Integrated genomic and phenotypic analysis of an endophytic bacterium reveals biocontrol and plant growth-promoting mechanisms

Root rot threatens Salvia miltiorrhiza yield and quality. We isolated an endophytic bacterium, Paenibacillus polymyxa DS-S6, from healthy plant stems that showed strong antifungal activity against Fusarium solani and other phytopathogens. The strain exhibited multiple plant growth-promoting traits, including phosphate solubilization, siderophore production, and secretion of indole-3-acetic acid-like compounds. Pot experiments confirmed that DS-S6 significantly promoted seedling growth and suppressed Fusarium root rot. The complete 5.84 Mb genome revealed 18 biosynthetic gene clusters, with five showing 100% similarity to known antifungal lipopeptide clusters. LC-MS confirmed production of fusaricidins and paenibacillin. GFP-tagged DS-S6 successfully colonized rhizosphere and internal tissues for at least 50 days. This integrated analysis positions DS-S6 as a promising multi-functional candidate for sustainable biocontrol and growth promotion in S . miltiorrhiza cultivation.