Intercropping Shapes the Metabolome and Microbiome of Medicinal Giant Lily (Cardiocrinum giganteum) in Bamboo, Chinese Fir, and Mixed 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.