Genomic and Metabolomic Characterization of Bacillus velezensis CMC-6 Reveals Biocontrol Potential Against Potato Fusarium Wilt

Background Potato Fusarium wilt, caused primarily by Fusarium oxysporum , is a significant soil-borne disease posing a serious threat to global potato production, with yield losses reaching 30-78% in continuously cropped fields. While Bacillus -based biocontrol agents offer promising, environmentally sustainable alternatives to chemical fungicides, comprehensive mechanistic studies integrating genomic and metabolomic approaches remain limited, particularly regarding the identification of key biosynthetic gene clusters (BGCs) and their associated antifungal metabolites responsible for disease suppression. Understanding the molecular basis of biocontrol activity is essential for developing effective biological control strategies. Results A multifunctional biocontrol strain, Bacillus velezensis CMC-6, was isolated from potato rhizosphere soils in Inner Mongolia, China. The strain exhibited strong antagonistic activity against F. oxysporum (76.37% inhibition) and demonstrated broad-spectrum antifungal effects against six additional phytopathogens, including Rhizoctonia solani , Alternaria alternata , and Botrytis cinerea . Functional characterization revealed multiple plant growth-promoting traits, including indole-3-acetic acid (IAA) production (12.24 mg/L), inorganic phosphate solubilization, and secretion of cell wall-degrading hydrolytic enzymes (cellulase, ligninase, pectinase, and protease activities). Whole-genome sequencing identified a circular chromosome of 3,929,792 bp containing 3,694 predicted protein-coding genes and 13 biosynthetic gene clusters (BGCs) encoding secondary metabolites, including macrolactin, bacillaene, fengycin, difficidin, surfactin, bacillibactin, and bacilysin, indicating strong biosynthetic capacity to produce bioactive lipopeptides and polyketides. Comparative metabolomics analysis using LC-MS/MS further revealed significant upregulation of antifungal/antibiotic-related metabolites, notably fumigaclavine B, dioscin, and fungichromin, which correlated with enhanced inhibitory activity against target pathogens. Greenhouse experiments demonstrated a control efficacy of 79.23% against Fusarium wilt and a 27.69% increase in plant biomass. Field trials across three Inner Mongolian sites achieved control efficacies of 35.53%, 47.51%, and 58.43%, accompanied by consistent yield gains exceeding 17.57% and a maximum increase of 27.43%. Conclusion This study provides comprehensive genomic and metabolomic evidence supporting B. velezensis CMC-6 as a multifunctional biocontrol agent with significant potential for the sustainable integrated management of potato Fusarium wilt. The integrated multi-omics approach elucidated the molecular basis of its antagonistic activity and provides valuable microbial resources for developing effective bioformulations in agricultural practice. These findings advance our understanding of Bacillus -mediated biocontrol mechanisms and support the development of environmentally friendly disease management strategies.