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

The search for sustainable agricultural solutions to reduce pesticide use is increasingly urgent, particularly under the growing pressures of climate change. Microorganisms from extreme environments offer valuable potential for biocontrol applications due to their unique adaptive traits, enabling survival under conditions such as high temperature, salinity and water scarcity. While Trichoderma species are well-known biocontrol agents, many strains perform poorly in extreme soils with high salinity or alkaline pH. Here, we characterize Trichoderma harzianum T9, an isolate from the alkaline desert soils of Nuevo León, México, that demonstrates exceptional resilience. T. harzianum T9 displayed significantly greater biocontrol efficiency against phytopathogenic fungi from strawberry plants compared with other strains. Genome sequencing, phylogenomics and SNP-based variant analysis revealed numerous genes involved in secondary metabolism with elevated nucleotide substitution rates. Metabologenomics predicted chemical variations, primarily in peptaibols, and identified six additional compounds through biosynthetic gene cluster (BGC) prediction, likely contributing to its strong antifungal capacity. These findings position T. harzianum T9 as a promising biocontrol agent for managing phytopathogens in degraded soils, offering an eco-friendly approach for sustainable agriculture. The unique genomic and metabolic traits of T9 highlight the untapped potential of microorganisms from extreme environments in advancing innovative strategies for crop protection and soil restoration.