Site- and Compartment-Associated Differentiation of Root Microbiomes in Rhododendron yunnanense

Root-associated microbiomes vary across environmental settings and root compartments, but these patterns remain poorly understood in wild woody plants. Here, we compared bacterial and fungal communities in the rhizosphere and root endosphere of Rhododendron yunnanense across four montane sampling sites in Yunnan, China, using 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing. α-diversity differences were mainly reflected in amplicon sequence variant (ASV) richness, whereas Shannon and Simpson diversity varied less among site–compartment combinations. Bray–Curtis community composition was significantly associated with sampling site, root compartment, and their interaction for both bacteria and fungi. Stable and core ASV analyses further showed limited overlap between the rhizosphere and endosphere. Under the predefined core criteria, only three bacterial ASVs were shared between compartments, while no fungal ASV qualified as a shared core member. The extent of stable-ASV overlap varied among sampling sites and differed between bacterial and fungal communities. Indicator-value analysis, paired abundance testing, and Random Forest classification converged on a smaller set of compartment-associated genera. Thirteen taxonomically interpretable genera were retained for main-text interpretation, including five bacterial genera associated with the endosphere and eight fungal genera, of which Phialocephala was associated with the rhizosphere. Together, these results show that sampling site and root compartment are both associated with marked differentiation of the R. yunnanense root microbiome. The low overlap of stable and core taxa further indicates substantial microbial turnover between the rhizosphere and endosphere, providing a basis for future functional validation of compartment-associated taxa.