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.
Authors
- Vivian Ng (ORCID: https://orcid.org/0000-0001-8941-6931)
- Alfredo Herrera‐Estrella (ORCID: https://orcid.org/0000-0002-4589-6870)
- Matteo Lorito
- Natalia Martínez-Reyes (ORCID: https://orcid.org/0000-0001-6560-417X)
- Mukesh Dubey (ORCID: https://orcid.org/0000-0001-7393-366X)
- Stephen J. Mondo (ORCID: https://orcid.org/0000-0001-5797-0647)
- Komal Chenthamara
- Andrei Stecca Steindorff (ORCID: https://orcid.org/0000-0002-2052-2848)
- Debbie Brown
- Mikael Brandström Durling (ORCID: https://orcid.org/0000-0001-6485-197X)
- Robert L. Mach (ORCID: https://orcid.org/0000-0003-2375-7244)
- Oded Yarden
- Ekaterina Shelest (ORCID: https://orcid.org/0000-0002-9751-6702)
- Sheridan L. Woo (ORCID: https://orcid.org/0000-0001-8611-6140)
- Philipp Kainz (ORCID: https://orcid.org/0000-0001-7970-370X)
- Sabrina Sarrocco (ORCID: https://orcid.org/0000-0002-7080-8369)
- Sumitha K. Reddy
- RRP de Vries (ORCID: https://orcid.org/0000-0002-2730-4683)
- Matthias Schmal (ORCID: https://orcid.org/0000-0002-3592-4882)
- Lea Atanasova (ORCID: https://orcid.org/0000-0002-1751-277X)
- Mohammad Javad Rahimi (ORCID: https://orcid.org/0000-0002-8444-8608)
- Tamás Marik (ORCID: https://orcid.org/0000-0002-0434-5685)
- Attila Szücs (ORCID: https://orcid.org/0000-0001-9733-4135)
- Adrian Tsang (ORCID: https://orcid.org/0000-0002-5892-4797)
- Daniel Flatschacher (ORCID: https://orcid.org/0000-0001-8221-9695)
- Magnus Karlsson (ORCID: https://orcid.org/0000-0001-6098-138X)
- Christian Zimmermann (ORCID: https://orcid.org/0000-0002-6440-2100)
- M. Miskei
- Randy M. Berka
- Edoardo Piombo (ORCID: https://orcid.org/0000-0003-2830-1967)
- Jasmyn Pangilinan (ORCID: https://orcid.org/0000-0001-7966-3496)
- Gelsomina Manganiello (ORCID: https://orcid.org/0000-0003-1502-1595)
- Jomal Rodrigues Barbosa-Filho
- Susanne Zeilinger (ORCID: https://orcid.org/0000-0003-3112-0948)
- Michael Mayrhofer-Reinhartshuber
- Guan Pang (ORCID: https://orcid.org/0000-0002-9922-7074)
- Alan Kuo
- Daum Chris
- Monika Schmoll
- Priscila Chaverri
- Mingyue Ding
- R. Riley
- E. Drula
- K. Labutti
- Tamás Emri
- László Kredics
- Renwei Gao
- Rosa Hermosa
- Gunseli Bayram Akcapinar
- Enrique Monte
- Marie-Claude Moisan
- István Pócsi
- Thomas Ebner
- Anna Lipzen
- Feng M. Cai
- Christian P. Kubicek
- Raphaela Castro Georg
- Irina S. Druzhinina
- Wolfgang Hinterdobler
- Scott E. Baker
- Igor V. Grigoriev
- Peijie Chen
- Bernard Henrissat
- Mao Peng
- Siqi Jiang
Institutions
- University of Pisa (IT)
- Nanjing Agricultural University (CN)
- Centre National de la Recherche Scientifique (FR)
- University of Vienna (AT)
- Agricultural Research Service (US)
- University of Debrecen (HU)
- TU Wien (AT)
- Lawrence Berkeley National Laboratory (US)
- Nanjing Normal University (CN)
- Sun Yat-sen University (CN)
- Universidad de Salamanca (ES)
- Universität Innsbruck (AT)
- National Center for Agricultural Utilization Research (US)
- Joint Genome Institute (US)
- Hebrew University of Jerusalem (IL)
- Aix-Marseille Université (FR)
- University of Szeged (HU)
- Royal Botanic Gardens, Kew (GB)
- Environmental Molecular Sciences Laboratory (US)
- Swedish University of Agricultural Sciences (SE)
- Acıbadem University (TR)
- Bowie State University (US)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Westerdijk Fungal Biodiversity Institute (NL)
- Federico II University Hospital (IT)
- Concordia University (CA)
- University of Portsmouth (GB)
- Universidade Federal de Goiás (BR)
- University of Naples Federico II (IT)
- University of California, Davis (US)
- Universidad de León (ES)
- Wageningen University & Research (NL)
- BOKU University (AT)
- University of California, Berkeley (US)
- Technical University of Denmark (DK)
Publication Details
- Journal
- Nature Microbiology
- Published
- 2026-03-03
- DOI
- https://doi.org/10.1038/s41564-026-02260-3
- Citations
- 1
- Primary Topic
- Plant-Microbe Interactions and Immunity
- Type
- article
- Field-Weighted Citation Impact
- 31.34
Funders
- National Science Foundation
- U.S. Department of Energy
- U.S. Department of Agriculture
- Joint Genome Institute
- National Natural Science Foundation of China
- Ministry of Education of the People's Republic of China
- Conselho Nacional de Desenvolvimento Científico e Tecnológico
- Sveriges Lantbruksuniversitet
- Fundação de Amparo à Pesquisa do Estado de Goiás
- Nanjing Agricultural University
- Office of Science
- Agricultural Research Service