Observational study links Rosa roxburghii phenotypic variation to rhizosphere microbes and climate

Plant phenotypic variation represents an important expression of diversity among populations and their responses to heterogeneous environments. However, the factors associated with such variation remain incompletely characterized. In this study, we examined eight phenotypic traits of Rosa roxburghii across environmentally heterogeneous sites and characterized rhizosphere bacterial and fungal communities using 16S rRNA and ITS high-throughput sequencing. Marker taxa were identified, and statistical analyses were applied to explore associations between microbial patterns, climatic context, and phenotypic traits. Our results revealed significant differences among populations in fruit length, fruit width, and stem diameter. Microbial community analyses indicated inter-population divergence in both bacterial and fungal communities, with fungi showing relatively stronger compositional differentiation. Using complementary analytical approaches (LEfSe, LASSO, and sPLS-DA), we identified a consensus set of 12 marker taxa, including six bacterial and six fungal genera. Correlation analyses suggested that fungal markers exhibited broader associations with phenotypic traits than bacterial markers, and regression analyses indicated that fungal markers were statistically associated with variation in fruit size. Stem diameter showed associations with both climatic variables and microbial markers. Overall, phenotypic variation in R. roxburghii was associated with patterns in rhizosphere microbial communities and climatic context, highlighting complex relationships that warrant further investigation. This study contributes descriptive insights into plant–microbe and environment–phenotype associations and provides a foundation for future work aimed at elucidating underlying mechanisms.