Genome sequencing and functional analysis of potential Trichoderma species for controlling Pythium schmitthenneri-Induced root rot in olive trees

Root rot disease caused by Pythium schmitthenneri is a significant challenge in olive ( Olea europaea L.) cultivation. Due to the limitations of chemical controls, this study explores the potential of Trichoderma species as a sustainable alternative with an overview in the genetic properties involved in it. Eight Trichoderma isolates were obtained from olive roots and identified using rDNA internal transcribed spacer (ITS) sequences, revealing four species: T. harzianum , T. longibrachiatum , T. virens , and T. viride . Among these, T. harzianum T-BM6 and T. virens T-KH4, showed 81.4% and 69.57% inhibition rates of pathogen growth, respectively, in vitro . Greenhouse trials demonstrated that these isolates reduced disease severity to 18.75% for T-BM6 and 31.25% for T-KH4. All isolates produced cellulase, with T-BM6 exhibiting high cellulolytic activity. Genomic analysis highlighted key genes related to the MAPK signaling pathway, sulfur metabolism, and inositol phosphate metabolism in T-BM6, and phenylalanine, tyrosine, and tryptophan metabolism in T-KH4. These results suggest that T. harzianum T-BM6 and T. virens T-KH4 are promising candidates for biological control, offering a sustainable alternative to chemical treatments for managing olive root rot. • Eight Trichoderma isolates inhibited Pythium schmitthenneri growth by up to 81.4% in vitro. • Greenhouse trials showed significant reduction in root rot severity in treated olive trees. • Trichoderma harzianum T-BM6 and Trichoderma virens T-KH4 were most effective against root rot. • Genomic analysis identified MAPK signaling and phenylalanine metabolism pathways as crucial for biocontrol efficacy.