Artificial Cultivation Reshapes Soil Nutrient Heterogeneity, Microbial Community Structure, and Multi-Nutrient Cycling Drivers of the Endangered Medicinal Plant Sinopodophyllum hexandrum

Artificial cultivation of the endangered medicinal plant Sinopodophyllum hexandrum is a key strategy for resource protection and supply, yet cultivation can cause soil degradation and microbial disorder, while the effect of cultivation on the microbial community and its relationship with soil nutrients remains unclear. This study aimed to explore the effects of artificial cultivation on the soil–microorganism–nutrient cycling system of Sinopodophyllum hexandrum, a rare medicinal plant. We compared three groups (Native-wild, Mix-wild, Mix-cultivated) by analyzing soil physicochemical properties, microbial diversity, community structure, co-occurrence networks, and multi-nutrient cycling drivers. Geographic position drove spatial (landscape scale) heterogeneity of soil nutrients, while cultivation shaped its vertical (soil depth) counterpart. Cultivation altered the natural vertical nutrient pattern via surface fertilization, causing nutrient surface retention. Microbial communities exhibited wild-specific/cultivation-specific responses, bacteria were slightly more sensitive to cultivation effect than fungi. Cultivation altered microbial network complexity depending on the host and increased instability, with only bacterial network associations correlating with soil factors. Fungal diversity and specific taxa became core drivers of multi-nutrient cycling. This study clarifies cultivation’s regulatory mechanism on S. hexandrum’s soil–microorganism system, providing a basis for optimizing cultivation management and protecting this endangered species.