Yi-Tun ChoHIENG MING TINGBo-Wei WangYi-Chen TsaiHao-Yung WangYu-Liang YangHiran Anjana Ariyawansa2025-12-052025-12-052025-10-30https://www.scopus.com/record/display.uri?eid=2-s2.0-105021035984&origin=resultslisthttps://scholars.lib.ntu.edu.tw/handle/123456789/734334Welsh onion cultivation in Taiwan faces a significant threat from a foliar disease complex caused by three major pathogens: Stemphylium vesicarium, Colletotrichum spaethianum , and C. circinans . As an alternative to conventional fungicides, the biocontrol agent Bacillus velezensis 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 C. spaethianum . The interaction between these two lipopeptides was determined to be additive, not synergistic, against C. spaethianum . Furthermore, volatile organic compounds (VOCs) from GFB08 significantly inhibited C. spaethianum while unexpectedly stimulating the growth of C. circinans , 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.enBioactive secondary metabolitesBiocontrol agentComparative genomic analysisFermentation optimizationPlant growth promotion[SDGs]SDG2journal article10.1016/j.crmicr.2025.100503