detect indigenous and contaminant microbial cells in a drill core sample. Precision rock sectioning coupled with infrared, fluorescence, and electron microscopy imaging of the rock section with submicron resolution revealed microbial colonization in veins filled with clay minerals. The entry and exit of microbial cells in the veins are severely limited by tight packing with clay minerals, the formation of which supplies energy sources for long-term habitability. Further microbiological characterization of drilled rock cores from the Bushveld Igneous Complex will expand the understanding of microbial evolution in deep igneous rocks over 2 billion years.},
}

South Africa
*Bacteria/isolation & purification/classification
Geologic Sediments/microbiology
Minerals/analysis/metabolism
Clay/chemistry
Soil Microbiology

@article {pmid39354152,
year = {2024},
author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and , and , and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM},
title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39354152},
issn = {2058-5276},
support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; },
abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.},
}

@article {pmid39350412,
year = {2024},
author = {Khan, A and Abass, S and Nizami, SAI and Shariq, M and Zahiruddin, S and Parveen, B and Parveen, R},
title = {The Gut Health Revolution: Herbs and Dietary Phytochemicals in Balancing Gut Microbiota for Optimal Human Health.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010313921240923125946},
pmid = {39350412},
issn = {1873-4316},
abstract = {The gut microbiota is a varied population of microorganisms that live in the human gastrointestinal system. Emerging research emphasizes the importance of this microbial ecology in general health and its influence on a variety of disorders. The review explores the synergy between herbal treatment and traditional medicine, emphasizing their cultural significance and therapeutic benefits. It delves into the intricate relationship between herbal remedies, traditional healing practices, and their sustained usage over centuries. The review highlights the pivotal role of the gut microbiota in herbal medicine, elucidating how treatments influence the gastrointestinal microorganisms, impacting overall health. Dietary phytochemicals are underscored for their significance in herbal medicine and nutritional well-being, along with the interdependence of plant extracts and botanicals. The investigation explores the molecular connections between phytoconstituents and gut microbiota, aiming to deepen the understanding of herbal medicine's tailored approach to specific health challenges. The summary concludes by emphasizing herbal treatments' unique ability to regulate gut flora, contributing to overall gastrointestinal wellbeing. In closing, the review provides a concise overview, serving as a valuable resource for integrative medicine research, with recommendations for future exploration of herbal medicine's potential in healthcare.},
}

@article {pmid39349736,
year = {2024},
author = {Karačić, S and Suarez, C and Hagelia, P and Persson, F and Modin, O and Martins, PD and Wilén, BM},
title = {Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22742},
pmid = {39349736},
issn = {2045-2322},
mesh = {*Oxidation-Reduction ; *Manganese/metabolism ; *Iron/metabolism ; *Construction Materials/microbiology ; Corrosion ; *Biofilms/growth & development ; Nitrogen/metabolism ; Sulfur/metabolism ; Steel/chemistry ; Bacteria/metabolism/genetics ; Hydrogen-Ion Concentration ; },
abstract = {The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.},
}

*Oxidation-Reduction
*Manganese/metabolism
*Iron/metabolism
*Construction Materials/microbiology
Corrosion
*Biofilms/growth & development
Nitrogen/metabolism
Sulfur/metabolism
Steel/chemistry
Bacteria/metabolism/genetics
Hydrogen-Ion Concentration

@article {pmid38546802,
year = {2024},
author = {Stephenson, MM and Coleman, ME and Azzolina, NA},
title = {Trends in Burdens of Disease by Transmission Source (USA, 2005-2020) and Hazard Identification for Foods: Focus on Milkborne Disease.},
journal = {Journal of epidemiology and global health},
volume = {14},
number = {3},
pages = {787-816},
pmid = {38546802},
issn = {2210-6014},
mesh = {Humans ; *Foodborne Diseases/epidemiology ; United States/epidemiology ; *Disease Outbreaks/statistics & numerical data ; Animals ; *Milk/microbiology ; Cost of Illness ; Hazard Analysis and Critical Control Points/methods ; Food Microbiology ; },
abstract = {BACKGROUND: Robust solutions to global, national, and regional burdens of communicable and non-communicable diseases, particularly related to diet, demand interdisciplinary or transdisciplinary collaborations to effectively inform risk analysis and policy decisions.

OBJECTIVE: U.S. outbreak data for 2005-2020 from all transmission sources were analyzed for trends in the burden of infectious disease and foodborne outbreaks.

METHODS: Outbreak data from 58 Microsoft Access[®] data tables were structured using systematic queries and pivot tables for analysis by transmission source, pathogen, and date. Trends were examined using graphical representations, smoothing splines, Spearman's rho rank correlations, and non-parametric testing for trend. Hazard Identification was conducted based on the number and severity of illnesses.

RESULTS: The evidence does not support increasing trends in the burden of infectious foodborne disease, though strongly increasing trends were observed for other transmission sources. Morbidity and mortality were dominated by person-to-person transmission; foodborne and other transmission sources accounted for small portions of the disease burden. Foods representing the greatest hazards associated with the four major foodborne bacterial diseases were identified. Fatal foodborne disease was dominated by fruits, vegetables, peanut butter, and pasteurized dairy.

CONCLUSION: The available evidence conflicts with assumptions of zero risk for pasteurized milk and increasing trends in the burden of illness for raw milk. For future evidence-based risk management, transdisciplinary risk analysis methodologies are essential to balance both communicable and non-communicable diseases and both food safety and food security, considering scientific, sustainable, economic, cultural, social, and political factors to support health and wellness for humans and ecosystems.},
}

Humans
*Foodborne Diseases/epidemiology
United States/epidemiology
*Disease Outbreaks/statistics & numerical data
Animals
*Milk/microbiology
Cost of Illness
Hazard Analysis and Critical Control Points/methods
Food Microbiology

@article {pmid39349195,
year = {2024},
author = {Cheng, X and Zhao, R and Bodelier, PLE and Song, Y and Yang, K and Tuovinen, OH and Wang, H},
title = {Differential response of subterranean microbiome to exogenous organic matter input in a cave ecosystem.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176584},
doi = {10.1016/j.scitotenv.2024.176584},
pmid = {39349195},
issn = {1879-1026},
abstract = {As a recurrent climatic phenomenon in the context of climate change, extreme rainstorms induce vertical translocation of organic matter and increase moisture content in terrestrial ecosystems. However, it remains unclear whether heavy rainstorms can impact microbial communities in the deep biosphere by modulating organic matter input. In this study, we present findings on the different responses of bacterial and fungal communities in a subsurface cave to rainstorms and moisture variations through field surveys and microcosm experiments. During periods of rainstorms, the influx of dissolved organic matter (DOM) from soil overlying the cave into cave sediments significantly enhanced the correlation between core bacteria and environmental factors, particularly fluorescence spectral indices. The resource utilization of core bacteria was diminished, while the functional diversity of core fungi remained relatively unaltered. We also performed simulated experiments with restricted external DOM inputs, in which DOM content was observed to decrease and microbial diversity increase in response to artificially increased moisture content (MC). The niche breadth of core bacteria decreased and became more closely associated with DOM as the MC increased, while the niche breadth of core fungi remained predominantly unchanged. Compared to fungi, cave bacteria exhibited higher sensitivity towards variations in DOM. The core microbiome can efficiently utilize the available organic matter and participate in nitrogen- and sulfur-related metabolic processes. The study systematically revealed distinct microbial responses to rainstorm events, thereby providing valuable insights for future investigations into energy utilization within deep biospheres.},
}

@article {pmid39349071,
year = {2024},
author = {Toporowska, M and Żebracki, K and Mazur, A and Mazur-Marzec, H and Šulčius, S and Alzbutas, G and Lukashevich, V and Dziga, D and Mieczan, T},
title = {Biodegradation of microcystins by microbiota of duckweed Spirodela polyrhiza.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143436},
doi = {10.1016/j.chemosphere.2024.143436},
pmid = {39349071},
issn = {1879-1298},
abstract = {Cyanobacteria-produced allelochemicals, including hepatotoxic microcystins (MCs), exert an inhibitory effect on macrophyte growth. However, the role of macrophyte-associated bacteria and algae (macrophyte microbiota) in mitigating these immediate negative effects of cyanotoxins remains poorly understood. In this paper, we analyzed the biodegradation of microcystin-RR, MC-LR, and MC-LF by microbiota of the macrophyte Spirodela polyrhiza. The biodegradation of two MC variants was observed and LC-MS/MS analysis allowed identifying the degradation products of MC-RR (m/z 1011, 984, 969, 877, 862, 820, and 615) and MC-LR (m/z 968 and 653), including eight previously unreported products. No degradation products of MC-LF were detected, suggesting its stability and resistance under experimental conditions. NGS-based profiling of microbial consortia revealed no major differences in bacterial community composition across experimental treatments. Taxa previously reported as capable of MC degradation have been found in S. polyrhiza microbiota. Furthermore, the presence of genes encoding putative microcystinase homologues and the formation of new linear intermediates suggest a biochemical pathway that is similar, but not identical to previously reported. The ability of aquatic plant microbiota to biodegrade MCs holds environmental significance, and further studies in this field are required.},
}

@article {pmid39346682,
year = {2024},
author = {Child, HT and Wierzbicki, L and Joslin, GR and Tennant, RK},
title = {Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.},
journal = {Access microbiology},
volume = {6},
number = {9},
pages = {},
pmid = {39346682},
issn = {2516-8290},
abstract = {Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.},
}

@article {pmid39346007,
year = {2024},
author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ},
title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae111},
pmid = {39346007},
issn = {2730-6151},
abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.},
}

@article {pmid39340684,
year = {2024},
author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A},
title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {120},
pmid = {39340684},
issn = {1432-184X},
mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention & control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; },
abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.},
}

Animals
*Solanum lycopersicum/microbiology/parasitology
*Soil Microbiology
*Rhizosphere
*Bacillus/genetics/physiology
*Plant Roots/microbiology/parasitology
*Pest Control, Biological
Plant Diseases/parasitology/prevention & control/microbiology
Trichoderma/physiology/genetics
Tylenchoidea/physiology
Microbiota
Antinematodal Agents/pharmacology
Biological Control Agents/pharmacology
Bacteria/genetics/classification

@article {pmid39340560,
year = {2024},
author = {Charalampous, G and Kormas, KA and Antoniou, E and Kalogerakis, N and Gontikaki, E},
title = {Distinct Communities of Bacteria and Unicellular Eukaryotes in the Different Water Masses of Cretan Passage Water Column (Eastern Mediterranean Sea).},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {381},
pmid = {39340560},
issn = {1432-0991},
support = {1874//Hellenic Foundation for Research and Innovation/ ; 1510//Hellenic Foundation for Research and Innovation/ ; },
mesh = {Mediterranean Sea ; *Bacteria/classification/genetics/isolation & purification ; *Eukaryota/classification/genetics/isolation & purification ; *Seawater/microbiology ; *Microbiota ; *RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Phylogeny ; Ecosystem ; },
abstract = {Elucidating marine microbiota diversity and dynamics holds significant importance due to their role in maintaining vital ecosystem functions and services including climate regulation. This work aims to contribute in the understanding of microbial ecology and networking in one of the world's most understudied marine regions, the Eastern Mediterranean Sea. High-throughput 16S and 18S rRNA gene sequencing analysis was applied to study the diversity of bacteria and unicellular eukaryotes in the different water masses of the Cretan Passage during two seasonally-different sampling expeditions. We assumed that microbial associations differ between the surface and deepwater masses and created co-occurrence networks to evaluate this hypothesis. Our results unveiled vertical variations in both bacterial and unicellular eukaryotic diversity with species fluctuations indicative of seasonality being recorded in the surface water mass. Heterotrophic taxa and grazers related to organic matter degradation and nutrient cycling were enriched in the deepest water layers. Moreover, surface waters presented a higher number of microbial associations indicating abundant ecological niches compared to the deepest layer, possibly related to the lack of bottom-up resources in the oligotrophic deep ocean. Overall, our data provide insight in a heavily stressed, yet underexplored, marine area that requires further research to unravel the ecological roles of marine microbes. To our knowledge, this is the first study that combines molecular biology tools to provide data on both planktic prokaryotes and unicellular eukaryotes across the different water masses in this marine region of the Eastern Mediterranean basin.},
}

Mediterranean Sea
*Bacteria/classification/genetics/isolation & purification
*Eukaryota/classification/genetics/isolation & purification
*Seawater/microbiology
*Microbiota
*RNA, Ribosomal, 18S/genetics
RNA, Ribosomal, 16S/genetics
Biodiversity
Phylogeny
Ecosystem

@article {pmid39340556,
year = {2024},
author = {Fernandez de Landa, G and Alberoni, D and Braglia, C and Baffoni, L and Fernandez de Landa, M and Revainera, PD and Quintana, S and Zumpano, F and Maggi, MD and Di Gioia, D},
title = {The Gut Microbiome of Two Wild Bumble Bee Species Native of South America: Bombus pauloensis and Bombus bellicosus.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {121},
pmid = {39340556},
issn = {1432-184X},
support = {777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; 777760//European Commission/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Nosema/physiology/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; South America ; },
abstract = {South America is populated by a wide range of bumble bee species that represent an important source of biodiversity, supporting pollination services in natural and agricultural ecosystems. These pollinators provide unique specific microbial niches, populated by a wide number of microorganisms such as symbionts, environmental opportunistic bacteria, and pathogens. Recently, it was demonstrated how microbial populations are shaped by trophic resources and environmental conditions but also by anthropogenic pressure, which strongly affects microbes' functionality. This study is focused on the impact of different land uses (natural reserve, agroecosystem, and suburban) on the gut microbiome composition of two South American bumble bees, Bombus pauloensis and Bombus bellicosus. Gut microbial DNA extracted from collected bumble bees was sequenced on the Illumina MiSeq platform and correlated with land use. Nosema ceranae load was analyzed with qPCR and correlated with microbiome data. Significant differences in gut microbiome composition between the two wild bumble bee species were highlighted, with notable variations in α- and β-diversity across study sites. Bombus bellicosus showed a high abundance of Pseudomonas, a genus that includes environmental saprobes, and was found to be the second major taxa populating the gut microbiome, probably indicating the vulnerability of this host to environmental pollution. Pathogen analysis unveils a high prevalence of N. ceranae, with B. bellicosus showing higher susceptibility. Finally, Gilliamella exhibited a negative correlation with N. ceranae, suggesting a potential protective role of this commensal taxon. Our findings underscore the importance of considering microbial dynamics in pollinator conservation strategies, highlighting potential interactions between gut bacteria and pathogens in shaping bumble bee health.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome
*Nosema/physiology/isolation & purification/genetics
*Bacteria/classification/genetics/isolation & purification
Biodiversity
South America

@article {pmid39340548,
year = {2024},
author = {Radouane, N and Errafii, K and Mouhib, S and Mhand, KA and Legeay, J and Hijri, M},
title = {Potential Plant-To-Plant Transmission: Shared Endophytic Bacterial Community Between Ziziphus lotus and Its Parasite Cuscuta epithymum.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {119},
pmid = {39340548},
issn = {1432-184X},
support = {Projects AS-77 and AS-85//OCP Group/ ; },
mesh = {*Cuscuta/physiology/microbiology/genetics ; *Ziziphus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Endophytes/genetics/physiology/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; Host-Parasite Interactions ; DNA, Bacterial/genetics ; },
abstract = {Microbiota associated with host-parasite relationships offer an opportunity to explore interactions among plants, parasites, and microbes, thereby contributing to the overall complexity of community structures. The dynamics of ecological interactions between parasitic plants and their hosts in arid environments remain largely understudied, especially in Africa. This study aimed to examine the bacterial communities of Cuscuta epithymum L. (clover dodder), an epiphytic parasitic plant, and its host, Ziziphus lotus L. (jujuba), in an arid environment. Our goal was to uncover the ecological complexities of microbial communities within the framework of plant-plant interactions. We conducted a comprehensive analysis of the bacterial composition and diversity within populations of the C. epithymum parasite, the infected- and non-infected jujuba host, and their interface at the shoots of the host. This involved amplicon sequencing, targeting the V5-V6 regions of the 16S rRNA gene. A total of 5680 amplicon sequence variants (ASVs) were identified, with Pseudomonadota, Bacillota, and Actinobacteriota being prevalent phyla. Among the bacterial communities, three genera were dominant: Cutibacterium, Staphylococcus, and Acinetobacter. Interestingly, analyses of alpha-diversity (p = 0.3 for Shannon index and p = 0.5 for Simplon index) and beta-diversity (PERMANOVA, with p-values of 0.6 and 0.3) revealed no significant differences between Cuscuta-infected and non-infected jujube shrubs, suggesting a shared shoot endophytic bacteriome. This finding advances our comprehension of microbial communities linked to plant-parasite interactions in the arid environments of Africa. Further research on various hosts is required to confirm plant-to-plant bacterial transmission through Cuscuta infection. Additionally, studies on functional diversity, cytology, ecophysiology and the mechanisms by which bacterial communities transferred between host and parasite are necessary.},
}

*Cuscuta/physiology/microbiology/genetics
*Ziziphus/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Endophytes/genetics/physiology/classification/isolation & purification
*Bacteria/genetics/classification/isolation & purification
Host-Parasite Interactions
DNA, Bacterial/genetics

@article {pmid39338505,
year = {2024},
author = {Shah, H and Trivedi, M and Gurjar, T and Sahoo, DK and Jergens, AE and Yadav, VK and Patel, A and Pandya, P},
title = {Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091831},
pmid = {39338505},
issn = {2076-2607},
abstract = {The changing notion of "companion animals" and their increasing global status as family members underscores the dynamic interaction between gut microbiota and host health. This review provides a comprehensive understanding of the intricate microbial ecology within companion animals required to maintain overall health and prevent disease. Exploration of specific diseases and syndromes linked to gut microbiome alterations (dysbiosis), such as inflammatory bowel disease, obesity, and neurological conditions like epilepsy, are highlighted. In addition, this review provides an analysis of the various factors that impact the abundance of the gut microbiome like age, breed, habitual diet, and microbe-targeted interventions, such as probiotics. Detection methods including PCR-based algorithms, fluorescence in situ hybridisation, and 16S rRNA gene sequencing are reviewed, along with their limitations and the need for future advancements. Prospects for longitudinal investigations, functional dynamics exploration, and accurate identification of microbial signatures associated with specific health problems offer promising directions for future research. In summary, it is an attempt to provide a deeper insight into the orchestration of multiple microbial species shaping the health of companion animals and possible species-specific differences.},
}

@article {pmid39338496,
year = {2024},
author = {Denux, M and Armenteros, M and Weber, L and Miller, CA and Sántha, K and Apprill, A},
title = {Coral Reef Water Microbial Communities of Jardines de la Reina, Cuba.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091822},
pmid = {39338496},
issn = {2076-2607},
abstract = {Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean's 'Crown Jewel' reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms.},
}

@article {pmid39338466,
year = {2024},
author = {Lauzon, J and Caron, D and Lazar, CS},
title = {The Saint-Leonard Urban Glaciotectonic Cave Harbors Rich and Diverse Planktonic and Sedimentary Microbial Communities.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091791},
pmid = {39338466},
issn = {2076-2607},
support = {RGPIN-2019-06670//Natural Sciences and Engineering Research Council/ ; },
abstract = {The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allow for studying a yet unknown fraction of the Earth's biodiversity. The Saint-Leonard cave in Montreal City (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet 13,000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the Saint-Leonard cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryote communities living in the groundwater (0.1 µm- and 0.2 µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave's galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave's groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.},
}

@article {pmid39338465,
year = {2024},
author = {Cruz, LG and Shen, FT and Chen, CP and Chen, WC},
title = {Dose Effect of Polyethylene Microplastics Derived from Commercial Resins on Soil Properties, Bacterial Communities, and Enzymatic Activity.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091790},
pmid = {39338465},
issn = {2076-2607},
support = {MOST 110-2313-B-005-015-//National Science and Technology Council/ ; },
abstract = {Soils are the largest reservoir of microplastics (MPs) on earth. Since MPs can remain in soils for a very long time, their effects are magnified. In this study, different concentrations of polyethylene (PE) MPs derived from commercial resins (0%, 1%, 7%, and 14%, represented as MP_0, MP_1, MP_7, and MP_14) were added to soils to assess the changes in the soils' chemical properties, enzyme activities, and bacterial communities during a 70-day incubation period. The results show that PE MP treatments with low concentrations differed from other treatments in terms of exchangeable Ca and Mg, whereas at high concentrations, the pH and availability of phosphate ions differed. Fluorescein diacetate (FDA), acid phosphatase (ACP), and N-acetyl-β-d-glucosaminidase (NAG) enzyme activities exhibited a dose-related trend with the addition of the PE MPs; however, the average FDA and ACP activities were significantly affected only by MP_14. Changes in the microbial communities were observed at both the phylum and family levels with all PE MP treatments. It was revealed that even a low dosage of PE MPs in soils can affect the functional microbes, and a greater impact is observed on those that can survive in polluted environments with limited resources.},
}

@article {pmid39338425,
year = {2024},
author = {Lyu, G and Hu, J and Ma, J},
title = {Variation in Bacterial and Fungal Communities in Soils from Three Major Apple Pear (Pyrus bretschneideri Rehd.) Orchards.},
journal = {Microorganisms},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/microorganisms12091751},
pmid = {39338425},
issn = {2076-2607},
support = {41571304//National Natural Science Foundation of China/ ; },
abstract = {Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3[-]-N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.},
}

@article {pmid39338386,
year = {2024},
author = {Galinytė, D and Bernatoniene, J and Žilius, M and Rysevaitė-Kyguolienė, K and Savickas, A and Karosienė, J and Briedis, V and Pauža, DH and Savickienė, N},
title = {In Vitro Study of Cyano-Phycocyanin Release from Hydrogels and Ex Vivo Study of Skin Penetration.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/ph17091224},
pmid = {39338386},
issn = {1424-8247},
abstract = {BACKGROUND: This study explored the most suitable materials for incorporating cyano-phycocyanin (C-PC) into hydrogels, focusing on maintaining the C-PC's long-term structural integrity and stabilityNext, the release of C-PC from the hydrogels and its skin penetration were investigated.

METHODS: A series of 1% (w/w) C-PC hydrogels was prepared using various gelling agents and preservatives. Spectrophotometric measurements compared the amount of C-PC in the hydrogels to the initially added amount. After selecting the most suitable gelling agent and preservative, two C-PC hydrogels, with and without propylene glycol (PG) (Sigma-Aldrich, St. Louis, MO, USA), were produced for further testing. In vitro release studies utilized modified Franz-type diffusion cells, while ex vivo skin-permeation studies employed Bronaugh-type cells and human skin. Confocal laser scanning microscopy analyzed C-PC accumulation in the skin.

RESULTS: The findings demonstrated that sodium alginate (Sigma-Aldrich, St. Louis, MO, USA), hydroxyethyl cellulose (HEC) (Sigma-Aldrich, St. Louis, MO, USA), and Soligel[TM] (Givaudan, Vernier, Switzerland) are effective biopolymers for formulating hydrogels while maintaining C-PC stability. After 6 h, C-PC release from the hydrogel containing PG was approximately 10% or 728.07 (±19.35) μg/cm[2], significantly higher than the nearly 7% or 531.44 (±26.81) μg/cm[2] release from the hydrogel without PG (p < 0.05). The ex vivo qualitative skin-permeation study indicated that PG enhances C-PC penetration into the outermost skin layer.

CONCLUSION: PG's ability to enhance the release of C-PC from the hydrogel, coupled with its capacity to modify the skin barrier ex vivo, facilitates the penetration of C-PC into the stratum corneum.},
}

@article {pmid39335049,
year = {2024},
author = {Afonso, L and Grzegorczyk, KG and Salomão, JM and Basso, KR and Alves, LC and Silva, MCD and Chryssafidis, AL and Gionco-Cano, B and Yamada-Ogatta, SF and Andrade, G},
title = {Fluopsin C Promotes Biofilm Removal of XDR Acinetobacter baumannii and Presents an Additive Effect with Polymyxin B on Planktonic Cells.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/antibiotics13090875},
pmid = {39335049},
issn = {2079-6382},
support = {439754/2018-6//National Council for Scientific and Technological Development/ ; 406016/2022-4//National Council for Scientific and Technological Development/ ; },
abstract = {Acinetobacter baumannii emerged as one of the most important pathogens for the development of new antimicrobials due to the worldwide detection of isolates resistant to all commercial antibiotics, especially in nosocomial infections. Biofilm formation enhances A. baumannii survival by impairing antimicrobial action, being an important target for new antimicrobials. Fluopsin C (FlpC) is an organocupric secondary metabolite with broad-spectrum antimicrobial activity. This study aimed to evaluate the antibiofilm activity of FlpC in established biofilms of extensively drug-resistant A. baumannii (XDRAb) and the effects of its combination with polymyxin B (PolB) on planktonic cells. XDRAb susceptibility profiles were determined by Vitek 2 Compact, disk diffusion, and broth microdilution. FlpC and PolB interaction was assessed using the microdilution checkerboard method and time-kill kinetics. Biofilms of XDRAb characterization and removal by FlpC exposure were assessed by biomass staining with crystal violet. Confocal Laser Scanning Microscopy was used to determine the temporal removal of the biofilms using DAPI, and cell viability using live/dead staining. The minimum inhibitory concentration (MIC) of FlpC on XDRAb was 3.5 µg mL[-1]. Combining FlpC + PolB culminated in an additive effect, increasing bacterial susceptibility to both antibiotics. FlpC-treated 24 h biofilms reached a major biomass removal of 92.40 ± 3.38% (isolate 230) using 7.0 µg mL[-1] FlpC. Biomass removal occurred significantly over time through the dispersion of the extracellular matrix and decreasing cell number and viability. This is the first report of FlpC's activity on XDRAb and the compound showed a promissory response on planktonic and sessile cells, making it a candidate for the development of a new antimicrobial product.},
}

@article {pmid39332295,
year = {2024},
author = {Tapia, N and Gallardo-Bustos, C and Rojas, C and Vargas, IT},
title = {Long-term evaluation of soil-based bioelectrochemical green roof systems for greywater treatment.},
journal = {Journal of environmental management},
volume = {370},
number = {},
pages = {122643},
doi = {10.1016/j.jenvman.2024.122643},
pmid = {39332295},
issn = {1095-8630},
abstract = {Water scarcity has generated the need to identify new sources. Due to its low organic contaminant load, greywater reuse has emerged as a potential alternative. Moreover, the search for decentralized treatment systems in urban areas has prompted research on using green roofs for greywater treatment. However, the performance of organic matter removal is limited by the type of substrate and height of the growing media. Bioelectrochemical systems (BESs) improve treatment performance by providing an additional electron acceptor (the electrode). In this study, nine reactors under three different conditions, i.e., open circuit (OC), microbial fuel cell (MFC), and microbial electrolysis cell (MEC), were built to evaluate the treatment of synthetic greywater in a substrate-growing medium composed of perlite and coconut fiber and operated in batch-cycle mode for 397 days. The results suggested that using BESs enables greywater treatment and the removal of pollutants to levels that allow their reuse for irrigation. Furthermore, electrical conductivity was reduced from 732.4 ± 41.2 μS/cm[2] in OC to 637.32 ± 22.73 μS/cm[2] and 543.15 ± 19.69 μS/cm[2] in MEC and MFC, respectively. The soluble chemical oxygen demand in the latter treatments reached 76% removal, compared to levels above the OC, which only reached approximately 67%. Microbial community analysis revealed differences, mainly in the cathodes, showing a higher development of Flavobacterium, Azospirillum, and Zoogloea in MFCs, which could explain the higher levels of organic matter removal in the other conditions, suggesting that the BES could produce an enrichment of beneficial bacterial groups for treatment. Therefore, implementing BESs in green roofs enables sustainable long-term greywater treatment.},
}

@article {pmid39331293,
year = {2024},
author = {Bianchelli, J and Sagua, MI and Quiroga, MP and Nuozzi, G and Fernández, J and Schiaffino, MR},
title = {Temporal dynamics of Legionella (Proteobacteria, Legionellaceae) in two Pampean shallow lakes from Argentina.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39331293},
issn = {1614-7499},
support = {PICT 0891-2017//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICTO 00006-2019//Agencia Nacional de Promoción Científica y Tecnológica/ ; SIB 2053-2022//Universidad Nacional del Noroeste de la Provincia de Buenos Aires/ ; },
abstract = {Aquatic systems have traditionally played a key role in the development of human life, providing multiple ecosystem services to society and being a reservoir for a wide biodiversity of organisms. Among them, bacteria belonging to Legionella stand out, mainly because they are of great interest both in the field of microbial ecology and public health, since some of them turn out to be pathogenic for humans. The aim of this work was to study the monthly temporal dynamics of Legionella spp. and its relationship with the environmental variables measured in two Pampean shallow lakes (Gómez and Carpincho, Buenos Aires Province, Argentina). The analysis was carried out using a quantitative approach by real-time polymerase chain reaction (qPCR) and a non-quantitative approach using bacterial diversity data obtained by next-generation sequencing (NGS), using the Illumina MiSeq platform. Our results showed that the overall Legionella abundance was very high in the studied Pampean shallow lakes. Notably, fluctuations in dissolved organic carbon and temperature influenced the dynamics shifts in Legionella abundances. Correlation analyses between Legionella reads from NGS and copy numbers obtained through qPCR revealed positive relationships, unveiling distinctions attributable to the diverse sequence processing algorithms employed in the analysis of NGS data.},
}

@article {pmid39330355,
year = {2024},
author = {Abbà, S and Valentini, B and Stefanini, I},
title = {Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/jof10090595},
pmid = {39330355},
issn = {2309-608X},
support = {RGP0060/2021//HFSP/ ; 20225SXSHY//PRIN 2022/ ; },
abstract = {Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.},
}

@article {pmid39328926,
year = {2024},
author = {Duque-Granda, D and Vivero-Gómez, RJ and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX},
title = {Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae).},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {44},
number = {},
pages = {e00857},
pmid = {39328926},
issn = {2215-017X},
abstract = {Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.},
}

@article {pmid39327479,
year = {2024},
author = {Tavaddod, S and Dawson, A and Allen, RJ},
title = {Bacterial aggregation triggered by low-level antibiotic-mediated lysis.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {90},
pmid = {39327479},
issn = {2055-5008},
support = {682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; BB/R012415/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; 682237//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; *Escherichia coli/drug effects/genetics ; *Bacteriolysis/drug effects ; Biofilms/drug effects/growth & development ; Microbial Sensitivity Tests ; },
abstract = {Suspended bacterial aggregates play a central role in ocean biogeochemistry, industrial processes and probably many clinical infections - yet the factors that trigger aggregation remain poorly understood, as does the relationship between suspended aggregates and surface-attached biofilms. Here we show that very low doses of cell-wall targeting antibiotic, far below the minimal inhibitory concentration, can trigger aggregation of Escherichia coli cells. This occurs when a few cells lyse, releasing extracellular DNA - thus, cell-to-cell variability in antibiotic response leads to population-level aggregation. Although lysis-triggered aggregation echoes known trigger mechanisms for surface-attached biofilms, these aggregates may have different ecological implications since they do not show increased biofilm-forming potential or increased antibiotic resistance. Our work contributes to understanding the nature of bacterial aggregates and the factors that trigger their formation, and the possible consequences of widespread low-dose antibiotic exposure in the environment and in the body.},
}

*Anti-Bacterial Agents/pharmacology
*Escherichia coli/drug effects/genetics
*Bacteriolysis/drug effects
Biofilms/drug effects/growth & development
Microbial Sensitivity Tests

@article {pmid39244747,
year = {2024},
author = {Bayer, B and Liu, S and Louie, K and Northen, TR and Wagner, M and Daims, H and Carlson, CA and Santoro, AE},
title = {Metabolite release by nitrifiers facilitates metabolic interactions in the ocean.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae172},
pmid = {39244747},
issn = {1751-7370},
mesh = {*Seawater/microbiology ; *Nitrification ; Oceans and Seas ; Nitrites/metabolism ; Heterotrophic Processes ; Microbial Interactions ; Metabolome ; Coculture Techniques ; Ammonia/metabolism ; },
abstract = {Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.},
}

*Seawater/microbiology
*Nitrification
Oceans and Seas
Nitrites/metabolism
Heterotrophic Processes
Microbial Interactions
Metabolome
Coculture Techniques
Ammonia/metabolism

@article {pmid39327101,
year = {2024},
author = {Goldman, AD and Fournier, GP},
title = {The very early evolution of biological complexity.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2024.09.001},
pmid = {39327101},
issn = {0168-9525},
abstract = {All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been a complex cellular organism. A new study by Moody et al. shows that this ancestor was not only a complex cell, but also lived within a microbial ecology likely inhabited by other complex cells.},
}

@article {pmid39326062,
year = {2024},
author = {Sun, X and Favier, A and Folmar, J and Pyenson, NC and Sanchez, A and Rebolleda-Gómez, M},
title = {Metabolic Plasticity Shapes Microbial Communities across a Temperature Gradient.},
journal = {The American naturalist},
volume = {204},
number = {4},
pages = {381-399},
doi = {10.1086/731997},
pmid = {39326062},
issn = {1537-5323},
mesh = {*Temperature ; *Microbiota ; Bacteria/metabolism ; Fermentation ; Carbon/metabolism ; Ecosystem ; },
abstract = {AbstractA central challenge in community ecology is understanding and predicting the effects of abiotic factors on community assembly. In particular, microbial communities play a central role in the ecosystem, but we do not understand how changing factors like temperature are going to affect community composition or function. In this article, we studied the self-assembly of multiple communities in synthetic environments to understand changes in microbial community composition based on metabolic responses of different functional groups along a temperature gradient. In many microbial communities, different microbial functional groups coexist through the partitioning of carbon sources in an emergent trophic structure (cross-feeding). In this system, respirofermentative bacteria display a preference for the sugars supplied as the only carbon source but secrete secondary carbon sources (organic acids) that are more efficiently consumed by obligate respirators. As a consequence of this trophic structure, the metabolic plasticity of the respirofermenters has downstream consequences for the relative abundance of respirators across temperatures. We found that the effects of different temperatures on microbial composition can largely be described by an increase in fermentation by-products with increasing temperatures from the respirofermentative bacteria. This research highlights the importance of metabolic plasticity and metabolic trade-offs in predicting species interactions and community dynamics across abiotic gradients.},
}

*Temperature
*Microbiota
Bacteria/metabolism
Fermentation
Carbon/metabolism
Ecosystem

@article {pmid39321934,
year = {2024},
author = {Liu, YC and Ramiro-Garcia, J and O'Connor, S and Paulo, LM and Maria Braguglia, C and Cristina Gagliano, M and O'Flaherty, V},
title = {Microbial community response to temperature reduction during anaerobic treatment of long chain fatty acids-containing wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131529},
doi = {10.1016/j.biortech.2024.131529},
pmid = {39321934},
issn = {1873-2976},
abstract = {Acclimating mesophilic biomass to low temperatures have been used to start-up psychrophilic anaerobic reactors, but limited microbial information is available during the acclimation. To investigate microbial responses to temperature reductions, duplicate lab-scale anaerobic digestion (AD) reactors were operated for 166 days, with the temperature being reduced from 37 °C to 15 °C, using synthetic long chain fatty acid (LCFA)-containing wastewater as the feedstock. The acclimated biomass at 15 °C exhibited efficient removal of organic matter (total COD>75 %, soluble COD>88 %, and LCFA>99 %). Temperature reductions lead to significant reductions in microbiome diversity. Fermentative bacteria were highly dynamic and functional redundant during temperature reductions. Smithella was the dominant syntrophic bacteria involved in LCFA degradation coupled with Methanothrix and Methanocorpusculum at 15 °C. Membrane modifications and compatible cellular solutes production were triggered by temperature reductions as microbial response to cold stress. This study provided molecular insights in microbial acclimation to low temperatures for psychrophilic AD.},
}

@article {pmid39319483,
year = {2024},
author = {Rasmussen, KL and Thieringer, PH and Nevadomski, S and Martinez, AM and Dawson, KS and Corsetti, FA and Zheng, XY and Lv, Y and Chen, X and Celestian, AJ and Berelson, WM and Rollins, NE and Spear, JR},
title = {Living to Lithified: Construction and Preservation of Silicified Biomarkers.},
journal = {Geobiology},
volume = {22},
number = {5},
pages = {1-30},
doi = {10.1111/gbi.12620},
pmid = {39319483},
issn = {1472-4669},
support = {/NASA/NASA/United States ; //Geological Society of America/ ; },
mesh = {*Biomarkers/analysis ; Cyanobacteria/metabolism ; Geologic Sediments/microbiology/chemistry ; Bacteria/metabolism ; Hot Springs/microbiology/chemistry ; },
abstract = {Whole microorganisms are rarely preserved in the fossil record but actively silicifying environments like hot springs provide an opportunity for microbial preservation, making silicifying environments critical for the study of microbial life through time on Earth and possibly other planetary bodies. Yet, the changes that biosignatures may undergo through lithification and burial remain unconstrained. At Steep Cone Geyser in Yellowstone National Park, we collected microbial material from (1) the living system across the active outflows, (2) the silicified areas adjacent to flows, and (3) lithified and buried material to assess the preservation of biosignatures and their changes across the lithification transect. Five biofabrics, built predominantly by Cyanobacteria Geitlerinema, Pseudanabaenaceae, and Leptolyngbya with some filamentous anoxygenic phototrophs contributions, were identified and tracked from the living system through the process of silicification/lithification. In the living systems, δ[30]Si values decrease from +0.13‰ in surficial waters to -2‰ in biomat samples, indicating a kinetic isotope effect potentially induced by increased association with actively growing biofabrics. The fatty acids C16:1 and iso-C14:0 and the hydrocarbon C17:0 were disentangled from confounding signals and determined to be reliable lipid biosignatures for living biofabric builders and tenant microorganisms. Builder and tenant microbial biosignatures were linked to specific Cyanobacteria, anoxygenic phototrophs, and heterotrophs, which are prominent members of the living communities. Upon lithification and burial, silicon isotopes of silicified biomass began to re-equilibrate, increasing from δ[30]Si -2‰ in living biomats to -0.55‰ in lithified samples. Active endolithic microbial communities were identified in lithified samples and were dominated by Cyanobacteria, heterotrophic bacteria, and fungi. Results indicate that distinct microbial communities build and inhabit silicified biofabrics through time and that microbial biosignatures shift over the course of lithification. These findings improve our understanding of how microbial communities silicify, the biomarkers they retain, and transitionary impacts that may occur through lithification and burial.},
}

*Biomarkers/analysis
Cyanobacteria/metabolism
Geologic Sediments/microbiology/chemistry
Bacteria/metabolism
Hot Springs/microbiology/chemistry

@article {pmid38949619,
year = {2024},
author = {Jibrin, MO and Sharma, A and Mavian, CN and Timilsina, S and Kaur, A and Iruegas-Bocardo, F and Potnis, N and Minsavage, GV and Coutinho, TA and Creswell, TC and Egel, DS and Francis, DM and Kebede, M and Miller, SA and Montelongo, MJ and Nikolaeva, E and Pianzzola, MJ and Pruvost, O and Quezado-Duval, AM and Ruhl, GE and Shutt, VM and Maynard, E and Maeso, DC and Siri, MI and Trueman, CL and Salemi, M and Vallad, GE and Roberts, PD and Jones, JB and Goss, EM},
title = {Phylodynamic Insights into Global Emergence and Diversification of the Tomato Pathogen Xanthomonas hortorum pv. gardneri.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {MPMI04240035R},
doi = {10.1094/MPMI-04-24-0035-R},
pmid = {38949619},
issn = {0894-0282},
abstract = {The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. Xanthomonas hortorum pv. gardneri is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despite active global research on the pathogens that cause tomato and pepper bacterial spot disease. Given the recently documented global distribution of X. hortorum pv. gardneri, our objective was to examine genomic diversification associated with its emergence. We sequenced the genomes of X. hortorum pv. gardneri strains collected in eight countries to examine global population structure and pathways of emergence using phylodynamic analysis. We found that strains isolated post-1990 group by region of collection and show minimal impact of recombination on genetic variation. A period of rapid geographic expansion in X. hortorum pv. gardneri is associated with acquisition of a large plasmid conferring copper tolerance by horizontal transfer and coincides with the burgeoning hybrid tomato seed industry through the 1980s. The ancestry of X. hortorum pv. gardneri is consistent with introduction to hybrid tomato seed production and dissemination during the rapid increase in trade of hybrid seeds. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
}

@article {pmid39317790,
year = {2024},
author = {Knorr, MA and Contosta, AR and Morrison, EW and Muratore, TJ and Anthony, MA and Stoica, I and Geyer, KM and Simpson, MJ and Frey, SD},
title = {Unexpected sustained soil carbon flux in response to simultaneous warming and nitrogen enrichment compared with single factors alone.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {39317790},
issn = {2397-334X},
abstract = {Recent observations document that long-term soil warming in a temperate deciduous forest leads to significant soil carbon loss, whereas chronic soil nitrogen enrichment leads to significant soil carbon gain. Most global change experiments like these are single factor, investigating the impacts of one stressor in isolation of others. Because warming and ecosystem nitrogen enrichment are happening concurrently in many parts of the world, we designed a field experiment to test how these two factors, alone and in combination, impact soil carbon cycling. Here, we show that long-term continuous soil warming or nitrogen enrichment when applied alone followed the predicted response, with warming resulting in significant soil carbon loss and nitrogen fertilization tending towards soil carbon gain. The combination treatment showed an unanticipated response, whereby soil respiratory carbon loss was significantly higher than either single factor alone, but without a concomitant decline in soil carbon storage. Observations suggest that when soils are exposed to both factors simultaneously, plant carbon inputs to the soil are enhanced, counterbalancing soil carbon loss and helping maintain soil carbon stocks near control levels. This has implications for both atmospheric CO2 emissions and soil fertility and shows that coupling two important global change drivers results in a distinctive response that was not predicted by the behaviour of the single factors in isolation.},
}

@article {pmid39311575,
year = {2024},
author = {Han, C-J and Huang, J-P and Chiang, M-R and Jean, OSM and Nand, N and Etebari, K and Shelomi, M},
title = {The hindgut microbiota of coconut rhinoceros beetles (Oryctes rhinoceros) in relation to their geographical populations.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0098724},
doi = {10.1128/aem.00987-24},
pmid = {39311575},
issn = {1098-5336},
abstract = {The coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB's microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.IMPORTANCECoconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.},
}

@article {pmid39311333,
year = {2024},
author = {Deo, R and Lakra, U and Ojha, M and Nigam, VK and Sharma, SR},
title = {Exopolysaccharides in microbial interactions: signalling, quorum sensing, and community dynamics.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/14786419.2024.2405867},
pmid = {39311333},
issn = {1478-6427},
abstract = {Microbial interactions within diverse ecosystems are intricately governed by the dynamic interplay of exopolysaccharides (EPSs) produced by microorganisms. This review delves into the multifaceted roles of EPS in microbial signalling, quorum sensing (QS), and community dynamics, highlighting their significance in orchestrating cooperative behaviours and shaping community structures. EPSs serve as pivotal signalling molecules, influencing chemical communication and promoting intricate interactions among microorganisms. The integration of EPS into QS mechanisms adds an additional layer of complexity, allowing microorganisms to assess population density and synchronise communal responses. Furthermore, EPSs actively contribute to community dynamics by influencing spatial organisation, adhesion, and resistance to environmental stressors. By providing comprehensive knowledge of EPS dynamics, this review offers valuable insights into microbial ecology, serving as a foundational resource for future research. It will benefit the research community by advancing our understanding of microbial ecosystems, with broad applications in biotechnology, environmental science, and beyond.},
}

@article {pmid39297874,
year = {2024},
author = {Castledine, M and Pennycook, J and Newbury, A and Lear, L and Erdos, Z and Lewis, R and Kay, S and Sanders, D and Sünderhauf, D and Buckling, A and Hesse, E and Padfield, D},
title = {Characterizing a stable five-species microbial community for use in experimental evolution and ecology.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {9},
pages = {},
doi = {10.1099/mic.0.001489},
pmid = {39297874},
issn = {1465-2080},
mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; Ecology ; Biological Evolution ; Microbial Interactions ; },
abstract = {Model microbial communities are regularly used to test ecological and evolutionary theory as they are easy to manipulate and have fast generation times, allowing for large-scale, high-throughput experiments. A key assumption for most model microbial communities is that they stably coexist, but this is rarely tested experimentally. Here we report the (dis)assembly of a five-species microbial community from a metacommunity of soil microbes that can be used for future experiments. Using reciprocal invasion-from-rare experiments we show that all species can coexist and we demonstrate that the community is stable for a long time (~600 generations). Crucially for future work, we show that each species can be identified by their plate morphologies, even after >1 year in co-culture. We characterise pairwise species interactions and produce high-quality reference genomes for each species. This stable five-species community can be used to test key questions in microbial ecology and evolution.},
}

*Soil Microbiology
*Microbiota
*Bacteria/genetics/classification/isolation & purification
Ecology
Biological Evolution
Microbial Interactions

@article {pmid39303870,
year = {2024},
author = {McDonagh, F and Tumeo, A and Murray, EK and Hallahan, B and Miliotis, G},
title = {Complete genome of Escherichia coli sequence type 73 with acquired blaTEM-1 and high genotypic virulence load identified in human saliva.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2024.08.011},
pmid = {39303870},
issn = {2213-7173},
abstract = {OBJECTIVES: Escherichia coli sequence type (ST) 73 is a pandemic lineage of the ExPEC (Extraintestinal Pathogenic E. coli) family associated with conserved virulence. We report the complete genome of a genomically hypervirulent E. coli ST73 strain isolated from the oral cavity of a patient with a diagnosis of treatment resistant schizophrenia and receiving clozapine treatment.

METHODS: E. coli strain GABEEC132 underwent second and third generation sequencing with Illumina and Oxford-Nanopore-Technologies (ONT) platforms. Antibiotic Resistance Genes (ARGs) and Virulence Factors (VFs) were bioinformatically identified using the NCBI-AMR-Finder-Plus database and Virulence-Factors-database (VFDB), respectively. To contextualize the genome within a broader epidemiological framework, phylogenetic analysis was conducted using representative genomes of E. coli ST73 O6:H1 (n=55).

RESULTS: E. coli strain GABEEC132 was identified as possessing the O6:H1 serotype and classified within the B2 phylogroup. The strain exhibited a high genomic virulence load, encoding for 194 VFs. Additionally, it encoded three ARGs, including an acquired blaTEM-1 located on a rep_cluster_2350 8 237 Kb mobilisable plasmid, presenting phenotypic resistance to ampicillin and piperacillin.

CONCLUSION: This report provides novel insights into the oral prevalence of genotypically hypervirulent and drug-resistant E. coli ST73, a pandemic lineage.},
}

@article {pmid39303138,
year = {2024},
author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and Lopez-Garcia, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlic, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R},
title = {Global freshwater distribution of Telonemia protists.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae177},
pmid = {39303138},
issn = {1751-7370},
abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remains unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analysed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.},
}