{"title":"Sulphur-Acquisition Pathways for Cysteine Synthesis Confer a Fitness Advantage to Bacteria in Plant Extracts","authors":"Kazuya Ishikawa, Saki Yamaguchi, Taketo Tsukaoka, Makoto Tsunoda, Kazuyuki Furuta, Chikara Kaito","doi":"10.1111/1462-2920.70126","DOIUrl":"10.1111/1462-2920.70126","url":null,"abstract":"<p>Bacteria and plants are closely associated with human society, in fields such as agriculture, public health, the food industry, and waste disposal. Bacteria have evolved nutrient-utilisation systems adapted to achieve the most efficient growth in their major habitats. However, empirical evidence to support the significance of bacterial nutrient utilisation in adaptation to plants is limited. Therefore, we investigated the genetic and nutritional factors required for bacterial growth in plant extracts by screening an <i>Escherichia coli</i> gene-knockout library in vegetable-based medium. Mutants lacking genes involved in sulphur assimilation, whereby sulphur is transferred from sulphate to cysteine, exhibited negligible growth in vegetable-based medium or plant extracts, owing to the low cysteine levels. The reverse transsulphuration pathway from methionine, another pathway for donating sulphur to cysteine, occurring in bacteria such as <i>Bacillus subtilis</i>, also played an important role in growth in plant extracts. These two sulphur-assimilation pathways were more frequently observed in plant-associated than in animal-associated bacteria. Sulphur-acquisition pathways for cysteine synthesis thus play a key role in bacterial growth in plant-derived environments such as plant residues and plant exudates.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70126","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jake D. Schumacher, Nicholas Dusek, Marcela Mendoza-Suárez, Barney A. Geddes
{"title":"Adaptation of Plasmid-ID Technology for Evaluation of N2-Fixing Effectiveness and Competitiveness for Root Nodulation in the Sinorhizobium–Medicago System","authors":"Jake D. Schumacher, Nicholas Dusek, Marcela Mendoza-Suárez, Barney A. Geddes","doi":"10.1111/1462-2920.70118","DOIUrl":"10.1111/1462-2920.70118","url":null,"abstract":"<div>\u0000 \u0000 <p>Maximising the nitrogen fixation occurring in rhizobia-legume associations represents an opportunity to sustainably reduce nitrogen fertiliser inputs in agriculture. High-throughput measurement of symbiotic traits has the potential to accelerate the identification of elite rhizobium/legume associations and enable novel research approaches. Plasmid-ID technology, recently deployed in <i>Rhizobium leguminosarum</i>, facilitates the concurrent assessment of rhizobium nitrogen-fixing effectiveness and competitiveness for root nodulation. This study adapts Plasmid-ID technology to function in <i>Sinorhizobium</i> species that are central models for studying rhizobium-legume associations and form economically important symbioses with alfalfa. New Sino-Plasmid-IDs were developed and tested for stability and their ability to measure competitiveness for root nodulation and nitrogen-fixing effectiveness. Rhizobial competitiveness is measured by identifying strain-specific nucleotide barcodes using next-generation sequencing, whereas effectiveness is measured by GFP fluorescence driven by the synthetic <i>nifH</i> promoter. Sino-Plasmid-IDs allow researchers to efficiently study competitiveness and effectiveness in a multitude of <i>Sinorhizobium</i> strains simultaneously.</p>\u0000 </div>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jesper R. van Dijk, Jeanine S. Geelhoed, Nicole Geerlings, Jiji Alingapoyil Choyikutty, Henricus T. S. Boschker, Erik Verbruggen, Filip J. R. Meysman
{"title":"Inactive “Ghost” Cells Do Not Affect Motility and Long-Range Electron Transport in Filamentous Cable Bacteria","authors":"Jesper R. van Dijk, Jeanine S. Geelhoed, Nicole Geerlings, Jiji Alingapoyil Choyikutty, Henricus T. S. Boschker, Erik Verbruggen, Filip J. R. Meysman","doi":"10.1111/1462-2920.70117","DOIUrl":"10.1111/1462-2920.70117","url":null,"abstract":"<p>Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation over centimetre-long distances. These filaments contain so-called “ghost cells”, which display a highly reduced cytoplasmic content and a lack of metabolic activity. However, the origin and abundance of these ghost cells are not well understood, raising questions about their formation and potential impact on the functioning of the entire filaments. Here, we quantified the abundance of ghost cells in cable bacteria via a targeted propidium iodide staining technique and investigated their morphology and possible origin. Microscopy revealed that ghost cells are present in filaments under in situ conditions, and hence, they are not an artefact from filament sampling. Interestingly, filaments containing ghost cells retained gliding motility, as well as the capacity for long-distance electron transport, thus suggesting that the functionality of the filament as a whole remains largely unaffected by the presence of these ghost cells. Noteworthy is the higher frequency of ghost cells near the ends of filaments, and within filament fragments retrieved from oxic environments. Our findings provide new insights into the adaptive strategies of filamentous bacteria, highlighting their ability to maintain functionality at the organism level despite the fact that some individual cells are no longer metabolically active.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jia-Ying Wang, Vincent Dunon, Vimac Nolla Ardevol, Jérémie Béguet, Sven Jechalke, Ellen Pauwelyn, Rob Lavigne, Kornelia Smalla, Fabrice Martin-Laurent, Dirk Springael
{"title":"Dynamics of IS1071 and Its Accessory Gene Functions During Start-Up of an On-Farm Biopurification System","authors":"Jia-Ying Wang, Vincent Dunon, Vimac Nolla Ardevol, Jérémie Béguet, Sven Jechalke, Ellen Pauwelyn, Rob Lavigne, Kornelia Smalla, Fabrice Martin-Laurent, Dirk Springael","doi":"10.1111/1462-2920.70120","DOIUrl":"10.1111/1462-2920.70120","url":null,"abstract":"<div>\u0000 \u0000 <p>Insertion sequences (IS) are drivers of bacterial diversification by facilitating recruitment and horizontal transfer of adaptive genes involving composite transposon structures, but their evolutionary role at the community level is rarely addressed. This study explores the dynamics of IS<i>1071</i> and the cargo of IS<i>1071</i>-associated putative composite transposons in the establishment of a pesticide-degrading microbiome in an on-farm biopurification system (BPS)—which treats pesticide-contaminated wastewater and is considered a hotspot of microbial evolution—during the crucial start-up phase. Pesticide mineralisation assays and quantitative PCR targeting pesticide catabolic genes showed that the microbial community, upon feeding on the pesticide-contaminated wastewater, rapidly evolved into a pesticide-degrading microbiome. Concomitantly, an increase in the relative abundances of several mobile genetic elements, including IS<i>1071</i>, was observed, as well as a striking enrichment of xenobiotic catabolic genes in the cargo of putative IS<i>1071</i>-flanked composite transposons. The IS<i>1071</i> cargo catabolic genes diversified over time and were mainly of Betaproteobacterial origin. Clear changes in community composition were observed both in the total bacterial community and the Betaproteobacterial community. We conclude that IS<i>1071</i> supports the rapid establishment of pesticide catabolism in the BPS microbiome, highlighting the contribution of IS elements to microbial community adaptation to environmental changes.</p>\u0000 </div>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrew T. Crombie, Chloe L. Wright, Ornella Carrión, Laura E. Lehtovirta-Morley, J. Colin Murrell
{"title":"Isoprene Production by Sphagnum Moss Is Balanced by Microbial Uptake, as Revealed by Selective Inhibitors","authors":"Andrew T. Crombie, Chloe L. Wright, Ornella Carrión, Laura E. Lehtovirta-Morley, J. Colin Murrell","doi":"10.1111/1462-2920.70114","DOIUrl":"10.1111/1462-2920.70114","url":null,"abstract":"<p>Northern peatlands, ecosystems which store enormous amounts of carbon, and yet are major sources of methane and plant-derived volatiles including isoprene, are predicted to be greatly affected by climate change. Isoprene, the major volatile secondary metabolite released by plants, can support the carbon and energy needs of a variety of bacteria. Here we show that <i>Sphagnum</i> moss from an acidic bog harboured highly active isoprene degraders which consumed the vast majority of the plant-produced isoprene, preventing its release to the atmosphere. We quantified the potential for microbial isoprene uptake in the moss and, using alkyne inhibitors specific to either isoprene monooxygenase of <i>bona fide</i> isoprene degraders, or to the enzymes of other microbes capable of its fortuitous co-oxidation, we show that methane utilizers, for example, did not oxidise significant isoprene in incubations. Our technique enabled the separate quantification of plant isoprene production and microbial uptake, revealing that although atmospheric isoprene concentrations are typically low, the microbes contained in, or in close association with the moss were capable of isoprene uptake at the plant-generated isoprene concentration. Analysis of the bacterial community suggested that the isoprene degraders in this environment belonged to novel groups distinct from extant strains with this capability.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70114","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144220157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samantha C. Waterworth, Susan Egbert, John Sorensen, Barry R. O'Keefe, John A. Beutler
{"title":"A Biosynthetic and Taxonomic Atlas of the Global Lichen Holobiont","authors":"Samantha C. Waterworth, Susan Egbert, John Sorensen, Barry R. O'Keefe, John A. Beutler","doi":"10.1111/1462-2920.70112","DOIUrl":"10.1111/1462-2920.70112","url":null,"abstract":"<p>Lichens are pioneer species in several ecosystems, and as such are found in a variety of geographic regions and environments. Here, inspection of metagenomic data from 794 lichen samples from 34 countries reveals the presence of a complex holobiont harbouring remarkable biosynthetic capabilities, particularly in the bacterial consortia, a component that has been somewhat underappreciated. While bacteria were consistently present, their abundance varied among lichen taxa. Common bacterial genera included <i>Microbacterium</i>, <i>Terribacillus</i>, and <i>JABEUN01</i> (an <i>Acidimicrobiaceae</i> bacterium awaiting Latin binomial naming assignment) albeit in low abundance. <i>Lichenihabitans</i> and <i>Sphingomonas</i> genera were moderately abundant, present in approximately 30% of samples, and exhibited an enrichment in the number of biosynthetic gene clusters (BGCs) predicted to encode secondary metabolites (biosynthetic potential). We found that both fungal and bacterial biosynthetic repertoires appeared to follow genus-specific patterns but that there was greater relative homogeneity of BGCs in the fungal genera. The substantial biosynthetic diversity within lichen holobionts is evident in our findings, with the lichen-associated bacteria emerging as a promising potential source for sustainable drug discovery.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70112","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144213924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jianwei Zhang, Zhiying Guo, Jie Liu, Xianzhang Pan, Yanan Huang, Xiaodan Cui, Yuanyuan Wang, Yang Jin, Jing Sheng
{"title":"Capabilities and Limitations of Air-Dried Soils in Microbial Biogeography: A Regional-Scale Comparative Analysis","authors":"Jianwei Zhang, Zhiying Guo, Jie Liu, Xianzhang Pan, Yanan Huang, Xiaodan Cui, Yuanyuan Wang, Yang Jin, Jing Sheng","doi":"10.1111/1462-2920.70111","DOIUrl":"10.1111/1462-2920.70111","url":null,"abstract":"<div>\u0000 \u0000 <p>Air-dried soil archives offer valuable potential for studying long-term microbial dynamics, yet systematic evaluations across large spatial scales with paired fresh-soil comparisons remain limited. Here, we systematically evaluated the effects of 1-month air-drying on microbial biogeography across 244 paddy fields in eastern China. Results showed that air-drying significantly altered communities by reducing diversity through the elimination of rare taxa while enriching desiccation-resistant phyla like Firmicutes, Chloroflexi and Actinobacteria. These compositional shifts further triggered functional bias, enhancing fermentation/methanogenesis pathways while suppressing nitrogen cycling processes. Despite these alterations, air-dried samples maintained remarkable fidelity to key ecological patterns observed in fresh soils. Multivariate analyses demonstrated strong structural concordance between paired samples, with soil pH consistently emerging as the primary environmental driver in both data sets. This preservation of biogeographical relationships occurred despite significant changes in underlying ecological mechanisms. Air-dried soil communities exhibited increased stochastic assembly, reduced niche breadth and simplified co-occurrence networks with altered keystone taxa, indicative of a two-phase process: deterministic filtering of drought-sensitive taxa followed by stochastic reorganisation among survivors. Overall, our findings provide a framework for utilising soil archives in microbial ecology, showing that while air-drying introduces predictable distortions, samples retain essential ecological information for reconstructing historical microbial–environmental relationships at large scales.</p>\u0000 </div>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marion Margaux Lemoine, Thomas Wöhner, Martin Kaltenpoth
{"title":"Microbial Community Dynamics in Natural Drosophila melanogaster Populations Across Seasons","authors":"Marion Margaux Lemoine, Thomas Wöhner, Martin Kaltenpoth","doi":"10.1111/1462-2920.70104","DOIUrl":"10.1111/1462-2920.70104","url":null,"abstract":"<p>Many insects benefit from gut microbes that contribute to digestion, detoxification, nutrient supplementation or defence. Although abiotic and biotic factors are known to shape insect-associated microbial communities, the seasonal dynamics and their potential impact on host fitness remain poorly studied. Here we investigated the temporal changes in bacterial and fungal communities associated with the model organism <i>Drosophila melanogaster</i> over 5 months. Our results reveal high inter-individual variation, but also consistent changes in microbial communities of three wild <i>D. melanogaster</i> populations from early spring to late summer. These changes were driven by specific indicator species, particularly Acetobacteraceae bacteria (<i>Gluconobacter</i> and <i>Komagataeibacter</i>) and Saccharomycetales yeasts (<i>Pichia</i>, <i>Starmerella</i>, <i>Kregervanrija</i>, <i>Hanseniaspora</i>, <i>Saccharomycopsis</i>, <i>Priceomyces</i> and <i>Dipodascopsis</i>). The temporal dynamics were not accompanied by differences in the total bacterial or fungal abundance, and alpha-diversity only changed across sampling months for the fungal but not the bacterial communities. While the changes in <i>D. melanogaster</i>-associated microbial communities are likely driven by the exposure to seasonally changing microbial environments and diets, they may have important impacts on host fitness. Elucidating the potential adaptive value of seasonally changing microbial communities will enhance our understanding of how symbiotic microbes may contribute to ecological niche shifts and geographic range expansions in insects.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 6","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Robbert van Himbeeck, Stefan Geisen, Casper van Schaik, Sven van den Elsen, Roeland Berendsen, André Bertran, Egbert Schepel, Johannes Helder
{"title":"Patchy Distribution of Potato Cyst Nematodes Within Single Arable Fields Reveals Local Disease Suppressiveness Mediated by Disparate Microbial Communities","authors":"Robbert van Himbeeck, Stefan Geisen, Casper van Schaik, Sven van den Elsen, Roeland Berendsen, André Bertran, Egbert Schepel, Johannes Helder","doi":"10.1111/1462-2920.70113","DOIUrl":"10.1111/1462-2920.70113","url":null,"abstract":"<p>Disease suppressiveness is a complex phenomenon that is assumed to be the resultant of the actions of local microbial antagonists. Exploitation of disease suppressiveness as a tool to manage pathogens is hindered by our poor understanding of this phenomenon. Here we investigated soil microbiome-based suppression of potato cyst nematodes (PCN), and to this end, four apparently homogeneous potato fields with an unexplained non-homogeneous PCN distribution were selected. We hypothesised that this patchy PCN distribution resulted from local variation in disease suppressiveness. Under controlled greenhouse conditions, we confirmed the overall suppressiveness of these soils vis-à-vis PCN and soils were gamma-irradiated to corroborate the biotic origin of this suppression. Subsequent DNA-based analysis of the microbial community in the potato rhizosphere revealed suppressiveness-related contrasts in community composition between suppressive and conducive patches. Elevated abundances of fungal (e.g., <i>Metacordyceps chlamydosporia</i>) and bacterial (e.g., <i>Pseudomonas fluorescens</i>) nematode antagonists were positively associated with PCN suppressive patches. Distinct sets of antagonists were found to be associated with PCN suppression despite the geographical closeness of the locations under investigation. Our findings confirm the biotic origin of local PCN suppressiveness and reveal that disparate microbial communities could achieve similar outcomes.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70113","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144140333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Corentin Morvan, Magloire P. Nekoua, Chaldam J. Mbani, Cyril Debuysschere, Enagnon K. Alidjinou, Didier Hober
{"title":"Enteroviruses in Water: Epidemiology, Detection and Inactivation","authors":"Corentin Morvan, Magloire P. Nekoua, Chaldam J. Mbani, Cyril Debuysschere, Enagnon K. Alidjinou, Didier Hober","doi":"10.1111/1462-2920.70109","DOIUrl":"10.1111/1462-2920.70109","url":null,"abstract":"<p>Enteroviruses are small non-enveloped RNA viruses commonly found in environmental water samples. Worldwide analysis of water provides evidence of the broad distribution of enteroviruses. In addition to their medical importance, they are used as markers of faecal contamination of water. This review focuses on water-borne human enteroviruses and their transmission. Methods for detecting enteroviruses in water are also presented as well as current strategies to control these enteric viruses in water.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"27 5","pages":""},"PeriodicalIF":4.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.70109","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}