Metabolomic Analysis of Specific Metabolites in Codonopsis pilosula Soil Under Different Stubble Conditions

To investigate the soil-specific metabolites of Codonopsis pilosula under different stubble management practices, this study analyzed differentially abundant metabolites in the rhizosphere soils of rotational (DS) and continuous (LS) cropping systems via liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomic approaches. The results revealed that 66 metabolites, including amino acids and their derivatives, nucleic acids, alcohols, organic acids, amines, fatty acids, purines, and sugars, were significantly different (p < 0.05) between the DS and LS groups. Under continuous cropping, the levels of amines, fatty acids, organic acids, and sugars in the rhizosphere soil were significantly greater (p < 0.05) than those under rotational cropping, whereas the levels of amino acids and their derivatives, nucleic acids, and purines and pyrimidines were significantly lower (p < 0.05). KEGG pathway enrichment analysis revealed that these differentially abundant metabolites were enriched in metabolic pathways such as amino acid metabolism (e.g., alanine, aspartate, and glutamate metabolism), carbon metabolism, the cAMP signaling pathway, ABC transporter proteins, phenylalanine metabolism, and the biosynthesis of plant secondary metabolites. These metabolic pathways were involved in osmoregulation, energy supply, and resilience in plants. In conclusion, inter-root soil metabolites in rotational and continuous cropping of Codonopsis pilosula were able to influence soil physicochemical properties and microbial populations by participating in various biological processes.