Reduced soil microbial diversity and altered co-occurrence networks associated with Phytophthora nicotianae infection in flue-cured tobacco fields

Reduced soil microbial diversity and altered co-occurrence networks associated with Phytophthora nicotianae infection in flue-cured tobacco fields | 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 Reduced soil microbial diversity and altered co-occurrence networks associated with Phytophthora nicotianae infection in flue-cured tobacco fields Ayodeji Bello, Jing Yuan, Ran Yang, Jiayu Dong, Kamal Chhetri, and 7 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9011956/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Phytophthora nicotianae is a persistent and highly destructive soilborne oomycete that causes black shank of tobacco and continues to threaten its production despite integrated management. Recent studies highlight the potential to harness microbiomes for plant disease suppression; however, it is poorly understood how soil microbial communities respond to P. nicotianae and how these responses relate to black shank severity under field conditions. Results We examined relationships among soil physicochemical properties, microbial community features, P. nicotianae DNA levels, and black shank outcomes in three flue-cured tobacco fields sampled repeatedly throughout a growing season. Phytophthora nicotianae DNA levels were correlated with soil physicochemical properties. The field with the lowest disease pressure had higher alpha diversity, the simplest bacterial network, and a moderately complex fungal network. In contrast, the field with the highest black shank mortality showed the lowest alpha diversity, the most complex bacterial network, and the least complex fungal network. Over the growing season, microbial alpha diversity decreased, and disease outcomes were associated with field-specific shifts in microbial community composition. Trichoderma , Fusarium , and Globodera were most abundant in the high-disease field, whereas multiple bacterial groups within Firmicutes, Proteobacteria, and Actinobacteriota were negatively associated with P. nicotianae in the lower-disease fields. Conclusion Our study indicates that P. nicotianae infection is associated with soil physiochemical properties and field-dependent patterns in microbial diversity, community composition, network topology, and several microbial taxa. These results provide a foundation for future research to experimentally test candidate microbe-pathogen relationships and, where supported, inform the development of microbiome-informed management approaches. Soil microbial community network patterns Phytophthora nicotianae black shank Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryData20260225.xlsx SourceData19.xlsx Cite Share Download PDF Status: Posted 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-9011956","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":601026389,"identity":"b7566322-c5f1-47c7-b441-b44d831d1d3a","order_by":0,"name":"Ayodeji Bello","email":"","orcid":"","institution":"Virginia Tech","correspondingAuthor":false,"prefix":"","firstName":"Ayodeji","middleName":"","lastName":"Bello","suffix":""},{"id":601026394,"identity":"702c9bef-21da-4e72-9e04-4b9a65cc32ef","order_by":1,"name":"Jing Yuan","email":"","orcid":"","institution":"Connecticut Agricultural Experiment Station","correspondingAuthor":false,"prefix":"","firstName":"Jing","middleName":"","lastName":"Yuan","suffix":""},{"id":601026395,"identity":"ddf214f1-dff5-470a-89c2-600779a218a0","order_by":2,"name":"Ran Yang","email":"","orcid":"","institution":"Virginia Tech","correspondingAuthor":false,"prefix":"","firstName":"Ran","middleName":"","lastName":"Yang","suffix":""},{"id":601026396,"identity":"d88d95c0-cc45-4495-87c7-93a05df85168","order_by":3,"name":"Jiayu Dong","email":"","orcid":"","institution":"Virginia Tech","correspondingAuthor":false,"prefix":"","firstName":"Jiayu","middleName":"","lastName":"Dong","suffix":""},{"id":601026400,"identity":"9eda7d59-7ac4-440b-97d6-ea8fbb9da867","order_by":4,"name":"Kamal Chhetri","email":"","orcid":"","institution":"Virginia Tech","correspondingAuthor":false,"prefix":"","firstName":"Kamal","middleName":"","lastName":"Chhetri","suffix":""},{"id":601026407,"identity":"2215a93f-1bde-426d-a9f9-af7aa559e497","order_by":5,"name":"Priyanka Gangwar","email":"","orcid":"","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Priyanka","middleName":"","lastName":"Gangwar","suffix":""},{"id":601026408,"identity":"372a084e-cb39-4974-bf6b-4c00ea07fb1a","order_by":6,"name":"Ruizhu Shi","email":"","orcid":"","institution":"Beijing University of Agriculture","correspondingAuthor":false,"prefix":"","firstName":"Ruizhu","middleName":"","lastName":"Shi","suffix":""},{"id":601026409,"identity":"7552ac22-bada-4661-86fb-93f10120e812","order_by":7,"name":"Ryan Stewart","email":"","orcid":"","institution":"Virginia Tech","correspondingAuthor":false,"prefix":"","firstName":"Ryan","middleName":"","lastName":"Stewart","suffix":""},{"id":601026410,"identity":"74c604d7-631f-477d-9f5d-b077b197013b","order_by":8,"name":"Zhenshan Chen","email":"","orcid":"","institution":"Virginia Tech","correspondingAuthor":false,"prefix":"","firstName":"Zhenshan","middleName":"","lastName":"Chen","suffix":""},{"id":601026413,"identity":"30a4faaa-ec46-45cf-a332-300045481574","order_by":9,"name":"Yiming Feng","email":"","orcid":"","institution":"Virginia Tech","correspondingAuthor":false,"prefix":"","firstName":"Yiming","middleName":"","lastName":"Feng","suffix":""},{"id":601026415,"identity":"ed9f6be0-8540-41d2-b905-2d4bd15d69de","order_by":10,"name":"T. 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Recent studies highlight the potential to harness microbiomes for plant disease suppression; however, it is poorly understood how soil microbial communities respond to \u003cem\u003eP. nicotianae\u003c/em\u003e and how these responses relate to black shank severity under field conditions.\u003c/p\u003e \u003cp\u003e \u003cb\u003eResults\u003c/b\u003e \u003c/p\u003e \u003cp\u003eWe examined relationships among soil physicochemical properties, microbial community features, \u003cem\u003eP. nicotianae\u003c/em\u003e DNA levels, and black shank outcomes in three flue-cured tobacco fields sampled repeatedly throughout a growing season. \u003cem\u003ePhytophthora nicotianae\u003c/em\u003e DNA levels were correlated with soil physicochemical properties. The field with the lowest disease pressure had higher alpha diversity, the simplest bacterial network, and a moderately complex fungal network. In contrast, the field with the highest black shank mortality showed the lowest alpha diversity, the most complex bacterial network, and the least complex fungal network. Over the growing season, microbial alpha diversity decreased, and disease outcomes were associated with field-specific shifts in microbial community composition. \u003cem\u003eTrichoderma\u003c/em\u003e, \u003cem\u003eFusarium\u003c/em\u003e, and \u003cem\u003eGlobodera\u003c/em\u003e were most abundant in the high-disease field, whereas multiple bacterial groups within Firmicutes, Proteobacteria, and Actinobacteriota were negatively associated with \u003cem\u003eP. nicotianae\u003c/em\u003e in the lower-disease fields.\u003c/p\u003e \u003cp\u003e \u003cb\u003eConclusion\u003c/b\u003e \u003c/p\u003e \u003cp\u003eOur study indicates that \u003cem\u003eP. nicotianae\u003c/em\u003e infection is associated with soil physiochemical properties and field-dependent patterns in microbial diversity, community composition, network topology, and several microbial taxa. These results provide a foundation for future research to experimentally test candidate microbe-pathogen relationships and, where supported, inform the development of microbiome-informed management approaches.\u003c/p\u003e","manuscriptTitle":"Reduced soil microbial diversity and altered co-occurrence networks associated with Phytophthora nicotianae infection in flue-cured tobacco fields","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-13 17:02:46","doi":"10.21203/rs.3.rs-9011956/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"9e88fefa-b8f5-45d6-a4db-6c3a9efe3ea5","owner":[],"postedDate":"March 13th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-04-07T09:42:48+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-13 17:02:46","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9011956","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9011956","identity":"rs-9011956","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}