@article {pmid39703713,
year = {2024},
author = {Sheng, Y and Zeng, X and Zhao, L and Li, Y},
title = {Editorial: Microbial involvement in biogeochemical cycling and contaminant transformations at land-water ecotones.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1525521},
pmid = {39703713},
issn = {1664-302X},
}

@article {pmid39701829,
year = {2024},
author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM},
title = {An interdisciplinary perspective of the built-environment microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae166},
pmid = {39701829},
issn = {1574-6941},
abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.},
}

@article {pmid39701529,
year = {2024},
author = {Firkins, JL and Henderson, EL and Duan, H and Pope, PB},
title = {International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25863},
pmid = {39701529},
issn = {1525-3198},
abstract = {Although cellulose has received the most attention, further research is needed for a complete comprehension of other fiber components in forage and nonforage fiber sources corresponding with the array of enzymes needed for depolymerization and resulting fermentation of sugars. The carbohydrate-active enzymes (CAZymes) have been described in detail herein, although new information will no doubt accumulate in the future. Known CAZymes are attributed to taxa that are easily detected via 16S rRNA gene profiling techniques, but such approaches have limitations. We describe how closely related species or strains expand into different niches depending on diet and the dynamic availability of remaining fibrous substrates. Moreover, expression of CAZymes and other enzymes such as in fermentation pathways can shift among strains and even within strains over time of incubation. We describe unique fibrolytic components of bacteria, protozoa, and fungi while emphasizing the development of consortia that efficiently increase neutral detergent fiber degradability (NDFD). For example, more powerful genome-centric functional omics approaches combined with expanded bioinformatics and network analyses are needed to expand our current understanding of ruminal function and the bottlenecks that lead to among-study variation in NDFD. Specific examples highlighted include our lack of fundamental understanding why starch limits NDFD, whereas moderate inclusion of rumen-degraded protein, certain supplemental fatty acids (especially palmitic), and supplemental sugars sometimes stimulates NDFD. Current and future research must uncover deeper complexity in the rumen microbiome through a combination of approaches described herein to be followed by validation using novel cultivation studies and, ultimately, NDFD measured in vivo for integration with ruminant productivity traits.},
}

@article {pmid39699229,
year = {2024},
author = {Anuforo, PC and Würz, B and Wick, LY and Kallies, R},
title = {Draft genome sequences of Pseudomonas chengduensis strain BW1 and Sphingobium sp. strain MK2 isolated from oil sands process-affected water.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0067724},
doi = {10.1128/mra.00677-24},
pmid = {39699229},
issn = {2576-098X},
abstract = {Draft genomes of two phenanthrene-degrading bacterial isolates from oil sands process-affected water (OSPW) in Alberta, Canada were sequenced. Both isolates grew in close association on agar plates and were difficult to obtain axenically. They represent novel Pseudomonas chengduensis and Sphingobium sp. strains with genomes of 5.5 and 4.1 Mbases length, respectively.},
}

@article {pmid39699221,
year = {2024},
author = {Lustermans, JJM and Sereika, M and Burdorf, LDW and Albertsen, M and Schramm, A and Marshall, IPG},
title = {Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0125924},
doi = {10.1128/msystems.01259-24},
pmid = {39699221},
issn = {2379-5077},
abstract = {UNLABELLED: Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.

IMPORTANCE: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.},
}

@article {pmid39698295,
year = {2024},
author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C},
title = {Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae050},
pmid = {39698295},
issn = {2730-6151},
abstract = {The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.},
}

@article {pmid39697668,
year = {2024},
author = {Roy, A and Ghosh, A and Bhadury, P},
title = {Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove.},
journal = {Access microbiology},
volume = {6},
number = {8},
pages = {},
pmid = {39697668},
issn = {2516-8290},
abstract = {Mangrovibacter sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed in silico analyses of the genome of Mangrovibacter sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.},
}

@article {pmid39695543,
year = {2024},
author = {Qin, K and Qing, J and Wang, Q and Li, Y},
title = {Epidemiological shifts in chronic kidney disease: a 30-year global and regional assessment.},
journal = {BMC public health},
volume = {24},
number = {1},
pages = {3519},
pmid = {39695543},
issn = {1471-2458},
support = {82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020SYS01//Key Laboratory Construction Plan Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; 2020XM21//Key Project of Shanxi Provincial Health Commission/ ; },
mesh = {Humans ; *Renal Insufficiency, Chronic/epidemiology/mortality ; Male ; Incidence ; *Global Health/statistics & numerical data ; Female ; Middle Aged ; Adult ; Prevalence ; Aged ; *Global Burden of Disease ; Risk Factors ; Disability-Adjusted Life Years ; Adolescent ; Young Adult ; Quality-Adjusted Life Years ; },
abstract = {BACKGROUND: Chronic kidney disease (CKD) presents a growing global health challenge, with significant variability in disease burden across different regions and countries. This study aimed to analyze the trends in incidence, prevalence, mortality, and disability-adjusted life years (DALYs) for CKD from 1990 to 2019, utilizing data from the Global Burden of Disease Study.

METHODS: We conducted an in-depth study on the global and age-standardized incidence, prevalence, mortality, and DALYs of CKD, and assessed trends over a 30-year period. Additionally, we explored the associations between healthcare access and quality (HAQ), the Socio-Demographic Index (SDI), and CKD. Furthermore, we conducted a detailed analysis of six risk factors closely related to CKD, and based on these findings, provided strong evidence for enhancing the management of CKD.

RESULTS: In 2019, there were 18,986,903 cases of CKD, with an average annual percent change (AAPC) of 1.82 (95% CI = 1.8 to 1.82) in incidence since 1990. The age-standardized incidence rate increased from 192.45 per 100,000 in 1990 to 233.65 per 100,000 in 2019. Prevalence also rose, with a total of 69,729,430 cases in 2019 and an AAPC of 1.19 (95% CI = 1.19 to 1.2). Mortality and DALYs have increased correspondingly, with the mortality rate reaching 18.29 per 100,000 and total DALYs at 41,538,592 in 2019. The analysis showed that higher HAQ levels are associated with better outcomes in terms of lower mortality and DALY rates, whereas lower HAQ levels correlate with poorer outcomes. In addition, high fasting plasma glucose and high systolic blood pressure are the main contributors to CKD-related deaths, with their population attributable fraction (PAF) significantly decreasing as the SDI decreases.

CONCLUSION: The burden of CKD has significantly increased over the past three decades, influenced by demographic changes and variations in healthcare quality and access. Effective public health strategies and improvements in healthcare delivery are needed to address the disparities in CKD outcomes globally.},
}

Humans
*Renal Insufficiency, Chronic/epidemiology/mortality
Male
Incidence
*Global Health/statistics & numerical data
Female
Middle Aged
Adult
Prevalence
Aged
*Global Burden of Disease
Risk Factors
Disability-Adjusted Life Years
Adolescent
Young Adult
Quality-Adjusted Life Years

@article {pmid39695352,
year = {2025},
author = {Moore, M and Whittington, HD and Knickmeyer, R and Azcarate-Peril, MA and Bruno-Bárcena, JM},
title = {Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2440120},
doi = {10.1080/19490976.2024.2440120},
pmid = {39695352},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Bacteria/metabolism/classification/isolation & purification/genetics ; Feces/microbiology ; Lactose/metabolism ; Dietary Fiber/metabolism ; Oligosaccharides/metabolism ; Amino Sugars ; },
abstract = {Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL[-1]) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Bacteria/metabolism/classification/isolation & purification/genetics
Feces/microbiology
Lactose/metabolism
Dietary Fiber/metabolism
Oligosaccharides/metabolism
Amino Sugars

@article {pmid39694113,
year = {2024},
author = {Van Peteghem, L and Matassa, S and Sakarika, M},
title = {Fueling the protein transition: Can waste-derived ethanol enable efficient and high-quality microbial protein production?.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131990},
doi = {10.1016/j.biortech.2024.131990},
pmid = {39694113},
issn = {1873-2976},
abstract = {Meeting the protein needs of a growing population will require significant resources. In this context, microbial protein (MP) offers a nutritious and versatile protein source from recovered resources. This meta-analysis of over 100 studies examines the efficiency and nutritional quality of MP production using ethanol. Ethanol, a feedstock derived from CO2 and biological waste, is used by various microorganisms, and has an established role in the food sector. Results show that ethanol-based MP production is technically feasible for food applications, reaching biomass concentrations of 14-230 g/L and productivities of 11-13 g/L/h. The protein content of MP correlates with productivity, and the nutritional quality of ethanol-grown MP matches common sources like pork and tofu. Lastly, operational choices affect the techno-economic feasibility of using waste-derived ethanol and other recovered resources. This meta-analysis highlights the potential of ethanol-grown MP, though further research is needed to close existing knowledge gaps.},
}

@article {pmid39693383,
year = {2024},
author = {Arrington, EC and Tarn, J and Kivenson, V and Nunn, BL and Liu, RM and Paul, BG and Valentine, DL},
title = {Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae247},
pmid = {39693383},
issn = {1751-7370},
abstract = {Aqueous-soluble hydrocarbons dissolve into the ocean's interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.},
}

@article {pmid39693347,
year = {2024},
author = {Sun, X and Buchanan, PJ and Zhang, IH and San Roman, M and Babbin, AR and Zakem, EJ},
title = {Ecological dynamics explain modular denitrification in the ocean.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {52},
pages = {e2417421121},
doi = {10.1073/pnas.2417421121},
pmid = {39693347},
issn = {1091-6490},
support = {LS-FMME-00871981//Simons Foundation (SF)/ ; OCE-2138890 and OCE-2142998//NSF (NSF)/ ; N/A//MIT School of Science MathWorks Science Fellowship/ ; 2125142//NSF (NSF)/ ; },
mesh = {*Denitrification/physiology ; *Oceans and Seas ; *Ecosystem ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Nitrous Oxide/metabolism ; Oxygen/metabolism ; Bacteria/metabolism ; },
abstract = {Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3[-]→NO2[-]→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2[-] and N2O in a NO3[-]-filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3[-]→NO2[-] module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3[-]→NO2[-] module. Results also capture observations that NO3[-] is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.},
}

*Denitrification/physiology
*Oceans and Seas
*Ecosystem
Seawater/microbiology/chemistry
Nitrogen/metabolism
Nitrous Oxide/metabolism
Oxygen/metabolism
Bacteria/metabolism

@article {pmid39692747,
year = {2024},
author = {Wallace, EJ and O'Dwyer, J and Dolan, EB and Burke, LP and Wylie, R and Bellavia, G and Straino, S and Cianfarani, F and Ciotti, G and Serini, S and Calviello, G and Roche, ET and Mitra, T and Duffy, GP},
title = {Actuation-Mediated Compression of a Mechanoresponsive Hydrogel by Soft Robotics to Control Release of Therapeutic Proteins.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2401744},
doi = {10.1002/advs.202401744},
pmid = {39692747},
issn = {2198-3844},
support = {713690//Horizon 2020/ ; 812865//Horizon 2020/ ; GOIPD/2020/157//Irish Research Council/ ; 13/RC/2073/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {Therapeutic proteins, the fastest growing class of pharmaceuticals, are subject to rapid proteolytic degradation in vivo, rendering them inactive. Sophisticated drug delivery systems that maintain protein stability, prolong therapeutic effects, and reduce administration frequency are urgently required. Herein, a mechanoresponsive hydrogel is developed contained within a soft robotic drug delivery (SRDD) device. In a step-change from previously reported systems, pneumatic actuation of this system releases the cationic therapeutic protein Vascular Endothelial Growth Factor (VEGF) in a bioactive form which is required for therapeutic angiogenesis, the growth of new blood vessels, in numerous clinical conditions. The ability of the SRDD device to release bioactive VEGF in a spatiotemporal manner from the hydrogel is tested in diabetic rats - a model in which angiogenesis is difficult to stimulate. Daily actuation of the SRDD device in the diabetic rat model significantly increased cluster of differentiation 31+ (CD31+) blood vessel number (p = 0.0335) and the diameter of alpha-smooth muscle actin+ (α-SMA+) blood vessels (p = 0.0025) compared to passive release of VEGF from non-actuated devices. The SRDD device combined with the mechanoresponsive hydrogel offers the potential to deliver an array of bioactive therapeutics in a spatiotemporal manner to mimic their natural release in vivo.},
}

@article {pmid39691821,
year = {2024},
author = {Ghosh, A and Bhambra, SK and Chandrasekaran, R and Bhadury, P},
title = {Genome description of a potentially new species of Streptomyces isolated from the Indian Sundarbans mangrove.},
journal = {Access microbiology},
volume = {6},
number = {12},
pages = {},
pmid = {39691821},
issn = {2516-8290},
abstract = {A potentially new species of Streptomyces was isolated from station 177 of the Sundarbans Seasonal Time Series in the Indian Sundarbans mangrove. The isolate was cultured from a sediment sample on TYS medium of salinity 15. Sequencing and annotation of the 16S rRNA showed 100% identity against S. laurentii NPS17 against GenBank/ENA/DDBJ. Annotation of the whole genome against the GTDB database showed closest identity with S. terrae SKN60 and belongs to the same clade as S. roseicoloratus TRM44457T and S. laurentii ATCC 31255. The genome is ~7.2 Mb and has a G+C% of 73%. The average amino acid identity was 85.01% with S. roseicoloratus and 80.34% with S. roseolus. The assembly reflected the presence of all essential genes and had 19 biosynthetic gene clusters predicted.},
}

@article {pmid39689568,
year = {2024},
author = {Sumerta, IN and Ruan, X and Howell, K},
title = {The forgotten wine: Understanding palm wine fermentation and composition.},
journal = {International journal of food microbiology},
volume = {429},
number = {},
pages = {111022},
doi = {10.1016/j.ijfoodmicro.2024.111022},
pmid = {39689568},
issn = {1879-3460},
abstract = {Palm wine is an alcoholic beverage that has existed for centuries and has important economic and socio-culture values in many tropical and sub-tropical countries. Lesser known than other types of wines, palm wine is made by spontaneous fermentation of palm sap by naturally occurring microbial communities. The palm sap ecosystem has unique microbial composition and diversity, which determines the composition of the eventual wine and is likely affected by geographical distinctiveness. While these features are well understood in grape and rice wine, these features have not been understood in palm wine. Here, we gather information of microbial communities and metabolite profiles from published studies, covering a wide range of methodologies and regions to better understand the causal links between the principal microbial species and major metabolites of palm wine. We assessed palm wine quality across production regions and local practices to provide general characteristics of palm wine and identify specific regional information. These will provide better understandings to the function of microbial communities and metabolite diversity, the contribution of regional variations and to ensure product quality in this unique, yet overlooked, fermented beverage.},
}

@article {pmid39689238,
year = {2024},
author = {Yang, Q and Defoirdt, T},
title = {Weak selection for resistance to quorum sensing inhibition during multiple host infection cycles.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae251},
pmid = {39689238},
issn = {1751-7370},
abstract = {Quorum sensing inhibition is a promising novel approach to control bacterial infections. However, it is not clear whether quorum sensing inhibition will impose selective pressure for the spread of resistance against quorum sensing inhibition in pathogen populations. Previous research tried to answer this question by using synthetic growth media, and this revealed that whether or not resistance will spread completely depends on the environment in which it is studied. Therefore, the spread of resistance should be studied in the environment where it ultimately matters: in vivo during infection of a host. Here, using quorum sensing inhibitor-susceptible and -resistant mimics, we show that resistance to quorum sensing inhibition does not spread in host-associated populations of Vibrio campbellii during up to 35 cycles of infection and transmission if the initial frequency of the resistance is low in the pathogen population, whereas it further increases to 100% if it is already prevalent. However, even in the latter case, the resistance spreads at a slower pace than resistance to antibiotics spreads under the same conditions.},
}

@article {pmid39689178,
year = {2024},
author = {Li, G and Liu, T and Xie, W and Liu, Z and Li, H and Whalen, JK and Jousset, A and Wei, Z},
title = {Metabolites limiting predator growth wane with prey biodiversity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {52},
pages = {e2410210121},
doi = {10.1073/pnas.2410210121},
pmid = {39689178},
issn = {1091-6490},
support = {32201399//MOST | National Natural Science Foundation of China (NSFC)/ ; 32171640//MOST | National Natural Science Foundation of China (NSFC)/ ; KYQN2023048//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2022YFD1500302//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Animals ; *Biodiversity ; *Nematoda/physiology ; *Food Chain ; *Predatory Behavior/physiology ; Microbiota/physiology ; Bacteria/metabolism/classification ; Soil Microbiology ; },
abstract = {Predator-prey interactions are a major driver of microbiome dynamics, but remain difficult to predict. While several prey traits potentially impact resistance to predation, their effects in a multispecies context remain unclear. Here, we leverage synthetic bacterial communities of varying complexity to identify traits driving palatability for nematodes, a main consumer of bacteria in soil. We assessed trophic interactions between four nematode species and 122 bacterial isolates, across a gradient of prey biodiversity ranging from single species to 50 species. Nematode size, a proxy for prey palatability, varied strongly with prey community composition and could be predicted by metabolic and morphological properties of the prey. However, the influence of prey traits on predators depended on biodiversity. Secondary metabolites drove palatability in monoculture, but this effect vanished under increasing prey biodiversity, where prey size became the dominant predictors of nematode size. Although idiosyncratic properties are often emphasized in the literatures, our results suggest that in biodiverse assemblages, the composition of available prey and their traits are more reliable predictors of predator-prey interactions. This study offers valuable insights into microbial ecology in the context of predator-prey interactions, as cryptic microbial responses can be guided by deductions based on generalizable biological traits.},
}

Animals
*Biodiversity
*Nematoda/physiology
*Food Chain
*Predatory Behavior/physiology
Microbiota/physiology
Bacteria/metabolism/classification
Soil Microbiology

@article {pmid39687379,
year = {2024},
author = {Lee, D and Oliveira, FCC and Conant, RT and Kim, M},
title = {Microbial community assembly across agricultural soil mineral mesocosms revealed by 16S rRNA gene amplicon sequencing data.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {111125},
doi = {10.1016/j.dib.2024.111125},
pmid = {39687379},
issn = {2352-3409},
abstract = {Increasing atmospheric carbon dioxide (CO2) concentrations are impacting the global climate, resulting in significant interest in soil carbon sequestration as a mitigation strategy. While recognized that mineral-associated organic matter (MAOM) in soils is mainly formed through microbial activity, our understanding of microbial-derived MAOM formation processes remains limited due to the complexity of the soil environment. To gain insights into this issue, we incubated fresh soil samples for 45 days with one of three mineral additions: Sand, Kaolinite+Sand, or Illite+Sand. 16S rRNA V3/V4 gene amplicon sequencing was then conducted on samples using an Illumina NextSeq 2000 flow cell. The reads were analyzed and taxonomically assigned with QIIME2 v2023.5.1 and SILVA 138. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA1124235. This dataset is important and useful as it provides valuable insights into the interactions between soil minerals and microbial communities, which can inform strategies for enhancing soil carbon sequestration and mitigating climate change. Moreover, it serves as a crucial reference for future studies, offering a foundational understanding of microbial dynamics in soil systems and guiding further research in microbial ecology and carbon cycling.},
}

@article {pmid39683937,
year = {2024},
author = {Liu, S and Teng, L and Ping, J},
title = {Graphitic Carbon Nitride Confers Bacterial Tolerance to Antibiotics in Wastewater Relating to ATP Depletion.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {23},
pages = {},
doi = {10.3390/molecules29235780},
pmid = {39683937},
issn = {1420-3049},
support = {62105175//National Natural Science Foundation of China/ ; ZR2021QF058//Natural Science Foundation of Shandong Province/ ; 2022PY036//The Education and Industry Integration Pilot Project of Qilu University of Technology/ ; 432413/01090//Start-up fund of Tianjin Renai College/ ; },
mesh = {*Graphite/chemistry ; *Wastewater/microbiology/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Adenosine Triphosphate/metabolism ; Nitrogen Compounds/chemistry ; Staphylococcus aureus/drug effects ; Ofloxacin/pharmacology ; Drug Resistance, Bacterial/drug effects ; Reactive Oxygen Species/metabolism ; Microbial Sensitivity Tests ; Water Purification/methods ; },
abstract = {Graphitic carbon nitride (C3N4) is a kind of visible light-responsive photocatalyst that has been of great interest in wastewater treatment. However, its environmental impact and biological effect remains to be elucidated. This study investigated the effect of C3N4 nanosheets on bacterial abundance and antibiotic tolerance in wastewater. Interestingly, as compared to the wastewater containing the antibiotic ofloxacin alone, the wastewater containing both ofloxacin and C3N4 had much higher numbers of total living bacteria, but lower levels of the ofloxacin-resistant bacteria and the ofloxacin-resistant gene qnrS. The model bacterium Staphylococcus aureus was then used to explore the mechanism of C3N4-induced antibiotic tolerance. The nanosheets neither adsorbed the antibiotic nor promoted drug efflux, uncovering that drug adsorption and efflux were not involved in antibiotic tolerance. Further investigations revealed that the nanosheets, like arsenate and menadione, drastically reduced ATP levels and induced the production of reactive oxygen species for enhanced antibiotic tolerance. This study revealed an antibiotic-tolerating mechanism associated with C3N4-induced ATP depletion, and shed a light on the effect of photocatalysts on microbial ecology during their application in wastewater treatment.},
}

*Graphite/chemistry
*Wastewater/microbiology/chemistry
*Anti-Bacterial Agents/pharmacology
*Adenosine Triphosphate/metabolism
Nitrogen Compounds/chemistry
Staphylococcus aureus/drug effects
Ofloxacin/pharmacology
Drug Resistance, Bacterial/drug effects
Reactive Oxygen Species/metabolism
Microbial Sensitivity Tests
Water Purification/methods

@article {pmid39682491,
year = {2024},
author = {Suriyasathaporn, W and Kongkaew, A and Intanon, M and Srithanasuwan, A and Saipinta, D and Pangprasit, N and Thongtharb, A and Chuasakhonwilai, A and Chaisri, W},
title = {Non-aureus Staphylococci Cause the Spontaneous Cure or Persistent Infection of Major Bovine Mastitis Pathogens in the Murine Mammary Glands.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/ani14233526},
pmid = {39682491},
issn = {2076-2615},
support = {FF66/017//The Fundamental Fund, Chiang Mai University/ ; },
abstract = {The microbial ecology in mastitis involves the interactions between bacteria and the mammary gland environment. Poor mastitis control, for which understanding these microbial relationships is crucial, increases the risk of mastitis and co-infections. The aim of this study was to determine the pathogenesis and bacterial ecology of murine mammary glands following intramammary infection (IMI) with S. aureus (AU), S. agalactiae (SA), and four isolates of selected non-aureus staphylococci (NAS), as well as co-infections of AU or SA with NAS. Selected NAS demonstrated resistance to growth inhibition after co-culture with AU and SA and were proven to be protective in vitro against AU and SA. Both single infections and co-infections of AU, SA, two selected isolates of S. hominis (NAS1 and NAS2), and two selected isolates of S. chromogens (NAS3 and NAS4) were injected into the murine mammary glands at 10[5] CFU/mL. After 72 h of inoculation, the results showed that AU, AU-NAS2, and AU-NAS3 expressed severe inflammation with clinical signs of mastitis. The persistence of AU was found for AU, NAS3, and AU-NAS3, whereas the persistence of SA was found for SA-NAS1, SA-NAS3, and SA-NAS, although single SA could not persist. Interestingly, NAS2 in both the single- and co-IMIs with AU or SA resulted in a spontaneous cure 72 h after the IMI. In conclusion, some NAS have beneficial results because they can eliminate S. aureus and S. agalactiae, but some NAS have negative effects because they can support persistent S. agalactiae infection. These results may be used to explain both the advantages and disadvantages of NAS on farms with poor mastitis control. In addition, the beneficial S. hominis may initiate natural live antibiotics and reduce antibiotic resistance problems.},
}

@article {pmid39681734,
year = {2024},
author = {Rajendran, D and Vinayagam, S and Sekar, K and Bhowmick, IP and Sattu, K},
title = {Symbiotic Bacteria: Wolbachia, Midgut Microbiota in Mosquitoes and Their Importance for Vector Prevention Strategies.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {154},
pmid = {39681734},
issn = {1432-184X},
mesh = {*Wolbachia/physiology ; Animals ; *Symbiosis ; *Gastrointestinal Microbiome ; *Mosquito Vectors/microbiology ; Culicidae/microbiology ; Mosquito Control/methods ; },
abstract = {Mosquito-borne illnesses pose a significant threat to eradication under existing vector management measures. Chemo-based vector control strategies (use of insecticides) raise a complication of resistance and environmental pollution. Biological control methods are an alternative approach to overcoming this complication arising from insecticides. The mosquito gut microbiome is essential to supporting the factors that involve metabolic regulation and metamorphic development (from juvenile to adult), as well as the induction of an immune response. The induced immune response includes the JAK-STAT, IMD, and Toll pathways due to the microbial interaction with the midgut cells (MG cells) that prevent disease transmission to humans. The aforementioned sequel to the review provides information about endosymbiont Wolbachia, which contaminates insect cells, including germline and somatic cytoplasm, and inhibits disease-causing pathogen development and transmission by competing for resources within the cell. Moreover, it reduces the host population via cytoplasmic incompatibility (CI), feminization, male killing, and parthenogenesis. Furthermore, the Cif factor in Wolbachia is responsible for CI induction that produces inviable cells with the translocating systems and the embryonic defect-causing protein factor, WalE1 (WD0830), which manipulates the host actin. This potential of Wolbachia can be used to design a paratransgenic system to control vectors in the field. An extracellular symbiotic bacterium such as Asaia, which is grown in the growth medium, is used to transfer lethal genes within itself. Besides, the genetically transferred symbiotic bacteria infect the wild mosquito population and are easily manifold. So, it might be suitable for vector control strategies in the future.},
}

*Wolbachia/physiology
Animals
*Symbiosis
*Gastrointestinal Microbiome
*Mosquito Vectors/microbiology
Culicidae/microbiology
Mosquito Control/methods

@article {pmid39681034,
year = {2024},
author = {Fu, Y and Hu, F and Wang, F and Xu, M and Jia, Z and Amelung, W and Mei, Z and Han, X and Virta, M and Jiang, X and Tiedje, JM},
title = {Field-based evidence for the prevalence of soil antibiotic resistomes under long-term antibiotic-free fertilization.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109202},
doi = {10.1016/j.envint.2024.109202},
pmid = {39681034},
issn = {1873-6750},
abstract = {Growing evidence suggests that the use of manure containing residual antibiotics universally leads to an increase in soil antibiotic resistance genes (ARGs). However, there is limited understanding of the influence of long-term antibiotic-free fertilization and the differences between antibiotic-free manure and chemical fertilizer on soil ARGs. This study aimed to quantify the assembly patterns of the antibiotic resistome by in situ probing bacterial community and environmental variations in field soils that have been subjected to long-term exposure to chemical fertilizer and/or manure from animals without antibiotic amendments. Long-term fertilization slightly impacts the diversity of antibiotic resistomes, with 85.5 % of total ARGs and mobile genetic elements (MGEs) being common across all treatment types, while significantly increasing their abundances from 0.68 to a maximum of 0.90 copies/16S rRNA. The rise in ARG abundances was less pronounced when using antibiotic-free manure compared to chemical fertilizer, particularly for Rank Ⅱ ARGs. However, when antibiotic-free manure and chemical fertilizer were combined, a significant increase in nutrients (such as available nitrogen and organic matter) and MGEs occurred, leading to the enrichment of soil microbial populations, especially in certain resistant species, and Rank Ⅰ and Ⅱ ARGs. Despite the influence of various factors like bacterial communities, soil properties, heavy metals, and MGEs, the MGEs had the most significant standardized effects on shaping ARGs through both direct and indirect pathways. Our findings indicates that while of antibiotic-free manure can lower the risk of antibiotic residues and promote sustainable farming practices, it may not fully eliminate the prevalence of ARGs, highlighting the need for more comprehensive strategies to address antibiotic resistance in agriculture rather than simply prohibiting the use of antibiotics.},
}

@article {pmid39680930,
year = {2024},
author = {Li, XY and Zhu, CW and Chen, S and Xiang, Q and Lu, C and Lin, XY and Chen, QL},
title = {Elevated CO2 Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO2 Enrichment (FACE) Experiment.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09625},
pmid = {39680930},
issn = {1520-5851},
abstract = {Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO2 on seed resistomes remains poorly understood. Here, a free-air CO2 enrichment system was used to examine the impact of elevated CO2 on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO2 levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO2 levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO2 level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO2 directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO2 on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.},
}

@article {pmid39680691,
year = {2024},
author = {Yang, JC and Lagishetty, V and Aja, E and Arias-Jayo, N and Chang, C and Hauer, M and Katzka, W and Zhou, Y and Sedighian, F and Koletic, C and Liang, F and Dong, TS and Situ, J and Troutman, R and Buri, H and Bhute, S and Simpson, CA and Braun, J and Jacob, N and Jacobs, JP},
title = {Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae250},
pmid = {39680691},
issn = {1751-7370},
abstract = {Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three cohorts of specific pathogen-free mice spanning two facilities. Of these region-specific microbes, the health-linked genus Akkermansia was consistently enriched in the lumen of the small intestine compared to the colon. Predictive functional modeling on 16S rRNA gene amplicon sequencing data recapitulated in shotgun sequencing data revealed increased microbial central metabolism, lipolytic fermentation, and cross-feeding in the small intestine, whereas butyrate synthesis was colon-enriched. Neuroactive compound metabolism also demonstrated regional specificity, including small intestine-enriched gamma-aminobutyric acid degradation and colon-enriched tryptophan degradation. Specifically, the jejunum and ileum stood out as sites with high predicted metabolic and neuromodulation activity. Differences between luminal and mucosal microbiomes within each site of the gastrointestinal tract were largely facility-specific, though there were a few consistent patterns in microbial metabolism in specific pathogen-free mice. These included luminal enrichment of central metabolism and cross-feeding within both the small intestine and the colon, and mucosal enrichment of butyrate synthesis within the colon. Across three cohorts of germ-free mice colonized with mice or human stool, compositional and functional region specificity were inconsistently reproduced. These results underscore the importance of investigating the spatial variation of the gut microbiome to better understand its impact on host physiology.},
}

@article {pmid39679708,
year = {2024},
author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H},
title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0102824},
doi = {10.1128/aem.01028-24},
pmid = {39679708},
issn = {1098-5336},
abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.},
}

@article {pmid39679616,
year = {2024},
author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D},
title = {Gut microbiota genome features associated with brain injury in extremely premature infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2410479},
doi = {10.1080/19490976.2024.2410479},
pmid = {39679616},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification/metabolism ; Genome, Bacterial ; Cohort Studies ; },
abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.},
}

*Gastrointestinal Microbiome
Humans
Infant, Newborn
*Infant, Extremely Premature
*Brain Injuries/microbiology/genetics
*Feces/microbiology
Female
Male
Bacteria/genetics/classification/isolation & purification/metabolism
Genome, Bacterial
Cohort Studies

@article {pmid39675658,
year = {2024},
author = {Yan, R and Xu, X and Niu, Y and Ying, S and Cai, J and Chen, R and Gu, Y and Kan, H},
title = {Microbial Diversity and Environmental Determinants at Shanghai Hongqiao Railway Station: A Comprehensive Microbial Assessment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125534},
doi = {10.1016/j.envpol.2024.125534},
pmid = {39675658},
issn = {1873-6424},
abstract = {The COVID-19 pandemic has underscored the importance of indoor environmental management in transportation hubs, which are critical for pathogen transmission due to high foot traffic. However, research has primarily focused on subways, with limited studies on train stations. In this study, samples were collected at the Shanghai Hongqiao Railway Station in winter, spring, and summer. Microbial DNA was extracted from collected indoor surfaces and ambient air samples and then analyzed through high-throughput 16S rRNA gene sequencing. Alongside sample collection, environmental data were recorded. Alpha diversity was greatest in winter, followed by summer, and least in spring within the train station environment. Surface samples exhibited higher alpha diversity compared to air samples, with no notable difference between indoor and outdoor air. Beta diversity showed significant variation across seasons and locations, with seasonal changes more pronounced than spatial ones, primarily due to differences between air and surface samples rather than indoor and outdoor environments. Key determinants of microbial community structure included CO2, temperature, illuminance, and passenger volume. The microbial community in train stations originates from various sources, with contributions from both natural elements (like wastewater/sludge, soil, and plants) and human sources (such as gastrointestinal, oral, and dermal flora). This study highlights the microbial ecology of train stations, emphasizing the need for microbial surveillance and management in transportation settings.},
}

@article {pmid39673336,
year = {2024},
author = {Liu, J and He, Y and Qiu, Z and Fahad, S and Zhao, S and Zhu 朱, M墨},
title = {Erysiphe russellii Causing Powdery Mildew on Oxalis corniculata L. in Central China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-24-2249-PDN},
pmid = {39673336},
issn = {0191-2917},
abstract = {Oxalis corniculata L. (Creeping woodsorrel) is a perennial plant of the genus Oxalis in Oxalidaceae family, which has the high ornamental and medicinal value. Extracts of creeping woodsorrel are used as antioxidants and cholinesterase inhibitors and for anti-inflammatory, antiseptic, analgesic, antirheumatic ache, and antimicrobial purposes (Leporatti et al. 2003). In June 2024, powdery mildew was found on the leaves of Creeping woodsorrel in Xinxiang City, Henan Province, China (113.925°E, 35.294°N). About 100 plants were examined and 80 % were infected with disease symptoms, i.e. curling and senescence. The white masses were on the both sides of plant leaves covering up to 90% of the leaves area. The slightly or straight curved conidiophores (n = 50) were 68 to 99× 6 to 12 μm in size and consisted of foot cells, shorter cells and singly conidia. The ellipsoidal to oval conidia (n =50), were 26 to 10 ×11 to 5 μm in size and had a length/width ratio of 1.6 to 2.2. These morphological characteristics were similar to the previously reported Creeping woodsorrel powdery mildew fungus, Erysiphe russellii (Thuong et al. 2017; Takamatsu et al. 2015). Following previously described methods (White et al. 1990; Bradshaw et al. 2022; Zhu et al. 2022), the ITS (ribosomal transcribed spacer), GAPDH (glyceraldehyde-3-phosphate dehydrogenase), RPB2 (RNA polymerase II), GS (glutamine synthetase) and CAM (calmodulin) gene regions of three isolates were amplified with specific primers ITS1/ITS4 (ITS1 5'-TCCGTAGGTGAACCTGCGG-3'; ITS4 5'-TCCTCCGCTTATTGATATGC-3'), PMGAPDH1/PMGAPDH3R (PMGAPDH1 5'-GGAATGGCTATGCGTGTACC-3'; PMGAPDH3R 5'-CCCCATTCGTTGTCGTACCATG-3'), CAM1/CAM4R (CAM1 5'-CTTTGCATCATGAGTTGGAC-3'; CAM4R 5'-GGCTCGAAAAATGAAAGATACCG-3'), Rpb2_4/Rpb2_6R (Rpb2_4 5'-GCAAGCTCAACTGCTGGTG-3'; Rpb2_6R 5'-TCCAGCGATGTGCTGTTGG-3'), GSPM2/GSPM3R (GSPM2 5'-CCAATCAGTTACTGTTTGTTCCC-3'; GSPM3R 5'-GGACTTCCTGATATTATGCC3'). Sanger sequencing results showed that each sequence of the three isolates were the same. Then sequences of one isolate were uploaded in GenBank (Accession No. PQ044579, PQ149219, PQ149220, PQ149221and PQ149222, respectively). The sequences were 100% identical to those of a previously reported E russellii on O. corniculata (Thuong et al. 2017; Takamatsu et al. 2015). The pathogen and the previously reported E russellii are clustered in the same branch in the phylogenetic tree (Thuong et al. 2017; Takamatsu et al. 2015). The pathogenicity was tested according to the method previously described (Zhu et al. 2021). By blowing conidia on infected leaves with pressurized air, the fungus was inoculated onto the leaves of three healthy plants (three-month-old), with three uninoculated plants (three-month-old) treated as controls. The infected plants and the control plants were placed in the culture room with the temperature 23 °C, humidity 50% and light/Dark 16/8 h, respectively. 10-12 days post inoculation, the leaves of the inoculated plants showed signs and symptoms of powdery mildew, while the control group was unaffected. The pathogen of the infected plant disease was re-examined by morphological characteristics and was similar to the original fungus. The pathogenicity tests were repeated three times and same results were obtained. Therefore, the pathogen was identified and confirmed as E russellii (isolate ER-ZM2024). Previously, E russellii was reported on Oxalis corniculata L. in Japan and Korea (Thuong et al. 2017; Takamatsu et al. 2015). To the best our knowledge, this is the first report of powdery mildew caused by E russellii on O. corniculata L. in central China. This identification of E russellii on O. corniculata L. provides a new perspective for the study of the disease. The results of this study provide the sequences of E russellii for further phylogenetic analysis.},
}

@article {pmid39665561,
year = {2024},
author = {Unzueta-Martínez, A and Girguis, PR},
title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0109424},
doi = {10.1128/aem.01094-24},
pmid = {39665561},
issn = {1098-5336},
abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.

IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.},
}

@article {pmid39660837,
year = {2024},
author = {Lewin, GR},
title = {mSphere of Influence: How the single cell contributes to the collective.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043124},
doi = {10.1128/msphere.00431-24},
pmid = {39660837},
issn = {2379-5042},
abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.},
}

@article {pmid39659497,
year = {2024},
author = {Ritsch, M and Brait, N and Harvey, E and Marz, M and Lequime, S},
title = {Endogenous viral elements: insights into data availability and accessibility.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae099},
pmid = {39659497},
issn = {2057-1577},
abstract = {Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR ('findable, accessible, interoperable, and reusable') principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.},
}

@article {pmid39657855,
year = {2024},
author = {Gu, Z and He, L and Liu, T and Xing, M and Feng, L and Luo, G},
title = {Exploring Strategies for Kitchen Waste Treatment and Remediation from the Perspectives of Microbial Ecology and Genomics.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143925},
doi = {10.1016/j.chemosphere.2024.143925},
pmid = {39657855},
issn = {1879-1298},
abstract = {Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes were increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.},
}

@article {pmid39657789,
year = {2024},
author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1115},
pmid = {39657789},
issn = {1362-4962},
support = {KICH1.LWV04.21.013//NWO/ ; 101000392//Horizon 2020/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; 547394769//German Research Foundation/ ; //University of Sydney/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; IM230100154//Australian Research Council Industry Fellowship/ ; //Hans Fischer Society/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; 101117891-MeDiSyn//ERC Starting/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; //Department of Biotechnology/ ; //National Agri-Food Biotechnology Institute/ ; 101087181//EU/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; 2021YFA0909500//National Key Research and Development Program of China/ ; 32170080//National Natural Science Foundation of China/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 21K06336//KAKENHI/ ; 21/07038-0//São Paulo Research Foundation/ ; VI.Veni.202.130//NWO Talent/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 222676//USDA Evans-Allen Research/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; //University of Illinois/ ; 802736//European Union Horizon 2020/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; //NWO Merian/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101066127//European Union/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; K12 GM068524/GM/NIGMS NIH HHS/United States ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Alexander von Humboldt-Stiftung/ ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; NE/T010959/1//Signals in the Soil/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; 495740318//German Research Foundation/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; 101072485//European Union's Horizon/ ; //European Regional Development Fund/ ; 802736//European Union's Horizon 2020/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; //Swiss Federal Government/ ; PS00349981//Fulbright/ ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; DM60066//Italian Ministry of Research/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; NA22NOS4200050//NERRS/ ; BB/V005723/2//BBSRC/ ; 1347411//CONAHCYT/ ; T32GM136583/NH/NIH HHS/United States ; 101130799//European Union's Horizon/ ; CFB 2.0//Novo Nordisk Foundation/ ; //Basic Science Research Program/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; //Werner Siemens Foundation/ ; OCENW.XL21.XL21.088//NWO-XL/ ; DNRF137//Danish National Research Foundation/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; CBET-2032243//U.S. National Science Foundation/ ; //Delta Stewardship Council Delta Science Program/ ; //European Union's Horizon 2020 Research/ ; 852600//Innovation Program ERC St/ ; 101072485//European Union's Horizon Europe/ ; //Conahcyt Mexico International PhD Studentship/ ; //Strathclyde University Global Research Scholarship/ ; 3141-00013A//Innovation Fund Denmark/ ; K445/2022//Leibniz Association/ ; 23/01956-2//São Paulo Research Foundation/ ; DGE 2241144//NSF GRFP/ ; 024.004.014//MiCRop Consortium/ ; CF22-1239//Carlsberg Foundation/ ; 102022750//SINTEF/ ; 102029187//SEP AGREE/ ; 102024676-14//POS BIOINFO 2024/ ; 101106349//Marie Sklodowska-Curie/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //National Research Fund of Ukraine/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //German Academic Scholarship Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; //Department of Biotechnology/ ; //University Grants Commission/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; GNT2021638//National Health and Medical Research Council/ ; DP230102668//Australian Research Council Discovery Project/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 865738/ERC_/European Research Council/International ; T32-GM136629//Chemical-Biology Interface Training/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; 101099528//European Innovation Council/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; //Swedish Pharmaceutical Society PostDoc/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; //Saarland University/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; AUFF-E-2022-9-42//AUFF/ ; 101055020-COMMUNITY//ERC Advanced/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; 10.55776/P 34036//Austrian Science Fund/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; },
abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}

@article {pmid39651958,
year = {2024},
author = {Werlang, CA and Sahoo, JK and Cárcarmo-Oyarce, G and Stevens, C and Uzun, D and Putnik, R and Hasturk, O and Choi, J and Kaplan, DL and Ribbeck, K},
title = {Selective Biofilm Inhibition through Mucin-Inspired Engineering of Silk Glycopolymers.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.4c12945},
pmid = {39651958},
issn = {1520-5126},
abstract = {Mucins are key components of innate immune defense and possess remarkable abilities to manage pathogenic microbes while supporting beneficial ones and maintaining microbial homeostasis at mucosal surfaces. Their unique properties have garnered significant interest in developing mucin-inspired materials as novel therapeutic strategies for selectively controlling pathogens without disrupting the overall microbial ecology. However, natural mucin production is challenging to scale, driving the need for simpler materials that reproduce mucin's bioactivity. In this work, we generated silk-based glycopolymers with different monosaccharides (GalNAc, GlcNAc, NeuNAc, GlcN, and GalN) and different grafting densities. Using the oral cavity as a model system, we treated in vitro cultures of pathogenic Streptococcus mutans and commensal Streptococcus sanguinis with our glycopolymers, finding that silk-tethered GalNAc uniquely prevented biofilm formation without affecting overall bacterial growth of either species. This relatively simple material reproduced mucin's virulence-neutralizing effects while maintaining biocompatibility. These mucin-inspired materials represent a valuable tool for preventing infection-related harm and offer a strategy for the domestication of pathogens in other environments.},
}

@article {pmid39651889,
year = {2024},
author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG},
title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0171224},
doi = {10.1128/spectrum.01712-24},
pmid = {39651889},
issn = {2165-0497},
abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.

IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.},
}

@article {pmid39644970,
year = {2024},
author = {Tumeo, A and McDonagh, F and Kovarova, A and Ryan, K and Clarke, C and Miliotis, G},
title = {Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2024.11.018},
pmid = {39644970},
issn = {2213-7173},
abstract = {OBJECTIVES: While Escherichia coli phylogroup-A is typically associated with commensal strains, some isolates can harbour virulence and exhibit multidrug-resistant (MDR) phenotypes. We report the draft genome of a rare instance of carbapenem, fosfomycin and colistin resistant E. coli phylogroup-A, isolated as part of routine screening of a human patient in a clinical setting in Ireland.

METHODS: E. coli E230738 was identified using MALDI-ToF/MS. Antibiotic susceptibility testing was performed using the Sensitire-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST).

RESULTS: E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs (17 acquired). Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to predicted chromosomal blaNDM-5. Colistin resistance appeared associated with acquired mcr-1.1. Despite lacking fosfomycin-inactivating-enzymes, fosfomycin resistance was observed, possibly due to efflux pumps. 47 chromosomal VFs were identified, involved in adhesion and iron acquisition amongst others. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. Phylogenetic analysis showed the closest relative being a strain from the UK differing by 851 genes.

CONCLUSION: This is a first detected instance of a blaNDM-5 and mcr-1.1 co-occurring in E. coli in Ireland. The MDR profile of E. coli E230738 highlights the growing public health threat posed by the dissemination of MDR E. coli lineages with limited treatment options and underscores the need for clinical screening coupled with genomic surveillance to better understand evolving MDR patterns in E. coli.},
}

@article {pmid39642168,
year = {2024},
author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M},
title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.},
journal = {PLoS computational biology},
volume = {20},
number = {12},
pages = {e1012627},
doi = {10.1371/journal.pcbi.1012627},
pmid = {39642168},
issn = {1553-7358},
abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.},
}

@article {pmid39641603,
year = {2024},
author = {Grimm, H and Lorenz, J and Straub, D and Joshi, P and Shuster, J and Zarfl, C and Muehe, EM and Kappler, A},
title = {Nitrous oxide is the main product during nitrate reduction by a novel lithoautotrophic iron(II)-oxidizing culture from an organic-rich paddy soil.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0126224},
doi = {10.1128/aem.01262-24},
pmid = {39641603},
issn = {1098-5336},
abstract = {Microbial nitrate reduction coupled to iron(II) oxidation (NRFeOx) occurs in paddy soils due to high levels of dissolved iron(II) and regular application of nitrogen fertilizer. However, to date, there is no lithoautotrophic NRFeOx isolate or enrichment culture available from this soil environment. Thus, resulting impacts on greenhouse gas emissions during nitrate reduction (i.e., nitrous oxide [N2O]) and on toxic metalloid (i.e., arsenic) mobility can hardly be investigated. We enriched a lithoautotrophic NRFeOx culture, culture HP (Huilongpu paddy, named after its origin), from a paddy soil (Huilongpu Town, China), which was dominated by Gallionella (71%). The culture reduced 0.45 to 0.63 mM nitrate and oxidized 1.76 to 2.31 mM iron(II) within 4 days leading to N2O as the main N-product (62%-88% N2O-N of total reduced NO3[-]-N). Nitrite was present as an intermediate at a maximum of 0.16 ± 0.1 mM. Cells were associated with, but mostly not encrusted by, poorly crystalline iron(III) minerals (ferrihydrite). Culture HP performed best below an iron(II) threshold of 2.5-3.5 mM and in a pH range of 6.50-7.05. In the presence of 100 µM arsenite, only 0%-18% of iron(II) was oxidized. Due to low iron(II) oxidation, arsenite was not immobilized. However, the proportion of N2O-N of total reduced NO3[-]-N decreased from 77% to 30%. Our results indicate that lithoautotrophic NRFeOx occurs even in organic-rich paddy soils, resulting in denitrification and subsequent N2O emissions. The obtained novel enrichment culture allows us to study the impact of lithoautotrophic NRFeOx on arsenic mobility and N2O emissions in paddy soils.IMPORTANCEPaddy soils are naturally rich in iron(II) and regularly experience nitrogen inputs due to fertilization. Nitrogen fertilization increases nitrous oxide emissions as it is an intermediate product during nitrate reduction. Microorganisms can live using nitrate and iron(II) as electron acceptor and donor, respectively, but mostly require an organic co-substrate. By contrast, microorganisms that only rely on nitrate, iron(II), and CO2 could inhabit carbon-limited ecological niches. So far, no isolate or consortium of lithoautotrophic iron(II)-oxidizing, nitrate-reducing microorganisms has been obtained from paddy soil. Here, we describe a lithoautotrophic enrichment culture, dominated by a typical iron(II)-oxidizer (Gallionella), that oxidized iron(II) and reduced nitrate to nitrous oxide, negatively impacting greenhouse gas dynamics. High arsenic concentrations were toxic to the culture but decreased the proportion of nitrous oxide of the total reduced nitrate. Our results suggest that autotrophic nitrate reduction coupled with iron(II) oxidation is a relevant, previously overlooked process in paddy soils.},
}

@article {pmid39637856,
year = {2024},
author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA},
title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.10.069},
pmid = {39637856},
issn = {1879-0445},
abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.},
}

@article {pmid39637512,
year = {2024},
author = {Wilkie, I and Orellana, LH},
title = {Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126562},
doi = {10.1016/j.syapm.2024.126562},
pmid = {39637512},
issn = {1618-0984},
abstract = {Members of the phylum Verrucomicrobiota play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (Seribacter gen. Nov., Chordibacter gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.},
}

@article {pmid39633812,
year = {2024},
author = {Bauchinger, F and Seki, D and Berry, D},
title = {Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1454634},
pmid = {39633812},
issn = {1664-302X},
abstract = {Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance.},
}

@article {pmid39633134,
year = {2024},
author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK},
title = {Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {153},
pmid = {39633134},
issn = {1432-184X},
support = {20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; Republic of Korea ; *Microbiota ; *Skin/microbiology ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Gills/microbiology ; Biological Evolution ; Species Specificity ; },
abstract = {Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts' divergence times showed that the differences in microbial communities in all three body parts were related to the hosts' divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.},
}

Animals
Republic of Korea
*Microbiota
*Skin/microbiology
*Phylogeny
*RNA, Ribosomal, 16S/genetics
*Fishes/microbiology
*Symbiosis
*Bacteria/classification/genetics/isolation & purification
Gills/microbiology
Biological Evolution
Species Specificity

@article {pmid39633061,
year = {2024},
author = {Paduano, S and Marchesi, I and Valeriani, F and Frezza, G and Facchini, MC and Romano Spica, V and Bargellini, A},
title = {Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {152},
pmid = {39633061},
issn = {1432-184X},
mesh = {*Bacteria/genetics/classification/isolation & purification ; Italy ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Clay/chemistry ; Biodiversity ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Mineral Waters/microbiology ; Phylogeny ; },
abstract = {Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus, Thauera, Pelobacter, and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2-4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation.},
}

*Bacteria/genetics/classification/isolation & purification
Italy
*RNA, Ribosomal, 16S/genetics
*Microbiota
*Clay/chemistry
Biodiversity
High-Throughput Nucleotide Sequencing
DNA, Bacterial/genetics
Mineral Waters/microbiology
Phylogeny

@article {pmid39632307,
year = {2024},
author = {Delmoitié, B and Sakarika, M and Rabaey, K and De Wever, H and Regueira, A},
title = {Tailoring non-axenic lactic acid fermentation from cheese whey permeate targeting a flexible lactic acid platform.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123529},
doi = {10.1016/j.jenvman.2024.123529},
pmid = {39632307},
issn = {1095-8630},
abstract = {Lactic acid (LA) is an important biobased platform chemical, with potential applications in synthetising a wide range of chemical products or serving as feedstock for various bioprocesses. Industrial LA production via pure culture fermentation is characterized by high operational costs and utilizes food-grade sugars, thereby reducing the feasibility of LA applications. In this context, our research focussed on valorising the largest dairy side stream, cheese whey permeate, through the use of mixed microbial communities. We evaluated the effect of different operational parameters (temperature, pH and hydraulic retention time) in non-axenic fermentations on productivity, yield, concentration, optical purity, and community. Our findings revealed that operating at mildly thermophilic conditions (45 °C) resulted in highly selective LA production, and significantly augmented the LA yield, and productivity, compared to higher temperatures (50-55 °C). In addition, operating at circumneutral pH conditions (6.0-6.5) led to significantly increased the LA fermentation performance compared to the conventional acid pH conditions (≤5.5). This led to an unprecedented LA productivity of 27.4 g/L/h with a LA yield of 70.0% which is 2.5 times higher compared to previous reported maximum. Additionally, varying pH levels influenced the optical purity of LA: we achieved an optical L-LA purity of 98.3% at pH 6.0-6.5, and an optical D-LA purity of 91.3% at a pH of 5.5. A short hydraulic retention time of less than 12 h was crucial for selective LA production. This process also yielded a microbial biomass composed of 90.3-98.6% Lactobacillus delbrueckii, which could be potentially valorised as probiotic or protein ingredient in food or feed products. Our work shows that by careful selection of operational conditions, the overall performance can be significantly increased compared to the state-of-the-art. These results highlight the potential of non-sterile LA fermentation and show that careful selection of simple reactor operation parameters can maximize process performance. A preliminary assessment suggests that valorising EU cheese whey permeate could increase LA and poly-LA production by 40 and 125 times, respectively. This could also lead to the production of 4,000 kton protein-rich biomass, potentially reducing CO2 emissions linked to EU food and feed production by 4.87% or 2.77% respectively.},
}

@article {pmid39629059,
year = {2024},
author = {Pecsi, EL and Forbes, S and Guillemette, F},
title = {Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate.},
journal = {Journal of geophysical research. Biogeosciences},
volume = {129},
number = {12},
pages = {e2024JG008355},
pmid = {39629059},
issn = {2169-8953},
abstract = {Organic by-products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois-Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein-like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic-like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A-horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold-climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.},
}

@article {pmid39628456,
year = {2024},
author = {Sinclair, JS and Buchner, D and Gessner, MO and Müller, J and Pauls, SU and Stoll, S and Welti, EAR and Bässler, C and Buse, J and Dziock, F and Enss, J and Hörren, T and Künast, R and Li, Y and Marten, A and Morkel, C and Richter, R and Seibold, S and Sorg, M and Twietmeyer, S and Weis, D and Weisser, W and Wiggering, B and Wilmking, M and Zotz, G and Frenzel, M and Leese, F and Haase, P},
title = {Effects of land cover and protected areas on flying insect diversity.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e14425},
doi = {10.1111/cobi.14425},
pmid = {39628456},
issn = {1523-1739},
support = {//Hessisches Landesamt für Umwelt und Geologie/ ; //LOEWE Centre for Translational Biodiversity Genomics/ ; 871128//EU Horizon project eLTER PLUS/ ; },
abstract = {Widespread insect losses are a critical global problem. Mitigating this problem requires identifying the principal drivers across different taxa and determining which insects are covered by protected areas. However, doing so is hindered by missing information on most species owing to extremely high insect diversity and difficulties in morphological identification. To address this knowledge gap, we used one of the most comprehensive insect DNA metabarcoding data sets assembled (encompassing 31,846 flying insect species) in which data were collected from a network of 75 Malaise traps distributed across Germany. Collection sites encompass gradients of land cover, weather, and climate, along with differences in site protection status, which allowed us to gain broader insights into how insects respond to these factors. We examined changes in total insect biomass, species richness, temporal turnover, and shifts in the composition of taxa, key functional groups (pollinators, threatened species, and invasive species), and feeding traits. Lower insect biomass generally equated to lower richness of all insects and higher temporal turnover, suggesting that biomass loss translates to biodiversity loss and less stable communities. Spatial variability in insect biomass and composition was primarily driven by land cover, rather than weather or climate change. As vegetation and land-cover heterogeneity increased, insect biomass increased by 50% in 2019 and 56% in 2020 and total species richness by 58% and 33%, respectively. Similarly, areas with low-vegetation habitats exhibited the highest richness of key taxa, including pollinators and threatened species, and the widest variety of feeding traits. However, these habitats tended to be less protected despite their higher diversity. Our results highlight the value of heterogeneous low vegetation for promoting overall insect biomass and diversity and that better protection of insects requires improved protection and management of unforested areas, where many biodiversity hotspots and key taxa occur.},
}

@article {pmid39624182,
year = {2024},
author = {Wirth, JS and Katz, LS and Williams, GM and Chen, JC},
title = {primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.},
journal = {Journal of open source software},
volume = {9},
number = {101},
pages = {},
pmid = {39624182},
issn = {2475-9066},
abstract = {In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An "ingroup" refers to a group of microbes that are the primary focus of study or interest. Conversely, an "outgroup" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.},
}

@article {pmid39621250,
year = {2024},
author = {Lin, X and Lin, C and Li, X and Yao, F and Guo, X and Wang, M and Zeng, M and Yuan, Y and Xie, Q and Huang, X and Jiao, X},
title = {Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39621250},
issn = {1976-3794},
support = {201224106490150//Shantou Science and Technology Project/ ; },
abstract = {To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.},
}

@article {pmid39619625,
year = {2024},
author = {Sakarika, M and Matassa, S and Carvajal-Arroyo, JM and Ganigué, R},
title = {Editorial: Microbial biorefineries for a more sustainable, circular economy.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1512756},
doi = {10.3389/fbioe.2024.1512756},
pmid = {39619625},
issn = {2296-4185},
}

@article {pmid39612478,
year = {2024},
author = {Zhao, Y and Ran, W and Xu, W and Song, Y},
title = {ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0188924},
doi = {10.1128/spectrum.01889-24},
pmid = {39612478},
issn = {2165-0497},
abstract = {The rhizospheres of plants and soil microorganisms are intricately interconnected. Tea trees are cultivated extensively on the karst plateau of Guizhou Province, China; however, the understanding of the interactions among fungal communities, community taxa, and diseases impacting tea tree in the soil rhizosphere is limited. Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. This study utilized the internal transcribed spacer high-throughput sequencing technology to explore the symbiotic relationship between rhizosphere fungi and plant disease feedback in multiple tea estates across the Guizhou Plateau. The ecological preferences and environmental thresholds of fungi were investigated via environmental variables. Furthermore, a correlation was established between different taxa and individual soil functions. Research has indicated that tea leaf blight disrupts symbiotic connections among fungal groups. For various taxa, we found that numerous taxa consistently maintained core positions within the community, whereas rare taxa were able to stabilize due to a high proportion of positive effects. Additionally, abundant taxa presented a wider range of environmental feedback, whereas the rare taxon diversity presented a stronger positive association with the soil Z score. This study contributes to our understanding of the importance of rare taxa in plant rhizosphere soil processes. Emphasis should be placed on the role of rare taxa in pest and disease control within green agriculture while also strengthening systematic development and biogeographical research related to rare taxa in this region.IMPORTANCEIn this study, based on internal transcribed spacer high-throughput sequencing, fungal communities in the rhizosphere soil of tea trees and their interactions with the environment in karst areas were reported, and the symbiotic relationships of different fungal taxa and their feedback to the environment were described in detail by using the knowledge of microbial ecology. On this basis, it was found that tea tree diseases affect the symbiotic relationships of fungal taxa. At the same time, we found that rare taxa have stronger cooperative relationships in response to environmental changes and explored their participation in soil processes based on fungal trait sets. This study will provide basic data for the development of modern agriculture in tea gardens and theoretical basis for the sustainable prevention and control of tea tree diseases.},
}

@article {pmid39611982,
year = {2024},
author = {Kou, Z and Liu, J and Tohti, G and Zhu, X and Zheng, B and Zhu, Y and Zhang, W},
title = {Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {151},
pmid = {39611982},
issn = {1432-184X},
support = {2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; },
mesh = {*Rhizosphere ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; *Desert Climate ; *Seasons ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; },
abstract = {Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0-30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3-22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.},
}

*Rhizosphere
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
*Desert Climate
*Seasons
Plant Roots/microbiology
Soil/chemistry
Microbiota

@article {pmid39611949,
year = {2024},
author = {Makumbi, JP and Leareng, SK and Pierneef, RE and Makhalanyane, TP},
title = {Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {150},
pmid = {39611949},
issn = {1432-184X},
support = {UID 110717//National Research Foundation of South Africa/ ; UID 110717//National Research Foundation of South Africa/ ; },
mesh = {*Microbiota/drug effects ; Humans ; *Ecotoxicology ; Animals ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Public Health ; Drug Resistance, Microbial ; },
abstract = {The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.},
}

*Microbiota/drug effects
Humans
*Ecotoxicology
Animals
Risk Assessment
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial
Public Health
Drug Resistance, Microbial

@article {pmid39611829,
year = {2024},
author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K},
title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0137624},
doi = {10.1128/spectrum.01376-24},
pmid = {39611829},
issn = {2165-0497},
abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.

IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.},
}

@article {pmid39611809,
year = {2024},
author = {Mermans, F and Chatzigiannidou, I and Teughels, W and Boon, N},
title = {Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100924},
doi = {10.1128/msystems.01009-24},
pmid = {39611809},
issn = {2379-5077},
abstract = {Determination of bacterial community composition in synthetic communities is critical for understanding microbial systems. The community composition is typically determined through bacterial plating or through PCR-based methods, which can be labor-intensive, expensive, or prone to bias. Simultaneously, flow cytometry has been suggested as a cheap and fast alternative. However, since the technique captures the phenotypic state of bacterial cells, accurate determination of community composition could be affected when bacteria are co-cultured. We investigated the performance of flow cytometry for quantifying oral synthetic communities and compared it to the performance of strain specific qPCR and 16S rRNA gene amplicon sequencing. Therefore, axenic cultures, mock communities and co-cultures of oral bacteria were prepared. Random forest classifiers trained on flow cytometry data of axenic cultures were used to determine the composition of the synthetic communities, as well as strain specific qPCR and 16S rRNA gene amplicon sequencing. Flow cytometry was shown to have a lower average root mean squared error and outperformed the PCR-based methods in even mock communities (flow cytometry: 0.11 ± 0.04; qPCR: 0.26 ± 0.09; amplicon sequencing: 0.15 ± 0.01). When bacteria were co-cultured, neither flow cytometry, strain-specific qPCR, nor 16S rRNA gene amplicon sequencing resulted in similar community composition. Performance of flow cytometry was decreased compared with mock communities due to changing phenotypes. Finally, discrepancies between flow cytometry and strain-specific qPCR were found. These findings highlight the challenges ahead for quantifying community composition in co-cultures by flow cytometry.IMPORTANCEQuantification of bacterial composition in synthetic communities is crucial for understanding and steering microbial interactions. Traditional approaches like plating, strain-specific qPCR, and amplicon sequencing are often labor-intensive and expensive and limit high-throughput experiments. Recently, flow cytometry has been suggested as a swift and cheap alternative for quantifying communities and has been successfully demonstrated on simple bacterial mock communities. However, since flow cytometry measures the phenotypic state of cells, measurements can be affected by differing phenotypes. Especially, changing phenotypes resulting from co-culturing bacteria can have a profound effect on the applicability of the technique in this context. This research illustrates the feasibility and challenges of flow cytometry for the determination of community structure in synthetic mock communities and co-cultures.},
}

@article {pmid39609949,
year = {2024},
author = {Almela, P and Elser, JJ and Giersch, JJ and Hotaling, S and Rebbeck, V and Hamilton, TL},
title = {Laboratory Experiments Suggest a Limited Impact of Increased Nitrogen Deposition on Snow Algae Blooms.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70052},
doi = {10.1111/1758-2229.70052},
pmid = {39609949},
issn = {1758-2229},
support = {2113783//National Science Foundation/ ; 2113784//National Science Foundation/ ; },
mesh = {*Nitrogen/metabolism/analysis ; *Snow/chemistry ; *Phosphorus/metabolism/analysis ; *Eutrophication ; *Biomass ; },
abstract = {Snow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor likely contributing is nutrient availability, specifically nitrogen and phosphorus. The nutrient requirements of the taxa responsible for these blooms are not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of nitrogen and phosphorus. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface. Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of nutrient conditions. However, the molar ratio of nitrogen to phosphorus at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for phosphorus for snow algae and highlights phosphorus availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo. Snow algae can thrive across a range of nitrogen (N) and phosphorus (P) conditions, with a higher P requirement for optimal growth. Our study suggests that increased N deposition may have a limited impact on snow algae bloom occurrence and size, emphasising P as a key factor influencing these blooms and their potential to accelerate snow melt by lowering albedo.},
}

*Nitrogen/metabolism/analysis
*Snow/chemistry
*Phosphorus/metabolism/analysis
*Eutrophication
*Biomass

@article {pmid39609930,
year = {2024},
author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE},
title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {98},
pmid = {39609930},
issn = {2524-6372},
abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.

RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.

CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.},
}

@article {pmid39608606,
year = {2024},
author = {Young Lee, J and Hyeon Jo, Y and Hee Kim, T and Eun Lee, S and Seo Hong, E and Sun Kang, T},
title = {Microbial and Sensory Characteristics of Traditional Watery Kimchi (Dongchimi) Fortified with Probiotics.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100422},
doi = {10.1016/j.jfp.2024.100422},
pmid = {39608606},
issn = {1944-9097},
abstract = {Dongchimi, a traditional Korean watery kimchi, relies on complex interactions among diverse lactic acid bacteria (LAB) to maintain its freshness and quality. Recently, dongchimi has gained attention as a health-promoting food due to its content of probiotics and prebiotics. In this study, six probiotic strains were employed into dongchimi fermentation, and its sensory and microbial characteristics were evaluated. The LAB-enriched dongchimi demonstrated superior sensory preference (63%) and significantly higher LAB counts (average 5.2 × 10[7] CFU/ml) compared to traditional dongchimi. Furthermore, microbial diversity between the LAB-enriched and traditional dongchimi was analyzed during the fermentation process using both culture-dependent Sanger sequencing and culture-independent metabarcoding techniques, employing 16S ribosomal RNA gene sequences. Lactiplantibacillus plantarum was identified as the dominant probiotic strain in both types of dongchimi, while other probiotics, including Bifidobacterium bifidum, B. animalis, Limosilactobacillus Fermentum, and Heyndrickxia coagulans, were exclusively detected in the LAB-enriched dongchimi. In conclusion, Lactiplanti. plantarum and Limosi. Fermentum were identified as the most effective probiotics for dongchimi fermentation. These results offer critical insights into the microbial ecology and probiotic strains essential for optimizing synbiotic dongchimi, thereby reinforcing health claims related to probiotics and prebiotics.},
}

@article {pmid39605469,
year = {2024},
author = {Woodruff, GC and Moser, KA and Wang, J},
title = {The Bacteria of a Fig Microcommunity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.22.624729},
pmid = {39605469},
issn = {2692-8205},
abstract = {UNLABELLED: Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach towards tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata such as foundress wasp number and nematode occupancy were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 3,000 OTUs were detected, and microbial communities were dominated by members of Proteobacteria , Bacteroidota , and Actinobacteriota . Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. Nematodes likewise had no detectable impact on microbial alpha diversity, although nematodes were associated with a modest change in microbial community composition. A handful of OTUs (associated with the genera Kosokonia , Ochobactrum , and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.

IMPORTANCE: Unraveling why different species live in different places is a longstanding open question in ecology, and it is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata , a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Likewise, we found that nematode occupancy impacts microbial composition but not alpha diversity. Moreover, we show that as the number of foundress wasps increases, the microbial alpha diversity decreases. Finally, we identified OTUs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a microcommunity wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.},
}

@article {pmid39604741,
year = {2024},
author = {de Freitas, AS and Carlos, FS and Martins, GL and Monteiro, GGTN and Roesch, LFW},
title = {Bacterial Resilience and Community Shifts Under 11 Draining-Flooding Cycles in Rice Soils.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {149},
pmid = {39604741},
issn = {1432-184X},
mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Floods ; *Soil/chemistry ; Brazil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Ecosystem ; },
abstract = {Flooded rice cultivation, accounting for 75% of global rice production, significantly influences soil redox potential, element speciation, pH, and nutrient availability, presenting challenges such as extensive water usage and altered soil properties. This study investigates bacterial community dynamics in rice soils subjected to repeated draining and flooding in Rio Grande do Sul, Brazil. We demonstrate that bacterial communities exhibit remarkable resilience (the capacity to recover after being altered by a disturbance) but cannot remain stable after long-term exposure to environmental changes. The beta diversity analysis revealed four distinct community states after 11 draining/flooding cycles, indicating resilience over successive environment changes. However, the consistent environmental disturbance reduced microbial resilience, causing the bacterial community structure to shift over time. Those differences were driven by substitutions of taxa and functions and not by the loss of diversity. Notable shifts included a decline in Acidobacteria and an increase in Proteobacteria and Chloroflexi. Increased Verrucomicrobia abundance corresponded with lower pH levels. Functional predictions suggested dynamic metabolic responses, with increased nitrification during drained cycles and a surge in fermenters after the sixth cycle. Despite cyclic disturbances, bacterial communities exhibit resilience, contributing to stable ecosystem functioning in flooded rice soils. These findings enhance our understanding of microbial adaptation, providing insights into sustainable rice cultivation and soil management practices.},
}

*Oryza/microbiology
*Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Floods
*Soil/chemistry
Brazil
Microbiota
RNA, Ribosomal, 16S/genetics
Hydrogen-Ion Concentration
Ecosystem

@article {pmid39603473,
year = {2024},
author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T},
title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131878},
doi = {10.1016/j.biortech.2024.131878},
pmid = {39603473},
issn = {1873-2976},
abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %∼74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.},
}

@article {pmid39601575,
year = {2024},
author = {Maguire, M and Serna, C and Montero Serra, N and Kovarova, A and O'Connor, L and Cahill, N and Hooban, B and DeLappe, N and Brennan, W and Devane, G and Cormican, M and Morris, D and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP},
title = {Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0090424},
doi = {10.1128/spectrum.00904-24},
pmid = {39601575},
issn = {2165-0497},
abstract = {Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.},
}

@article {pmid39601521,
year = {2024},
author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS},
title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0063724},
doi = {10.1128/mra.00637-24},
pmid = {39601521},
issn = {2576-098X},
abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.},
}

@article {pmid39597739,
year = {2024},
author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H},
title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112350},
pmid = {39597739},
issn = {2076-2607},
support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; },
abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.},
}

@article {pmid39597685,
year = {2024},
author = {Zhang, K and Chen, X and Shi, X and Yang, Z and Yang, L and Liu, D and Yu, F},
title = {Endophytic Bacterial Community, Core Taxa, and Functional Variations Within the Fruiting Bodies of Laccaria.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112296},
pmid = {39597685},
issn = {2076-2607},
support = {202205AD160036//the Yunnan Technology Innovation/ ; 42077072//the National Natural Science Foundation of Management Practices China/ ; },
abstract = {Macrofungi do not exist in isolation but establish symbiotic relationships with microorganisms, particularly bacteria, within their fruiting bodies. Herein, we examined the fruiting bodies' bacteriome of seven species of the genus Laccaria collected from four locations in Yunnan, China. By analyzing bacterial diversity, community structure, and function through 16S rRNA sequencing, we observed the following: (1) In total, 4,840,291 high-quality bacterial sequences obtained from the fruiting bodies were grouped into 16,577 amplicon sequence variants (ASVs), and all samples comprised 23 shared bacterial ASVs. (2) The Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex was found to be the most abundant and presumably coexisting bacterium. (3) A network analysis revealed that endophytic bacteria formed functional groups, which were dominated by the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Novosphingobium, and Variovorax. (4) The diversity, community structure, and dominance of ecological functions (chemoheterotrophy and nitrogen cycling) among endophytic bacteria were significantly shaped by geographic location, habitat, and fungal genotype, rather than fruiting body type. (5) A large number of the endophytic bacteria within Laccaria are bacteria that promote plant growth; however, some pathogenic bacteria that pose a threat to human health might also be present. This research advances our understanding of the microbial ecology of Laccaria and the factors shaping its endophytic bacterial communities.},
}

@article {pmid39597671,
year = {2024},
author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E},
title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112281},
pmid = {39597671},
issn = {2076-2607},
support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; },
abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.},
}

@article {pmid39597543,
year = {2024},
author = {Wu, D and He, X and Lu, Y and Gao, Z and Chong, Y and Hong, J and Wu, J and Deng, W and Xi, D},
title = {Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112154},
pmid = {39597543},
issn = {2076-2607},
abstract = {With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.},
}

@article {pmid39597512,
year = {2024},
author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP},
title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112121},
pmid = {39597512},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.},
}

@article {pmid39596705,
year = {2024},
author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF},
title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111010},
pmid = {39596705},
issn = {2079-6382},
support = {FAPESP//001/ ; },
abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.},
}

@article {pmid39592542,
year = {2024},
author = {Kaur, T and Devi, R and Negi, R and Kour, H and Singh, S and Khan, SS and Kumari, C and Kour, D and Chowdhury, S and Kapoor, M and Rai, AK and Rustagi, S and Shreaz, S and Yadav, AN},
title = {Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39592542},
issn = {1874-9356},
abstract = {Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3[¯], NH4[+]) and solubilized forms (K[+], H2PO4[-] and HPO4[2-]). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.},
}

@article {pmid39587399,
year = {2024},
author = {Trevathan-Tackett, SM and Kepfer-Rojas, S and Malerba, M and Macreadie, PI and Djukic, I and Zhao, J and Young, EB and York, PH and Yeh, SC and Xiong, Y and Winters, G and Whitlock, D and Weaver, CA and Watson, A and Visby, I and Tylkowski, J and Trethowan, A and Tiegs, S and Taylor, B and Szpikowski, J and Szpikowska, G and Strickland, VL and Stivrins, N and Sousa, AI and Sinutok, S and Scheffel, WA and Santos, R and Sanderman, J and Sánchez-Carrillo, S and Sanchez-Cabeza, JA and Rymer, KG and Ruiz-Fernandez, AC and Robroek, BJM and Roberts, T and Ricart, AM and Reynolds, LK and Rachlewicz, G and Prathep, A and Pinsonneault, AJ and Pendall, E and Payne, R and Ozola, I and Onufrock, C and Ola, A and Oberbauer, SF and Numbere, AO and Novak, AB and Norkko, J and Norkko, A and Mozdzer, TJ and Morgan, P and Montemayor, DI and Martin, CW and Malone, SL and Major, M and Majewski, M and Lundquist, CJ and Lovelock, CE and Liu, S and Lin, HJ and Lillebo, A and Li, J and Kominoski, JS and Khuroo, AA and Kelleway, JJ and Jinks, KI and Jerónimo, D and Janousek, C and Jackson, EL and Iribarne, O and Hanley, T and Hamid, M and Gupta, A and Guariento, RD and Grudzinska, I and da Rocha Gripp, A and González Sagrario, MA and Garrison, LM and Gagnon, K and Gacia, E and Fusi, M and Farrington, L and Farmer, J and de Assis Esteves, F and Escapa, M and Domańska, M and Dias, ATC and de Los Santos, CB and Daffonchio, D and Czyryca, PM and Connolly, RM and Cobb, A and Chudzińska, M and Christiaen, B and Chifflard, P and Castelar, S and Carneiro, LS and Cardoso-Mohedano, JG and Camden, M and Caliman, A and Bulmer, RH and Bowen, J and Boström, C and Bernal, S and Berges, JA and Benavides, JC and Barry, SC and Alatalo, JM and Al-Haj, AN and Adame, MF},
title = {Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02116},
pmid = {39587399},
issn = {1520-5851},
abstract = {Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of "recalcitrant" (rooibos tea) and "labile" (green tea) organic matter (OM) decomposition. Freshwater wetlands and tidal marshes had the highest tea mass remaining, indicating a greater potential for carbon preservation in these ecosystems. Recalcitrant OM decomposition increased with elevated temperatures throughout the decay period, e.g., increase from 10 to 20 °C corresponded to a 1.46-fold increase in the recalcitrant OM decay rate constant. The effect of elevated temperature on labile OM breakdown was ecosystem-dependent, with tidally influenced wetlands showing limited effects of temperature compared with freshwater wetlands. Based on climatic projections, by 2050 wetland decay constants will increase by 1.8% for labile and 3.1% for recalcitrant OM. Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming, but the extent and direction of this effect at a large scale is dependent on ecosystem and OM characteristics. Understanding local versus global drivers is necessary to resolve ecosystem influences on carbon preservation in wetlands.},
}

@article {pmid39586934,
year = {2024},
author = {Rong, X and Liu, X and Du, F and Aanderud, ZT and Zhang, Y},
title = {Biocrusts Mediate the Niche Distribution and Diversity of Ammonia-Oxidizing Microorganisms in the Gurbantunggut Desert, Northwestern China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {148},
pmid = {39586934},
issn = {1432-184X},
support = {2022TSYCCX0007//the Xinjiang Tianshan Youth Talent Top Project/ ; 2022D01D083//the Key Fund Projects of the Natural Science Foundation of Xinjiang/ ; U2003214//the National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics/metabolism/classification ; *Desert Climate ; *Ammonia/metabolism ; *Soil Microbiology ; China ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Oxidation-Reduction ; Soil/chemistry ; Biodiversity ; Ecosystem ; Seasons ; Microbiota ; Nitrification ; },
abstract = {Biological soil crusts (biocrusts) play pivotal ecological roles in regulating nitrogen cycling within desert ecosystems. While acknowledging the essential role played by ammonia-oxidizing microorganisms in nitrogen transformation, there remains a paucity of understanding concerning how disturbances to biocrusts impact the diversity and spatial distribution patterns among ammonia oxidizer communities within temperate deserts. This investigation delved into assessing how 4 years' worth of removing biocrust influenced niche differentiation between nitrifying archaea and bacteria while also examining its effects on shaping community structures of predominant ammonia-oxidizing archaea (AOA) within the Gurbantunggut Desert soils. Despite notable variations in abundance of ammonia-oxidizing microbes across distinct soil depths throughout different seasons, it became apparent that removing biocrust significantly altered both the abundance and niche pattern for AOA alongside their bacterial counterparts during winter and summer periods. Notably dominating over their bacterial counterparts within desert soils, AOA displayed their highest archaeal to bacterial amoA gene copy ratio (6549-fold higher) at a soil depth of 5-10 cm during summer. Moreover, substantial impacts were observed upon AOA diversity along with compositional changes following such perturbation events. The aftermath saw an emergence of more diffuse yet dynamic AOA communities, especially noticeable amidst winter when nitrogen and water limitations were relatively alleviated. In summary, our findings underscore how interactions between biocrust coverages alongside factors like soil temperature, total carbon content, or NO3[-]_N concentrations govern niches occupied by ammoxidation communities whilst influencing assemblage processes too. The sensitivity shown by dominant AOAs towards biocrust removal further underscores how biocrust coverage influences nitrogen transformation processes while potentially involving other communities and functions in desert ecosystems.},
}

*Archaea/genetics/metabolism/classification
*Desert Climate
*Ammonia/metabolism
*Soil Microbiology
China
*Bacteria/metabolism/genetics/classification/isolation & purification
*Oxidation-Reduction
Soil/chemistry
Biodiversity
Ecosystem
Seasons
Microbiota
Nitrification

@article {pmid39587087,
year = {2024},
author = {Whalen, ED and Grandy, AS and Geyer, KM and Morrison, EW and Frey, SD},
title = {Microbial trait multifunctionality drives soil organic matter formation potential.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10209},
pmid = {39587087},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism ; *Carbon/metabolism ; Biomass ; Organic Chemicals/metabolism ; },
abstract = {Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.},
}

*Soil Microbiology
*Soil/chemistry
*Fungi/metabolism
*Carbon/metabolism
Biomass
Organic Chemicals/metabolism

@article {pmid39585925,
year = {2024},
author = {Richards, TA and Eme, L and Archibald, JM and Leonard, G and Coelho, SM and de Mendoza, A and Dessimoz, C and Dolezal, P and Fritz-Laylin, LK and Gabaldón, T and Hampl, V and Kops, GJPL and Leger, MM and Lopez-Garcia, P and McInerney, JO and Moreira, D and Muñoz-Gómez, SA and Richter, DJ and Ruiz-Trillo, I and Santoro, AE and Sebé-Pedrós, A and Snel, B and Stairs, CW and Tromer, EC and van Hooff, JJE and Wickstead, B and Williams, TA and Roger, AJ and Dacks, JB and Wideman, JG},
title = {Reconstructing the last common ancestor of all eukaryotes.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002917},
doi = {10.1371/journal.pbio.3002917},
pmid = {39585925},
issn = {1545-7885},
abstract = {Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.},
}

@article {pmid39583547,
year = {2024},
author = {Yang, X and Gänzle, M and Wang, R},
title = {Editorial: How the application of antimicrobial hurdles in meat processing facilities shapes microbial ecology.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501925},
pmid = {39583547},
issn = {1664-302X},
}

@article {pmid39348267,
year = {2024},
author = {Clegg, T and Pawar, S},
title = {Variation in thermal physiology can drive the temperature-dependence of microbial community richness.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.84662},
pmid = {39348267},
issn = {2050-084X},
support = {NERC QMEE Centre for Doctoral Training NE/P012345/1//Natural Environment Research Council/ ; RF-2020-653\2//Leverhulme Trust/ ; NE/M020843/1//NERC Natural Environment Research Council/ ; NE/S000348/1//NERC Natural Environment Research Council/ ; },
mesh = {*Temperature ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Bacterial Physiological Phenomena ; },
abstract = {Predicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes, current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here, we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.},
}

*Temperature
*Microbiota/physiology
Bacteria/classification/genetics/metabolism
Biodiversity
Bacterial Physiological Phenomena

@article {pmid39578630,
year = {2024},
author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK},
title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28934},
pmid = {39578630},
issn = {2045-2322},
support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; },
mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.},
}

*Metagenomics/methods
*Soil Microbiology
Soil/chemistry
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Metagenome

@article {pmid39572704,
year = {2024},
author = {Li, J and Göbel, F and Hsu, HY and Koch, JN and Hager, N and Flegler, WA and Tanabe, TS and Dahl, C},
title = {YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1548},
pmid = {39572704},
issn = {2399-3642},
support = {Da 351/8-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/14-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Signal Transduction ; *Bacterial Proteins/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; Biological Transport ; },
abstract = {Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.},
}

*Sulfur/metabolism
*Oxidation-Reduction
*Signal Transduction
*Bacterial Proteins/metabolism/genetics
*Gene Expression Regulation, Bacterial
Biological Transport

@article {pmid39572621,
year = {2024},
author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM},
title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28890},
pmid = {39572621},
issn = {2045-2322},
support = {07939716/2020//Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; },
abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.},
}

Humans
*Helicobacter pylori/pathogenicity/genetics
*Helicobacter Infections/microbiology/pathology
*Stomach Neoplasms/microbiology/pathology
*Gastritis/microbiology/pathology
Virulence
*Gastric Mucosa/microbiology/pathology
Male
Female
RNA, Ribosomal, 16S/genetics
Middle Aged
Aged
Metaplasia/microbiology
Adult
Gastrointestinal Microbiome

@article {pmid39572453,
year = {2024},
author = {Méndez, A and Sanmartín, P and Balboa, S and Trueba-Santiso, A},
title = {Environmental Proteomics Elucidates Phototrophic Biofilm Responses to Ornamental Lighting on Stone-built Heritage.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {147},
pmid = {39572453},
issn = {1432-184X},
support = {04_IN606D_2021_2598528//Programa de Doutoramento Industrial - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; RYC2020-029987-I//Ramón y Cajal contract - Spanish State Research Agency (AEI)/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; },
mesh = {*Biofilms/radiation effects/growth & development ; *Proteomics ; Light ; Phototrophic Processes ; Cyanobacteria/metabolism/radiation effects/physiology ; Chlorophyta/radiation effects/metabolism/physiology ; Proteome ; Lighting ; },
abstract = {Recent studies are showing that some lights suitable for illuminating the urban fabric (i.e. that do not include the red, green and blue sets of primary colours) may halt biological colonisation on monuments, mainly that caused by phototrophic subaerial biofilms (SABs), which may exacerbate the biodeterioration of substrates. However, the light-triggered mechanisms that cause changes in the growth of the phototrophs remain unknown. Environmental proteomics could be used to provide information about the changes in the SAB metabolism under stress inflicted by nocturnal lighting. Here, laboratory-produced SABs, composed of Chlorophyta, Streptophyta and Cyanobacteriota, were subjected to three types of lighting used for monuments: cool white, warm white and amber + green (potentially with a biostatic effect). A control without light (i.e. darkness) was also included for comparison. The nocturnal lighting impaired the capacity of the SABs to decompose superoxide radicals and thus protect themselves from oxidative stress. Cool white and warm white light both strongly affected the proteomes of the SABs and reduced the total peptide content, with the extent of the reduction depending on the genera of the organisms involved. Analysis of the photo-damaging effect of amber + green light on the biofilm metabolism revealed a negative impact on photosystems I and II and production of photosystem antenna protein-like, as well as a triggering effect on protein metabolism (synthesis, folding and degradation). This research provides, for the first-time, a description of the proteomic changes induced by lighting on SABs colonising illuminated monuments in urban areas.},
}

*Biofilms/radiation effects/growth & development
*Proteomics
Light
Phototrophic Processes
Cyanobacteria/metabolism/radiation effects/physiology
Chlorophyta/radiation effects/metabolism/physiology
Proteome
Lighting

@article {pmid39571806,
year = {2024},
author = {Graham, A and Thorn, C and McDonagh, M and O'Donnell, C and Nolan, S and Kirwan, SF and O'Connor, S and Nzeteu, CO and Montoya, ACV and Bartle, A and Hall, A and Abberton, C and Friel, R and Waters, SM and O'Flaherty, V},
title = {Development and in-vitro assessment of novel oxygen-releasing feed additives to reduce enteric ruminant methane emissions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177598},
doi = {10.1016/j.scitotenv.2024.177598},
pmid = {39571806},
issn = {1879-1026},
abstract = {Ruminant livestock contribute significantly to global methane production and mitigation of which is of utmost importance. Feed additives represent a cost-effective means of achieving this. A potential target for such additives is rumen Oxidative Reduction Potential (ORP), a parameter which influences CH4 production rates, with methanogenesis occurring optimally at ORPs below -300 mV. Thus, a controlled elevation of rumen ORP represents a potentially benign means of methanogen suppression. This research involved assessing a range of oxygen-releasing compounds for their ability to increase rumen ORP and inhibit methanogenesis, using the in-vitro rumen simulation technique (RUSITEC). Seven potential CH4 inhibitors were tested in a 21-day trial monitoring biogas volume, CH4 content, ORP, digestibility, ammonia, and volatile fatty acids concentration. The additives evaluated included: liquid peroxide (H2O2) and urea hydrogen peroxide (UHP), as well as slower reacting species (calcium and magnesium peroxide), in addition to encapsulated liquid H2O2 for controlled, slow release. Consistent CH4 reductions of >50 % were observed from all additives. Reduced neutral detergent fibre (NDF) digestibility and a reduction in total volatile fatty acids (VFAs) was observed for some treatments, but MgO2 and encapsulated H2O2 reduced CH4 volume by 62 % and 58 %, respectively, and had no detrimental effects on digestibility (p > 0.05) or on VFA production. Ex-situ ORP measurements demonstrated significant increases in ORP upon addition of the additives, with MgO2 and encapsulated H2O2 inducing a more moderate effect suggesting a controlled additive release was achieved with the slow-release format of encapsulated liquid H2O2. Thus, potential slow-release forms deemed suitable to progress to bolus or pellet format in-vivo were identified and could enable a longer-lasting suppression of methanogens within the rumen, facilitating application in both intensive and pasture-based production systems.},
}

@article {pmid39571521,
year = {2024},
author = {Zuo, J and Yang, S and Grossart, HP and Xiao, P and Zhang, H and Sun, R and Li, G and Jiang, H and Zhao, Q and Jiao, M and Cheng, Y and Wang, Z and Geng, R and Ma, Z and Li, R},
title = {Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu.},
journal = {Water research},
volume = {269},
number = {},
pages = {122784},
doi = {10.1016/j.watres.2024.122784},
pmid = {39571521},
issn = {1879-2448},
abstract = {River ecosystems face escalating challenges due to altered flow regimes from human activities, such as urbanization with hydrological modifications. Understanding the role of microbial communities for ecosystems with changing flow regimes is still incomplete and remains at the frontier of aquatic microbial ecology. In particular, influences of riverine backward flow on the aquatic biota remain largely unknown. Therefore, we examined the impact of backward flow on the cyanobacterial, total prokaryotic, and eukaryotic communities in the Changdougang River, which naturally flows into Lake Taihu, through environmental DNA metabarcoding. We analyzed the differences in community diversity, assembly, and ecological network stability among groups under backward, weak, and forward flow direction conditions. Non-metric multidimensional scaling showed higher variations in communities of groups across flow direction conditions than seasonal groups. Variations in alpha and beta diversity showed that cyanobacterial and total prokaryotic communities experienced strong homogenization under backward flow conditions, whereas the ecological uniqueness of the eukaryotic community decreased. Assembly of the three flow-related communities was primarily governed by drift and dispersal limitation in stochastic processes. However, in the cyanobacterial community, homogeneous selection in deterministic processes increased from 22.79 % to 42.86 % under backward flow, aligning with trends observed in the checkerboard score (C-score). More importantly, the topological properties of ecological networks and the degree of average variation revealed higher stability in the cyanobacterial community compared to total prokaryotic and eukaryotic communities. Considering the variations in cohesion, the network stability in the cyanobacterial community decreased under backward flow. Our findings emphasize the distinct and sequentially diminishing responses of cyanobacterial, total prokaryotic, and eukaryotic communities to backward flowing rivers. This knowledge is crucial for maintaining ecological health of rivers, assessing the complex ecological impacts on hydrological engineering, and formulating sustainable water management strategies.},
}

@article {pmid39570409,
year = {2024},
author = {Xu, H and Zhang, Y and Fan, D and Meng, S and Fan, L and Song, C and Qiu, L and Li, D and Fang, L and Liu, Z and Bing, X},
title = {Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {145},
pmid = {39570409},
issn = {1432-184X},
support = {2023JBFR01//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; CARS-46//the earmarked fund for CARS/ ; 2023TD18//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
mesh = {*Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Aquaculture ; *Rhizosphere ; *Feces/microbiology ; Animals ; Biofilms ; Fishes/microbiology ; Water Microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.},
}

*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Aquaculture
*Rhizosphere
*Feces/microbiology
Animals
Biofilms
Fishes/microbiology
Water Microbiology
Ecosystem
RNA, Ribosomal, 16S/genetics

@article {pmid39570377,
year = {2024},
author = {Jensen, IC and Schramm, A and Offenberg, J},
title = {Fungus Fighters: Wood Ants (Formica polyctena) and Their Associated Microbes Inhibit Plant Pathogenic Fungi.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {146},
pmid = {39570377},
issn = {1432-184X},
support = {NNF21OC0071665//Novo Nordisk Fonden/ ; NNF21OC0071665//Novo Nordisk Fonden/ ; 34009-19-1562//Internationalt Center for Forskning i Økologisk Jordbrug og Fødevaresystemer/ ; },
mesh = {*Ants/microbiology/physiology ; Animals ; *Plant Diseases/microbiology/prevention & control ; Malus/microbiology ; Fungi/physiology/classification ; Antibiosis ; Bacteria/classification/drug effects/isolation & purification ; Ascomycota/physiology/drug effects ; },
abstract = {Plant diseases cost the global economy billions of US dollars every year. The problem has mainly been addressed by using chemical pesticides, but recently, the use of ants has shown promising effects against plant pathogens. However, the mechanisms accounting for these effects have not yet been determined. One possible explanation is antimicrobial microorganisms associated with ants. Through controlled laboratory experiments, we investigated the inhibitory effects of wood ants (Formica polyctena) and their associated microorganisms against economically important plant pathogenic fungi. All live ants, extracts from crushed ants, and extracts from washed ants significantly inhibited the apple brown rot (Monilinia fructigena) while yielding the growth of other microbes. Furthermore, all investigated wood ants transferred microorganisms to their surroundings within 10 s when walking across a surface. We isolated the most dominant microorganisms deposited by walking ants and from washed ant extracts (i.e., strains likely found on the surface of ants), resulting in four bacterial cultures and one yeast. Two of these isolates, strain I3 (most closely related to Pseudomonas sichuanensis and P. entomophila) and strain I1b (most closely related to Bacillus mycoides), showed inhibitory effects against apple brown rot and apple scab (Venturia inaequalis), while strain I3 also inhibited gray mold (Botrytis cinerea) and Fusarium head blight (Fusarium graminearum). These results suggest that wood ants have potential as biological control agents against commercially relevant plant pathogens, and that their inhibitory effect might be at least partially caused by antibiotic compounds produced by their associated microorganisms.},
}

*Ants/microbiology/physiology
Animals
*Plant Diseases/microbiology/prevention & control
Malus/microbiology
Fungi/physiology/classification
Antibiosis
Bacteria/classification/drug effects/isolation & purification
Ascomycota/physiology/drug effects

@article {pmid39568064,
year = {2024},
author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB},
title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on Southern African dryland soil microbial communities.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae157},
pmid = {39568064},
issn = {1574-6941},
abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggest that they are functionally stable, and that they could be functional even under harsher conditions, such as those expected with climate change.},
}

@article {pmid39567391,
year = {2024},
author = {Vezina, B and Cooper, HB and Wisniewski, JA and Parker, MH and Jenney, AWJ and Holt, KE and Wyres, KL},
title = {Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {144},
pmid = {39567391},
issn = {1432-184X},
support = {DP200103364//Australian Research Council/ ; DP200103364//Australian Research Council/ ; APP1176192//National Health and Medical Research Council/ ; },
mesh = {*Klebsiella pneumoniae/genetics/metabolism/growth & development ; *Culture Media/chemistry ; *Genome, Bacterial ; Histidine/metabolism ; Mutation ; Whole Genome Sequencing ; },
abstract = {Bacteria are typically isolated on rich media to maximise isolation success, removing them from their native evolutionary context. This eliminates selection pressures, enabling otherwise deleterious genomic events to accumulate. Here, we present a cautionary tale of these 'quiet mutations' which can persist unnoticed in bacterial culture lines. We used a combination of microbiological culture (standard and minimal media conditions), whole genome sequencing and metabolic modelling to investigate putative Klebsiella pneumoniae L-histidine auxotrophs. Additionally, we used genome-scale metabolic modelling to predict auxotrophies among completed public genomes (n = 2637). Two sub-populations were identified within a K. pneumoniae frozen stock, differing in their ability to grow in the absence of L-histidine. These sub-populations were the same 'strain', separated by eight single nucleotide variants and an insertion sequence-mediated deletion of the L-histidine biosynthetic operon. The His[-] sub-population remained undetected for > 10 years despite its inclusion in independent laboratory experiments. Genome-scale metabolic models predicted 0.8% public genomes contained ≥ 1 auxotrophy, with purine/pyrimidine biosynthesis and amino acid metabolism most frequently implicated. We provide a definitive example of the role of standard rich media culture conditions in obscuring biologically relevant mutations (i.e. nutrient auxotrophies) and estimate the prevalence of such auxotrophies using public genome collections. While the prevalence is low, it is not insignificant given the thousands of K. pneumoniae that are isolated for global surveillance and research studies each year. Our data serve as a pertinent reminder that rich-media culturing can cause unnoticed wild-type domestication.},
}

*Klebsiella pneumoniae/genetics/metabolism/growth & development
*Culture Media/chemistry
*Genome, Bacterial
Histidine/metabolism
Mutation
Whole Genome Sequencing

@article {pmid39567372,
year = {2024},
author = {Issifu, S and Acharya, P and Kaur-Bhambra, J and Gubry-Rangin, C and Rasche, F},
title = {Biological Nitrification Inhibitors with Antagonistic and Synergistic Effects on Growth of Ammonia Oxidisers and Soil Nitrification.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {143},
pmid = {39567372},
issn = {1432-184X},
support = {RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; URF150571//Royal Society University Research Fellowship/ ; },
mesh = {*Nitrification ; *Soil Microbiology ; *Ammonia/metabolism ; *Soil/chemistry ; Archaea/metabolism/drug effects/growth & development ; Oxidation-Reduction ; Rhizosphere ; Bacteria/metabolism/drug effects/growth & development ; },
abstract = {Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis, while others showed antagonism against N. europaea, N. multiformis, and N. viennensis. Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification.},
}

*Nitrification
*Soil Microbiology
*Ammonia/metabolism
*Soil/chemistry
Archaea/metabolism/drug effects/growth & development
Oxidation-Reduction
Rhizosphere
Bacteria/metabolism/drug effects/growth & development

@article {pmid39565130,
year = {2024},
author = {Yu, C and Yu, M and Ma, R and Wei, S and Jin, M and Jiao, N and Zheng, Q and Zhang, R and Feng, X},
title = {A novel Alteromonas phage with tail fiber containing six potential iron-binding domains.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0093424},
doi = {10.1128/spectrum.00934-24},
pmid = {39565130},
issn = {2165-0497},
abstract = {Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.},
}

@article {pmid39563404,
year = {2024},
author = {Chari, NR and Muratore, TJ and Frey, SD and Winters, CL and Martinez, G and Taylor, BN},
title = {Long-Term Soil Warming Drives Different Belowground Responses in Arbuscular Mycorrhizal and Ectomycorrhizal Trees.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17550},
doi = {10.1111/gcb.17550},
pmid = {39563404},
issn = {1365-2486},
support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; },
mesh = {*Mycorrhizae/physiology ; *Trees/microbiology/physiology/growth & development ; *Soil/chemistry ; *Plant Roots/microbiology ; *Global Warming ; Biomass ; Soil Microbiology ; Carbon/metabolism/analysis ; Nitrogen/metabolism/analysis ; Climate Change ; Temperature ; },
abstract = {The ability of trees to acquire soil nutrients under future climate conditions will influence forest composition and function in a warmer world. Rarely are multiple belowground carbon allocation pathways measured simultaneously in large global change experiments, restricting our understanding of how trees may shift their allocation of resources to different nutrient acquisition mechanisms under future climates. Leveraging a 20-year soil warming experiment, we show that ectomycorrhizal (EM) trees reduce mycorrhizal colonization and root exudation while increasing fine root biomass, while arbuscular mycorrhizal (AM) trees largely maintained their belowground carbon allocation patterns in warmer soils. We suggest that AM trees may be better adapted to thrive under global warming due to higher rates of nitrogen mineralization in warmer soils and the ability of their mycorrhizal symbiont to acquire mineralized inorganic nutrients, whereas EM trees may need to alter their belowground carbon allocation patterns to remain competitive as global temperatures rise.},
}

*Mycorrhizae/physiology
*Trees/microbiology/physiology/growth & development
*Soil/chemistry
*Plant Roots/microbiology
*Global Warming
Biomass
Soil Microbiology
Carbon/metabolism/analysis
Nitrogen/metabolism/analysis
Climate Change
Temperature

@article {pmid39561700,
year = {2024},
author = {Partida-Martínez, LP},
title = {Laila P. Partida-Martínez.},
journal = {Current biology : CB},
volume = {34},
number = {22},
pages = {R1121-R1122},
doi = {10.1016/j.cub.2024.09.085},
pmid = {39561700},
issn = {1879-0445},
mesh = {*Symbiosis ; Fungi/physiology ; Plants/microbiology ; History, 21st Century ; History, 20th Century ; },
abstract = {Interview with Laila Partida-Martínez, who studies microbial ecology, fungal-bacterial symbioses and plant-microbe interactions at the Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav).},
}

*Symbiosis
Fungi/physiology
Plants/microbiology
History, 21st Century
History, 20th Century

@article {pmid39561304,
year = {2024},
author = {Vargas Ribera, PR and Kim, N and Venbrux, M and Álvarez-Pérez, S and Rediers, H},
title = {Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0302954},
pmid = {39561304},
issn = {1932-6203},
mesh = {*Agrobacterium tumefaciens/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Agrobacterium/genetics ; Genome, Bacterial ; DNA, Bacterial/genetics ; },
abstract = {Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacterium tumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.},
}

*Agrobacterium tumefaciens/genetics
*Phylogeny
RNA, Ribosomal, 16S/genetics
Agrobacterium/genetics
Genome, Bacterial
DNA, Bacterial/genetics

@article {pmid39560406,
year = {2024},
author = {Ye, Y-Q and Ye, M-Q and Zhang, X-Y and Huang, Y-Z and Zhou, Z-Y and Feng, Y-J and Du, Z-J},
title = {Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0053524},
doi = {10.1128/msystems.00535-24},
pmid = {39560406},
issn = {2379-5077},
abstract = {The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.},
}

@article {pmid39558480,
year = {2024},
author = {Zechner, EL and Kienesberger, S},
title = {Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2430423},
pmid = {39558480},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/genetics/classification/drug effects ; Animals ; *Host Microbial Interactions ; Mutagens/metabolism ; Polyketides/metabolism/pharmacology ; Enterotoxins/metabolism ; Peptides ; },
abstract = {The human intestinal tract is densely colonized by a microbial community that is subject to intense competition. Bacteria in this complex habitat seek to outcompete their neighbors for nutrients and eliminate competitors with antibacterial toxins. Antagonism can be mediated by diverse effectors including toxic proteins and small molecule inhibitors that are released extracellularly or delivered by specialized secretion systems to targeted cells. Two prototypical microbiota-derived enterotoxins, colibactin and tilimycin, and the newly discovered family of indolimines represent an expanding group of non-proteinaceous small molecules which specifically target DNA. In addition to cell killing, they generate mutations and genome instability in intoxicated microbes and host cells alike. They have been studied in detail because of their direct toxicity to human cells and important etiological roles in intestinal pathologies. Increasing evidence, however, reveals that these commensal genotoxins are also mediators of interbacterial antagonism, which impacts gut microbial ecology. In this review, we illustrate the functional versatility of commensal genotoxins in the gut ecosystem.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Bacteria/metabolism/genetics/classification/drug effects
Animals
*Host Microbial Interactions
Mutagens/metabolism
Polyketides/metabolism/pharmacology
Enterotoxins/metabolism
Peptides

@article {pmid39557685,
year = {2024},
author = {Mai, N and Foysal, MJ and Timms, VJ and Pearson, LA and Romanis, CS and Mills, TJT and Powell, JR and Neilan, BA},
title = {Seasonal and Spatial Dynamics of Fungal Leaf Endophytes in Eucalyptus crebra (Narrow-Leaved Ironbark).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {142},
pmid = {39557685},
issn = {1432-184X},
support = {CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; FF0883440//Australian Research Council/ ; },
mesh = {*Eucalyptus/microbiology ; *Seasons ; *Endophytes/isolation & purification/classification/genetics ; *Plant Leaves/microbiology ; *Fungi/classification/isolation & purification/genetics ; Biodiversity ; Ascomycota/genetics/isolation & purification ; Basidiomycota/isolation & purification/genetics/classification ; },
abstract = {Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.},
}

*Eucalyptus/microbiology
*Seasons
*Endophytes/isolation & purification/classification/genetics
*Plant Leaves/microbiology
*Fungi/classification/isolation & purification/genetics
Biodiversity
Ascomycota/genetics/isolation & purification
Basidiomycota/isolation & purification/genetics/classification

@article {pmid39551884,
year = {2024},
author = {Mamo, Z and Abera, S and Tafesse, M},
title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {12},
pages = {384},
pmid = {39551884},
issn = {1573-0972},
support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; },
mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; },
abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.},
}

*Solid Waste
*Bacteria/classification/genetics/metabolism
*Waste Disposal Facilities
*Microbiota
*Metagenomics
Phylogeny
Refuse Disposal
Biodegradation, Environmental
Drug Resistance, Microbial/genetics
Soil Microbiology

@article {pmid39551202,
year = {2024},
author = {Duran, C and Bouchard, A and Agogué, H and Dupuy, C and Duran, R and Cravo-Laureau, C},
title = {Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177523},
doi = {10.1016/j.scitotenv.2024.177523},
pmid = {39551202},
issn = {1879-1026},
abstract = {Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.},
}

@article {pmid39549623,
year = {2024},
author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L},
title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122727},
doi = {10.1016/j.watres.2024.122727},
pmid = {39549623},
issn = {1879-2448},
abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.},
}

@article {pmid39549075,
year = {2024},
author = {de la Sovera, V and Bovio-Winkler, P and Zinola, G and Etchebehere, C},
title = {Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {519},
pmid = {39549075},
issn = {1432-0614},
support = {SNI//ANII/ ; SNI//ANII/ ; SNI//ANII/ ; (II/FVF/2019/121).//Carlos Vaz Ferreira/ ; },
mesh = {*Methane/metabolism ; *Biomass ; *Bioreactors/microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Archaea/genetics/metabolism/classification ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Microbiota ; Biodegradation, Environmental ; },
abstract = {Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.},
}

*Methane/metabolism
*Biomass
*Bioreactors/microbiology
*Bacteria/genetics/metabolism/classification/isolation & purification
*Archaea/genetics/metabolism/classification
Anaerobiosis
*RNA, Ribosomal, 16S/genetics
*Sewage/microbiology
Microbiota
Biodegradation, Environmental

@article {pmid39546027,
year = {2024},
author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M},
title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {141},
pmid = {39546027},
issn = {1432-184X},
mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; },
abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.},
}

*Carbon-Sulfur Lyases/genetics/metabolism
*Metagenomics
*Phylogeny
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
Archaea/genetics/enzymology/classification
Groundwater/microbiology
Metagenome
Seawater/microbiology

@article {pmid39545996,
year = {2024},
author = {Scheelings, TF and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {140},
pmid = {39545996},
issn = {1432-184X},
mesh = {Animals ; *Turtles/microbiology ; *Cloaca/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Fresh Water/microbiology ; Australia ; Gastrointestinal Microbiome ; Biodiversity ; },
abstract = {The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.},
}

Animals
*Turtles/microbiology
*Cloaca/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Fresh Water/microbiology
Australia
Gastrointestinal Microbiome
Biodiversity

@article {pmid39545729,
year = {2024},
author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC},
title = {Enriching the future of public health microbiology with hybridization bait capture.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0006822},
doi = {10.1128/cmr.00068-22},
pmid = {39545729},
issn = {1098-6618},
abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.},
}