1 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
2 State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China. caif8@mail.sysu.edu.cn.
3 Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Key lab of organic-based fertilizers of China, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, China.
4 Department of Biotechnology and Food Science, BOKU University, Vienna, Austria.
5 Microbial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
6 Department of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, Brazil.
7 Department of Medical Biotechnology, Institute of Health Sciences, Acibadem University, Istanbul, Turkey.
8 USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA.
9 Department of Natural Sciences, Bowie State University, Bowie, MD, USA.
10 Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.
11 Department of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
12 Aix Marseille Univ, CNRS, INRAE, AFMB, Marseille, France.
13 Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
14 Department of Microbiology, University of Innsbruck, Innsbruck, Austria.
15 KOLAIDO GmbH, Altenrhein, Switzerland.
16 Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary.
17 HUN-REN-UD Fungal Stress Biology Research Group, Debrecen, Hungary.
18 Jiangsu Key Laboratory for Pathogens and Ecosystems, Jiangsu Engineering and Technology Research Centre for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
19 Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark.
20 Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain.
21 Advanced Genomics Unit, Center for Research and Advanced Studies, Irapuato, Mexico.
22 MyPilz GmbH, Vienna, Austria.
23 Department of Biotechnology and Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
24 Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
25 University of Leon, Ponferrada, Spain.
26 KML Vision GmbH, Graz, Austria.
27 Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
28 Wageningen University, Wageningen, Netherlands.
29 Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
30 Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
31 Department of Pharmacy, University of Naples Federico II, Naples, Italy.
32 Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
33 School of Biological Sciences, University of Portsmouth, Portsmouth, UK.
34 ADM, Davis, CA, USA.
35 Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, USA.
36 Royal Botanic Gardens, Kew, Richmond, UK. i.druzhinina@kew.org.

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.