Daniel Martak, Thibault Bourdin, Benoit Valot, Audrey Laboissière, Frédéric Lirussi, Xavier Bertrand, Edward Topp, Didier Hocquet
Antimicrobial resistance (AMR) is a serious global health threat, yet the drivers of its spread among humans are not fully understood. Antibiotics can enter the human gastrointestinal tract through the food chain, leading to the presence of low concentrations in the gut microbiota. However, the role of such traces in promoting the implantation of drug-resistant pathogens in the gut microbiota has never been explored in a controlled experimental setting. Using an in vitro model of the human gut microbiota, we tested whether traces of 19 antibiotics used in both human and veterinary medicine, alone or in combination, lead to the enrichment of Gram-negative pathogens producing extended-spectrum β-lactamases or carbapenemases. 28 strains of Gram-negative pathogens epidemic in humans (10 Escherichia coli, 6 Klebsiella pneumoniae, 5 Enterobacter hormaechei, 4 Acinetobacter baumannii, 3 Pseudomonas aeruginosa) were tested. We found that antibiotics at levels similar to those measured in the feces of healthy individuals (fluoroquinolones, 1–100 μg L−1; trimethoprim, 100 μg L−1; a mixture of fifteen veterinary antibiotics, 10–20 μg L−1) enriched the human gut microbiota with those resistant pathogens. Overall, the present study indicates that dietary consumption of some antibiotics can result in concentrations in the human colon sufficiently high to favor the implantation of exogenous antibiotic-resistant pathogens. These findings highlight the need to reassess permissible antibiotic concentrations in food and critically evaluate agricultural practices contributing to the contamination of animal- and plant-based products.
{"title":"Foodborne antibiotics enrich human gut microbiota with pathogens producing extended-spectrum β-lactamases and carbapenemases","authors":"Daniel Martak, Thibault Bourdin, Benoit Valot, Audrey Laboissière, Frédéric Lirussi, Xavier Bertrand, Edward Topp, Didier Hocquet","doi":"10.1093/ismejo/wrag008","DOIUrl":"https://doi.org/10.1093/ismejo/wrag008","url":null,"abstract":"Antimicrobial resistance (AMR) is a serious global health threat, yet the drivers of its spread among humans are not fully understood. Antibiotics can enter the human gastrointestinal tract through the food chain, leading to the presence of low concentrations in the gut microbiota. However, the role of such traces in promoting the implantation of drug-resistant pathogens in the gut microbiota has never been explored in a controlled experimental setting. Using an in vitro model of the human gut microbiota, we tested whether traces of 19 antibiotics used in both human and veterinary medicine, alone or in combination, lead to the enrichment of Gram-negative pathogens producing extended-spectrum β-lactamases or carbapenemases. 28 strains of Gram-negative pathogens epidemic in humans (10 Escherichia coli, 6 Klebsiella pneumoniae, 5 Enterobacter hormaechei, 4 Acinetobacter baumannii, 3 Pseudomonas aeruginosa) were tested. We found that antibiotics at levels similar to those measured in the feces of healthy individuals (fluoroquinolones, 1–100 μg L−1; trimethoprim, 100 μg L−1; a mixture of fifteen veterinary antibiotics, 10–20 μg L−1) enriched the human gut microbiota with those resistant pathogens. Overall, the present study indicates that dietary consumption of some antibiotics can result in concentrations in the human colon sufficiently high to favor the implantation of exogenous antibiotic-resistant pathogens. These findings highlight the need to reassess permissible antibiotic concentrations in food and critically evaluate agricultural practices contributing to the contamination of animal- and plant-based products.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"68 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chen Zhang, Siavash Atashgahi, Tom N P Bosma, Hauke Smidt
Marine sediments harbour diverse organohalide-respiring bacteria (OHRB), but their functional roles and metabolic interactions remains poorly understood. To investigate these interactions, we obtained and characterized a debrominating consortium from Aarhus Bay marine sediments. The consortium transformed 2,6-dibromophenol (2,6-DBP) to phenol under sulfate-reducing conditions, with bacterial growth demonstrating respiratory energy conservation. Metagenomic analysis and binning revealed five new species-level populations (>85% complete, <3% contaminated) dominated by Desulforhopalus (bin.5). Critically, bin.5 encodes a thiolytic tetrachloro-p-hydroquinone (TPh-) reductive dehalogenase (RDase), previously characterized only in aerobic bacteria, representing evidence of this enzyme functioning in a strictly anaerobic sulfate-reducing bacterium. Two additional populations (Desulfoplanes bin.3 and Marinifilaceae bin.4) encoded two and one putative respiratory corrinoid-dependent RDase, respectively. Transcription of all four RDase genes was rapidly induced upon 2,6-DBP addition, indicating multi-population response. Acetylene inhibited debromination post-transcriptionally without affecting RDase gene transcription, or sulfate metabolism, confirming RDase-mediated catalysis. Genome analysis indicated bin.5 encodes a near-complete vitamin B12 biosynthesis pathway (lacking only cbiJ, which can be bypassed through alternative reductases), consistent with debromination activity independent of exogenous B12 addition. Comparative genomics identified Marinifilum and Ancylomarina as candidate OHRB taxa, substantially expanding known phylogenetic diversity of marine organohalide respirers. This work reveals previously unrecognized biochemical versatility in anaerobic dehalogenation and demonstrates metabolic self-sufficiency enabling organohalide respiration in oligotrophic marine sediments.
{"title":"Organohalide respiration by a Desulforhopalus -dominated community","authors":"Chen Zhang, Siavash Atashgahi, Tom N P Bosma, Hauke Smidt","doi":"10.1093/ismejo/wrag007","DOIUrl":"https://doi.org/10.1093/ismejo/wrag007","url":null,"abstract":"Marine sediments harbour diverse organohalide-respiring bacteria (OHRB), but their functional roles and metabolic interactions remains poorly understood. To investigate these interactions, we obtained and characterized a debrominating consortium from Aarhus Bay marine sediments. The consortium transformed 2,6-dibromophenol (2,6-DBP) to phenol under sulfate-reducing conditions, with bacterial growth demonstrating respiratory energy conservation. Metagenomic analysis and binning revealed five new species-level populations (&gt;85% complete, &lt;3% contaminated) dominated by Desulforhopalus (bin.5). Critically, bin.5 encodes a thiolytic tetrachloro-p-hydroquinone (TPh-) reductive dehalogenase (RDase), previously characterized only in aerobic bacteria, representing evidence of this enzyme functioning in a strictly anaerobic sulfate-reducing bacterium. Two additional populations (Desulfoplanes bin.3 and Marinifilaceae bin.4) encoded two and one putative respiratory corrinoid-dependent RDase, respectively. Transcription of all four RDase genes was rapidly induced upon 2,6-DBP addition, indicating multi-population response. Acetylene inhibited debromination post-transcriptionally without affecting RDase gene transcription, or sulfate metabolism, confirming RDase-mediated catalysis. Genome analysis indicated bin.5 encodes a near-complete vitamin B12 biosynthesis pathway (lacking only cbiJ, which can be bypassed through alternative reductases), consistent with debromination activity independent of exogenous B12 addition. Comparative genomics identified Marinifilum and Ancylomarina as candidate OHRB taxa, substantially expanding known phylogenetic diversity of marine organohalide respirers. This work reveals previously unrecognized biochemical versatility in anaerobic dehalogenation and demonstrates metabolic self-sufficiency enabling organohalide respiration in oligotrophic marine sediments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146048042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Guillaume Chesneau, Alba Noel, Dimitri Bréard, Alice Boulanger, Martial Briand, Sophie Bonneau, Chrystelle Brin, Marion Fischer-Le Saux, Yujia Liu, Andrew Hendrickson, Torben Nielsen, Alain Sarniguet, David Guilet, Adam Arkin, Lauren Lui, Matthieu Barret
The seed is a habitat with limited resources and space. Although it is widely accepted that microbial competition is a key driver of the assembly of seed-associated microbial communities, the underlying mechanisms of this competition are not well understood. The initial objective of this work was to assess the importance of contact-independent microbial competition between the phytopathogenic bacterium Xanthomonas campestris pv. campestris 8004 (Xcc8004) and 30 strains representative of the bacterial populations most commonly associated with radish (Raphanus sativus) seeds. We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.
{"title":"Lactuchelins represent lipopeptide siderophores produced by Pseudomonas lactucae that inhibit Xanthomonas campestris","authors":"Guillaume Chesneau, Alba Noel, Dimitri Bréard, Alice Boulanger, Martial Briand, Sophie Bonneau, Chrystelle Brin, Marion Fischer-Le Saux, Yujia Liu, Andrew Hendrickson, Torben Nielsen, Alain Sarniguet, David Guilet, Adam Arkin, Lauren Lui, Matthieu Barret","doi":"10.1093/ismejo/wrag003","DOIUrl":"https://doi.org/10.1093/ismejo/wrag003","url":null,"abstract":"The seed is a habitat with limited resources and space. Although it is widely accepted that microbial competition is a key driver of the assembly of seed-associated microbial communities, the underlying mechanisms of this competition are not well understood. The initial objective of this work was to assess the importance of contact-independent microbial competition between the phytopathogenic bacterium Xanthomonas campestris pv. campestris 8004 (Xcc8004) and 30 strains representative of the bacterial populations most commonly associated with radish (Raphanus sativus) seeds. We identified Pseudomonas lactucae CFBP 13502 as a potent inhibitor of Xcc8004, mediated by exometabolites, specifically induced by certain seed-borne strains. Transcriptomic analysis linked this inducible activity to the upregulation of a gene cluster encoding a lipopeptide siderophore. Targeted gene deletion in P. lactucae CFBP 13502 confirmed that this cluster is essential for antagonism against Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, strongly supporting iron chelation as the underlying mechanism. Through comparative metabolomics, we elucidated the structure of a family of lipopeptide siderophores, produced by P. lactucae CFBP 13502, which we named lactuchelins. Our findings provide molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"101 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikhil R Chari,Kristen M DeAngelis,Arturo A Aguilar,A Li Han Chan,Grace A Burgin,Serita D Frey,Benton N Taylor
Root exudation, the export of soluble carbon compounds from living plant roots into soil, is an important pathway for soil carbon formation, but high rates of exudation can also induce rapid soil organic matter decomposition - a phenomenon known as the priming effect. Long-term soil warming associated with climate change could alter exudation rates and impact soil microbes by changing soil carbon chemistry. We hypothesized that warming-induced changes to exudation rate combined with direct effects of long-term warming on soil microbial communities would regulate the microbial priming effect. We tested this hypothesis with an artificial root exudate experiment using intact soil cores from a long-term soil warming experiment in a temperate forest. We found that chronic soil warming did not alter soil carbon formation from exudates, but did reduce the exudate-induced priming effect; exudation caused greater soil carbon loss in unwarmed than warmed soils. We used DNA stable isotope probing with 16S ribosomal RNA gene and shotgun metagenomic sequencing to determine whether long-term warming affected which microbes consume 13carbon-labeled artificial exudates. We found significant differences in bacterial community composition and relative gene abundances of 13carbon-enriched compared to natural abundance DNA. Both soil bacterial community composition and specific enzyme-coding gene families were strongly correlated with soil carbon priming in unwarmed treatments, but these effects were absent in warmed treatments. Our results suggest that the root exudate-induced priming effect is mediated by microbial biomass, community structure, and gene abundance, and that chronic warming reduces the priming effect by altering these microbial variables.
{"title":"Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.","authors":"Nikhil R Chari,Kristen M DeAngelis,Arturo A Aguilar,A Li Han Chan,Grace A Burgin,Serita D Frey,Benton N Taylor","doi":"10.1093/ismejo/wrag002","DOIUrl":"https://doi.org/10.1093/ismejo/wrag002","url":null,"abstract":"Root exudation, the export of soluble carbon compounds from living plant roots into soil, is an important pathway for soil carbon formation, but high rates of exudation can also induce rapid soil organic matter decomposition - a phenomenon known as the priming effect. Long-term soil warming associated with climate change could alter exudation rates and impact soil microbes by changing soil carbon chemistry. We hypothesized that warming-induced changes to exudation rate combined with direct effects of long-term warming on soil microbial communities would regulate the microbial priming effect. We tested this hypothesis with an artificial root exudate experiment using intact soil cores from a long-term soil warming experiment in a temperate forest. We found that chronic soil warming did not alter soil carbon formation from exudates, but did reduce the exudate-induced priming effect; exudation caused greater soil carbon loss in unwarmed than warmed soils. We used DNA stable isotope probing with 16S ribosomal RNA gene and shotgun metagenomic sequencing to determine whether long-term warming affected which microbes consume 13carbon-labeled artificial exudates. We found significant differences in bacterial community composition and relative gene abundances of 13carbon-enriched compared to natural abundance DNA. Both soil bacterial community composition and specific enzyme-coding gene families were strongly correlated with soil carbon priming in unwarmed treatments, but these effects were absent in warmed treatments. Our results suggest that the root exudate-induced priming effect is mediated by microbial biomass, community structure, and gene abundance, and that chronic warming reduces the priming effect by altering these microbial variables.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"219 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145971747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kang Zhou,Yue Deng,Chenghuan Zhu,Long Yang,Jing Zhang,Weidong Chen,Nobuhiro Suzuki,Guoqing Li,Mingde Wu
Despite extensive exploration of fungal viromes (mycoviromes), the ecological roles of mycoviruses remain poorly understood. Hence, we investigated the virome of Leptosphaeria biglobosa (an important fungal pathogen of rapeseed) from different geographic origins to determine the impacts of external factors on virome composition and their role in fungal ecological adaptation. The viromes of different L. biglobosa groups were investigated, and viral diversity correlated positively with field disease incidence and host diversity, but negatively with the altitude of the strain collection sites. A positive single-stranded RNA virus, namely, Leptosphaeria biglobosa letobirnavirus 1 (LbLV1), one of the core virome members (predominant viruses that constitute the majority of the viral community), has a significantly high incidence in L. biglobosa populations in winter rapeseed in southern China but a low incidence in L. biglobosa populations in spring rapeseed in northern China. Further laboratory and field tests revealed that LbLV1 could increase the ability of L. biglobosa to oversummer at average temperatures ranging from 23°C to 34°C in the winter rapeseed region of China. Therefore, the variation in LbLV1 incidence between winter and spring rapeseed should be a consequence of LbLV1-mediated adaptation to climate and cropping patterns. Furthermore, one gene, namely Lbhsp12, significantly induced by the hypothetical protein of LbLV1, is responsible for LbLV1-mediated thermal tolerance. Our findings indicate that mycovirome composition reflects environmental constraints, and core viruses can drive ecological adaptation by modulating host stress responses.
{"title":"Core virome shapes adaptation of a phytopathogenic fungus to climate and cropping patterns.","authors":"Kang Zhou,Yue Deng,Chenghuan Zhu,Long Yang,Jing Zhang,Weidong Chen,Nobuhiro Suzuki,Guoqing Li,Mingde Wu","doi":"10.1093/ismejo/wrag001","DOIUrl":"https://doi.org/10.1093/ismejo/wrag001","url":null,"abstract":"Despite extensive exploration of fungal viromes (mycoviromes), the ecological roles of mycoviruses remain poorly understood. Hence, we investigated the virome of Leptosphaeria biglobosa (an important fungal pathogen of rapeseed) from different geographic origins to determine the impacts of external factors on virome composition and their role in fungal ecological adaptation. The viromes of different L. biglobosa groups were investigated, and viral diversity correlated positively with field disease incidence and host diversity, but negatively with the altitude of the strain collection sites. A positive single-stranded RNA virus, namely, Leptosphaeria biglobosa letobirnavirus 1 (LbLV1), one of the core virome members (predominant viruses that constitute the majority of the viral community), has a significantly high incidence in L. biglobosa populations in winter rapeseed in southern China but a low incidence in L. biglobosa populations in spring rapeseed in northern China. Further laboratory and field tests revealed that LbLV1 could increase the ability of L. biglobosa to oversummer at average temperatures ranging from 23°C to 34°C in the winter rapeseed region of China. Therefore, the variation in LbLV1 incidence between winter and spring rapeseed should be a consequence of LbLV1-mediated adaptation to climate and cropping patterns. Furthermore, one gene, namely Lbhsp12, significantly induced by the hypothetical protein of LbLV1, is responsible for LbLV1-mediated thermal tolerance. Our findings indicate that mycovirome composition reflects environmental constraints, and core viruses can drive ecological adaptation by modulating host stress responses.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145949643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Michael Hoffert, Evan Gorman, Manuel E Lladser, Noah Fierer
Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmental preferences. This diversity makes it challenging to interpret ecological patterns in microbiomes and understand why individual taxa, or assemblages, may vary across space and time. Although we can use information from the rapidly growing databases of bacterial genomes to infer traits, we still need an approach to organize what we know, or think we know, about bacterial taxa to match taxonomic and phylogenetic information to trait inferences. Inspired by the periodic table of the elements, we have constructed a “periodic table” of bacterial taxa to organize and visualize monophyletic groups of bacteria based on the distributions of key traits predicted from genomic data. By analyzing 50 745 genomes across 31 bacterial phyla, we used the Haar-like wavelet transformation, a model-free transformation of trait data, to identify clades of bacteria which are nearly uniform with respect to six selected traits - oxygen tolerance, autotrophy, chlorophototrophy, maximum potential growth rate, GC content, and genome size. The identified functionally uniform clades of bacteria are presented in a concise periodic table-like format to facilitate identification and exploration of bacterial lineages in trait space. While our approach could be improved and expanded in the future, we demonstrate its utility for integrating phylogenetic information with genome-derived trait values to improve our understanding of the bacterial diversity found in environmental and host-associated microbiomes.
{"title":"Constructing a “periodic table” of bacteria to map diversity in trait space","authors":"Michael Hoffert, Evan Gorman, Manuel E Lladser, Noah Fierer","doi":"10.1093/ismejo/wraf289","DOIUrl":"https://doi.org/10.1093/ismejo/wraf289","url":null,"abstract":"Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmental preferences. This diversity makes it challenging to interpret ecological patterns in microbiomes and understand why individual taxa, or assemblages, may vary across space and time. Although we can use information from the rapidly growing databases of bacterial genomes to infer traits, we still need an approach to organize what we know, or think we know, about bacterial taxa to match taxonomic and phylogenetic information to trait inferences. Inspired by the periodic table of the elements, we have constructed a “periodic table” of bacterial taxa to organize and visualize monophyletic groups of bacteria based on the distributions of key traits predicted from genomic data. By analyzing 50 745 genomes across 31 bacterial phyla, we used the Haar-like wavelet transformation, a model-free transformation of trait data, to identify clades of bacteria which are nearly uniform with respect to six selected traits - oxygen tolerance, autotrophy, chlorophototrophy, maximum potential growth rate, GC content, and genome size. The identified functionally uniform clades of bacteria are presented in a concise periodic table-like format to facilitate identification and exploration of bacterial lineages in trait space. While our approach could be improved and expanded in the future, we demonstrate its utility for integrating phylogenetic information with genome-derived trait values to improve our understanding of the bacterial diversity found in environmental and host-associated microbiomes.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marine diazotrophs are microscopic planktonic organisms ubiquitous in the ocean, that play a major ecological role: they supply nitrogen to the surface ocean biosphere, an essential but scarce nutrient in ~60% of the global ocean. Over the past decades, they have attracted considerable attention, with numerous studies providing key insights into their diversity, lifestyle, biogeographical distribution, and biogeochemical role in planktonic ecosystems. An increasing number of studies show that these microbes regulate marine productivity and shape the food web by alleviating nitrogen limitation, thereby contributing to carbon sequestration to the deep ocean. Yet, the diazotroph-derived organic carbon exported to the deep ocean is still poorly quantified, limiting robust estimates of the ocean’s contribution to CO₂ sequestration and climate change mitigation under present and future conditions. This knowledge gap reflects the complexity of diazotroph export pathways to the deep ocean, whose quantification and variability drivers remain difficult to resolve with current methods. This review aims to synthesize current knowledge on the role of diazotrophs in their interactions with the food web and the biological carbon pump, reanalyze existing datasets, identify key knowledge gaps, and propose future research directions.
{"title":"Impact of Diazotrophs on Marine Food Webs and the Biological Carbon Pump: Progress and Remaining Challenges","authors":"Sophie Bonnet, Hugo Berthelot, Ilana Berman-Frank","doi":"10.1093/ismejo/wraf291","DOIUrl":"https://doi.org/10.1093/ismejo/wraf291","url":null,"abstract":"Marine diazotrophs are microscopic planktonic organisms ubiquitous in the ocean, that play a major ecological role: they supply nitrogen to the surface ocean biosphere, an essential but scarce nutrient in ~60% of the global ocean. Over the past decades, they have attracted considerable attention, with numerous studies providing key insights into their diversity, lifestyle, biogeographical distribution, and biogeochemical role in planktonic ecosystems. An increasing number of studies show that these microbes regulate marine productivity and shape the food web by alleviating nitrogen limitation, thereby contributing to carbon sequestration to the deep ocean. Yet, the diazotroph-derived organic carbon exported to the deep ocean is still poorly quantified, limiting robust estimates of the ocean’s contribution to CO₂ sequestration and climate change mitigation under present and future conditions. This knowledge gap reflects the complexity of diazotroph export pathways to the deep ocean, whose quantification and variability drivers remain difficult to resolve with current methods. This review aims to synthesize current knowledge on the role of diazotrophs in their interactions with the food web and the biological carbon pump, reanalyze existing datasets, identify key knowledge gaps, and propose future research directions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nusrat Nahar, Pu-Ting Dong, Jing Tian, Alex S Grossman, Erik L Hendrickson, Kristopher A Kerns, Mary Ellen Davey, Batbileg Bor, Jeffrey S McLean, Xuesong He
Saccharibacteria (formerly TM7) are a group of environmentally diverse, ultrasmall bacteria with highly reduced genomes belonging to Patescibacteria (formerly Candidate Phyla Radiation), a newly identified bacterial lineage accounting for over a quarter of microbial diversity. Nanosynbacter lyticus strain TM7x was isolated from the human oral cavity and was the first culture representative of Saccharibacteria. It displays an obligate episymbiotic lifestyle where TM7x lives on the surface of its bacterial host Schaalia odontolytica strain XH001. Saccharibacteria rely on host bacteria for growth. TM7x multiplies through budding division, and daughter cells can disassociate from host bacteria during their horizontal transmission stage and establish symbiosis with new bacterial hosts. However, how these metabolically constrained symbionts maintain their viability and infectivity during their horizontal transmission phase, when they are disassociated from hosts, remains poorly understood. By applying targeted mutagenesis using recently developed genetic tools for Saccharibacteria, we demonstrate that the TM7x-encoded arginine deiminase system (ADS) plays a critical role in ATP production and impacts TM7x-host bacterium interaction. Furthermore, we present the first empirical evidence showing that TM7x can uptake and utilize glucose via the glycolysis pathway. Glycolysis is particularly important for episymbiont ATP production under anoxic conditions during horizontal transmission between hosts. Our study demonstrates that TM7x employs two ATP-generating metabolic pathways, ADS and glycolysis, to ensure its viability and infectivity under different microenvironments when disassociated from its hosts during horizontal transmission, a critical phase of its life cycle.
{"title":"Ultrasmall episymbiont Nanosynbacter lyticus employs multiple ATP-generating metabolic pathways during horizontal transmission","authors":"Nusrat Nahar, Pu-Ting Dong, Jing Tian, Alex S Grossman, Erik L Hendrickson, Kristopher A Kerns, Mary Ellen Davey, Batbileg Bor, Jeffrey S McLean, Xuesong He","doi":"10.1093/ismejo/wraf288","DOIUrl":"https://doi.org/10.1093/ismejo/wraf288","url":null,"abstract":"Saccharibacteria (formerly TM7) are a group of environmentally diverse, ultrasmall bacteria with highly reduced genomes belonging to Patescibacteria (formerly Candidate Phyla Radiation), a newly identified bacterial lineage accounting for over a quarter of microbial diversity. Nanosynbacter lyticus strain TM7x was isolated from the human oral cavity and was the first culture representative of Saccharibacteria. It displays an obligate episymbiotic lifestyle where TM7x lives on the surface of its bacterial host Schaalia odontolytica strain XH001. Saccharibacteria rely on host bacteria for growth. TM7x multiplies through budding division, and daughter cells can disassociate from host bacteria during their horizontal transmission stage and establish symbiosis with new bacterial hosts. However, how these metabolically constrained symbionts maintain their viability and infectivity during their horizontal transmission phase, when they are disassociated from hosts, remains poorly understood. By applying targeted mutagenesis using recently developed genetic tools for Saccharibacteria, we demonstrate that the TM7x-encoded arginine deiminase system (ADS) plays a critical role in ATP production and impacts TM7x-host bacterium interaction. Furthermore, we present the first empirical evidence showing that TM7x can uptake and utilize glucose via the glycolysis pathway. Glycolysis is particularly important for episymbiont ATP production under anoxic conditions during horizontal transmission between hosts. Our study demonstrates that TM7x employs two ATP-generating metabolic pathways, ADS and glycolysis, to ensure its viability and infectivity under different microenvironments when disassociated from its hosts during horizontal transmission, a critical phase of its life cycle.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145847493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Youngho Kwon, Jisu Choi, Sung Hoon Kim, Pil Joo Kim, So-Myeong Lee, Jin-Kyung Cha, Hyeonjin Park, Ju-Won Kang, Su-Min Jo, Youn-Sig Kwak, Dajeong Kim, Woo-Jae Kim, Jong-Hee Lee, Choong-Min Ryu
Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line, Saeilmi, particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation or promoting microbial symbiosis. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele’s dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. This study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars
{"title":"Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits","authors":"Youngho Kwon, Jisu Choi, Sung Hoon Kim, Pil Joo Kim, So-Myeong Lee, Jin-Kyung Cha, Hyeonjin Park, Ju-Won Kang, Su-Min Jo, Youn-Sig Kwak, Dajeong Kim, Woo-Jae Kim, Jong-Hee Lee, Choong-Min Ryu","doi":"10.1093/ismejo/wraf284","DOIUrl":"https://doi.org/10.1093/ismejo/wraf284","url":null,"abstract":"Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line, Saeilmi, particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation or promoting microbial symbiosis. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele’s dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. This study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145847494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jiyu Xie, Xinli Sun, Tao Wen, Yaoqiang Bai, Tong Qian, Shunjuan Hu, Lihao Chen, Pan Wang, Youzhi Miao, Ruifu Zhang, Ákos T Kovács, Zhihui Xu, Qirong Shen
Bacteria-Fungi Interactions play a crucial role in soil nutrient cycling and plant disease suppression. Bacillus and Trichoderma exhibit antagonism when inoculated on laboratory media, global soil sample analysis reveals a positive correlation between these two genera in addition to enhanced plant-pathogen Fusarium oxysporum suppression and plant growth promotion. Here, we assess cross-kingdom interactions within artificial model communities of Bacillus velezensis and Trichoderma guizhouense. Transcriptomic profiling revealed that in the presence of fungi, the key stress sigma factor of B. velezensis activates expression of biosynthetic genes for antimicrobial secondary metabolite production. Among these, surfactin induces T22azaphilone production in T. guizhouense that hinders oxidative stress. Both surfactin and T22azaphilone contribute to Bacillus and Trichoderma maintenance in soil in the presence of Fusarium oxysporum. Finally, Fusarium oxysporum-secreted fusaric acid temporarily inhibits B. velezensis growth whereas it is efficiently degraded by T. guizhouense. These metabolite-mediated interactions reveal how competing soil microorganisms could form effective alliances that ultimately enhance plant protection against soil-borne pathogens.
{"title":"Metabolite interactions mediate beneficial alliances between Bacillus and Trichoderma for effective Fusarium wilt control","authors":"Jiyu Xie, Xinli Sun, Tao Wen, Yaoqiang Bai, Tong Qian, Shunjuan Hu, Lihao Chen, Pan Wang, Youzhi Miao, Ruifu Zhang, Ákos T Kovács, Zhihui Xu, Qirong Shen","doi":"10.1093/ismejo/wraf283","DOIUrl":"https://doi.org/10.1093/ismejo/wraf283","url":null,"abstract":"Bacteria-Fungi Interactions play a crucial role in soil nutrient cycling and plant disease suppression. Bacillus and Trichoderma exhibit antagonism when inoculated on laboratory media, global soil sample analysis reveals a positive correlation between these two genera in addition to enhanced plant-pathogen Fusarium oxysporum suppression and plant growth promotion. Here, we assess cross-kingdom interactions within artificial model communities of Bacillus velezensis and Trichoderma guizhouense. Transcriptomic profiling revealed that in the presence of fungi, the key stress sigma factor of B. velezensis activates expression of biosynthetic genes for antimicrobial secondary metabolite production. Among these, surfactin induces T22azaphilone production in T. guizhouense that hinders oxidative stress. Both surfactin and T22azaphilone contribute to Bacillus and Trichoderma maintenance in soil in the presence of Fusarium oxysporum. Finally, Fusarium oxysporum-secreted fusaric acid temporarily inhibits B. velezensis growth whereas it is efficiently degraded by T. guizhouense. These metabolite-mediated interactions reveal how competing soil microorganisms could form effective alliances that ultimately enhance plant protection against soil-borne pathogens.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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