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

IF 19.4 1区生物学 Q1 MICROBIOLOGY

Nature Microbiology Pub Date : 2026-03-03 DOI:10.1038/s41564-026-02260-3

Andrei S. 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, Chris Daum, Elodie 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, Kurt LaButti, Anna Lipzen, Matteo Lorito, Robert L. Mach, Gelsomina Manganiello, Tamás Marik, Natalia Martinez-Reyes, Michael Mayrhofer-Reinhartshuber, Márton Miskei, Marie-Claude Moisan, Stephen Mondo, Enrique Monte, Vivian Ng, Guan Pang, Jasmyn Pangilinan, Mao Peng, Edoardo Piombo, István Pócsi, Mohammad Javad Rahimi, Sumitha K. Reddy, Robert Riley, Sabrina Sarrocco, Matthias Schmal, Monika Schmoll, Attila Szűcs, Sheridan L. Woo, Oded Yarden, Susanne Zeilinger, Christian Zimmermann, Ekaterina Shelest, Adrian Tsang, Randy Berka, Ronald P. de Vries, Igor V. Grigoriev, Irina S. Druzhinina

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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. Analysis of 37 genomes together with more than 140 phenotypic traits links genomic features to ecological fitness and lifestyle diversity in Trichoderma fungi.

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表型基因组学揭示了可持续农业中木霉的生态学和进化。

木霉真菌通过抑制植物病害和提高作物性能来支持可持续农业。然而，木霉的新兴致病性需要进一步的生态和遗传表征。在这里，我们使用机器学习将37种木霉菌株的基因组数据与140多种表型性状相关联，包括代谢多样性、生物相互作用、耐受性和生殖策略。我们确定木霉是一个古老的，遗传上有凝聚力和生理上多样化的属，孢子能够在水中萌发并通过空气和水滴传播。代谢偏好表明对真菌寄生和生态位（如树栖微生物垫）的普遍适应，以及更广泛的腐养多样性。我们的分析结果与近亲之间的特征位移和远缘谱系的趋同进化一致，这两个过程都形成了生态可塑性和特征，包括扩散模式、陆地化或内生作用。我们的研究结果表明，虽然一些木霉物种表现出生物安全问题，但其巨大的生态生理多样性使开发安全的靶向生物效应剂成为可能。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nature Microbiology Immunology and Microbiology-Microbiology

CiteScore

44.40

自引率

1.10%

发文量

226

期刊介绍： Nature Microbiology aims to cover a comprehensive range of topics related to microorganisms. This includes: Evolution: The journal is interested in exploring the evolutionary aspects of microorganisms. This may include research on their genetic diversity, adaptation, and speciation over time. Physiology and cell biology: Nature Microbiology seeks to understand the functions and characteristics of microorganisms at the cellular and physiological levels. This may involve studying their metabolism, growth patterns, and cellular processes. Interactions: The journal focuses on the interactions microorganisms have with each other, as well as their interactions with hosts or the environment. This encompasses investigations into microbial communities, symbiotic relationships, and microbial responses to different environments. Societal significance: Nature Microbiology recognizes the societal impact of microorganisms and welcomes studies that explore their practical applications. This may include research on microbial diseases, biotechnology, or environmental remediation. In summary, Nature Microbiology is interested in research related to the evolution, physiology and cell biology of microorganisms, their interactions, and their societal relevance.