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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: Trichoderma ecogenomics elucidates convergent adaptations enhancing fungal fitness

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

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. 2026. Trichoderma ecogenomics elucidates convergent adaptations enhancing fungal fitness. Nature Microbiology . https://Resource 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.