Linking Host Provenance, Microbial Assembly, and Environmental Legacy Effects in the Root-Associated Microbiome of Tripterygium wilfordii Hook f.

Plant-associated microbiomes play critical roles in regulating plant growth, nutrient acquisition, and stress adaptation. However, whether geographically distinct plant provenances retain heritable signatures that influence microbiome assembly under uniform environmental conditions remains poorly understood. In this study, 16S rRNA amplicon sequencing was employed to characterize root-associated bacterial communities of clonally propagated Tripterygium wilfordii derived from nine provenances and cultivated under identical soil conditions, with additional sampling from native populations. Host provenance significantly affected community composition, explaining 27.0% and 32.6% of the variation in rhizosphere and endophytic communities, respectively. Rhizosphere bacterial diversity differed significantly among provenances, whereas endophytic communities showed stronger differentiation in community structure and deterministic host selection. Although native plants exhibited lower bacterial diversity, they recruited more potential plant growth-promoting bacteria compared with transplanted plants. Environmental factors, particularly historical mean annual precipitation and longitude of native habitats, significantly influenced community diversity and structure. Distance–decay patterns demonstrated that root-associated bacterial communities retained climatic imprints from their native provenances despite cultivation under common-garden conditions. This study provides evidence that plant provenance can leave persistent microbial signatures and highlights the importance of integrating host genetic background and microbiome characteristics to understand ecological adaptation and improve germplasm utilization in medicinal plants.