Integrating genomics and targeted metabolite profiling to elucidate disease-suppression mechanisms of Bacillus velezensis GFB08

Welsh onion cultivation in Taiwan faces a significant threat from a foliar disease complex caused by three major pathogens: <i>Stemphylium vesicarium, Colletotrichum spaethianum</i>, and <i>C. circinans</i>. As an alternative to conventional fungicides, the biocontrol agent <i>Bacillus velezensis</i> GFB08 was systematically characterised through an integrated genomic and targeted metabolite profiling approach. The 3.89 Mbp genome harbored biosynthetic gene clusters for key lipopeptides, and comparative genomics revealed a mersacidin-like BGC, a feature variably present in B. velezensis, indicating enhanced antimicrobial potential. Metabolite profiling identified fengycin and bacillomycin D as the primary antifungal compounds. Bioassays demonstrated that purified fengycin exhibited potent, broad-spectrum activity against all three pathogens, while bacillomycin D displayed species-specific effects, significantly inhibiting only <i>C. spaethianum</i>. The interaction between these two lipopeptides was determined to be additive, not synergistic, against <i>C. spaethianum</i>. Furthermore, volatile organic compounds (VOCs) from GFB08 significantly inhibited <i>C. spaethianum</i> while unexpectedly stimulating the growth of <i>C. circinans</i>, highlighting the complexity of its biocontrol mechanisms. Among these VOCs, acetic acid was highly effective, providing complete inhibition at a concentration of 0.1 µL/mL. The strain also demonstrated a significant plant growth-promoting effect, which was limited to the seed stage. This study provides the first integrative genomic-metabolite-functional characterization of a Welsh onion biocontrol strain GFB08, clarifying its multi-modal mechanisms and highlighting the role of mersacidin-associated genomic features and pathogen-specific VOC responses in biocontrol efficacy.