Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes

Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes Hirokazu Toju, Mikihito Noguchi, Kenta Suzuki, Hiroaki Fujita This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7962497/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Root-associated fungi and bacteria play pivotal roles in plant nutrient acquisition and stress tolerance. However, identifying the keystone taxa that have the greatest impacts on below-ground microbial assembly remains a major challenge. Here, we present a statistical framework for identifying microbes that could govern the assembly rules of complex plant microbiomes. Using more than 1,000 root samples collected from a cool-temperate forest, we reconstructed the architecture of “assembly landscapes” that depict the probability distributions of community states. We found that several endophytic fungi ( Oidiodendron , Cladophialophora , Hyaloscypha , and Meliniomyces ) could reorganize assembly landscape topography, potentially driving drastic shifts in mycorrhizal symbiotic types in host plants associated with both ectomycorrhizal and arbuscular mycorrhizal fungi ( Populus , Acer , and Juglans ). Furthermore, cross-kingdom effects of uncharacterized bacteria (e.g., Thermosporothrix ) on fungal community assembly were detected. We also found that prokaryotic communities underwent transitions among states characterized respectively by core (common) members, Pseudomonadota, and Actinomycetota under the disproportionate influence of " Candidatus Udaeobacter " and several endophytic fungi. Thus, data-driven inference of assembly landscapes will advance our understanding of underappreciated drivers of ecosystem-scale processes. Biological sciences/Ecology/Community ecology Earth and environmental sciences/Environmental sciences Physical sciences/Mathematics and computing/Computational science Biological sciences/Microbiology/Microbial communities/Microbiome Biological sciences/Computational biology and bioinformatics Full Text Additional Declarations Yes there is potential Competing Interest. HT is the founder and director of Sunlit Seedlings Ltd. Other authors declare no competing interests. Supplementary Files SupplementaryInformation.pdf Supplementary Information rs.pdf Reporting Summary Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7962497","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":541577685,"identity":"2e1f0707-df6d-4e8a-a2d8-8f1dee9f0b21","order_by":0,"name":"Hirokazu 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Other authors declare no competing interests.","formattedTitle":"Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-7962497/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7962497/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eRoot-associated fungi and bacteria play pivotal roles in plant nutrient acquisition and stress tolerance. However, identifying the keystone taxa that have the greatest impacts on below-ground microbial assembly remains a major challenge. Here, we present a statistical framework for identifying microbes that could govern the assembly rules of complex plant microbiomes. Using more than 1,000 root samples collected from a cool-temperate forest, we reconstructed the architecture of \u0026ldquo;assembly landscapes\u0026rdquo; that depict the probability distributions of community states. We found that several endophytic fungi (\u003cem\u003eOidiodendron\u003c/em\u003e, \u003cem\u003eCladophialophora\u003c/em\u003e, \u003cem\u003eHyaloscypha\u003c/em\u003e, and \u003cem\u003eMeliniomyces\u003c/em\u003e) could reorganize assembly landscape topography, potentially driving drastic shifts in mycorrhizal symbiotic types in host plants associated with both ectomycorrhizal and arbuscular mycorrhizal fungi (\u003cem\u003ePopulus\u003c/em\u003e, \u003cem\u003eAcer\u003c/em\u003e, and \u003cem\u003eJuglans\u003c/em\u003e). Furthermore, cross-kingdom effects of uncharacterized bacteria (e.g., \u003cem\u003eThermosporothrix\u003c/em\u003e) on fungal community assembly were detected. We also found that prokaryotic communities underwent transitions among states characterized respectively by core (common) members, Pseudomonadota, and Actinomycetota under the disproportionate influence of \"\u003cem\u003eCandidatus Udaeobacter\u003c/em\u003e\" and several endophytic fungi. Thus, data-driven inference of assembly landscapes will advance our understanding of underappreciated drivers of ecosystem-scale processes.\u003c/p\u003e","manuscriptTitle":"Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-10 03:37:47","doi":"10.21203/rs.3.rs-7962497/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"0a720cbf-531e-4496-9a78-c1e4915aca4f","owner":[],"postedDate":"November 10th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":57618912,"name":"Biological sciences/Ecology/Community ecology"},{"id":57618913,"name":"Earth and environmental sciences/Environmental sciences"},{"id":57618914,"name":"Physical sciences/Mathematics and computing/Computational science"},{"id":57618915,"name":"Biological sciences/Microbiology/Microbial communities/Microbiome"},{"id":57618916,"name":"Biological sciences/Computational biology and bioinformatics"}],"tags":[],"updatedAt":"2026-05-12T16:07:05+00:00","versionOfRecord":[],"versionCreatedAt":"2025-11-10 03:37:47","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7962497","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7962497","identity":"rs-7962497","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}