ISME communications最新文献

{"title":"Bark presence shifts fungal guild composition with varying effects on fungal diversity and biomass in a tropical forest.","authors":"Jean Evans Israel Codjia, Busayo Joshua Babalola, Weiming Hu, Yun-Qiang Yang, Sewanou H Honfo, Ekananda Paudel, Douglas Schaefer, Kun-Fang Cao, Jian-Chu Xu, Yong-Ping Yang, Rhett D Harrison, Gbadamassi G O Dossa","doi":"10.1093/ismeco/ycag258","DOIUrl":"10.1093/ismeco/ycag258","url":null,"abstract":"<p><p>Bark influences wood decomposition, but the mechanisms are unclear. We investigated fungal community composition, microbial biomass, and wood physicochemical condition during a wood decomposition experiment. We carried out a 2-year common garden experiment in a tropical seasonal rainforest, China, with logs from five tree species, comparing intact-bark versus bark-removed treatments over 0, 18, and 24 months of field exposure. We sequenced wood-inhabiting fungi, measured microbial biomass, and assessed wood chemical properties over time. We anticipated bark presence would alter fungal community composition and increase diversity, decay types, and microbial biomass. Wood with bark-removed had a higher relative abundance of Ascomycota, whereas bark presence fostered Basidiomycota. Soft rot fungi showed the highest relative abundance, followed by white rot fungi and brown rot fungi. However, bark presence was associated with higher relative abundance of white rot fungi, during early decay. Wood chemical properties and moisture (water content) availability, were correlated with the dominance of saprotrophs, rather than bark status. Despite compositional shifts, bark status did not influence fungal alpha diversity at the bark effects level. Bark status also did not directly influence fungal and bacterial biomass. Microbial biomass dynamics were instead linked to changes in wood physicochemical properties as decomposition progressed. Fungal community turnover dominated over time in bark-removed treatments, while bark presence redirected community assembly toward nestedness at the advanced decay stages. Overall, bark presence was linked with a shift toward more deterministic, habitat-filtered microbial community assembly, suggesting a multi-guild, multi-factor framework to predict bark effects on wood decay in forests.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag258"},"PeriodicalIF":6.4,"publicationDate":"2026-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overcoming gelling agent-derived inhibitory factors enables the cultivation of fastidious nitrifiers on solid media.","authors":"Zhiwei Peng, Atsushi Tamura, Tomonori Kindaichi, Akiyoshi Ohashi, Setsu Kato, Yutaka Nakashimada, Yoshiteru Aoi","doi":"10.1093/ismeco/ycag246","DOIUrl":"10.1093/ismeco/ycag246","url":null,"abstract":"<p><p>Nitrification is a key process in the global nitrogen cycle, yet the physiological characterization of nitrifiers remains limited due to their low culturability. Although culture-independent approaches have provided important ecological insights, they do not fully resolve the physiological properties of nitrifying microorganisms. Here, we show that common gelling agents (agar, agarose, and gellan gum) contain toxic substances that inhibit the growth of diverse nitrifying microorganisms as well as some heterotrophic bacteria. These inhibitory substances appear to be generated during autoclaving and act via mechanisms distinct from previously reported hydrogen peroxide. Removal of these inhibitory factors using a simple washing strategy enables colony formation in recalcitrant nitrifiers, including <i>Nitrososphaera</i> (ammonia-oxidizing archaea) and <i>Nitrospira</i> (nitrite-oxidizing bacteria). Application of this approach to environmental samples enabled the isolation of multiple difficult-to-culture nitrifying strains, including ammonia-oxidizing and nitrite-oxidizing microorganisms. Together, these findings demonstrate that the limited culturability of nitrifiers on solid medium is largely driven by gelling agent<b>-</b>derived inhibitory substances and can be overcome by a simple and broadly applicable strategy.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag246"},"PeriodicalIF":6.4,"publicationDate":"2026-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584200/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transfer potential of F-like plasmids in <i>Escherichia coli</i> differs by animal environment.","authors":"Sneha Sundar, Sebastian Bonhoeffer, Jana S Huisman","doi":"10.1093/ismeco/ycag256","DOIUrl":"10.1093/ismeco/ycag256","url":null,"abstract":"<p><p>Plasmids play a key role in the spread of virulence and antimicrobial resistance genes to new genetic backgrounds. Genetic variation in the transfer operon, which contains the genes responsible for conjugation, can lead to substantial differences in transfer potential even between closely-related plasmids. However, it is not clear how much genetic diversity there is in transfer operons of natural bacterial populations. Here, we analyse the prevalence and transfer potential of F-like plasmids, a clinically important family of plasmids in <i>Enterobacteriaceae</i>, by searching for the presence of essential conjugation genes in 1200 <i>Escherichia coli</i> genomes isolated from three livestock-associated environments. We find that the fraction of functionally complete F-like transfer operons was significantly higher in poultry than in bovine- and swine-associated bacteria. This difference was not captured in methods that use the presence of replication genes to estimate plasmid prevalence. Confounders such as the phylogenetic relatedness of <i>E. coli</i> or the presence of antibiotic resistance could not explain these significant differences in transfer potential. Instead, it seems the poultry environment selects for plasmids with high transfer potential, as it also contained more conjugative plasmid types per isolate. While we find environment-specific differences in overall plasmid frequency, patterns of transfer gene presence/absence were similar across the three environments. Regulatory and exclusion genes are the exception to this pattern, suggesting environment-specific modulation of transfer rates. This highlights the use of genomic data to uncover environment-specific differences in plasmid prevalence and transfer potential, revealing the selection pressures shaping horizontal gene transfer in these environments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag256"},"PeriodicalIF":6.4,"publicationDate":"2026-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13639103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogeny-guided curation reveals widespread misannotation of Asgard archaeal 16S rRNA gene sequences in public databases.","authors":"Agathe Struillou, Philippe Deschamps, David Moreira, Purificación López-García","doi":"10.1093/ismeco/ycag253","DOIUrl":"10.1093/ismeco/ycag253","url":null,"abstract":"<p><p>Accurate taxonomic assignment of 16S rRNA gene sequences is essential for the reliable interpretation of microbial community studies based on amplicon sequence data. Yet, it critically depends on the reliability of reference databases such as the Genome Taxonomy Database (GTDB) and the SILVA ribosomal RNA database. Here, we evaluate the consistency of taxonomic annotations within the Asgardarchaeota phylum, a lineage of major evolutionary and ecological interest. Using a phylogenetically curated set of GTDB-derived 16S rRNA gene sequences, we show that most of the affiliations of these sequences were consistent with the phylogenomic placement of their corresponding metagenome-assembled genomes (MAGs), although a small fraction of them exhibited clear inconsistencies likely resulting from erroneous binning to MAGs. In contrast, phylogenetic analyses of SILVA-derived 16S rRNA gene sequences including curated reference sequences revealed widespread taxonomic misannotation and/or limited resolution of taxon assignment. Specifically, many sequences annotated as Odinarchaeales robustly clustered within Lokiarchaeia, Heimdallarchaeia, Hermodarchaeia, or Sifarchaeia, leading to an artificial inflation of Odinarchaeales assignments and potentially biased ecological interpretations. To mitigate these issues, we constructed a curated reference dataset of Asgardarchaeota 16S rRNA gene sequences and generated phylogenetically validated taxonomic assignments across clustered entries, providing a resource for improved classification of environmental sequences. Our results demonstrate that widely used reference databases can contain systematic annotation errors that propagate across studies and distort ecological inference. Although illustrated using Asgard archaea, these limitations are likely pervasive across understudied microbial diversity, highlighting the need for routine phylogenetic validation and systematic curation of reference datasets.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag253"},"PeriodicalIF":6.4,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149076945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stage-specific cyanobacterial handoffs and heterotrophic subsidies underpin biocrust carbon accumulation.","authors":"Xian Zhang, Hua Li, Yingchun Han, Qi Li, Haijian Yang, Chunxiang Hu","doi":"10.1093/ismeco/ycag254","DOIUrl":"10.1093/ismeco/ycag254","url":null,"abstract":"<p><p>Inoculating cyanobacteria is a widely adopted strategy to accelerate biocrust formation and restore dryland soil functions, yet the in situ mechanisms sustaining microbial biomass carbon (MBC) accumulation under seasonal stress remain poorly understood. Here, we combined a field inoculation experiment with multi-omic profiling (amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics) and genome-scale metabolic modeling to track the circannual development of induced cyanobacterial biocrusts in Hopq Desert, China. Although the inoculated <i>Konicacronema</i> strain (formerly <i>Microcoleus</i>) maintained significant taxonomic dominance, metatranscriptomic and metaproteomic data revealed a striking functional handoff. <i>Microcoleus</i>-like populations drove rapid initial biocrust formation via the oxidative pentose-phosphate pathway and enzymatic antioxidant systems, whereas <i>Oscillatoria</i> assumed transcriptional dominance during harsher seasonal transitions through enhanced light harvesting, cyclic electron transport, and non-enzymatic photoprotection. Genome-scale metabolic modeling predicted that dominant cyanobacteria acted primarily as net importers, receiving amino acids, vitamins, cell-wall precursors, and phosphate from heterotrophic partners, while supplying inorganic sulfur and iron-sulfur clusters. Co-occurrence networks and life-history analyses further revealed that MBC maintenance was associated with a shift from growth-oriented resource mobilization toward acquisition-oriented strategies mediated by ABC transporters. Structural equation modeling confirmed that solar radiation and soil salinity govern MBC indirectly by influencing cyanobacterial composition and the balance between phototrophic assimilation and resource-acquisition strategies. These findings demonstrate that biocrust carbon accumulation is sustained by temporal functional division among cyanobacterial guilds and metabolic subsidies from heterotrophic partners, rather than by the persistent activity of a single pioneer strain, and provide a trait-based roadmap for designing resilient, multifunctional synthetic inocula for dryland restoration.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag254"},"PeriodicalIF":6.4,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13602264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omic stable isotope probing reveals <i>myo</i>-inositol metabolism by anaerobic gut bacteria in laying hens.","authors":"Harshita Naithani, Johannes Günther, Timur Yergaliyev, Amélia Camarinha-Silva, Jana Seifert","doi":"10.1093/ismeco/ycag257","DOIUrl":"10.1093/ismeco/ycag257","url":null,"abstract":"<p><p><i>Myo</i>-inositol (MI) is a dietary cyclitol and phytate hydrolysis product whose microbial fate in poultry is poorly understood. We combined ¹³C-labelled MI, metaproteomic stable-isotope probing (SIP), untargeted metaproteomics, and ¹³C-nuclear magnetic resonance metabolomics to map MI utilization by anaerobic bacterial enrichment cultures established from ileal and caecal digesta of laying hens. This integrative approach enables activity-resolved tracking of carbon flow from substrate to proteins and fermentation end products within a complex anaerobic community. We reconstructed, for the first time, a community-resolved pathway of MI degradation in the chicken gut, linking labelled metabolites to taxon-specific protein synthesis. MI metabolism was spatially structured, with rapid and sustained utilization in the caeca and delayed, host-variable activity in the ileum. Metaproteomic-SIP identified <i>Megamonas</i> as a dominant MI-assimilating genus in the caeca and implicated <i>Gallibacterium</i> as a previously unrecognized contributor in the ileum. Despite minimal shifts in community composition inferred from metaproteomics, protein expression profiles changed markedly, indicating that functional responses to MI occurred independently of taxonomic restructuring. Pathway reconstruction, supported by labelled and unlabelled proteins and labelled metabolite dynamics, revealed conversion of MI into central metabolic intermediates and short-chain fatty acids (SCFAs), providing a mechanistic framework for microbial MI utilization. Together, these findings establish stable isotope probing multi-omics as a powerful strategy for reconstructing metabolic pathways in complex microbiomes and demonstrate the metabolic potential of chicken gut-derived microbial communities to utilize MI under controlled anaerobic enrichment conditions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag257"},"PeriodicalIF":6.4,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149077018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel <i>Thermodesulfovibrionia</i> lineage largely supports sulfate reduction in sandy sediments of the southern Baltic Sea.","authors":"Judith Piontek, Thomas Schott, Patricia Roeser, Jens Kallmeyer, Michael Ernst Böttcher, Christiane Hassenrück, Klaus Jürgens","doi":"10.1093/ismeco/ycag255","DOIUrl":"https://doi.org/10.1093/ismeco/ycag255","url":null,"abstract":"<p><p>Sandy sediments of the coastal ocean are generally not considered a habitat for highly active sulfate-reducing microorganisms (SRM) due to fluctuations in oxygen concentrations and carbon availability. This study investigated the taxonomic composition and gene expression patterns of sulfate-reducing communities in both sandy, organic-poor sediments and muddy, organic-rich sediments in the mesohaline southern Baltic Sea. Our results revealed that a novel order-level lineage within the class <i>Thermodesulfovibrionia</i> (phylum <i>Nitrospirota</i>), named <i>Arenidesulfomonadales</i>, contributed significantly to sulfate reduction in the sandy sediments and supported sulfate reduction rates similar to those in the organic-rich, muddy sediments. In the sands, <i>Thermodesulfovibrionia</i> effectively competed with <i>Desulfobacterales</i>, which strongly dominated the sulfate-reducing communities in the organic-rich sediments. Metatranscriptomic data revealed that <i>Desulfobacterales</i> functioned as typical secondary fermenters in both sediment types and expressed nearly complete sets of genes for the catabolism of fermentation products such as lactate, propionate, and butyrate. In contrast, the gene expression profile of <i>Thermodesulfovibrionia</i> suggests that hydrogenotrophic sulfate reduction, coupled with carbon fixation via the Wood-Ljungdahl pathway and a reduced capacity to oxidize organic compounds, was a competitive metabolic strategy enabling sulfate reduction to proceed independently of fermentation-derived carbon. Overall, our results suggest that overlooked lineages of SRM may contribute to higher levels of sulfate reduction than previously assumed in the extensive areas of permeable sediments of coastal and shelf seas.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag255"},"PeriodicalIF":6.4,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13657043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149186711","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Orchard management alters citrus root and rhizosphere microbiomes with functional consequences for plant performance.","authors":"Nichole Ginnan, Riley Jones, Jessica Wu-Woods, Tariq Pervaiz, Ashraf El-Kereamy, Vanessa E T M Ashworth, Muhammad Imran Hamid, Emma K Dawson, Sarah L Strauss, Jason Stajich, Philippe Rolshausen, Caroline Roper","doi":"10.1093/ismeco/ycag248","DOIUrl":"10.1093/ismeco/ycag248","url":null,"abstract":"<p><p>Agricultural management practices act as ecological disturbances that can restructure soil and plant-associated microbial communities, but the functional consequences of these microbial shifts on crop performance remain poorly understood. Here, we examined how common orchard inputs, including wood mulch, glyphosate, and humic acid, affect citrus root and rhizosphere microbiomes, leaf nutrient trajectories, and tree performance over a 3-year field experiment. Mulch emerged as the dominant driver of fungal community composition and taxonomic turnover, enriching for saprophytic fungi. Conversely, bacterial communities responded primarily to interactions among applications, particularly mulch × glyphosate, which was associated with significant depletions of bacterial genera in roots and rhizospheres. These microbiome changes corresponded with reduced tree carbon assimilation, transpiration, and yield, and altered leaf nutrients dynamics. To verify whether the microbial shifts were contributing to these plant phenotypic changes, we conducted a greenhouse experiment using field-derived soil microbiota. Active microbiota from mulch-treated soils reduced citrus seedling establishment and root growth relative to microbiota from nonmulched soils, whereas heat-killed controls eliminated these negative effects, demonstrating a causal relationship between management-induced microbiota changes and decreases in plant performance. The effect of mulch-associated microbiota on root growth further depended on glyphosate history, paralleling field observations. Humic acid increased root growth regardless of microbiota activity and moderated decreases in shoot growth by mulch-associated microbiota. Together, these results show that management practices can restructure citrus microbiomes and generate community-level traits that influence plant performance, highlighting the importance of incorporating microbial ecology and microbiome information when devising crop management strategies.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag248"},"PeriodicalIF":6.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phosphorus acquisition among planktonic microbial communities across a salinity gradient.","authors":"Thomas Mollica, Elin Lindehoff, Daniel Lundin, Jarone Pinhassi, Malin Olofsson, Kristian Spilling, Hanna Farnelid, Catherine Legrand","doi":"10.1093/ismeco/ycag249","DOIUrl":"10.1093/ismeco/ycag249","url":null,"abstract":"<p><p>The Baltic Sea, with its pronounced gradient in temperature, salinity, and nutrient availability, provides a natural system to investigate microbial responses to eutrophication and climate change effects. While nutrient limitation in this system has been extensively studied, direct comparisons of phosphorus acquisition strategies across co-occurring prokaryotic and eukaryotic communities remain limited. This study provides a comprehensive analysis of how microbial plankton communities respond at the molecular level to shifts in phosphorus availability, by resolving both prokaryotic and eukaryotic strategies across spatial and seasonal gradients. By combining size-fractionation, community composition profiling, stoichiometry, and metatranscriptomics along a transect from the Bothnian Bay to the Bothnian Sea across spring and summer conditions, we identify both shared and domain-specific strategies of P acquisition. Results reveal that phosphorus acquisition is shaped by strong environmental gradients, with prokaryotes primarily relying on transporter-mediated uptake, while eukaryotes preferentially employ membrane remodelling and degradation pathways. These contrasting strategies varied across basins and seasons, reflecting differences in nutrient availability, temperature, and community structure. This integrative approach provides new insights into the functional ecology of microbial communities under shifting nutrient regimes and improves our ability to anticipate ecosystem response to eutrophication and climate change in the Baltic Sea.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag249"},"PeriodicalIF":6.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149077020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence.","authors":"Tim Goodall, Briony Jones, Amy C Thorpe, Robert I Griffiths, Hyun S Gweon, Daniel S Read, Richard Pywell, Susheel Bhanu Busi","doi":"10.1093/ismeco/ycag250","DOIUrl":"10.1093/ismeco/ycag250","url":null,"abstract":"<p><p>Restoring agriculturally degraded habitats to species-rich grasslands is a vital conservation objective. During restoration, how the soil resistome matures alongside microbial community composition and function remains unclear. Here, we tested two competing hypotheses: whether the soil resistome co-occurs through a microbial structural maturation, in which soil restoration is associated with higher-order biotic interactions, or whether antimicrobial resistance (AMR) is instead associated with the competitive pressures and high bacterial taxonomic richness found in disturbed, eutrophic arable land. Using a unique land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly following the cessation of agricultural activity. Our results demonstrate that AMR abundance increases significantly with restoration age, reaching a maximum in >143-year-old soils. The strongest predictor of this rise in AMR abundance was an increasing microbial eukaryotic signature rather than increasing microbial density, suggesting that resistome expansion is not associated with generalized spatial competition, but rather, co-occurs with structural maturation of the microbiome. We observed an order of magnitude increase in antibiotic biosynthetic potential, dominated by the emergence of streptomycin clusters. Microbial reorientation during soil maturation mirrors the expansion of a core resistome comprised of ancient, intrinsic mechanisms, such as Major Facilitator Superfamily (MFS) efflux pumps and RNA Polymerase-Binding Protein A (RbpA) target protection, in older soils. We demonstrate that endogenous AMR is a hallmark of healthy, restored soil ecosystems rather than a marker of anthropogenic soil degradation.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag250"},"PeriodicalIF":6.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13592167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}