Genomic insights into Bacillus velezensis FB-4 as a multifaceted biocontrol agent against Valsa canker caused by Valsa pyri on Korla fragrant pear

Abstract

Pear Valsa canker, caused by Valsa pyri , poses a severe threat to the sustainable cultivation of Korla fragrant pear. The environmental concerns associated with chemical fungicides have driven the search for biological control alternatives. Endophytic bacteria represent a promising resource for eco-friendly disease management. A previously isolated endophytic strain, Bacillus velezensis strain FB-4, from the bark of Korla fragrant pear, exhibited inhibitory activity against V. pyri in preliminary assays. This study aimed to characterize its biocontrol potential and investigate the underlying mechanisms through integrated phenotypic and genomic approaches. In dual-culture assays, strain FB-4 inhibited mycelial growth of V. pyri strain ALE2 by 85.51% and induced hyphal morphological abnormalities, including swelling, constriction, and distortion. The cell-free supernatant exhibited dose- and time-dependent antifungal activity, with complete inhibition at 10% (v/v) after 72 h of fermentation. On detached pear twigs, the 10% supernatant reduced lesion length by 74.84%. Strain FB-4 also showed broad-spectrum activity against six other phytopathogenic fungi. Phenotypic assays showed that strain FB-4 produces indole-3-acetic acid, siderophores, biofilm, and extracellular hydrolases (protease, cellulase, and amylase), and exhibits moderate salt (up to 6% NaCl) and cold (10–40 °C) tolerance. Whole-genome sequencing revealed a 3.89 Mb genome (GC content 46.5%) comprising 13 contigs, with 3,749 protein-coding genes. Phylogenetic and average nucleotide identity analyses assigned strain FB-4 to B. velezensis . Functional annotation identified genes and biosynthetic gene clusters predicted to be involved in antimicrobial compound production, plant growth promotion, and stress tolerance. UPLC-IMS-Q-TOF-MS analysis indicated the production of surfactin, iturin A, and bacillomycin lipopeptides, which are known for their membrane-disrupting activities, as well as with polyketides including macrolactin H, bacillaene, and difficidin. Comparative genomic analysis revealed that strain FB-4 harbors 10 strain-specific singleton genes, suggesting possible niche-specific adaptations. The combination of direct antifungal activity, broad-spectrum efficacy, and plant growth-promoting and stress-tolerance traits positions B. velezensis strain FB-4 as a promising candidate for further development as a biocontrol agent against pear Valsa canker. Future studies should focus on validating its efficacy under greenhouse and field conditions and elucidating the specific contribution of individual metabolites to the overall antifungal activity.