Unveiling tomato root-associated bacterial interactions responding to hairy root disease

Unveiling tomato root-associated bacterial interactions responding to hairy root disease | 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 Research Article Unveiling tomato root-associated bacterial interactions responding to hairy root disease Peiyang Huo, Pablo Vargas Ribera, Hans Rediers, Jan Aerts This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7363607/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 23 Nov, 2025 Read the published version in Environmental Microbiome → Version 1 posted 9 You are reading this latest preprint version Abstract Background : Hairy root disease (HRD), caused by rhizogenic Agrobacterium strains, is a significant disease threat to modern hydroponic greenhouses, which can result in up to 15% loss in yield. Our prior research has suggested increased alpha diversity after infection in hydroponic tomato root-associated microbiota. However, a more detailed investigation of how root-associated microbial components (MCs; clusters of weighted bacterial features) respond to disease and the underlying mechanisms remains lacking. To address this gap, we applied latent Dirichlet allocation (LDA) to analyze MCs from 12 Belgian commercial hydroponic tomato greenhouses. Using high-throughput amplicon sequencing of the 16S rRNA locus, three locations along each greenhouse irrigation system (beginning, middle, and end) were sampled at 5 time points throughout the 2018 growing season. Results : In this study, we used LDA to identify root-associated MCs and gained insights into temporal changes and new health status. First, we observed a structured temporal pattern from the early stage (ES; sampling time points 1 and 2) through a transitional stage (TS; sampling time point 3) to the late stage (LS; sampling time points 4 and 5), showing different MC trajectories by health status. Second, MC4 (characterised by Paenibacillus spp.) was pronounced for healthy greenhouses in the ES, MC7 (characterised by rhizogenic Agrobacterium spp., Devosia and Limnobacter amplicon sequence variants (ASVs)) was pronounced for pre-symptomatic status, while MC0 (characterized by Comamonadaceae spp. ASVs) were indicative of an intermediate state between healthy and infected conditions. Furthermore, the ratio between Paenibacillus ASV and rhizogenic Agrobacterium ASV can be used as a biomarker to assess greenhouse health status in both ES and LS. Conclusion : We investigated hydroponic tomato root-associated MCs responses to HRD using LDA, which revealed different MC trajectories in terms of plant health. Our study advances knowledge of hairy root disease regarding the mechanisms that can improve plant health monitoring in greenhouses and biocontrol strategies. From a computational perspective, we demonstrate how to apply LDA—a powerful analytical tool—to understudied subfields through visual analytics. Hairy Root Disease 16S rRNA amplicon sequencing Hydroponic Greenhouse Microbiota Agrobacterium Visual Analytics Latent Dirichlet Allocation Full Text Additional Declarations No competing interests reported. Supplementary Files Additionalfile1.docx Additionalfile2.pdf Additionalfile3.docx Additionalfile4.xlsx Cite Share Download PDF Status: Published Journal Publication published 23 Nov, 2025 Read the published version in Environmental Microbiome → Version 1 posted Editorial decision: Revision requested 25 Sep, 2025 Reviews received at journal 24 Sep, 2025 Reviewers agreed at journal 18 Sep, 2025 Reviews received at journal 15 Sep, 2025 Reviewers agreed at journal 11 Sep, 2025 Reviewers invited by journal 10 Sep, 2025 Editor assigned by journal 31 Aug, 2025 Submission checks completed at journal 14 Aug, 2025 First submitted to journal 13 Aug, 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-7363607","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":516628362,"identity":"be8b8544-273e-41fb-a299-6ac6a4d043e4","order_by":0,"name":"Peiyang Huo","email":"","orcid":"","institution":"KU Leuven","correspondingAuthor":false,"prefix":"","firstName":"Peiyang","middleName":"","lastName":"Huo","suffix":""},{"id":516628363,"identity":"ea1f7991-8f58-42cd-bf25-507b5f29ddb6","order_by":1,"name":"Pablo Vargas Ribera","email":"","orcid":"","institution":"Institute of Agrifood Research and 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AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Hairy Root Disease, 16S rRNA amplicon sequencing, Hydroponic Greenhouse, Microbiota, Agrobacterium, Visual Analytics, Latent Dirichlet Allocation","lastPublishedDoi":"10.21203/rs.3.rs-7363607/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7363607/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e: Hairy root disease (HRD), caused by rhizogenic Agrobacterium strains, is a significant disease threat to modern hydroponic greenhouses, which can result in up to 15% loss in yield. 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First, we observed a structured temporal pattern from the early stage (ES; sampling time points 1 and 2) through a transitional stage (TS; sampling time point 3) to the late stage (LS; sampling time points 4 and 5), showing different MC trajectories by health status. Second, MC4 (characterised by Paenibacillus spp.) was pronounced for healthy greenhouses in the ES, MC7 (characterised by rhizogenic Agrobacterium spp., Devosia and Limnobacter amplicon sequence variants (ASVs)) was pronounced for pre-symptomatic status, while MC0 (characterized by Comamonadaceae spp. ASVs) were indicative of an intermediate state between healthy and infected conditions. Furthermore, the ratio between Paenibacillus ASV and rhizogenic Agrobacterium ASV can be used as a biomarker to assess greenhouse health status in both ES and LS. \u0026nbsp;\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion\u003c/strong\u003e: We investigated hydroponic tomato root-associated MCs responses to HRD using LDA, which revealed different MC trajectories in terms of plant health. Our study advances knowledge of hairy root disease regarding the mechanisms that can improve plant health monitoring in greenhouses and biocontrol strategies. From a computational perspective, we demonstrate how to apply LDA—a powerful analytical tool—to understudied subfields through visual analytics.\u003c/p\u003e","manuscriptTitle":"Unveiling tomato root-associated bacterial interactions responding to hairy root disease","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-22 06:54:18","doi":"10.21203/rs.3.rs-7363607/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-09-25T13:47:12+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-24T15:57:58+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"236014722425469623849124251243936885115","date":"2025-09-18T12:58:49+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-15T12:23:07+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"246880243708293820357491080875629639456","date":"2025-09-11T04:52:01+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-10T20:32:37+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-31T14:07:11+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-15T00:54:40+00:00","index":"","fulltext":""},{"type":"submitted","content":"Environmental Microbiome","date":"2025-08-13T09:41:35+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"environmental-microbiome","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"sigs","sideBox":"Learn more about [Environmental Microbiome](https://environmentalmicrobiome.biomedcentral.com)","snPcode":"40793","submissionUrl":"https://submission.nature.com/new-submission/40793/3","title":"Environmental Microbiome","twitterHandle":"@bmc","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"52d247f4-2c54-4a01-8eb7-9fc88d06e7db","owner":[],"postedDate":"September 22nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-11-24T16:09:02+00:00","versionOfRecord":{"articleIdentity":"rs-7363607","link":"https://doi.org/10.1186/s40793-025-00822-2","journal":{"identity":"environmental-microbiome","isVorOnly":false,"title":"Environmental Microbiome"},"publishedOn":"2025-11-23 15:58:12","publishedOnDateReadable":"November 23rd, 2025"},"versionCreatedAt":"2025-09-22 06:54:18","video":"","vorDoi":"10.1186/s40793-025-00822-2","vorDoiUrl":"https://doi.org/10.1186/s40793-025-00822-2","workflowStages":[]},"version":"v1","identity":"rs-7363607","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7363607","identity":"rs-7363607","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}