The structure of rhizosphere microbial and endophytic communities of Coptis chinensis var. brevisepala: variations across different ecological niches

Coptis chinensis var. brevisepala is a valuable traditional Chinese medicinal plant, whose resources are severely depleted due to long-term overexploitation. However, the associations between its rhizosphere microbiome and habitat soil properties, as well as the composition and functions of endophytes, remain unclear. This study employed high-throughput sequencing to characterize rhizosphere microbial communities of C. chinensis var. brevisepala from four distribution sites, analyze their correlations with soil chemical properties, and explore the differences and functional traits of endophytic communities in distinct tissues (leaves, rhizomes, fibrous roots). A total of 177 core bacterial genera and 146 core fungal genera were detected in rhizosphere soils of the four sites. The dominant bacterial phyla were Proteobacteria, Acidobacteriota, and Actinobacteriota, with norankfXanthobacteraceae and Bradyrhizobium as the dominant genera. The dominant fungal phyla were Ascomycota and Basidiomycota, with Paraboeremia and Saitozyma as the dominant genera. Soil chemical properties exerted significant effects on both bacterial and fungal communities in the rhizosphere, among which soil pH and total nitrogen (TN) were the key drivers shaping rhizosphere microbial communities. For endophytes, 29 bacterial phyla (596 genera) and 12 fungal phyla (653 genera) were identified, with significant differences in diversity, richness, and dominant genera across tissues; leaves harbored the highest endophytic diversity. Functional prediction indicated that endophytic fungi were dominated by saprotrophy-related functional genes, and KEGG secondary functional annotation uncovered the presence of antimicrobial-related genes. This study clarifies the rhizosphere microbiome ecological traits and tissue-specific endophytic characteristics of C. chinensis var. brevisepala, providing a scientific basis for screening beneficial microorganisms to facilitate the restoration and reconstruction of this endangered medicinal plant.