Niches-driven changes in microbial communities contributes to medicinal compound accumulation in Panax notoginseng

Understanding how environmental gradients shape soil microbial communities and their functions is essential for optimizing medicinal plant cultivation. In this study, the rhizosphere microbial communities of Panax notoginseng (PN) were investigated along an altitudinal gradient in Southwest China, integrating amplicon sequencing, soil physicochemical analysis, and plant metabolite profiling. Results revealed that elevation was significantly related to soil carbon and phosphorus fractions, and microbial community composition, with a pronounced effect on fungal specialists. Null-model analysis suggested that homogeneous selected bacterial generalists exhibited more than 1.5 folds higher diversity and network connectivity compared to other subcommunities, which may contribute to microbial network stability, while stochastic process selected fungal specialists might be more responsive to elevation-associated changes and network complexity. Functional potential predicted using FUNGuild and PICRUSt2 suggested distinct ecological roles: bacterial generalists were enriched in nutrient-cycling genes, whereas fungal specialists were associated with symbiotic and saprotrophic lifestyles. Importantly, saponin contents in PN roots decreased with elevation and were positively correlated with mean annual temperature (MAT) but negatively correlated with soil organic carbon (SOC) and readily oxidizable carbon (ROC). Partial Least Squares modeling (Goodness-of-Fit, GOF = 0.548) indicated that fungal specialists and bacterial generalists might be associated with the effect of carbon pool and the ratio of SOC and total nitrogen (TN) on the accumulation of medical compound (saponins and flavonoids), separately (p < 0.05). These findings underscore the potential roles of bacterial generalists and fungal specialists in mediating plant-soil-microbe interactions and emphasize their ecological significance for the sustainable cultivation of PN amid changing environmental conditions. • Elevation induces shifts in rhizosphere microbial communities and their functional traits. • Bacterial generalists and fungal specialists complementarily contribute to microbial network stability and complexity. • Homogeneous selection drives community assembly within the bacterial generalist subcommunity. • Bacterial generalists and fungal specialists mediate the link between soil nutrients and bioactive compound accumulation. • This study provides a comprehensive framework integrating microbial ecology, soil chemistry, and plant metabolomics.