Trichoderma longibrachiatum LT9 from grape rhizosphere suppresses root rot by inhibiting pathogens and inducing plant resistance

Grape root rot caused by Fusarium acuminatum is a major threat to grape production, which currently relies heavily on chemical fungicides for control. From grape rhizosphere soil, we obtained 71 Trichoderma isolates representing seven distinct species. Trichoderma longibrachiatum isolate LT9 was selected based on its broad‑spectrum antimicrobial activity, as demonstrated through in vitro antagonism assays and evaluations of volatile organic compound and culture filtrate inhibitory effects. In pot experiments, LT9 pretreatment significantly reduced the incidence and disease index of grapevine root rot, achieving a control efficacy of 80.65%. This treatment also persistently induced the activity of defense enzymes—peroxidase, polyphenol oxidase, and superoxide dismutase—in the leaves, while reducing malondialdehyde content and increasing soluble sugar levels to enhance plant resistance.Transcriptome sequencing analysis revealed the dynamic transcriptional reprogramming triggered by LT9 treatment in grape plants. Under pathogen stress, both LT9 treatment alone and its co‑treatment with the pathogen significantly activated pathways related to plant–pathogen interaction, MAPK signaling, plant hormone signal transduction, and biosynthesis of secondary metabolites. Differential expression gene analysis further identified several key transcription factor families, including AP2/ERF‑ERF, MYB, WRKY, bHLH, and NAC, involved in regulating these defense responses. Protein–protein interaction network analysis screened multiple hub genes that played core regulatory roles at different time points. This study systematically elucidates the multi‑level mechanisms—pathogen inhibition, induced systemic resistance, and modulation of defense signaling—by which LT9 controls grape root rot, providing a foundation for developing efficient Trichoderma-based biocontrol agents.