Genome and antimicrobial compounds analysis of Bacillus subtilis M51 as a potential biocontrol agent against Fusarium oxysporum

Fusarium oxysporum is a common fungal pathogen of wheat that severely impacts plant growth and causes grain yield loss. The identification of potential biocontrol agents is important to complement agricultural management practices and reduce the use of chemical fungicides. This study investigated the potential mechanism of Bacillus subtilis strain M51 inhibition of F. oxysporum and analyzed secondary metabolite-related compounds based on M51 whole-genome sequencing results. The strain M51 was experimentally isolated from healthy wheat roots and identified as B. subtilis. This strain showed significant antagonistic effects against seven phytopathogenic fungi, with the highest inhibition rate of 64.35% observed against F. oxysporum YJ-2. Fusarium oxysporum treated with a crude extract of M51 fermentation broth produced rough and abnormally twisted mycelium, an increased number of branch nodes, and disruption of mycelial cell membranes. The activity of peroxidase in F. oxysporum treated with the crude extract was significantly reduced, whereas reactive oxygen species accumulation and malondialdehyde content were increased. Genome sequencing revealed that M51 contained a single circular chromosome 4,425,418 bp in length, with 4498 coding sequences and an average GC content of 43.05%. Genomic analysis revealed that it contained protein-encoding genes for the production of cellulase, lipopetides, indole-3-acetic acid, and iron carriers, for example, which assist in plant defense against pathogen infection and promote plant growth. Six lipopetides (surfactin, fengycin, bacillaene, bacillibactin, bacilysin, and subtilosin A) and small secondary metabolites (dimethyl carbate, aviglycine hydrochloride, butroxydim, D-limonene, latilure, and oryctalure) were detected from the M51 crude extract by UHPLC-QTOF-MS/MS. In addition, a pot experiment indicated that the sterile filtrate from M51 fermentation broth can promote the growth of wheat seedlings. These findings demonstrate the potential of M51 as a biological control agent against wheat root-rot fungi and provide a foundation for the development of novel secondary metabolites that effectively inhibit pathogenic fungi.