Pan-genomic analysis reveals ecological adaptation and biocontrol of Bacillus pumilus

Bacillus pumilus is known for its ecological resilience and plant-beneficial traits; however, the genomic basis of its biocontrol potential remains unclear. Here, we performed a comparative pan-genome analysis of ecologically diverse B. pumilus strains to explore the genetic determinants underlying plant association and antimicrobial activity. The species exhibited an open pan-genome containing 6035 gene clusters, including a conserved core genome of 3078 clusters and a diverse accessory genome. Functional annotation revealed conserved gene clusters involved in biofilm formation, sporulation, auxin biosynthesis, metal detoxification, short-chain fatty acid regulation, and nutrient-sensing regulators. Genome mining further identified conserved biosynthetic gene clusters encoding antimicrobial compounds and siderophores, including bacilysin and bacillibactin, which are associated with pathogen suppression and plant protection. Several of these strains also possessed unique gene clusters linked to nutrient acquisition, metal detoxification, and environmental adaptation. The universal presence of the chloramphenicol resistance gene (cat86) underscores a conserved adaptive trait. These findings indicate that the ecological versatility of B. pumilus is driven by a stable core genome combined with a dynamic accessory genome enriched in its secondary metabolite pathways, highlighting its potential for sustainable agriculture and biological control. This study presents original research findings based on comparative pan-genome analysis of Bacillus pumilus strains.