Multifunctional Bioactivity of Bacillus amyloliquefaciens SH-53: Analysis of Multiple Antagonistic and Synergistic Growth Promotion Mechanisms Based on Whole Genome

<i>Bacillus amyloliquefaciens</i> is an important agricultural microbial resource. This study focuses on the whole genome analysis and functional characterization of <i>B. amyloliquefaciens</i> SH-53, isolated from the Wuliang Mountain National Nature Reserve in Dali, Yunnan. The genomic feature analysis revealed that the genome of SH-53 contains 27 ribosomal RNA operons, 4078 protein-coding genes, and 250 prophage-related genes. Additionally, 12 biosynthetic gene clusters (BGCs) for secondary metabolites were predicted, of which 7 are novel gene clusters with unknown functions, showing significant differences compared to the known BGCs of conventional biocontrol strains. Functional potential analysis indicates that SH-53 possesses potential antagonistic activity against plant pathogenic bacteria and can colonize the plant rhizosphere through various mechanisms to exert growth-promoting effects. It is capable of synthesizing multiple antibacterial secondary metabolites, indole-3-acetic acid (IAA), iron carriers, secreting amylase, and efficiently utilizing sulfur sources. The genome also harbors a complete core gene network related to the induced systemic resistance (ISR) and supporting genes that maintain secondary metabolism homeostasis. In conclusion, <i>B. amyloliquefaciens</i> SH-53 exhibits rich biocontrol-related characteristics and unique secondary metabolic potential, indicating promising prospects for its development as an excellent biocontrol agent.