ISME Journal最新文献

{"title":"High molecular weight dissolved organic matter drives soil resistome proliferation by enhancing microbial competition and viral carbon metabolism.","authors":"Zi-Teng Liu, Xin-Di Zhao, Jia-Qi Li, Shu-Xin Li, Xianjin Tang, Si-Yu Zhang","doi":"10.1093/ismejo/wrag212","DOIUrl":"10.1093/ismejo/wrag212","url":null,"abstract":"<p><p>Soil organic carbon is a key determinant of microbial community structure and function, yet the role of dissolved organic matter (DOM) bioavailability in shaping the soil antibiotic resistome remains poorly understood. Here, we combined previous continental-scale field sampling across 18 provinces in China (n = 141) with additional microcosm experiments to investigate how DOM molecular weight influences soil antibiotic resistance gene (ARG) proliferation. Using Fourier transform ion cyclotron resonance mass spectrometry and metagenomic analyses, we found that soils enriched in high molecular weight (HMW) DOM harbored significantly greater ARG abundance and diversity compared to low molecular weight DOM soils. HMW DOM intensified microbial competition, as evidenced by a higher proportion of negative correlations in the co-occurrence network and lower niche breadth, favoring the enrichment of co-hosts that simultaneously carried ARGs, carbon metabolism genes, and biosynthetic gene clusters for antimicrobial compounds. Microcosm experiments confirmed that HMW DOM (lignin) addition significantly increased ARG transcript abundance (2.4-fold) and co-host relative abundance (2.3-fold), accompanied by a concurrent increase in transcribed viral auxiliary metabolic genes (2.5-fold) involved in complex carbon degradation. Structural equation modeling revealed that HMW DOM abundance and chemodiversity exerted the strongest positive effects on ARG abundance, primarily by shaping microbial community competition and metabolic potential. Collectively, our findings establish DOM bioavailability, particularly its molecular weight, as a critical yet previously overlooked driver of soil resistome development, challenging the conventional focus on total carbon content and highlighting the potential for molecular-level organic matter management to mitigate the spread of ARGs.</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/PMC13615529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148800964","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":"Deoxycholate induces proline provision from Escherichia coli to enhance Clostridioides difficile virulence.","authors":"Jingpeng Yang, Xilong Deng, Xiaoya Sheng, Yanan Li, Xuna Tang","doi":"10.1093/ismejo/wrag249","DOIUrl":"10.1093/ismejo/wrag249","url":null,"abstract":"<p><p>Clostridioides difficile infection (CDI) is a refractory enteritis. A key indicator of successful treatment and microbial restoration is the elevation of intestinal deoxycholate (DCA) levels. Nevertheless, a small proportion of patients experience disease recurrence despite this apparent metabolic recovery, the underlying mechanisms of which remain poorly understood. We investigated the ecological dynamics of Clostridioides difficile (CD) and Escherichia coli (EC) under DCA exposure, revealing that DCA exacerbates the severity of co-infection. Specifically, DCA promotes the formation of a robust and dense symbiotic biofilm that confers a substantial survival advantage to CD. Through a combination of in vitro co-culture and validation in a murine infection model, we demonstrated that EC produces substantial quantities of L-proline in response to DCA. This amino acid is converted to D-proline by the proline racemase and subsequently catabolized by the D-proline reductase in CD, thereby enhancing its environmental fitness and pathogenicity within the gut. The indispensable nature of this tripartite interaction was further corroborated using additional EC or CD strains, including isogenic mutants deficient in D-proline reductase, in subsequent murine infection models. These experiments collectively confirm that EC, proline, and the D-proline reductase are all essential components mediating the DCA-induced exacerbation of CDI. In summary, our study elucidates a mechanism by which a DCA environment promotes the exacerbation of CDI through a metabolic cross-feeding interaction between CD and EC. Specifically, EC-derived L-proline serves as a critical nutrient that enhances the fitness and pathogenicity of CD. This finding provides a plausible explanation for the paradoxical phenomenon of CDI recurrence in patients exhibiting elevated intestinal DCA levels.</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/PMC13634199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992274","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":"Galactosaminogalactan orchestrates Verticillium dahliae virulence and rhizosphere microbial ecology through multi-partite interactions.","authors":"Xueping Xu, Yingqing Tan, Sitong Xiecun, Junyao Wang, Wennan Zhao, Lei Wang, Renyu Dai, Liting Tang, Xianbi Li, Dan Jin, Yanhua Fan","doi":"10.1093/ismejo/wrag123","DOIUrl":"10.1093/ismejo/wrag123","url":null,"abstract":"<p><p>The infection of plants by soil-borne fungal pathogens is a complex process and depends on their adhere ability to host surfaces and interactions with the rhizosphere bacteria. In this study, we identify galactosaminogalactan (GAG) as a pivotal virulence determinant in the pathogenesis of Verticillium dahliae. By characterizing the VdGAG biosynthetic gene cluster, we show that the glycosyltransferase VdGtb is essential for GAG synthesis. The knockout of GAG increased fungal sensitivity to the cell wall-perturbing agent calcofluor white and reduced mycelial ball formation in liquid culture. The absence of GAG polysaccharides reduced root-binding capacity by 50% and increased cotton immune responses 1 day post fungal infection. The ΔVdGtb mutant exhibited a significant 30.5% decrease in the pathogenicity toward cotton seedlings compared with the wild type V991. Microbiome and bacterial enrichment analysis indicate that the GAG polysaccharides promote the enrichment of soil bacteria and alter the bacterial community structure in the plant rhizosphere. Several bacteria enriched by GAG-contained fungal cells, including Achromobacter animicus, Pseudomonas aeruginosa, and Acinetobacter pittii exhibited strong growth-inhibitory effects against V. dahliae and showed distinct effects on fungal virulence in a GAG-dependent manner. Together, these results reveal that GAG is not merely a cell wall component but a multi-functional molecule that orchestrates fungal protection, host infection, and inter-kingdom microbial communication.</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/PMC13245733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147965379","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":"Ruminosignatures associated with methane emissions and feed efficiency across geographies and cattle breeds.","authors":"Ioanna-Theoni Vourlaki, Ori Furman, Ilma Tapio, Le Luo Guan, Sinéad M Waters, David Kenny, Paul Smith, Stuart F Kirwan, David Kelly, Ross Evans, Raquel Quintanilla, Miriam Piles, Antonio Reverter, Pâmela A Alexandre, Fuyong Li, Philip C Garnsworthy, Paolo Bani, Phillip B Pope, Diego P Morgavi, Itzhak Mizrahi, Yuliaxis Ramayo-Caldas","doi":"10.1093/ismejo/wrag185","DOIUrl":"10.1093/ismejo/wrag185","url":null,"abstract":"<p><p>The cattle rumen microbiota represents a complex and dynamic ecosystem whose organization and relationship to host phenotypes are important for food security and environmental sustainability. We analyzed rumen microbiota profiles from 2496 cattle representing five breeds and production systems across five countries, identifying microbial co-abundance groups termed Ruminosignatures. We detected 14 distinct Ruminosignatures, including 2 observed across all populations dominated by Prevotella and UBA2810. Additional Ruminosignatures showed breed- and diet-specific patterns and collectively explained 96%-99% of variance in rumen microbial composition. Integrative cross-country analysis confirmed 10 out of 14 Ruminosignatures identified in cohort-specific analyses. Several Ruminosignatures were associated with methane emissions and feed efficiency traits and were partially under host genetic control, with heritability estimates ranging from 0.09 to 0.58. Structural equation modeling revealed consistent negative genetic and phenotypic correlations between the UBA2810-dominated Ruminosignature (RS_UBA2) and methane emissions across cohorts (rg = -0.40 to -0.65), with structural coefficients concordant in sign across all populations, supporting the expected direction of phenotypic response to selection on RS_UBA2. Meta-analysis confirmed positive associations of RS_UBA2 with average daily gain and negative associations with methane-related traits and feed conversion ratio. Functional genome-based predictions suggested RS_UBA2 may reduce methanogenesis through alternative hydrogen utilization pathways competing with methanogenic archaea. Production system type influenced both Ruminosignature occurrence and relationships with host phenotypes, emphasizing the relevance of context-specific strategies for microbiome modulation. Our findings highlight the potential of the Ruminosignatures framework for microbiome-informed breeding programs aimed at improving feed efficiency while reducing the environmental impact of cattle production.</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/PMC13573583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148425956","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":"Heterologous expression in E. coli reveals that bicarbonate transporter BicA2 mediates carbon uptake in marine Prochlorococcus spp.","authors":"Loraine M Rourke, Caitlin S Byrt, G Dean Price, Benedict M Long","doi":"10.1093/ismejo/wrag222","DOIUrl":"10.1093/ismejo/wrag222","url":null,"abstract":"<p><p>The widespread oceanic cyanobacterial Prochlorococcus genus is a major contributor to global carbon fixation, yet mechanisms enabling this lineage to elevate intracellular inorganic carbon as a substrate for photosynthesis remain unresolved. Cyanobacterial CO2-concentrating mechanisms typically rely on membrane-bound bicarbonate (HCO3-) transporters SbtA1, SbtA2, BicA and BCT1, and CO2-to-HCO3- conversion uptake systems (CO2 pumps; NDH-I3 and NDH-I4), to elevate a cellular HCO3- pool for use by Rubisco-containing carboxysomes. Evidence suggests Prochlorococcus harbours carboxysomes with a low-CO2-specificity Rubisco, implying a functional CCM dependent on active HCO3- uptake. However, canonical CO2 pumps are absent, leaving distant HCO3- transporter homologues, BicA2 and SbtA2, as prime candidates for HCO3- transport in this group. Yet these have not been functionally characterized. Here we demonstrate that BicA2 from P. marinus CCMP1375 mediates Na+-dependent HCO3- uptake in Escherichia coli, whereas BicA2 from P. marinus CCMP1986 is inactive in its native form but acquired transport function through a single amino acid substitution during adaptive laboratory evolution. These findings confirm BicA2 as a low-affinity, Na+-dependent bicarbonate transporter with variable flux, revealing a previously uncharacterized CCM component in Prochlorococcus. This mechanistic insight reshapes our understanding of carbon acquisition strategies in the most abundant photosynthetic organism on Earth and highlights evolutionary plasticity in transporter function with implications for global biogeochemical cycles.</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/PMC13588710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148842003","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":"Integration and regulation of stolen organelles in a marine protist.","authors":"Julian M Jacobs, Zachary L Reitz, Erica Lasek-Nesselquist, Amelie L'Etoile-Goga, Brittany N Sprecher, Matthew D Johnson, Holly V Moeller","doi":"10.1093/ismejo/wrag204","DOIUrl":"10.1093/ismejo/wrag204","url":null,"abstract":"<p><p>Chloroplast-stealing (a.k.a., \"kleptoplastidic\") plankton transiently obtain and integrate prey metabolic machinery into their own cells. To do so, they must address a series of challenges, including physical localization of acquired machinery, metabolic integration of organelles and their products, and maintenance of machinery. Here, we study this transient integration in the marine ciliate Mesodinium chamaeleon by pulse feeding the ciliate with cryptophyte algal prey (Storeatula major) and then tracking changes in ciliate cellular ultrastructure, physiology (growth and photosynthesis), and gene expression over time. We demonstrate a predictable series of changes, from the reconfiguration of metabolic activity fueled by recent ingestion, to a period of rapid growth, to a reduction in physiological performance as prey organelle number and functionality become limiting. Because M. chamaeleon also steals transcriptionally active prey nuclei, gene expression is a complex milieu of host and cryptophyte expression, with much of prey metabolism apparently intact in the new host, albeit at low levels. Collectively, our results highlight the holistic orchestration of stolen organelles to produce rapid-yet transient-growth in a new host.</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/PMC13592161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148671129","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":"Soil amelioration impacts viral ecology in saline-alkali lands.","authors":"Junxi Liu, Guixiang Zhou, Lin Chen, Yu Xiao, Yakov Kuzyakov, Congzhi Zhang, Ping Huang, Donghao Ma, Jiabao Zhang","doi":"10.1093/ismejo/wrag217","DOIUrl":"10.1093/ismejo/wrag217","url":null,"abstract":"<p><p>The continuous expansion of saline-alkali lands under climate change threatens food security and reduces soil carbon stocks. A common mitigation strategy is soil amelioration, which converts degraded soils back into a fertile and arable state. Microbes play critical roles in soil health and recovery. However, the viruses that infect these microbial communities, and their potential impacts during saline-alkali soil restoration, remain largely unknown. Here, we combined total soil metagenomics and viromics to investigate host-linked viral ecology across four major saline-alkali regions in China, each encompassing two soil amelioration statuses: saline-alkali and reclaimed. We found that viral community structure was shaped by both geography and soil amelioration status, with salinity and alkalinity emerging as key environmental factors. Viral populations were sensitive to soil restoration, showing strong amelioration-status endemism with functional adaptations. Virus-host dynamics ranged from reduced temperate viruses to abundance mismatches in those infecting key carbon-cycling microorganisms, including carbohydrate degraders. 13C-cellulose DNA-SIP experiments provided further support for this mismatch by tracing assimilated carbon transfer between active host and virus populations. Compared with saline-alkali soils, the relative abundance of hosts in restored soils increased from 39.0% to 61.0%, whereas the linked viruses decreased from 60.6% to 39.4%. Together, these findings reveal an underappreciated role of viruses in shaping saline-alkali soil amelioration trajectories, and could improve management strategies for degraded land recovery and carbon storage.</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/PMC13584217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148820010","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}