Composition, function and driving factors of microbial communities in rhizosphere soil and root endophyte of Codonopsis pilosula in different years

Root microbial communities influence plant health and response to environmental stress. While the succession of rhizosphere soil and endophytic microbial communities in the growth stage of perennial medicinal plant Codonopsis pilosula remains unclear. In this study, rhizosphere soil and root tissue samples of one-year, two-year and three-year C. pilosula were selected to determine the community composition and diversity of rhizosphere soil and root endophyte microorganisms based on high-throughput sequencing technology. The results showed that the composition and structure of microbial community in rhizosphere soil and root endophyte of C. pilosula were different in different planting years. The abundance of Proteobacteria has decreased significantly, while that of Acidobacteria and Ascomycota have increased significantly. The neutral community model showed that the bacteria were mainly affected by random assembly and fungi by deterministic assembly. The complexity of microbial network in rhizosphere soil was higher than that in the root endophyte, and the complexity of bacterial network was higher than that of fungal community. Environmental factors significantly affected the microbial diversity of C. pilosula root system, while the growth years had little effect on it. Soil protease (PRO), soil total nitrogen (TN) and microbial biomass carbon (MBC) were the key factors causing the changes of C. pilosula microbiome. This study provides insights into the dynamic changes and driving factors of root microbial community of C. pilosula, and provides a basis for regulating root microbial community in C. pilosula cultivation to improve the sustainability of agricultural production.