Remi Gschwind,Mehdi Bonnet,Anna Abramova,Victor Hugo Jarquín-Díaz,Marcus Wenne,Ulrike Löber,Nicolas Godron,Ioannis D Kampouris,Faina Tskhay,Fouzia Nahid,Chloé Debroucker,Maximilien Bui-Hai,Inès El Aiba,Uli Klümper,Thomas U Berendonk,Sofia K Forslund-Startceva,Rabaab Zahra,Johan Bengtsson-Palme,Etienne Ruppé
Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the "One Health" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a "Trojan Horse" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/L), including ꞵ-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.
{"title":"Cefiderocol resistance genes identified in environmental samples using functional metagenomics.","authors":"Remi Gschwind,Mehdi Bonnet,Anna Abramova,Victor Hugo Jarquín-Díaz,Marcus Wenne,Ulrike Löber,Nicolas Godron,Ioannis D Kampouris,Faina Tskhay,Fouzia Nahid,Chloé Debroucker,Maximilien Bui-Hai,Inès El Aiba,Uli Klümper,Thomas U Berendonk,Sofia K Forslund-Startceva,Rabaab Zahra,Johan Bengtsson-Palme,Etienne Ruppé","doi":"10.1093/ismejo/wrag010","DOIUrl":"https://doi.org/10.1093/ismejo/wrag010","url":null,"abstract":"Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the \"One Health\" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a \"Trojan Horse\" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/L), including ꞵ-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056918","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}
Jiao Xi, Hanxiang Tao, Ziyi Zhang, Biyao Lian, Wei Sun, Yang Zhang, Shuhai Bu, Xiaojun Yang, Xun Qian
Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife–human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal–human interface.
{"title":"Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes","authors":"Jiao Xi, Hanxiang Tao, Ziyi Zhang, Biyao Lian, Wei Sun, Yang Zhang, Shuhai Bu, Xiaojun Yang, Xun Qian","doi":"10.1093/ismejo/wrag009","DOIUrl":"https://doi.org/10.1093/ismejo/wrag009","url":null,"abstract":"Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife–human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal–human interface.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"88 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056026","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}
Na Han,Xianhui Peng,Tingting Zhang,Yujun Qiang,Xiuwen Li,Wen Zhang
Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters detected in >30% of individuals. Among these, plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes like cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples, validated by single-cell and Nanopore sequencing. Screening 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This suggests potential repeated cross-species transmission events, equipping pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat for fueling multidrug-resistant pathogens.
{"title":"Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.","authors":"Na Han,Xianhui Peng,Tingting Zhang,Yujun Qiang,Xiuwen Li,Wen Zhang","doi":"10.1093/ismejo/wrag004","DOIUrl":"https://doi.org/10.1093/ismejo/wrag004","url":null,"abstract":"Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters detected in >30% of individuals. Among these, plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a \"plug-and-play\" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes like cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples, validated by single-cell and Nanopore sequencing. Screening 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This suggests potential repeated cross-species transmission events, equipping pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat for fueling multidrug-resistant pathogens.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146021688","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}
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}
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