Comparative genomic analyses reveal key traits for biocontrol and the promotion of plant growth in Paenibacillus strains

Paenibacillus species have emerged as promising candidates for sustainable agriculture due to their functional versatility in plant growth promotion and biocontrol. We performed a comparative genomic analysis of 428 high-quality Paenibacillus genomes to assess their ecological adaptability and biotechnological potential. The analyzed strains originated from diverse environments, reflecting broad ecological distribution. Functional annotation revealed a widespread occurrence of plant growth-promoting traits (PGPTs), including phosphate and potassium solubilization, siderophore biosynthesis, nitrogen fixation, and phytohormone-related compounds. On average, the genomes contained 249 genes associated with biofertilization, 190 with phytohormone production, 97 linked to bioremediation, and around 322 involved in competitive exclusion. The open pan-genome configuration (b = 0.503) highlights notable genetic plasticity and ongoing gene acquisition. While the core genome was enriched in essential functions, accessory and unique fractions carried genes associated with environmental adaptation and niche specialization. Analysis of mobile genetic elements (MGEs) showed that some PGPT-related genes occur in mobile regions, suggesting horizontal gene transfer contributes to the dissemination of beneficial traits. Diverse BGCs, including those encoding Bacillopaline, Tridecaptin, Fusaricidin B, Paeninodin, and Polymyxin, were identified, many with antimicrobial potential. CAZyme profiling revealed abundant chitinases, supporting pathogen suppression capacity. No virulence factors were detected, and antibiotic resistance genes were rare, underscoring the genus’ low pathogenicity. Altogether, these findings position Paenibacillus as a genetically and functionally diverse group with strong potential as a safe, sustainable resource for developing biofertilizers and biopesticides.