Genomics and metabolomics assisted functional characterization of Bacillus velezensis D83 as a biocontrol and plant growth-promoting bacterium.

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.IMPORTANCED83 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.