Genomic and metabolomic insights into Trichoderma harzianum T9, a resilient biocontrol fungus from arid environments

The search for sustainable agricultural solutions to reduce pesticide dependence is urgent, particularly under the growing pressures of climate change. Although Trichoderma species are well-known biocontrol agents, many strains perform poorly in extreme soils characterized by high salinity or alkaline pH. Here, we characterize Trichoderma harzianum T9, an isolate from the alkaline desert soils of Nuevo León, Mexico, that exhibits exceptional ecological resilience. A competition assay revealed that T9 exhibits significantly higher biocontrol activity against the phytopathogenic fungi Macrophomina sp., Neopestaloptiosis rosae, and two strains of Fusarium sp., all major threats to strawberry production in Mexico, outperforming other Trichoderma strains. Genome sequencing and phylogenomics confirmed that T9 belongs to the T. harzianum species. SNP-based variant analysis revealed numerous genes involved in secondary metabolism with elevated nucleotide substitution rates, including a highly diverged polyketide synthase (PKS). Metabologenomics analysis predicted chemical variation primarily in peptaibols, while biosynthetic gene cluster (BGC) prediction identified six additional putative metabolites likely contributing to its strong antifungal activity. In this work, we also delineate the biosynthetic pathways underlying these seven compounds. Together, these findings position T. harzianum T9 as a highly promising biocontrol agent for managing phytopathogens in degraded soils, providing an eco-friendly strategy that supports sustainable agriculture. The distinctive genomic and metabolic traits of T9 highlight the untapped potential of microorganisms from extreme environments to drive innovative approaches for crop protection and soil restoration.