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

Trichoderma fungi support sustainable agriculture by suppressing plant diseases and improving crop performance. However, emerging pathogenicity of Trichoderma warrants further ecological and genetic characterization. Here we used machine learning to correlate genomic data from 37 Trichoderma strains with over 140 phenotypic traits, spanning metabolic versatility, biotic interactions, stress tolerance and reproductive strategies. We determined Trichoderma to be an ancient, genetically cohesive and physiologically diverse genus with spores capable of germination in water and dispersal via air and water droplets. Metabolic preferences indicate universal adaptation to mycoparasitism and to niches like arboreal microbial mats, alongside broader saprotrophic versatility. Our analyses are consistent with character displacement among close relatives and convergent evolution in distant lineages, with both processes shaping ecological plasticity and traits including dispersal modes, terrestrialization or endophytism. Our findings reveal that while some Trichoderma species show traits of biosafety concern, its vast ecophysiological diversity enables the development of safe, targeted bioeffectors.

Project(s)

Priority 4: Accelerated Taxonomy

Funder

Funder name	Awards
Royal Botanic Gardens, Kew
Nanjing Agricultural University, China
National Natural Science Foundation of China, China	32470020
National Science Foundation, United States	DEB-1638976 - DEB-1019972
Ministry of Education of the People's Republic of China, China	Fundamental and Interdisciplinary Disciplines Breakthrough Plan (JYB2025XDXM902)
Hungarian Research Network, Hungary
Agricultural Research Service, United States
Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil
Fundação de Amparo à Pesquisa do Estado de Goiás, Brazil
Sveriges Lantbruksuniversitet, Sweden