ISME Journal最新文献

{"title":"Contrasting salinity regimes reshape microbe-DOM coupling and reduce recalcitrant dissolved organic carbon preservation in a salt lake.","authors":"Xiding Wang, Yang Liu, Xinyue Yang, Ruikai Zhang, Xudong Liu, Fangru Nan, Qi Liu, Junping Lv, Jia Feng, Shulian Xie","doi":"10.1093/ismejo/wrag107","DOIUrl":"10.1093/ismejo/wrag107","url":null,"abstract":"<p><p>Salt lakes account for nearly half of the world's inland water area and play an irreplaceable role as \"carbon conversion and stabilization factories,\" making substantial contributions to the global carbon cycle. Central to this function is the transformation of dissolved organic carbon (DOC) and its accumulation into recalcitrant dissolved organic carbon (RDOC), which together underpin internal carbon processing in these systems. However, the pathways through which DOC is converted to RDOC in salt lakes, and how these pathways are shaped by salinity and microbial communities, remain poorly resolved. Here, using Yuncheng Salt Lake as a within-lake system, we combined field-based in situ characterization with long-term incubation experiments to examine how contrasting salinity regimes were associated with microbial and dissolved organic matter (DOM) variation. Higher salinity was associated with reduced bacterial and dissolved organic matter diversity, stronger deterministic bacterial assembly, and a restructured bacteria-DOM association network. Under the standardized nutrient-replete incubation conditions used here, samples from the higher-salinity regime exhibited higher biodegradable DOC, lower RDOC preservation, and greater overall DOC loss over the 100-day experimental timescale. Salinity-related differences in microbial community composition, metabolomic profiles, and dissolved organic matter characteristics were closely associated with variation in RDOC dynamics, suggesting that these carbon-processing differences were accompanied by coordinated microbial and metabolic reorganization. Together, these results provide process-relevant, condition-specific evidence that contrasting salinity regimes within Yuncheng Salt Lake were associated with differences in microbe-DOM coupling and in DOC/RDOC outcomes.</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/PMC13200285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845436","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":"Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept.","authors":"Wei Zhang, Ioannis Eleftherianos, Amr Mohamed, Guy Smagghe, George Joseph Chakkalakkal, Rasha Al-Akeel, Umut Toprak, Gianluca Tettamanti, Nemat Keyhani, David Renault","doi":"10.1093/ismejo/wrag137","DOIUrl":"10.1093/ismejo/wrag137","url":null,"abstract":"<p><p>Insect-associated microbiomes, as co-evolved members of the holobiont, play pivotal roles in host physiology, ecological resilience, and evolutionary innovation. This review synthesizes recent advances in understanding microbial symbionts' contributions to metabolic adaptation, insecticide detoxification, and immune modulation. Framed within hologenome theory-which posits host-microbe assemblages as units of natural selection-we explore co-evolutionary dynamics driving mutualistic specialization and adaptive plasticity. Cutting-edge tools like genome editing and metagenomics reveal how gut microbiota mediate cross-kingdom interactions, insecticide resistance, and reproductive fitness. Intriguingly, microbial symbionts can enhance host resistance through detoxification while sensitizing hosts to specific toxins, highlighting context-dependent trade-offs. Targeted manipulation of microbial consortia-via detoxification disruption or symbiont engineering-offers new avenues for sustainable pest control, though ecological risks demand rigorous biosafety protocols. A paradigm shift toward holobiont-centered models promises unified strategies for sustainable agriculture and biodiversity conservation in the Anthropocene.</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/PMC13310142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148037199","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":"Host and microbial factors influence bacterial colonization of the honey bee gut.","authors":"Silvia Moriano-Gutierrez, Aurélien Pirat, Audam Chhun, Aiswarya Prasad, Alexandra Szigeti, Méline Garcia, Lucie Kesner, Florent Mazel, Philipp Engel","doi":"10.1093/ismejo/wrag127","DOIUrl":"10.1093/ismejo/wrag127","url":null,"abstract":"<p><p>The guts of many animals are colonized by host-specific microbes, yet how host filtering (host-derived constraints) shapes microbial colonization and host specificity remains poorly understood. Here, we used gnotobiotic honey bees (Apis mellifera) as a model system to systematically assess colonization potential of a phylogenetically and ecologically diverse panel of 56 bacterial strains, spanning native symbionts, opportunistic bee-associated taxa, gut microbes from other bee species, and non-bee environmental isolates. Bacterial load and colonization frequency were quantified by strain-specific qPCR seven days post-inoculation, in monocolonization and with a synthetic community of native honeybee core bacteria. Bacterial load was highest for native strains and declined with increasing phylogenetic distance from native symbionts. Co-colonization with the synthetic community reduced bacterial load across all groups, but native strains were least affected. Across strains, KEGG pathway completeness correlated with bacterial load in some ecological groups; however, metabolic capacity did not fully explain colonization patterns, either in monocolonization or under competitive conditions. A key finding was that in vitro sensitivity to antimicrobial peptides (AMPs; apidaecin, abaecin, defensins, and hymenoptaecin) varied widely among strains and was highest in closely related bee-associated bacteria. Even highly successful colonizers such as Gilliamella and Snodgrassella were AMP-sensitive. AMP sensitivity showed a negative correlation with bacterial load, but not with the frequency of host colonization. These findings suggest that AMPs modulate symbiont abundance rather than acting as strict barriers to colonization. Overall, our results reveal that host filtering in the bee gut is multifaceted, integrating immune-mediated barriers, microbial traits, and competitive interactions.</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/PMC13293248/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147976876","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":"Rapid adaptation accelerates competitive suppression in a parasite community.","authors":"Samuel T E Greenrod, Daniel Cazares, Weronika Ślesak, Tobias E Hector, R Craig MacLean, Kayla C King","doi":"10.1093/ismejo/wrag114","DOIUrl":"10.1093/ismejo/wrag114","url":null,"abstract":"<p><p>Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to environmental sensitivity of infection steps and dependence on host fitness. Parasite populations might avoid extinction through evolutionary rescue-whereby rapid adaptation to stress enables persistence-but the impacts of adaptation to stress on parasite communities remain unclear. Here, we study the evolutionary and ecological impact of thermal stress in a simple parasite community by propagating populations of two viral parasites (bacteriophages φ14-1 and φLUZ19) of Pseudomonas aeruginosa in monoculture and co-culture under two thermal conditions: a control temperature (37°C) and a high temperature that restricts φ14-1 growth (42°C). We show that rapid thermal adaptation of φ14-1 facilitated persistence in monoculture. Rescue of this phage in co-culture made it a superior competitor, and it replaced φLUZ19 as the dominant phage at high temperature. We determine that thermal adaptation occurred through mutations in genes linked to attachment to bacterial hosts and within-host replication. We also show that competitive suppression by φ14-1 constrained φLUZ19 molecular evolution. Our findings suggest that rapid adaptation to environmental stress can prevent the extinction of some parasites but may inadvertently destabilise the community and facilitate further species loss. This work underscores the need to take an eco-evolutionary approach to predict the responses of communities to global climate change.</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/PMC13374857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148240533","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":"Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.","authors":"Xiao-Yu Zhu, Frances E Hopkins, Ruth Airs, Claire E Widdicombe, Bethany Wilkinson, Glen A Tarran, E Malcolm S Woodward, Ornella Carrión, Andrew R J Curson, Qianyao Ma, Libby Hanwell, Gui-Peng Yang, Joseph A Christie-Oleza, David J Lea-Smith, Xiao-Hua Zhang, Jonathan D Todd","doi":"10.1093/ismejo/wrag141","DOIUrl":"10.1093/ismejo/wrag141","url":null,"abstract":"<p><p>Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolize it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations, and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring-summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying that flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.</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/PMC13310141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148220453","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":"Bacterial family-VIII esterase displays dual activities: hydrolysis of polyester bioplastics and β-lactam antibiotics.","authors":"Harry Lerner, Diego Casaburi, Nele Charlott Meier, Léa Bernabeu, Marcel Eck, Stefan Mecking, David Schleheck","doi":"10.1093/ismejo/wrag203","DOIUrl":"10.1093/ismejo/wrag203","url":null,"abstract":"<p><p>The plastisphere is a unique ecosystem with microbes colonizing and potentially degrading plastic debris in the environment, provided that the polymers are enzymatically accessible as substrates to drive microbial growth. It also harbors an unusually high occurrence of antibiotic resistance genes, suggesting plastic debris as a potential vector for antibiotic-resistant microorganisms. In this study, we investigated microbial communities in forest soil degrading an emerging type of bioplastics, aliphatic long-chain polyesters (LCAPs). Sequencing analysis revealed a family-VIII esterase strongly associated with LCAP depolymerization that showed high structural similarity to type C β-lactamases. Structural modeling and substrate docking analysis indicated catalytically favorable binding of both LCAP and β-lactam antibiotics. Furthermore, the active site appeared to be located in a large, wide-open groove, rather than in a tunnel, resulting in a protein with a striking \"pac-man\"-like structure. Heterologous expression and in vitro activity testing confirmed its dual functionality as plastic depolymerase and β-lactam hydrolase. Sequence analysis indicated the enzyme as membrane-associated lipoprotein likely to be directed to the outer membrane. The membrane anchoring of the enzyme may offer striking microbial-ecological benefits, by preventing enzyme loss especially in aqueous environments, by increased catalytic efficiency through high enzyme concentration at the cell-plastic interface, and by spatially linking catalysis with membrane transport, thereby limiting monomer loss to non-producing plastisphere-community members (cheaters). Hence, our study highlighted a plastic depolymerizing enzyme with a striking substrate spectrum, bridging plastics and antibiotics degradation, and provides intriguing perspectives for understanding the microbial physiology, ecology, and evolution of (bio)plastic degradation in the environment.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13533575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148875744","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":"Mutations in legume genes that influence symbiosis create a complex selective landscape for rhizobial symbionts.","authors":"Sohini Guha, Regina B Bledsoe, Jeremy Sutherland, Brendan Epstein, Gwendolyn M Fry, Vikram Venugopal, Siva Sankari, Alejandra Gil-Polo, Garrett Levin, Barney A Geddes, Nevin D Young, Peter Tiffin, Liana T Burghardt","doi":"10.1093/ismejo/wrag005","DOIUrl":"10.1093/ismejo/wrag005","url":null,"abstract":"<p><p>In the mutualism between leguminous plants and rhizobial bacteria, rhizobia live inside root nodules, creating potential for host genes to shape the rhizobial selective environment. Many host genes that affect symbiosis have been identified; however, the extent to which these genes affect selection acting on rhizobia is unknown. In this study, we inoculated 18 Medicago truncatula symbiotic mutants (including mutants that alter Nodule Cysteine-Rich (NCR) peptide production, plant defence, and nodule number regulation) with a mixture of 86 Sinorhizobium meliloti strains. Most mutations resulted in reduced host benefits, but the effects on rhizobial benefit (i.e. relative strain fitness) varied widely, revealing widespread host-by-strain fitness interactions. Genome-wide association analyses identified variants on rhizobial replicons pSymA and pSymB as important in mediating strain fitness responses to host mutations. Whereas most top variants affected rhizobial fitness with one host mutation (limited effect variants), nine affected fitness across six or more host mutations. These pervasive variants occurred primarily on pSymA, the symbiotic replicon, and include fixL and some metabolic genes. In contrast to the limited effect variants, variants with pervasive positive effects on strain fitness when host genes were mutated tended to adversely affect fitness in wild-type hosts. Competition assays across Medicago genotypes confirmed a pervasive role for one candidate (malonyl-CoA synthase), and AlphaFold multimer modelling suggests that many rhizobial top candidates could interact with host NCR peptides. Our results reveal how host genetic mutations alter strain fitness, setting the stage for improving rhizobial inoculants and breeding legume hosts better adapted to multi-strain environments.</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/PMC12904279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146127436","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":"Distribution of a novel DsrEFH sulfur transferase suggests widespread sulfur oxidation capacity in sulfate reducers.","authors":"Lea Emilie Plum-Jensen, Marc Gregor Mohr, Tomohisa Sebastian Tanabe, Bo Wang, Simon Gregersen Echers, Nikoline Sanggård Madsen, Casper Thorup, Markéta Linhartová, Lars Peter Nielsen, Morten Kam Dahl Dueholm, Thomas Boesen, Ian Philip George Marshall, Christiane Dahl, Andreas Schramm","doi":"10.1093/ismejo/wrag130","DOIUrl":"10.1093/ismejo/wrag130","url":null,"abstract":"<p><p>Microbial sulfur cycling is typically divided into an oxidative and a reductive branch, with microbes driving either sulfide oxidation or sulfate reduction distinguished by their genomic setup. Paradoxically, filamentous cable bacteria perform electrogenic sulfide oxidation but contain genes indicative of sulfate reduction, including the reductive type of dissimilatory sulfite reductase (DsrAB), whereas they apparently lack the canonical sulfur transferase DsrEFH essential for sulfur oxidation. AlphaFold2 structure prediction of conserved cable bacteria proteins with unknown functions identified a protein complex resembling canonical DsrEFH (hereafter termed DsrEFH type II). In vitro characterization of heterologously expressed DsrEFH type II confirmed its sulfur transferase function and, together with site-directed mutagenesis, verified that the conserved cysteine, Cys67, is the active sulfur transfer residue. Genes encoding the novel DsrEFH type II were found in 985 prokaryotic genomes. They typically co-occurred with genes for reductive DsrAB in microbes characterized as sulfate reducers or sulfur disproportionators. This study not only fills an important gap in the sulfide oxidation pathway of cable bacteria, but also suggests that a wide range of sulfate reducing bacteria may be more metabolically versatile than currently understood, representing a major shift in the perception of this globally significant physiological group of microorganisms.</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/PMC13293266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007489","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":"Systems-level restoration of vaginal and gut microbiota by Lactobacillus helveticus 20838 alleviates Gardnerella vaginalis-induced dysbiosis.","authors":"Juewon Kim, Woo-Il Kim, Kyuyeon Lee, Nayeon Kim, Ah Young Hwang, Dong Ho Suh, Donghyun Cho, Yosep Ji, Hye-Ji Kang, Eun Sung Jung","doi":"10.1093/ismejo/wrag118","DOIUrl":"10.1093/ismejo/wrag118","url":null,"abstract":"<p><p>Bacterial vaginosis (BV), often driven by Gardnerella vaginalis overgrowth, is characterized by epithelial disruption, inflammation, and microbiome dysbiosis across the vaginal and gut ecosystems. Affecting a majority of women during their reproductive years, BV increases the risk of infection and reproductive complications. Here, we identify a novel probiotic strain, Lactobacillus helveticus 20838, exhibiting potent antagonistic activity against G. vaginalis and evaluate its ecological and immunological effects in a murine model of vaginitis. Comparative genomics revealed distinct adaptive and antimicrobial traits of L. helveticus 20838 relatives to the reference strain DPC4571. Both oral and intravaginal administration reduced G. vaginalis colonization, suppressed Tnf-α and Il-1β expression in vaginal tissue, and prevented pathological epithelial thickening. Multi-omics profiling of fecal and vaginal samples demonstrated restoration of microbial alpha and beta diversity disrupted by infection. The L. helveticus 20838 reduced dysbiosis-associated taxa such as Staphylococcaceae, whereas enriching protective Lactobacillus species, with intravaginal delivery achieving superior local recolonization of Lactobacillaceae. Collectively, these findings identify L. helveticus 20838 as a next-generation probiotic that alleviates G. vaginalis-induced dysbiosis by restoring microbial and immune homeostasis across interconnected mucosal niches, providing a systems-level framework for microbiota-targeted therapy in women's health.</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/PMC13245722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147965441","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":"Tissue-specific experimental evolution reveals adaptive trade-offs in the plant vascular pathogen Clavibacter michiganensis.","authors":"Raj Kumar Verma, Veronica Roman-Reyna, Nathan Benmoche, Evanson Ngugi, Eduard Belausov, Noa Sela, Maya Bar, Jonathan M Jacobs, Doron Teper","doi":"10.1093/ismejo/wrag110","DOIUrl":"10.1093/ismejo/wrag110","url":null,"abstract":"<p><p>The plant pathogenic bacterium Clavibacter michiganensis (Cm) is a systemic vascular pathogen that colonizes both xylem vessels and the intracellular apoplast during different stages of infection. To identify traits and loci associated with adaptation to these distinct host microenvironments, we conducted tissue-specific experimental evolution. Twenty independent Cm lineages were repeatedly passaged in either tomato stems or leaves to promote adaptation to vascular or apoplastic lifestyles, respectively. After fifteen passages, adapted clones were characterized for virulence and virulence-related traits. These characterizations demonstrated clear differential associations of virulence-associated traits with the adapted tissue. The majority of vascular-adapted clones displayed enhanced surface attachment, reduced cellulase activity, reduced exopolysaccharide (EPS) production, and attenuated virulence on tomato compared to the parent clone. In contrast, apoplast-adapted clones displayed reduced biofilm formation and enhanced EPS production and retained their virulence on tomato. Whole-genome sequencing of all adapted clones revealed candidate loci linked to tissue adaptation. Six of ten vascular-adapted clones carried two independent mutations in CMM_1284, a putative HipB/XRE-type transcriptional regulator. A CMM_1284 marker exchange mutant displayed phenotypes similar to vascular-adapted clones, suggesting a role for this regulator in vascular colonization. Together, these findings highlight the role of phenotypic plasticity in tissue adaptation of plant pathogens, showing that tissue-specific adaptation involves modulation of surface attachment, EPS production, and cell wall-degrading enzymes and suggest a trade-off between vascular persistence, supported by strong surface attachment, and systemic virulence, which depends on bacterial dispersal and migration.</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/PMC13298646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845390","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}