ArticleNature microbiology2026
Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture.
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Article in Nature microbiology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9citing papers in PubMed
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Who cites it
9 citing papers in PubMed.
- Phylogenomic and Comparative Genomic Analyses Reveal Deep Evolutionary Structure and Cryptic Diversity in the GenusInternational journal of molecular sciences · 2026Article
- Barcoded mutant library enables high-throughput functional genomics in a filamentous fungus.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- HarnessingPlants (Basel, Switzerland) · 2026Review
- Soil as a Battlefield and a Reservoir: Linking Soil Components to the Epidemiology of Soilborne Plant Diseases.Microbial ecology · 2026Review
- TrichoBase: a standardized genomic resource for comparative genomics of Trichoderma species.BMC genomic data · 2026Article
- Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture.Nature microbiology · 2026Article
- Regulatory adaptation of an accessory gene controls fungal halotolerance and niche expansion.The ISME journal · 2026Article
- Conserved storage-carbohydrate metabolic modules are rewired during germination ofFrontiers in fungal biology · 2026Article
- Four Unrecorded Species ofMycobiology · 2026Article
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Authors and funding
65 authors.
Andrei S Steindorff *US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-2052-2848
Feng M Cai *State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China. caif8@mail.sysu.edu.cn.ORCID http://orcid.org/0000-0003-2032-6190
Mingyue DingJiangsu 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.
Siqi JiangJiangsu 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.
Lea AtanasovaDepartment of Biotechnology and Food Science, BOKU University, Vienna, Austria.ORCID http://orcid.org/0000-0002-1751-277X
Scott E BakerMicrobial Molecular Phenotyping Group, Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.ORCID http://orcid.org/0000-0001-5085-3106
Jomal Rodrigues Barbosa-FilhoDepartment of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, Brazil.ORCID http://orcid.org/0000-0002-9375-4906
Gunseli Bayram AkcapinarDepartment of Medical Biotechnology, Institute of Health Sciences, Acibadem University, Istanbul, Turkey.ORCID http://orcid.org/0000-0002-6296-7415
Daren W BrownUSDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, USA.
Priscila ChaverriDepartment of Natural Sciences, Bowie State University, Bowie, MD, USA.ORCID http://orcid.org/0000-0002-8486-6033
Peijie ChenJiangsu 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.
Komal ChenthamaraDepartment of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
Chris DaumUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-3895-5892
Elodie DrulaAix Marseille Univ, CNRS, INRAE, AFMB, Marseille, France.ORCID http://orcid.org/0000-0002-9168-5214
Mukesh DubeyDepartment of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Mikael Brandström DurlingDepartment of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Daniel FlatschacherDepartment of Microbiology, University of Innsbruck, Innsbruck, Austria.ORCID http://orcid.org/0000-0001-8221-9695
Thomas EbnerKOLAIDO GmbH, Altenrhein, Switzerland.
Tamás EmriDepartment of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary.ORCID http://orcid.org/0000-0002-8850-6975
Renwei GaoJiangsu 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.
Raphaela Castro GeorgDepartment of Biochemistry and Molecular Biology, Federal University of Goiás, Goiânia, Brazil.
Bernard HenrissatDepartment of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark.ORCID http://orcid.org/0000-0002-3434-8588
Rosa HermosaInstitute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain.
Alfredo Herrera-EstrellaAdvanced Genomics Unit, Center for Research and Advanced Studies, Irapuato, Mexico.ORCID http://orcid.org/0000-0002-4589-6870
Wolfgang HinterdoblerMyPilz GmbH, Vienna, Austria.
Philipp KainzKOLAIDO GmbH, Altenrhein, Switzerland.
Magnus KarlssonDepartment of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
László KredicsDepartment of Biotechnology and Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
Christian P KubicekDepartment of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
Alan KuoUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-3514-3530
Kurt LaButtiUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-5838-1972
Anna LipzenUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-2293-9329
Matteo LoritoDepartment of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
Robert L MachDepartment of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.ORCID http://orcid.org/0000-0003-2375-7244
Gelsomina ManganielloDepartment of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
Tamás MarikDepartment of Biotechnology and Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
Natalia Martinez-ReyesFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.
Michael Mayrhofer-ReinhartshuberKML Vision GmbH, Graz, Austria.
Márton MiskeiHUN-REN-UD Fungal Stress Biology Research Group, Debrecen, Hungary.
Marie-Claude MoisanCentre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
Stephen MondoUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-5797-0647
Enrique MonteInstitute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain.
Vivian NgUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-8941-6931
Guan PangJiangsu 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.
Jasmyn PangilinanUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Mao PengFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.ORCID http://orcid.org/0000-0003-1676-0242
Edoardo PiomboDepartment of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
István PócsiDepartment of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary.ORCID http://orcid.org/0000-0003-2692-6453
Mohammad Javad RahimiDepartment of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
Sumitha K ReddyFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.
Robert RileyUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-0224-0975
Sabrina SarroccoDepartment of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
Matthias SchmalDepartment of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
Monika SchmollCentre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
Attila SzűcsDepartment of Biotechnology and Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
Sheridan L WooDepartment of Pharmacy, University of Naples Federico II, Naples, Italy.ORCID http://orcid.org/0000-0001-8611-6140
Oded YardenDepartment of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.ORCID http://orcid.org/0000-0002-4722-535X
Susanne ZeilingerDepartment of Microbiology, University of Innsbruck, Innsbruck, Austria.ORCID http://orcid.org/0000-0003-3112-0948
Christian ZimmermannDepartment of Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
Ekaterina ShelestSchool of Biological Sciences, University of Portsmouth, Portsmouth, UK.
Adrian TsangCentre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
Randy BerkaADM, Davis, CA, USA.
Ronald P de VriesFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands.ORCID http://orcid.org/0000-0002-4363-1123
Igor V GrigorievUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-3136-8903
Irina S DruzhininaRoyal Botanic Gardens, Kew, Richmond, UK. i.druzhinina@kew.org.ORCID http://orcid.org/0000-0003-2821-5268
Funding
National Natural Science Foundation of China (National Science Foundation of China) 32470020National Science Foundation (NSF) DEB-1638976NSF | National Science Board (NSB) DEB-1019972
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.
Indexed as
AgricultureBiological EvolutionPhenomicsTrichodermaGenome, FungalPhenotypePhylogenyPlant DiseasesSpores, Fungal
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