Plant-associated microbes play a crucial role in host growth, health, and stress resistance. Host plants significantly influence the assembly of their microbial communities. To examine the influence of plant provenance on bacterial composition and plant growth promoting (PGP) properties, we compared readily culturable bacteria isolated from the root interior and rhizosphere of Tripterygium wilfordii Hook f., a woody Chinese medicinal plant, across three provenances grown in different regions. Regardless of the host growing environment, the abundance of endophytic bacterial colonies followed the trend: Fujian provenances > Hunan provenances > Hubei provenances. A total of 227 isolates were classified into 21 genera from the root interior and 40 genera from the rhizosphere, with Pseudomonas and/or Bacillus as the dominant genera. The taxonomic composition varied across plant provenances and host growing environments. Plants from the same provenance but cultivated in different locations exhibited greater similarity in their endophytic bacterial composition. The majority of the assayed strains displayed one or more PGP traits. Local plants harbored a higher proportion of PGP strains than non-local plants. Our findings indicate that plant provenance significantly influences the composition of root-associated culturable bacteria, particularly endophytic communities. Plants in their native environments may recruit PGP bacteria to enhance their fitness.

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.