Transplantation-Driven Microbial Shifts and Keystone Taxa Enhance Medicinal Ingredients in Astragalus mongholicus

Root-associated microbes play a crucial role in plant growth, stress resistance and the accumulation of secondary metabolites. In this study, LC-MS analysis revealed that soil provenance exerts a decisive influence on the content of flavonoids and astragalosides in <i>Astragalus membranaceus</i>. Transplant assays revealed that each soil type acted as a selective filter, assembling distinct microbial communities in both the rhizosphere and root of <i>Astragalus membranaceus</i>. The rhizosphere taxa selected from Yangling soil specifically enhanced flavonoid levels, whereas the root taxa selected from TanChang soil drove higher astragaloside accumulation. SourceTracker revealed that seedling root-endosphere ASVs served as the primary inoculum for later communities, confirming strong priority effects among early colonizers. Keystones tightly linked to both metabolite contents and biomass belonging to <i>Caulobacteraceae</i>, <i>Acidimicrobiia</i>, <i>Sutterellaceae</i>, <i>Bradyrhizobium</i>, <i>Sphingomonas</i> and <i>Mesorhizobium</i> were isolated, and the SynComs were constructed. In Tanchang soil, SynComs inoculation raised Astragaloside IV (AST IV) and Calycosin-7-glucoside (CAG) contents by 52.30% and 55.73%, respectively; in Yangling soil, the same consortium increased Astragaloside I (AST I), Astragaloside II (AST II), AST IV and CAG by 29.38%, 39.04%, 54.97% and 58.98% compared to the uninoculated controls. Collectively, our work charts the transplantation-driven dynamics of root-associated bacterial communities and medicinal metabolites, pinpoints keystones that govern ingredient accumulation and delivers validated microbial strains for enhancing the quality and pharmaceutical value of <i>Astragalus mongholicus</i>.