Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization

Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization | 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 Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization Miriam Schalamun, Guofen Li, Wolfgang Hinterdobler, Dominik K. Großkinsky, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8098172/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 20 Jan, 2026 Read the published version in Scientific Reports → Version 1 posted 11 You are reading this latest preprint version Abstract Trichoderma harzianum is a filamentous ascomycete frequently applied as biocontrol agent in agriculture. While mycoparasitism and antagonism of Trichoderma spp. against fungal pathogens are well known, early fungal responses to the presence of a plant await broader investigation. Analyzing early stages of plant-fungus communication we show that T. harzianum B97 chemotropically responds to a plant extract and that both plant and fungus alter secondary metabolite secretion upon recognition. We developed a strategy for omics-analysis simulating conditions of early plant recognition eliciting a chemotropic response in the fungus and found 102 genes to be differentially regulated, including nitrate and nitrite reductases. Additionally, the previously uncharacterized P lant C ommunication A ssociated (PCA) gene cluster was strongly induced upon recognition of the plant, comprises a palindromic DNA motif and was essential for plant colonization. The PCA-cluster is only present in the Harzianum clade of Trichoderma and closely related to a homologous cluster in Metarhizium spp. Horizontal gene transfer (HGT) was detected for PCA-cluster genes by plants, while the cluster in T. harzianum is likely under balancing or positive selection. Hence, the PCA-cluster mediates early fungus-plant chemical communication and may be responsible for the high potential of T. harzianum and closely related species for biocontrol applications. Biological sciences/Microbiology Biological sciences/Molecular biology Biological sciences/Plant sciences Trichoderma harzianum Hypocrea lixii biocontrol plant protection plant-fungus interaction secondary metabolism MAMP (microbe-associated molecular pattern) interkingdom communication PCA cluster Full Text Additional Declarations Competing interest reported. The study was in part funded by Greencell, France Supplementary Files supplementaryfile1.xlsx Supplementaryfile2v5b250908.pdf supplementaryfile3.pdf supplementaryfile4.svg Cite Share Download PDF Status: Published Journal Publication published 20 Jan, 2026 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 25 Nov, 2025 Reviews received at journal 24 Nov, 2025 Reviews received at journal 20 Nov, 2025 Reviewers agreed at journal 20 Nov, 2025 Reviewers agreed at journal 20 Nov, 2025 Reviewers agreed at journal 20 Nov, 2025 Reviewers invited by journal 20 Nov, 2025 Editor invited by journal 20 Nov, 2025 Editor assigned by journal 17 Nov, 2025 Submission checks completed at journal 17 Nov, 2025 First submitted to journal 12 Nov, 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. 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-8098172","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":550464126,"identity":"15649104-a851-485f-a07d-318ca624cd79","order_by":0,"name":"Miriam Schalamun","email":"","orcid":"","institution":"AIT Austrian Institute of Technology GmbH","correspondingAuthor":false,"prefix":"","firstName":"Miriam","middleName":"","lastName":"Schalamun","suffix":""},{"id":550464127,"identity":"fdc1b1a0-720f-4853-8327-ccdb5546f839","order_by":1,"name":"Guofen Li","email":"","orcid":"","institution":"AIT Austrian Institute of Technology GmbH","correspondingAuthor":false,"prefix":"","firstName":"Guofen","middleName":"","lastName":"Li","suffix":""},{"id":550464129,"identity":"b6703ee8-4a77-4282-bfe2-d6998281137f","order_by":2,"name":"Wolfgang Hinterdobler","email":"","orcid":"","institution":"AIT Austrian Institute of Technology GmbH","correspondingAuthor":false,"prefix":"","firstName":"Wolfgang","middleName":"","lastName":"Hinterdobler","suffix":""},{"id":550464130,"identity":"9e509c86-6324-4c1c-a909-e758d0bd4a70","order_by":3,"name":"Dominik K. 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The study was in part funded by Greencell, France","formattedTitle":"Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization","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":"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},"keywords":"Trichoderma harzianum, Hypocrea lixii, biocontrol, plant protection, plant-fungus interaction, secondary metabolism, MAMP (microbe-associated molecular pattern), interkingdom communication, PCA cluster","lastPublishedDoi":"10.21203/rs.3.rs-8098172/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8098172/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cem\u003eTrichoderma harzianum\u003c/em\u003e is a filamentous ascomycete frequently applied as biocontrol agent in agriculture. While mycoparasitism and antagonism of \u003cem\u003eTrichoderma\u003c/em\u003e spp. against fungal pathogens are well known, early fungal responses to the presence of a plant await broader investigation. Analyzing early stages of plant-fungus communication we show that \u003cem\u003eT. harzianum\u003c/em\u003e B97 chemotropically responds to a plant extract and that both plant and fungus alter secondary metabolite secretion upon recognition. We developed a strategy for omics-analysis simulating conditions of early plant recognition eliciting a chemotropic response in the fungus and found 102 genes to be differentially regulated, including nitrate and nitrite reductases. Additionally, the previously uncharacterized \u003cspan type=\"ItalicUnderline\" class=\"ItalicUnderline\" name=\"Emphasis\"\u003eP\u003c/span\u003elant \u003cspan type=\"ItalicUnderline\" class=\"ItalicUnderline\" name=\"Emphasis\"\u003eC\u003c/span\u003eommunication \u003cspan type=\"ItalicUnderline\" class=\"ItalicUnderline\" name=\"Emphasis\"\u003eA\u003c/span\u003essociated (PCA) gene cluster was strongly induced upon recognition of the plant, comprises a palindromic DNA motif and was essential for plant colonization. The PCA-cluster is only present in the Harzianum clade of \u003cem\u003eTrichoderma\u003c/em\u003e and closely related to a homologous cluster in \u003cem\u003eMetarhizium\u003c/em\u003e spp. Horizontal gene transfer (HGT) was detected for PCA-cluster genes by plants, while the cluster in \u003cem\u003eT. harzianum\u003c/em\u003e is likely under balancing or positive selection.\u003c/p\u003e\u003cp\u003eHence, the PCA-cluster mediates early fungus-plant chemical communication and may be responsible for the high potential of \u003cem\u003eT. harzianum\u003c/em\u003e and closely related species for biocontrol applications.\u003c/p\u003e","manuscriptTitle":"Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-27 18:10:02","doi":"10.21203/rs.3.rs-8098172/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-11-25T09:36:21+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-24T07:30:22+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-21T03:55:03+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"158884343682359690105181591252464320800","date":"2025-11-21T03:29:00+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"153477996455972661407109236775228863783","date":"2025-11-21T01:11:09+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"262519658080104228875110765683089424134","date":"2025-11-20T13:47:37+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-11-20T13:09:10+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-11-20T09:12:01+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-11-17T10:04:49+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-11-17T10:03:42+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-11-12T15:53:01+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":"aea1e98c-98df-4a18-8bec-c398ebf8867b","owner":[],"postedDate":"November 27th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":58568900,"name":"Biological sciences/Microbiology"},{"id":58568901,"name":"Biological sciences/Molecular biology"},{"id":58568902,"name":"Biological sciences/Plant sciences"}],"tags":[],"updatedAt":"2026-01-26T16:06:08+00:00","versionOfRecord":{"articleIdentity":"rs-8098172","link":"https://doi.org/10.1038/s41598-025-33935-2","journal":{"identity":"scientific-reports","isVorOnly":false,"title":"Scientific Reports"},"publishedOn":"2026-01-20 15:58:58","publishedOnDateReadable":"January 20th, 2026"},"versionCreatedAt":"2025-11-27 18:10:02","video":"","vorDoi":"10.1038/s41598-025-33935-2","vorDoiUrl":"https://doi.org/10.1038/s41598-025-33935-2","workflowStages":[]},"version":"v1","identity":"rs-8098172","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8098172","identity":"rs-8098172","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}