| Summary: | Continuous cropping of the important achlorophyllous medicinal orchid <i>Gastrodia elata</i> Blume causes an imbalance in soil microecology leading to soil-borne diseases. However, the impacts on different land covers remain largely unknown. Hence, this study aimed to investigate changes in the soil nutrient composition and the global microbial community structure in rhizospheres of <i>G. elata</i> cultivated on a barren slope (HPGJ) and under a forest (LXT) using integrated shotgun metagenomics and an analysis of soil chemical properties. High-throughput sequencing revealed an increase in the abundance of Proteobacteria, Actinobacteria, Mucoromycota, Basidiomycota, and Ascomycota, which drive N- and C-cycling genes in HPGJ and LXT. Notably, the fungal community was significantly improved in the HPGJ (from 0.17% to 23.61%) compared to the LXT (from 0.2% to 2.04%). Consequently, mineral cycling was enhanced in the HPGJ, resulting in a more improved soil nutrient composition than in the LXT. The soil chemical properties analysis unveiled a significant increase in the contents of the total nitrogen, NO<sub>3</sub><sup>−</sup>-N, organic matter, total carbon, organic carbon, total sulfur, and total phosphorus in the HPGJ, while no changes were recorded in the LXT. It was noteworthy that the abundance of pathogenic microorganisms increased significantly in the HPGJ compared to the LXT. Our results provide supporting data to optimize <i>G. elata</i> cultivation on slopes.
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