ISME Journal最新文献

{"title":"Modulation of microbial communication by lipid exudates.","authors":"Mahmoud Gargouri, Philip D Bates, Stéphane Declerck","doi":"10.1093/ismejo/wrag156","DOIUrl":"10.1093/ismejo/wrag156","url":null,"abstract":"<p><p>Root exudates comprise a diverse mixture of nonpolar and amphiphilic compounds that are only partially recovered by aqueous extraction methods, yet can rival polar metabolites as carbon sources for microorganisms. Because many quorum sensing (QS) signals are fatty-acyl derivatives, lipid-rich microhabitats at the root-soil interface are likely to influence signal partitioning, persistence, and local QS thresholds. We propose a lipid-mediated framework in which plant-derived lipids modulate QS through four nodes: receptor mimicry/antagonism, quorum quenching, membrane/microenvironment regulation, and lipid-dependent resource gating. These mechanisms operate across two lipid-rich interfaces-the rhizosphere and the arbuscular mycorrhizal fungi hyphosphere-where host lipid fluxes may restructure microbial community composition. Combined with QS-sensitive changes in root exudation, this spatially structured lipid circuit could generate feedbacks influencing microbiome composition and function, with potential implications for microbiome engineering.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13372036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148267098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Upregulated jasmonate signaling shifts Arabidopsis microbiota interactions and stress adaptations through a positive feedback loop.","authors":"Tung-Tse Lu, Miguelito Isip, Chiao-Jung Han, Hung-Jui Shih, Syukur Syukur, Lai Loi Trinh, Silvina Perin, Yu-Chun Lin, Po-An Lin, Ka-Wai Ma","doi":"10.1093/ismejo/wrag146","DOIUrl":"10.1093/ismejo/wrag146","url":null,"abstract":"<p><p>The model plant Arabidopsis thaliana hosts diverse microbial communities collectively known as the microbiota. The plant microbiota is generally taxonomically structured and, in many cases, confers benefits to the plant host including plant growth promotion and enhanced stress tolerance. However, microbial imbalance can also result in deleterious effects, a phenomenon termed dysbiosis that was first coined in the gut microbiome field. To uncover the regulatory mechanism maintaining healthy plant homeostatic interactions with microbiota, we conducted screening using defined synthetic bacterial communities. We identified an Arabidopsis mutant displaying altered microbial profiles with an overall increase of microbial load and microbiota-dependent growth defects. Transcriptomic analyses combined with phytohormone quantification revealed that these phenotypes are attributed to an upregulation of the jasmonic acid (JA) signaling pathway in this mutant upon microbiota colonization. Furthermore, chemical treatment with different JA inducers reproduced similar phenotypes in wild-type plants, suggesting regulation through a positive feedback loop. Although activation of the JA pathway is typically associated with enhanced plant stress responses, our mutant exhibited reduced pathogen load at the expense of reduced plant growth and impaired salt tolerance. Together, our findings demonstrate that JA signaling not only orchestrates plant growth and defense but also plays a pivotal role in shaping plant-microbiota interactions. Controlled regulation of the JA signaling pathway is therefore essential to maintain balanced plant response to multiple environmental stressors.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13352530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148220476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrical signalling beyond diffusion-limited microbial interactions.","authors":"Paulo R F Rocha, Leïla Tirichine","doi":"10.1093/ismejo/wrag238","DOIUrl":"10.1093/ismejo/wrag238","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13615533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.","authors":"Sierra L Bedwell, Isabelle M Lakis, Allison R Megow, Angelina E Carpenter, Kevin D Ricks, Christopher J Fields, Jennifer A Lau, Rachel J Whitaker, Katy D Heath","doi":"10.1093/ismejo/wrag228","DOIUrl":"10.1093/ismejo/wrag228","url":null,"abstract":"<p><p>Though they jointly shape community responses to environmental perturbations, ecology and evolution are often examined separately, even in microorganisms where both occur over short timescales. Here, we examine ecological and evolutionary responses to 33 years of nitrogen fertilization using the legume-rhizobium mutualism. Pairing a manipulative inoculation study with full-length 16S rRNA gene amplicon sequencing and structural equation modeling allows us to synthesize across biological scales: whole bacterial community, genus Rhizobium, Rhizobium amplicon sequence variants (ASVs), and symbiosis plasmids. Clover's preferred partner decreases in N-addition soils, limiting host growth, while a diverse and largely uncharacterized Rhizobium community increases. This ecological change is compounded by a concurrent evolutionary degradation of symbiont partner quality via changing frequencies of symbiotic plasmids. Ecological (rarer symbionts) and evolutionary (inferior symbionts) processes each accounted for roughly half of this loss of host benefit, revealing that ecology and evolution jointly shape mutualism breakdown over the short timescales typical of microbial systems.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.","authors":"Lisa Jourdain, Aaron Leininger, Alan R Pacheco, Wenyu Gu","doi":"10.1093/ismejo/wrag145","DOIUrl":"10.1093/ismejo/wrag145","url":null,"abstract":"<p><p>Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion (AD) communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (permutational multivariate analysis of variance R2 = 0.21, P = .001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in ad emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13325402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148200561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Standardized and batch effect-independent technologies enable global collaboration in microbiome research.","authors":"Muzi Ge, Tomoya Maeda, Jingdi Li, Maryam Chaib De Mares, Emmanuel George Kifaro, Gizachew Haile Gidamo, Katsuyuki Shiroguchi, Andrew H Moeller, Zhibin Zhang, Jianshi Jin","doi":"10.1093/ismejo/wrag122","DOIUrl":"10.1093/ismejo/wrag122","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13285996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147934865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CHD-18 g-modulated Pseudomonas taxa support poplar salt tolerance.","authors":"Yangwenke Liao, Qingyue Zhang, Jiafeng Zheng, Jinchi Zhang, Tingting Dai, Fuyuan Zhu, Víctor J Carrión, Manuel Delgado-Baquerizo, Christian Sonne, Fuliang Cao, Xiaogang Li","doi":"10.1093/ismejo/wrag138","DOIUrl":"10.1093/ismejo/wrag138","url":null,"abstract":"<p><p>Against the background of global climate change, soil salinization has emerged as a major abiotic stressor constraining agroforestry productivity worldwide. Root-recruited microbes enhance plant stress resilience, and host-microbe interactions depend on plant root metabolism. Stress-tolerant plant genotypes exhibit a marked capacity to enrich beneficial root-associated microbes through specialized metabolic responses, thereby facilitating phenotypic plasticity. However, the molecular mechanisms underlying these plant-microbe interactions remain unclear. In this study, we compared salt tolerance among three poplar varieties under aseptic and non-aseptic conditions, and analyzed their rhizosphere bacterial community responses to salt stress. We found that microbial inoculation modulated poplar salt tolerance, and poplar shaped rhizosphere bacterial communities in a genotype-dependent manner. Transcriptome sequencing and targeted metabolomic analysis indicated that salt-tolerant poplar plants preferentially activate the phenylpropanoid biosynthesis pathway, accompanied by the enhanced root secretion of benzoic acid (BA) and salicylic acid (SA) and up-regulation of CHD-18 g encoding cinnamoyl-CoA hydratase/dehydrogenase. Overexpression of CHD-18 g increased rhizosphere Pseudomonas abundance by enhancing BA and SA biosynthesis. Binary interaction assays further showed that the BA-induced Pseudomonas taxa mitigated salt stress and promoted poplar growth under salt stress. Our findings propose a framework linking host gene expression, root metabolism, and key microbial taxa in conferring salt tolerance. This work uncovers a metabolic signaling mechanism by which trees shape their root microbiome to enhance stress adaptation, offering actionable genetic and ecological strategies for improving tree resilience in sustainable agroforestry systems.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13332713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148044581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aesculetin-mediated recruitment of denitrifying microbiota by resistant rapeseed suppresses Plasmodiophora brassicae via nitrate depletion.","authors":"Zhen Zhang, Xingfu Chen, Meihui Wu, Xiuxiu Liu, Lu Chang, Feng Rao, Yuanwei Zhou, Kenichi Tsuda, Chunyu Zhang, Jiasen Cheng, Jiatao Xie, Yang Lin, Yanping Fu, Daohong Jiang, Tao Chen","doi":"10.1093/ismejo/wrag061","DOIUrl":"10.1093/ismejo/wrag061","url":null,"abstract":"<p><p>Clubroot, caused by the protist pathogen Plasmodiophora brassicae, is a major threat to cruciferous crop production worldwide. Although plant microbiota is known to influence disease outcomes, the mechanisms underlying microbiota-mediated resistance remain unclear. Here, we investigated the role of plant microbiota in clubroot resistance using two Chinese rapeseed cultivars carrying resistance genes introduced through breeding and their susceptible parental lines. Microbiome profiling revealed that P. brassicae infection altered root and rhizosphere bacterial communities, with resistant cultivars displaying distinct assemblages. Functional prediction indicated an enrichment of denitrifying bacteria in the roots of resistant plants following pathogen challenge. Key denitrifying strains were isolated and assembled into a synthetic microbial community (SynCom18), which significantly suppressed clubroot development under both controlled and field conditions. In addition to reducing disease severity, microbial treatments improved agronomic traits, including yield and seed quality. Mechanistic analysis revealed a positive correlation between soil nitrate levels and disease severity. Denitrifying strains and SynCom18 likely suppressed the development of P. brassicae and enhanced plant immunity by reducing soil nitrate levels by ~39.4%. Metabolomic profiling revealed that aesculetin, as a dominant metabolite that is produced by resistance roots and excreted into the rhizosphere to recruit denitrifying bacteria. Our findings show that pathogen-infected clubroot-resistant rapeseed cultivars secrete aesculetin to recruit nitrate-depleting bacteria for resistance against P. brassicae. This study elucidates a tripartite microbiota-pathogen-soil nutrient interaction and provides a sustainable biocontrol strategy for cruciferous crops.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13215590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148037265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome-mediated polyphosphate accumulation enhances the resilience of sponge holobionts to future climate scenarios.","authors":"Bifu Gan, Chenyu Yang, Chenzheng Jia, Kai Wang, Jun Chen, Shaoxiong Ding, Jing Zhao","doi":"10.1093/ismejo/wrag128","DOIUrl":"10.1093/ismejo/wrag128","url":null,"abstract":"<p><p>Ocean warming is threatening the stability of marine ecosystems, yet the mechanisms underlying the resilience of foundational species like sponges remain poorly understood. Polyphosphate (PolyP), a key player in marine phosphorus burial, is hypothesized to play an important role in sponge stress adaptation. Here, we demonstrated that microbiome-mediated PolyP dynamics were closely associated with sponge adaptation to thermal stress. Field investigation of three sponge species (Spongia sp., Tedania sp., Haliclona simulans) revealed marked interspecific differences in PolyP accumulation, with Spongia sp. maintaining the highest PolyP levels. Strong seasonal fluctuations in sponge PolyP content, peaking in June and reaching a minimum in January, correlated with ambient temperature. We found that this variation was regulated by ppk1 gene expression levels rather than by altering the microbial composition. The ppk1-harboring microbial assemblages exhibited host specificity, and phylogenetic analysis uncovered sponge-specific clades of ppk1 genes. Laboratory warming experiments further confirmed the functional link: under acute heat stress, both the ppk1 gene of the symbiotic microorganisms and the inorganic pyrophosphatase (ppa) gene in the host were upregulated in Spongia sp. PolyP likely provide an energy source for the host, maintaining holobiont stability and leading to low mortality. Conversely, H. simulans, with limited PolyP supply, ultimately suffered 100% mortality. Our results establish a link whereby sponge-associated microbes, via ppk1 expression, modulate PolyP accumulation to support host oxidative phosphorylation and mitigate thermal stress. This microbiome-mediated physiological pathway contributes to our understanding of sponge climate resilience, offering new functional insights into holobiont persistence in a warming ocean.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13431277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148058202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic filtering accompanies functional expansion during long-term soil restoration.","authors":"Tim Goodall, Susheel Bhanu Busi, Briony Jones, Amy Thorpe, Robert I Griffiths, John Redhead, Lucy Hulmes, Sarah Hulmes, Lucy Ridding, Jodey Peyton, Gloria Pereira, Hyun Soon Gweon, Daniel S Read, Richard Pywell","doi":"10.1093/ismejo/wrag131","DOIUrl":"10.1093/ismejo/wrag131","url":null,"abstract":"<p><p>The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a decoupling between floral and edaphic recovery. While the diversity of vegetation recovered relatively rapidly, approaching ancient grassland levels within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age; this taxonomic contraction was conversely matched by an expansion in inferred metagenomic functional potential. This was reflected in increased functional gene richness and shifts in the relative abundance of specific SEED-annotated functions towards metabolic pathways associated with complex carbon cycling and stress tolerance. These shifts were congruent with the emergence of specific, unnamed genera belonging to Pseudomonadota and Actinomycetota, and the Bacillota species Pristimantibacillus. The soil ecosystem remained distinct from the 143-year stage even after 67 years of recovery, characterized by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13280953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147989957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}