Endophytic bacteria of Heracleum candicans as potential microbial sources for bioactive flavonoids

Heracleum candicans is a wild medicinal plant renowned for its anti-inflammatory-, analgesic-, and anti-osteoporosis-related properties, which have been attributed to its high flavonoid content. However, the community composition of endophytic bacteria across its various tissues and their potential roles in flavonoid accumulation remain unclear. To address this, we employed high-throughput sequencing to compare the diversity of endophytic bacteria in rhizosphere soil and different tissues of H. candicans collected in Xizang. Additionally, we utilized liquid chromatography-mass spectrometry analysis to detect the types and concentrations of flavonoids in the roots. A correlation analysis was performed to identify bacterial groups associated with flavonoid synthesis, and pure-culture methods were employed to screen and isolate target bacterial communities. Ultimately, a target strain was obtained through genetic and metabolite verification. Significant differences in microbial richness and diversity were identified across various H. candicans tissues, with each exhibiting its own dominant microbiota. A correlation analysis revealed that Bradyrhizobium , Bacillus , and Paenibacillus are key contributors to flavonoid accumulation. A total of 220 isolates were obtained through pure culture techniques. By screening for the flavonol synthase gene, conducting correlation analyses, and validating metabolites, eight bacterial strains were identified that produced 25 types of flavonoids, predominantly genistein, daidzein, daidzin, genistin, glycitein, and glycitin, and they all demonstrated significant antioxidant and antibacterial activities. Our findings enhance the understanding of plant–microbe interactions and provide materials and support for the development of functional bacteria capable of metabolizing flavonoids, as well as for the industrial production of their secondary metabolites.