Longitudinal metagenomic insights into soil, bark, and berry microbiomes under abandoned, bio- organic, and conventional cultivation in Tokaj vineyard

Longitudinal metagenomic insights into soil, bark, and berry microbiomes under abandoned, bio- organic, and conventional cultivation in Tokaj vineyard | 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 Longitudinal metagenomic insights into soil, bark, and berry microbiomes under abandoned, bio- organic, and conventional cultivation in Tokaj vineyard Peter David, Peter Fauszt, Maja Mikolas, Anna Anita Szilagyi-Racz, and 8 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7591151/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 10 You are reading this latest preprint version Abstract This two-year longitudinal metagenomic study in Tokaj, Hungary, profiled soil, bark, and grape berry microbiomes across three cultivation regimes (abandoned, bio-organic, conventional) and two vintages (2020–2021), using 16S rRNA and shotgun metagenomics coupled with climate-integrated, spatially matched sampling. Above-average genera (aaGs) were analyzed to assess soil-bark microbial overlap. Distinct clustering was observed, with higher aaG biomass in bark. Core taxa accounted for only 23.2% of genera but contributed equally to total biomass. Bark-specific taxa were more diverse and abundant. Random forest analysis identified cultivation-specific microbial signatures, positioning the bark microbiome as a sensitive bioindicator of vineyard management intensity. Bio-organic management favored the dominance of a few high-abundance bacterial and fungal indicators (e.g., Nakamurella flavida , Lophiostoma macrostomum ), whereas abandoned sites exhibited greater evenness but lower overall biomass. In bark-berry comparisons, bark microbiota was dominated by bacteria, whereas fungal reads prevailed in berries. Species overlap was minimal. Core taxa, present in both bark and berry microbiomes, were predominantly bacterial in bark (e.g., Microlunatus antarcticus , Kineococcus rubinsiae ) and fungal in berries (e.g., Aureobasidium pullulans , Hortaea werneckii ), with habitat-specific dominance typically exceeding a tenfold biomass difference. Fungal succession during ripening reflected vintage-specific climate: high rainfall in 2020 favored moisture-adapted taxa ( Cladosporium , Acidomyces ), whereas warm, sunny 2021 promoted thermotolerant and opportunistic species ( Aspergillus puulaauensis , Cryptococcus gattii ). Pathogens dominated both habitats, particularly in abandoned vineyards. Botrytis cinerea was the most abundant pathogen, with bioprotective taxa showing inverse patterns. Plasmopara viticola dominated in 2020, while Phaeoacremonium minimum and Aspergillus fumigatus were enriched in 2021. Targeted functional metagenomics of Botrytis -associated genes showed bark enriched in aroma biosynthesis, stress response, and cell wall-degrading functions. Abandoned vineyards carried the highest virulence gene load, while bio-organic systems favored degradation traits. Veraison-to-harvest shifts were evident in quorum sensing, phytotoxin, and bioprotection genes, indicating stage-specific pathogenic potential. Biological sciences/Ecology Earth and environmental sciences/Ecology Biological sciences/Microbiology Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryFile1.xlsx SupplementaryFile2.xlsx SupplementaryFile3.xlsx SupplementaryFile4.xlsx SupplementaryFile5.xlsx SupplementaryFile6.xlsx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 15 Dec, 2025 Reviews received at journal 06 Dec, 2025 Reviewers agreed at journal 29 Nov, 2025 Reviews received at journal 18 Nov, 2025 Reviewers agreed at journal 27 Oct, 2025 Reviewers invited by journal 27 Oct, 2025 Editor assigned by journal 22 Sep, 2025 Editor invited by journal 17 Sep, 2025 Submission checks completed at journal 16 Sep, 2025 First submitted to journal 16 Sep, 2025 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. 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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-7591151","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":535586795,"identity":"15f10b6b-e6ce-4932-8f5f-d6edb5be2f26","order_by":0,"name":"Peter David","email":"","orcid":"","institution":"University of Debrecen","correspondingAuthor":false,"prefix":"","firstName":"Peter","middleName":"","lastName":"David","suffix":""},{"id":535586796,"identity":"9db06350-3c15-4a42-b64b-a8eeb226a0fe","order_by":1,"name":"Peter Fauszt","email":"","orcid":"","institution":"University of 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vineyard","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"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":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific 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Distinct clustering was observed, with higher aaG biomass in bark. Core taxa accounted for only 23.2% of genera but contributed equally to total biomass. Bark-specific taxa were more diverse and abundant. Random forest analysis identified cultivation-specific microbial signatures, positioning the bark microbiome as a sensitive bioindicator of vineyard management intensity. Bio-organic management favored the dominance of a few high-abundance bacterial and fungal indicators (e.g., \u003cem\u003eNakamurella flavida\u003c/em\u003e, \u003cem\u003eLophiostoma macrostomum\u003c/em\u003e), whereas abandoned sites exhibited greater evenness but lower overall biomass.\u003c/p\u003e\u003cp\u003eIn bark-berry comparisons, bark microbiota was dominated by bacteria, whereas fungal reads prevailed in berries. Species overlap was minimal. Core taxa, present in both bark and berry microbiomes, were predominantly bacterial in bark (e.g., \u003cem\u003eMicrolunatus antarcticus\u003c/em\u003e, \u003cem\u003eKineococcus rubinsiae\u003c/em\u003e) and fungal in berries (e.g., \u003cem\u003eAureobasidium pullulans\u003c/em\u003e, \u003cem\u003eHortaea werneckii\u003c/em\u003e), with habitat-specific dominance typically exceeding a tenfold biomass difference.\u003c/p\u003e\u003cp\u003eFungal succession during ripening reflected vintage-specific climate: high rainfall in 2020 favored moisture-adapted taxa (\u003cem\u003eCladosporium\u003c/em\u003e, \u003cem\u003eAcidomyces\u003c/em\u003e), whereas warm, sunny 2021 promoted thermotolerant and opportunistic species (\u003cem\u003eAspergillus puulaauensis\u003c/em\u003e, \u003cem\u003eCryptococcus gattii\u003c/em\u003e).\u003c/p\u003e\u003cp\u003ePathogens dominated both habitats, particularly in abandoned vineyards. \u003cem\u003eBotrytis cinerea\u003c/em\u003e was the most abundant pathogen, with bioprotective taxa showing inverse patterns. \u003cem\u003ePlasmopara viticola\u003c/em\u003e dominated in 2020, while \u003cem\u003ePhaeoacremonium minimum\u003c/em\u003e and \u003cem\u003eAspergillus fumigatus\u003c/em\u003e were enriched in 2021. Targeted functional metagenomics of \u003cem\u003eBotrytis\u003c/em\u003e-associated genes showed bark enriched in aroma biosynthesis, stress response, and cell wall-degrading functions. Abandoned vineyards carried the highest virulence gene load, while bio-organic systems favored degradation traits. Veraison-to-harvest shifts were evident in quorum sensing, phytotoxin, and bioprotection genes, indicating stage-specific pathogenic potential.\u003c/p\u003e","manuscriptTitle":"Longitudinal metagenomic insights into soil, bark, and berry microbiomes under abandoned, bio- organic, and conventional cultivation in Tokaj vineyard","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-05 18:52:43","doi":"10.21203/rs.3.rs-7591151/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-12-15T14:43:08+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-06T10:08:43+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"5637754273147693423572870805888488392","date":"2025-11-30T01:41:55+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-18T11:31:06+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"188548857840475276370091015574598360265","date":"2025-10-27T06:16:00+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-10-27T05:32:24+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-09-22T13:41:26+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-09-17T12:21:50+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-09-16T08:50:28+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-09-16T08:41:46+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"64be7b88-ef05-4f10-9355-945067c48232","owner":[],"postedDate":"November 5th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":56941545,"name":"Biological sciences/Ecology"},{"id":56941546,"name":"Earth and environmental sciences/Ecology"},{"id":56941547,"name":"Biological sciences/Microbiology"}],"tags":[],"updatedAt":"2026-02-23T15:38:13+00:00","versionOfRecord":[],"versionCreatedAt":"2025-11-05 18:52:43","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7591151","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7591151","identity":"rs-7591151","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}