Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in Antibacterial Bacillus pumilus Strain SF-4

The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of B. pumilus strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with “biosynthesis of secondary metabolites, transport, and catabolism” (Q), “replication, recombination and repair” (L), and “unknown function” (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced B. pumilus SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 B. pumilus strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future.