Microbiome-mediated geo-authenticity of Panax quinquefolius L.: Linking soil nutrients, root-associated microbiomes, and metabolites

Panax quinquefolius L. (P. quinquefolius) is a high-value medicinal plant characterized by substantial regional differentiation in root secondary metabolite composition. Despite increasing evidence that environmental conditions and rhizosphere microorganisms jointly influence plant metabolic processes, the mechanistic pathways linking environmental gradients, microbial communities, and metabolite biosynthesis in P. quinquefolius remain largely unresolved. We performed an integrated multi-omics analysis by coupling LC-MS/MS-based metabolomic profiling with bacterial and fungal high-throughput sequencing in both rhizosphere and root endosphere across three major cultivation regions in China (Northeast, Northwest, and Shandong). Microbial co-occurrence networks, functional gene predictions, and multivariate correlation analyses were used to investigate how environmental and biotic factors shape metabolite profiles. Significant regional differences were observed in root metabolite composition, Shannon diversity, community structure, and nutrient-cycling gene abundance. Notably, roots from Shandong accumulated 17 triterpenoid saponins but only 3 terpenoid precursors compared to other regions, which was significantly associated with the decrease in total nitrogen, microbial diversity, and the enrichment of arbuscular mycorrhizal fungi (AMF) in the rhizosphere, highlighting the role of nutrients and microbial symbionts in stimulating secondary metabolism. Partial least squares structural equation modeling indicated that geographical differences exerted significant effects (path coefficients = 0.77) on metabolite accumulation via soil properties and microbial community composition. Our findings demonstrate that the geo-authentic accumulation of metabolites in P. quinquefolius roots is driven by the interactions among soil nutrients, microbial communities, and plant metabolism. Rhizosphere and endosphere microbiomes act as critical modulators of triterpenoid saponin biosynthesis, emphasizing their importance in determining the medicinal quality and Daodi characteristics of P. quinquefolius .