Habitat‑associated differences in rhizosphere microbiome of Polygonatum kingianum: a comparative study of wild and cultivated plants

Wild populations of Polygonatum kingianum , an important medicinal plant, are increasingly threatened by overharvesting, leading to the expansion of its cultivation. Rhizosphere microorganisms are critical for nutrient uptake, disease resistance and bioactive compound formation. However, the differences in the rhizosphere microbiome between wild and cultivated habitats remain unclear, and systematic studies on what these differences entail and how they may inform ecological cultivation of P. kingianum are still lacking. We found marked differences in soil physicochemical properties and enzyme activities between wild and cultivated P. kingianum rhizospheres. Compared with cultivated plants, wild plants had significantly higher levels of alkali‑hydrolyzable nitrogen (AHN), soil organic matter (SOM), available phosphorus (AP), and higher activities of urease (UE), sucrase (SC) and catalase (CAT), whereas pH and acid phosphatase (ACP) activity were significantly lower. Analysis of bioactive constituents showed that cultivated rhizomes accumulated more total polysaccharides and total saponins than wild ones, while the opposite pattern was observed for total phenolics. In terms of community composition, the dominant bacterial phyla in both groups were Acidobacteriota and Pseudomonadota, and the dominant fungal phyla were Basidiomycota and Ascomycota. At the genus level, Bradyrhizobium was enriched in the cultivated group as a bacterial differentially abundant taxon. Among fungal differentially abundant taxa, Lactifluus , Penicillifer and Volutella were the dominant genera in the cultivated group, whereas Subulicystidium was dominant in the wild group. Functional predictions revealed that bacterial communities in wild rhizospheres were enriched in central carbon and nitrogen metabolic pathways, such as the TCA cycle and pyrimidine metabolism, whereas those in cultivated rhizospheres were enriched in pathways related to xenobiotic biodegradation and metabolism. The fungal community in wild plants was dominated by saprotrophic functions, while cultivated plants showed a greater abundance of ectomycorrhizal functional groups. This study provides a comparative characterization of the rhizosphere microbiomes of wild and cultivated P. kingianum , highlighting habitat‑associated differences in microbial community structure, functional potential, and their links to soil properties and plant bioactive compounds. These findings offer a foundation for further studies on the ecological cultivation of P. kingianum .