Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture
Andrei Stecca Steindorff, Feng M. Cai, Mingyue Ding, Siqi Jiang, Lea Atanasova, Scott E. Baker, Jomal Rodrigues Barbosa-Filho, Gunseli Bayram Akcapinar, Daren W. Brown, Priscila Chaverri, Peijie Chen, Komal Chenthamara, Daum Chris, E. Drula, Mukesh Dubey, Mikael Brandström Durling, Daniel Flatschacher, Thomas Ebner, Tamás Emri, Renwei Gao, Raphaela Castro Georg, Bernard Henrissat, Rosa Hermosa, Alfredo Herrera‐Estrella, Wolfgang Hinterdobler, Philipp Kainz, Magnus Karlsson, László Kredics, Christian P. Kubicek, Alan Kuo, K. Labutti, Anna Lipzen, Matteo Lorito, Robert L. Mach, Gelsomina Manganiello, Tamás Marik, Natalia Martínez-Reyes, Michael Mayrhofer-Reinhartshuber, M. Miskei, Marie-Claude Moisan, Stephen J. Mondo, Enrique Monte, Vivian Ng, Guan Pang, Jasmyn Pangilinan, Mao Peng, Edoardo Piombo, István Pócsi, Mohammad Javad Rahimi, Sumitha K. Reddy, R. Riley, Sabrina Sarrocco, Matthias Schmal, Monika Schmoll, Attila Szücs, Sheridan L. Woo, Oded Yarden, Susanne Zeilinger, Christian Zimmermann, Ekaterina Shelest, Adrian Tsang, Randy M. Berka, Ronald P. de Vries, Igor V. Grigoriev, Irina S. Druzhinina
Abstract
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.