Fluorescent Pseudomonas spp. from Suppressive and Non-Suppressive Soils Share Genomic and Functional Traits Relevant to Fusarium graminearum Disease Suppression

Fluorescent Pseudomonas spp. from Suppressive and Non-Suppressive Soils Share Genomic and Functional Traits Relevant to Fusarium graminearum Disease Suppression | 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 Fluorescent Pseudomonas spp. from Suppressive and Non-Suppressive Soils Share Genomic and Functional Traits Relevant to Fusarium graminearum Disease Suppression Irena Todorović, Danis Abrouk, Martina Kyselková, Rubén López-Mondéjar, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7214815/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 06 Dec, 2025 Read the published version in BMC Genomics → Version 1 posted 10 You are reading this latest preprint version Abstract Background Soils suppressive to fungal pathogens harbor microbiomes that can inhibit disease development despite the presence of virulent pathogens and susceptible hosts. Fluorescent Pseudomonas are often implicated in such suppressiveness, but their genomic determinants and distribution in suppressive vs non-suppressive (i.e., conducive) soils remain unclear. Results We investigated the taxonomic and functional diversity of Pseudomonas populations from wheat rhizospheres in four agricultural soils with contrasting suppressiveness to Fusarium graminearum -induced seedling disease. rpoD -based metabarcoding and culture-dependent isolation revealed distinct Pseudomonas community structures linked to soil suppressiveness. However, major phylogenetic groups were shared across soils. From 406 isolates, 29 representative strains spanning seven subgroups of the P. fluorescens group were selected for whole-genome sequencing. Comparative genomics revealed 14 putative novel Pseudomonas genomospecies (dDDH < 70% with closest described type strains). Genomic screening revealed wide distribution of genes linked to biocontrol and plant-growth promotion, including siderophore biosynthesis, hormone modulation, phosphate solubilization, and production of antimicrobial compounds. Biosynthetic genes for phenazine and pyrrolnitrin were detected exclusively in P. chlororaphis strains isolated from suppressive soils, and rpoD alleles corresponding to these strains were not found in conducive soils within our metabarcoding dataset. Other traits such as hydrogen cyanide, ACC deaminase, and auxin biosynthesis were broadly distributed across isolates from all soils. Functional assays demonstrated variable expression of predicted traits, indicating regulatory or environmental influence. Several strains inhibited F. graminearum mycelial growth via volatile organic compounds, while two strains also reduced conidia germination, including isolates from both suppressive and conducive soils. Conclusions This study demonstrates that Pseudomonas genomic traits important for biocontrol are not restricted to suppressive soils, and that functional redundancy and context-dependent expression may shape the contribution of Pseudomonas to disease suppression. Our results highlight the need for integrative analyses combining community profiling, genome-based prediction, and phenotyping to better understand microbiome-mediated plant protection. The identification of novel genomospecies and lineage-specific biosynthetic traits advances our knowledge of Pseudomonas diversity in agricultural soils and supports future development of targeted microbial consortia. phytopathogens PGPR diversity biocontrol agents comparative genomics Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementarydata.docx Cite Share Download PDF Status: Published Journal Publication published 06 Dec, 2025 Read the published version in BMC Genomics → Version 1 posted Editorial decision: Revision requested 22 Oct, 2025 Reviews received at journal 21 Oct, 2025 Reviewers agreed at journal 08 Oct, 2025 Reviewers agreed at journal 08 Oct, 2025 Reviews received at journal 23 Sep, 2025 Reviewers agreed at journal 04 Sep, 2025 Reviewers invited by journal 04 Sep, 2025 Editor assigned by journal 29 Aug, 2025 Submission checks completed at journal 27 Aug, 2025 First submitted to journal 27 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-7214815","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":512407316,"identity":"58d9c738-5fd0-49e9-a9a1-120c84916463","order_by":0,"name":"Irena Todorović","email":"","orcid":"","institution":"National Institute of the Republic of Serbia, University of Belgrade","correspondingAuthor":false,"prefix":"","firstName":"Irena","middleName":"","lastName":"Todorović","suffix":""},{"id":512407317,"identity":"ad4fbef1-0276-4019-8135-d14f5bfc299f","order_by":1,"name":"Danis Abrouk","email":"","orcid":"","institution":"Université Claude 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Suppression","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"phytopathogens, PGPR, diversity, biocontrol agents, comparative genomics","lastPublishedDoi":"10.21203/rs.3.rs-7214815/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7214815/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eSoils suppressive to fungal pathogens harbor microbiomes that can inhibit disease development despite the presence of virulent pathogens and susceptible hosts. Fluorescent \u003cem\u003ePseudomonas\u003c/em\u003e are often implicated in such suppressiveness, but their genomic determinants and distribution in suppressive vs non-suppressive (i.e., conducive) soils remain unclear.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eWe investigated the taxonomic and functional diversity of \u003cem\u003ePseudomonas\u003c/em\u003e populations from wheat rhizospheres in four agricultural soils with contrasting suppressiveness to \u003cem\u003eFusarium graminearum\u003c/em\u003e-induced seedling disease. \u003cem\u003erpoD\u003c/em\u003e-based metabarcoding and culture-dependent isolation revealed distinct \u003cem\u003ePseudomonas\u003c/em\u003e community structures linked to soil suppressiveness. However, major phylogenetic groups were shared across soils. From 406 isolates, 29 representative strains spanning seven subgroups of the \u003cem\u003eP. fluorescens\u003c/em\u003e group were selected for whole-genome sequencing. Comparative genomics revealed 14 putative novel \u003cem\u003ePseudomonas\u003c/em\u003e genomospecies (dDDH\u0026thinsp;\u0026lt;\u0026thinsp;70% with closest described type strains). Genomic screening revealed wide distribution of genes linked to biocontrol and plant-growth promotion, including siderophore biosynthesis, hormone modulation, phosphate solubilization, and production of antimicrobial compounds. Biosynthetic genes for phenazine and pyrrolnitrin were detected exclusively in \u003cem\u003eP. chlororaphis\u003c/em\u003e strains isolated from suppressive soils, and \u003cem\u003erpoD\u003c/em\u003e alleles corresponding to these strains were not found in conducive soils within our metabarcoding dataset. Other traits such as hydrogen cyanide, ACC deaminase, and auxin biosynthesis were broadly distributed across isolates from all soils. Functional assays demonstrated variable expression of predicted traits, indicating regulatory or environmental influence. Several strains inhibited \u003cem\u003eF. graminearum\u003c/em\u003e mycelial growth via volatile organic compounds, while two strains also reduced conidia germination, including isolates from both suppressive and conducive soils.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eThis study demonstrates that \u003cem\u003ePseudomonas\u003c/em\u003e genomic traits important for biocontrol are not restricted to suppressive soils, and that functional redundancy and context-dependent expression may shape the contribution of \u003cem\u003ePseudomonas\u003c/em\u003e to disease suppression. Our results highlight the need for integrative analyses combining community profiling, genome-based prediction, and phenotyping to better understand microbiome-mediated plant protection. The identification of novel genomospecies and lineage-specific biosynthetic traits advances our knowledge of \u003cem\u003ePseudomonas\u003c/em\u003e diversity in agricultural soils and supports future development of targeted microbial consortia.\u003c/p\u003e","manuscriptTitle":"Fluorescent Pseudomonas spp. from Suppressive and Non-Suppressive Soils Share Genomic and Functional Traits Relevant to Fusarium graminearum Disease Suppression","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-10 19:44:19","doi":"10.21203/rs.3.rs-7214815/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-22T20:12:46+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-21T14:16:14+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"223945899900773225210197748551249195449","date":"2025-10-08T17:15:51+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"240670431925427060888751915372661216395","date":"2025-10-08T12:28:20+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-23T16:37:42+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"82562084544021484675793358950805347222","date":"2025-09-04T13:44:33+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-04T06:57:34+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-29T19:19:08+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-27T10:17:54+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-08-27T10:13:19+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"877ff0c1-9426-4d4c-8c9c-4e9c1fe09c08","owner":[],"postedDate":"September 10th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-12-08T16:04:02+00:00","versionOfRecord":{"articleIdentity":"rs-7214815","link":"https://doi.org/10.1186/s12864-025-12374-3","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2025-12-06 15:58:17","publishedOnDateReadable":"December 6th, 2025"},"versionCreatedAt":"2025-09-10 19:44:19","video":"","vorDoi":"10.1186/s12864-025-12374-3","vorDoiUrl":"https://doi.org/10.1186/s12864-025-12374-3","workflowStages":[]},"version":"v1","identity":"rs-7214815","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7214815","identity":"rs-7214815","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}