Intercropping affects soil microbial community structure significantly; however, the effects on understory medicinal plants in karst areas remain unclear. We investigated the effects of four intercropping systems (Moso bamboo, Chinese fir, bamboo-fir mixed forest, and forest gap) on the rhizosphere microbial communities of giant lily (Cardiocrinum giganteum), an economically important medicinal plant in China. We assessed the intercropping impact on rhizosphere microbial diversity, composition, and co-occurrence networks and identified key soil properties driving the changes. Bacterial and fungal diversity were assessed by 16S rRNA and ITS gene sequencing, respectively; soil physicochemical properties and enzyme activities were measured. Moso bamboo system had the highest fungal diversity, with relatively high bacterial diversity. It promoted a distinct microbial community structure with significant Actinobacteria and saprotrophic fungi enrichment. Soil organic carbon, total nitrogen, and available potassium were the most influential drivers of microbial community structure. Co-occurrence network analysis revealed that the microbial network in the Moso bamboo system was the most complex and highly interconnected, with a higher proportion of positive interactions and a greater number of keystone taxa. Thus, integrating Moso bamboo into intercropping systems can enhance soil fertility, microbial diversity, and ecological interactions in the giant lily rhizosphere in karst forests.

Intercropping is a promising strategy for sustainable medicinal plant cultivation, but its impact on plant–microbe interactions remains poorly understood. This study investigated the influence that intercropping giant lily (Cardiocrinum giganteum) with bamboo (BG), Chinese fir (FG), and mixed forests (MG) had on the giant lily metabolome and microbiome compared to a monoculture control (GG). Metabolomic analysis revealed that BG significantly increased the accumulation of terpenoids (e.g., yucalexin B22, 19.39-fold), alkaloids (e.g., anabasine, 2.97-fold), and steroids (e.g., O-acetyl-lariciresinol, 4.49-fold), while MG induced the production of stress-related metabolites (e.g., aflatoxin G2, 128.62-fold), and FG enhanced nitrogen metabolism (e.g., putrescine, 2.47-fold). Intercropping altered the rhizosphere and endophytic microbial communities, with BG enriching beneficial bacteria (e.g., Acidobacteria and Alphaproteobacteria) and FG promoting symbiotic fungi (e.g., Serendipita and Xylariales). Network analysis revealed strong correlations between specific microbial taxa (e.g., Bacillus and Ceratobasidiaceae) and key metabolites (e.g., norpandamarilactonine A, methylgingerol), indicating their potential roles in shaping the metabolic profiles of giant lily. These findings highlight the complex interplay between intercropping systems, microbial communities, and medicinal plant metabolism and provide a basis for developing targeted cultivation strategies to enhance the production of bioactive compounds in giant lily and other medicinal plants.