The B115 strain, isolated from the inter-root soil of healthy plants in a continuous cropping site of Panax notoginseng, was identified as Bacillus velezensis B115 by 16S rDNA sequence comparison and comparative genomic analysis. B115 is a strain of beneficial microorganisms present in the inter-root zone of plants, with favorable plant growth-promoting properties and antagonistic effects against the plant pathogen Fusarium oxysporum. However, the whole genome of B115 remains unclear, thus restricting its potential applications. To address this gap, the whole genome of B115 has been sequenced and annotated to elucidate the molecular mechanisms underlying its plant growth-promoting and antimicrobial activities. The genome analysis revealed that B115 comprises a single circular chromosome of 4,200,774 bp and a plasmid region 16,878 bp long, possessing a GC content of 45.95%. Moreover, 4349 protein-coding genes were predicted. Notably, the B115 genome contains a substantial number of genes (103) involved in the biosynthesis, transport, and catabolism of secondary metabolites. Through genome mining, 13 BGCs and 540 genes encoding secondary metabolites with predicted roles were identified, including members of the surfactin and fengycin families. Utilizing LC–MS/MS technologies, 2318 metabolites were detected in the fermentation broth of B. velezensis B115, encompassing compounds such as Corynebactin, Gamabufotalin, Pracinostat, Indoleacetic acid, (8)-Gingerol, Luteolin, Liquiritigenin, and other metabolites with antimicrobial, growth-promoting, antioxidant, and antitumor properties. By exploring secondary metabolite-related genes and predicting potential secondary metabolites from the B115 genome based on the whole-genome sequence results, we further elucidate the genomic basis for its ability to promote plant growth and inhibit pathogen activity.

Diseases triggered by phytopathogenic bacteria lead to substantial economic losses within the realm of agricultural production. Bacillus velezensis is an important agricultural biocontrol and plant growth-promoting bacterium. In this study, we evaluated the inhibitory ability of B. velezensis D83 against eight plant pathogenic fungi. D83 has a broad spectrum of antagonistic activity against these eight plant pathogens. In addition, our study found that D83 promotes seed germination and plant growth in maize and tobacco, and this growth-promoting ability is related to its growth-promoting properties such as indoleacetic acid production, nitrogen fixation, and phosphate solubilization. This effect of promoting plant growth is more effective than the microbial preparations on the market. A complete genome sequencing of D83 yielded a genome size of 3,929,757 bp and a GC content of 46.5%. The genome analysis identified 3,987 protein-coding genes. Gene clusters for the antimicrobial metabolites fengycin, surfactin , bacilysin, butirosin A/B, bacillaene, difficidin, macrolactin, surfactin, and bacilysin were identified in D83. Genes associated with plant growth promotion were also identified and analyzed. Analysis of the amplicons of genes associated with fengycin, surfactin, and iturin synthesis revealed that D83 has the capacity to encode the genes responsible for fengycin, surfactin, and iturin synthesis. In addition, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of D83 cell sediment extracts confirmed the presence of antifungal metabolites and plant growth-promoting hormones. These results suggested that D83 has the combined ability to promote plant growth and antagonize common plant pathogens and is a source for further development of antimicrobial compounds. IMPORTANCE: D83 has a broad-spectrum inhibitory effect on eight plant pathogenic fungi. D83 also demonstrated the properties of a variety of plant-promoting bacteria. Under in vitro conditions, D83 has the ability to promote the germination of maize and tobacco seeds, and in pot experiments, D83 has the ability to promote the growth of maize and tobacco seedlings and suggests that promotion is more pronounced than that of sterile water treatment (CK) and commercially available microbial preparations treatment (A). The gene cluster responsible for the production of the antimicrobial metabolites fengycin, surfactin, bacilysin, butirosin A/B, bacillaene, difficidin, macrolactin, surfactin, and bacilysin was identified in the D83 genome by genome prediction analysis. The genes responsible for fengycin, iturin, and surfactin biosynthesis were identified by D83 amplicon analysis. Furthermore, LC/MS analysis of D83 fermented extracts confirmed the presence of antifungal metabolites and plant growth substances.