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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #423873
Research Project: Innovative Food and Feed Safety Research to Eliminate Mycotoxin Contamination in Corn and other Crops

Location: Mycotoxin Prevention and Applied Microbiology Research

Title: Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture

Author
item STEINDORFF, ANDREI - Lawrence Berkeley National Laboratory
item CAI, FENG - Sun Yat-Sen University
item DING, MINGYUE - Sun Yat-Sen University
item JIANG, SIQI - Sun Yat-Sen University
item SHELEST, EKATERINA - University Of Portsmouth
item TSANG, ADRIAN - Concordia University
item BERKA, RANDY - Novozymes
item DE VRIES, RONALD - Westerdijk Fungal Biodiversity Institute
item GRIGORIEV, IGOR - Lawrence Berkeley National Laboratory
item DRUZHININA, IRINA - Royal Botanic Gardens, Kew
item Brown, Daren
item ATANASOVA, LEA - Austrian University
item BAKER, SCOTT - Austrian Academy Of Sciences
item BARBOSA-FILHO, JOMAL - Swedish University Of Agricultural Sciences
item AKCAPINAR, GUNSELI - Sabanci University
item CHAVERRI, PRISCILA - Bowie State University
item CHEN, PEIJIE - Auburn University
item CHENTHAMARA, KOMAL - Technische Universität Wien
item DAUM, CHRIS - Department Of Energy Joint Genome
item DRULA, ELODIE - Aix-Marseille University
item DUBEY, MUKESH - Uppsala University
item DURLING, MIKAEL - Uppsala University
item FLATSCHACHER, DANIEL - (NCE, CECR)networks Of Centres Of Exellence Of Canada, Centres Of Excellence For Commercilization A
item EBNER, THOMAS - Lexogen Gmbh
item EMRI, TAMAS - University Of Debrecen
item GAO, RENWEI - Jiangsu Academy Agricultural Sciences
item GEORG, RAPHAELA - Federal University Of Goias
item HENRISSAT, BERNARD - Technical University Of Denmark
item HERMOSA, ROSA - University Of Salamanca
item HERRERA ESTRELLA, ALFREDO - National Laboratory Of Genomics And Biodiversity
item HINTERDOBLER, WOLFGANG - Lexogen Gmbh
item KAINZ, PHILIPP - Lexogen Gmbh
item KARLSSON, MAGNUS - Uppsala University
item KREDICS, LASZLO - University Of Szeged
item KUBICEK, CHRISTIAN - Technische Universität Wien
item KUO, ALAN - Lawrence Berkeley National Laboratory
item LABUTTI, KURT - Lawrence Berkeley National Laboratory
item LIPZEN, ANNA - Lawrence Berkeley National Laboratory
item LORITO, MATTEO - The University Of Naples Federico Ii
item MACH, ROBERT - Technische Universität Wien
item MANGANIELLO, GELSOMINA - The University Of Naples Federico Ii
item MARIK, TAMAS - University Of Szeged
item MARTINEZ-REYES, NATALIA - Westerdijk Fungal Biodiversity Institute
item MAYRHOFER-REINHARTSH, MICHAEL - Lexogen Gmbh
item MISKEI, MARTON - University Of Debrecen
item MOISAN, MARIE-CLAUDE - Concordia University
item MONDO, STEPHEN - Lawrence Berkeley National Laboratory
item MONTE, ENRIQUE - University Of Salamanca
item NG, VIVIAN - Lawrence Berkeley National Laboratory
item PANG, GUAN - Nanjing Agricultural University
item PANGILINAN, JASMYN - Lawrence Berkeley National Laboratory
item PENG, MAO - Westerdijk Fungal Biodiversity Institute
item PIMBO, EDOARDO - Uppsala University
item POCSI, ISTVAN - University Of Debrecen
item RAHIMI, MOHAMMAD - Technische Universität Wien
item REDDY, SUMITHA - Westerdijk Fungal Biodiversity Institute
item RILEY, ROBERT - Lawrence Berkeley National Laboratory
item SARROCCO, SABRINA - University Of Pisa
item SCHMAL, MATTHIAS - Technische Universität Wien
item SCHMOLL, MONIKA - University Of Vienna
item SZUCS, ATTILA - University Of Szeged
item WOO, SHERIDAN - University Of Naples Federico Ii
item YARDEN, ODED - Hebrew University Of Jerusalem
item ZEILINGER, SUSANNE - University Of Innsbruck
item ZIMMERMAN, CHRISTIAN - Technische Universität Wien
item SHELEST, EKATERINA - University Of Portsmouth
item TSANG, ADRIAN - Concordia University
item BERKA, RANDY - Archer Daniels Midland
item DE VRIES, RONALD - Westerdijk Fungal Biodiversity Institute
item GRIGORIEV, IGOR - Lawrence Berkeley National Laboratory
item DRUZHININA, IRINA - Royal Botanic Gardens, Kew

Submitted to: Nature Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/8/2026
Publication Date: 3/3/2026
Citation: Steindorff, A., Cai, F.M., Ding, M., Jiang, S., Shelest, E., Tsang, A., Berka, R., De Vries, R.P., Grigoriev, I.V., Druzhinina, I.S., Brown, D.W., Atanasova, L., Baker, S.E., Barbosa-Filho, J.R., Akcapinar, G.B., Chaverri, P., Chen, P., Chenthamara, K., Daum, C., Drula, E., Dubey, M., Durling, M.B., Flatschacher, D., Ebner, T., Emri, T., Gao, R., Georg, R.C., Henrissat, B., Hermosa, R., Herrera Estrella, A., Hinterdobler, W., Kainz, P., Karlsson, M., Kredics, L., Kubicek, C.P., Kuo, A., Labutti, K., Lipzen, A., Lorito, M., Mach, R.L., Manganiello, G., Marik, T., Martinez-Reyes, N., Mayrhofer-Reinhartsh, M., Miskei, M., Moisan, M., Mondo, S., Monte, E., Ng, V., Pang, G., Pangilinan, J., Peng, M., Pimbo, E., Pocsi, I., Rahimi, M.J., Reddy, S.K., Riley, R., Sarrocco, S., Schmal, M., Schmoll, M., Szucs, A., Woo, S.L., Yarden, O., Zeilinger, S., Zimmerman, C., Shelest, E., Tsang, A., Berka, R., De Vries, R.P., Grigoriev, I.V., Druzhinina, I.S. 2026. Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture. Nature Microbiology. https://doi.org/10.1038/s41564-026-02260-3.
DOI: https://doi.org/10.1038/s41564-026-02260-3

Interpretive Summary: Trichoderma species are well known biological control agents that promote plant health and limit plant pathogenic fungi, including Fusarium. The application of Trichoderma in agriculture seed treatments or as foliar sprays improves plant productivity, soil health and reduces the use of chemical pesticides. To provide insights for a science-based assessment of the potential risks associated with the increased use of these fungi in agriculture, we analyzed genomic data from 37 different Trichoderma strains and correlated them with over 150 phenotypic traits. We found that Trichoderma is an ancient fungal genus with a diverse collection of regulatory genes, enzymes, transporters, and small secreted proteins that contribute to its ecological plasticity, superior stress resilience, and fitness vigor. We conclude that the vast genetic diversity of the genus allows for a judicious selection of safe and efficient Trichoderma strains beneficial for agriculture. This knowledge will be of use to plant pathologists, plant breeders, and other scientists focused on the development of novel strategies to control fungal plant diseases and limit fungal toxin contamination of grain to keep our food supply safe.

Technical Abstract: Plant-beneficial mycoparasitic fungi from the genus Trichoderma enhance eco-sustainable agriculture by controlling pathogens and improving plant immunity, stress tolerance, and crop yield. However, their occasional but increasing pathogenicity in plants, humans, and cultivated mushrooms necessitates a thorough risk assessment. This study utilized machine learning to analyze genomic data from 37 ecologically diverse Trichoderma strains, correlating them with over 150 phenotypic traits. Results depict Trichoderma as an ancient, genetically distinct, and polymorphic genus, possibly predominantly associated with arboreal phyllospheric microbial mats of tropical rainforests. Genomic analysis revealed the role of specific regulatory genes, enzymes, transporters, and small secreted proteins in Trichoderma fitness, propounding convergent evolution of physiological traits and mechanisms of ecological plasticity. Their superior stress resilience, fitness vigor, and edaphic competence of some commonly used strains beneficial for agriculture raises potential biosecurity concerns. However, the vast genetic diversity of the genus allows for judicious selection of safe and efficient Trichoderma strains.