Bacillus licheniformisYB06: A Rhizosphere–Genome-Wide Analysis and Plant Growth-Promoting Analysis of a Plant Growth-Promoting Rhizobacterium Isolated from Codonopsis pilosula

<i>Codonopsis pilosula</i>, commonly known as Dangshen, is a valuable medicinal plant, but its slow growth and susceptibility to environmental stress pose challenges for its cultivation. In pursuit of sustainable agricultural practices to enhance the yield and quality of Dangshen, the present study isolated a bacterial strain exhibiting plant growth-promoting potential from the rhizosphere of <i>C. pilosula</i>. This strain was subsequently identified as <i>Bacillus licheniformis</i>YB06. Assessment of its plant growth-promoting attributes revealed the potential of <i>B. licheniformis</i> YB06 as a biofertilizer. Whole-genome sequencing of <i>B. licheniformis</i> YB06 revealed a genome size of 4,226,888 bp with a GC content of 46.22%, harboring 4325 predicted protein-coding sequences. Genomic analysis of <i>B. licheniformis</i> YB06 revealed a diverse array of genes linked to induced systemic resistance (ISR) and plant growth-promoting (PGP) traits, encompassing phytohormone production, nitrogen assimilation and reduction, siderophore biosynthesis, phosphate solubilization, biofilm formation, synthesis of PGP-related amino acids, and flagellar motility. Seed germination assays demonstrated the positive effects of <i>B. licheniformis</i> YB06 on the germination and growth of <i>C. pilosula</i> seedlings. Furthermore, we explored various fertilization regimes, particularly the <i>B. licheniformis</i> YB06-based biofertilizer, were investigated for their impact on the structure and diversity of the <i>C. pilosula</i> rhizosphere soil bacterial community. Our findings revealed that fertilization significantly impacted soil bacterial composition and diversity, with the combined application of <i>B. licheniformis</i> YB06-based biofertilizer and organic fertilizer exhibiting a particularly pronounced enhancement of rhizosphere bacterial community structure and diversity. This study represents the first report on the beneficial effects of <i>B. licheniformis</i> YB06 on both the growth of <i>C. pilosula</i> and the composition of its rhizosphere soil microbial community. These findings provide a theoretical foundation and practical guidance for the development of novel bio-organic compound fertilizers, thereby contributing to the sustainable cultivation of <i>C. pilosula</i>.