Shaping of the core microbiome by ginsenosides in American ginseng across diverse habitats

Geographical environmental factors affect the secondary metabolism of plants and regulate rhizosphere microorganisms. However, the metabolite characteristics and rhizosphere microbial composition of American ginseng (Panax quinquefolius L., AG) from different sources remain unclear. In this study, high-throughput sequencing technology and metabolomics technology were used to analyze the microbial community structure and metabolite content in the rhizosphere soil of AG from different habitats, and the relationships between soil microorganisms and metabolites were analyzed. The results revealed that the diversity of rhizospheric soil bacterial and fungal communities in different habitats was unusual and affected the metabolite content. The bacterial genera strongly correlated with the triterpenoid saponins of AG included Bradyrhizobium and Pseudoxanthomonas. Among these, Bradyrhizobium was strongly negatively correlated with ginsenoside Rg1 (P < 0.001, r = - 0.8204), and Pseudoxanthomonas was strongly positively correlated with (PPD -2 H)-Glc-Glc-malonyl (P < 0.01, r = 0.6305). The fungal genera included Alternaria and Colletotrichum. Alternaria was strongly negatively correlated with ginsenoside F1 (P < 0.001, r = - 0.7434), and Colletotrichum was also strongly negatively correlated with ginsenoside F1 (P < 0.001, r = - 0.7106). The results revealed a complex correlation between rhizosphere-dominant microorganisms and the saponin content of AG, providing a theoretical basis for guiding rational cultivation planning and designing microbial fertilizers to enhance AG quality.