Pan-genome analysis ofPaenibacillus polymyxa strainsreveals the mechanism of plant growth promotion and biocontrol

Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species.Paenibacillus polymyxais a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representativeP. polymyxastrains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome ofP. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification ofP. polymyxastrains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, thenifcluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable inP. polymyxa. Analysis of antibiotic gene clusters inP. polymyxarevealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis ofP. polymyxawill help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use ofP. polymyxain agriculture.