Comparative Phenotypic, Genomic, and Transcriptomic Analyses of Two Contrasting Strains of the Plant Beneficial Fungus Trichoderma virens

Shikha Pachauri; Rinat Zaid; Pramod D Sherkhane; Jamela Easa; Ada Viterbo; Ilan Chet; Benjamin A Horwitz; Prasun K Mukherjee

doi:10.1128/spectrum.03024-22

Comparative Phenotypic, Genomic, and Transcriptomic Analyses of Two Contrasting Strains of the Plant Beneficial Fungus Trichoderma virens

Microbiol Spectr. 2023 Jan 31;11(2):e0302422. doi: 10.1128/spectrum.03024-22. Online ahead of print.

Authors

Shikha Pachauri^#^{1

2}, Rinat Zaid^#³, Pramod D Sherkhane¹, Jamela Easa³, Ada Viterbo⁴, Ilan Chet⁴, Benjamin A Horwitz³, Prasun K Mukherjee^{1

2}

Affiliations

¹ Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India.
² Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
³ Faculty of Biology, The Technion - Israel Institute of Technology, Haifa, Israel.
⁴ Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.

^# Contributed equally.

Abstract

Trichoderma virens is a beneficial fungus that helps plants fight pathogens and abiotic stresses and thereby enhances crop yields. Unlike other Trichoderma spp., there are two well-defined strains (P and Q) of T. virens, classified by secondary metabolites profiling, primarily the biosynthesis of the nonribosomal, strong antimicrobial agents gliotoxin (Q) and gliovirin (P). We have studied the phenotypic and biocontrol properties of two well-studied representative isolates (T. virens Gv29-8 and T. virens GvW/IMI304061) that represent a Q strain and a P strain of T. virens, respectively. We refined the genome assembly of the P strain using nanopore technology, and we compared it with the Q strain. The differences between the genomes include gene expansion in the Q strain. T. virens Gv29-8 is weaker than GvW as a mycoparasite on the broad host-range plant pathogen Sclerotium rolfsii, and it is ineffective as a biocontrol agent when applied to pathogen-infested soil. T. virens Gv29-8 proved to be phytotoxic to Arabidopsis seedlings, whereas the effect of T. virens GvW was not major. Both strains colonized the surface and outer cortex layer of tomato roots, with about 40% higher colonization by T. virens Gv29-8. T. virens Gv29-8 induced the expression of a larger set of tomato genes than did T. virens GvW, although some tomato genes were uniquely induced in response to T. virens GvW. We studied the comparative transcriptome response of T. virens Gv29-8 and T. virens GvW to S. rolfsii. A larger set of genes was regulated in T. virens GvW than in T. virens Gv29-8 in the presence of the plant pathogen. IMPORTANCE Trichoderma virens populations that were earlier classified into two strains (P and Q) based on secondary metabolites profiling are also phenotypically and genetically distinct, with the latter being ineffective in controlling the devastating, broad host range plant pathogen Sclerotium rolfsii. The two strains also provoke distinct as well as overlapping transcriptional responses to the presence of the plant and the pathogen. This study enriches our knowledge of Trichoderma-plant-pathogen interactions and identifies novel candidate genes for further research and deployment in agriculture.

Keywords: CEL-RNA-Seq; Trichoderma; biocontrol; comparative genomics; fungal-plant interaction; genomics; induced resistance; mycoparasitism; mycotrophy; nanopore sequencing; transcriptomics.