Genome mining and metabolite profiling uncover the biocontrol and plant growth-promoting capacities of Bacillus velezensis TCS001

• B . velezensis TCS001 contains a 4.12 Mb genome with 4,243 genes and 13 BGCs. • Metabolomics revealed 3,739 metabolites with antimicrobial and growth-promoting traits. • Iturin A4 showed the strongest antifungal effect among tested analogues. • Iturin A4 altered fungal genes for membrane, stress, transport and metabolism. • Multi-omics support TCS001 as a biocontrol and plant growth-promoting bacterium. Bacillus velezensis TCS001, isolated from Bohai Sea sediments, is a beneficial microbial strain exhibiting both plant growth-promoting properties and antagonistic activity against plant pathogens, with particularly efficacy against Botrytis cinerea . However, the whole genome of TCS001 remains unclear, thus restricting its potential applications. To address this gap, the whole genome of TCS001 has been sequenced and annotated to elucidate the molecular mechanisms underlying its plant growth promoting and antimicrobial activities. The genome analysis revealed that TCS001 comprises a single circular chromosome of 4,124,134 bp, possessing a GC content of 46.18 %. Moreover, 4243 protein-coding genes were predicted. Through genome mining, 13 BGCs encoding secondary metabolites with predicted roles were identified, including members of the surfactin, fengycin, and macrolactin families. Utilizing UHPLC–MS/MS technologies, a total of 2,277 metabolites in positive ion mode and 1,462 metabolites in negative ion mode were identified across the CFS and CLE of TCS001, encompassing compounds such as bergenin, gentiopicroside, mycophenolic acid, indole-3-butyric acid, gibberellin A89, A39, A125, arbutin, esculetin, gallic acid, protocatechuic acid, ponicidin, bruceine D,and other metabolites with antimicrobial, growth promoting, antioxidant, and antitumor properties. Three iturin analogues, namely iturin A2, A3, A4, were purified from the CLE.At 50 mg/L, iturin A2, A3, and A4 all showed above 70 % inhibition of B . cinerea mycelial growth, with iturin A4 (77.48 %) being more effective than A2 (72.82 %) and A3 (74.43 %). Transcriptomic analysis revealed that iturin A4 modulated the expression of genes involved in secondary metabolite biosynthesis, amino acid metabolism, and ABC transporters. These findings further elucidated the genomic basis for its ability to promote plant growth and inhibit pathogen activity.