Effects of Continuous Cropping of Codonopsis pilosula on Rhizosphere Soil Microbial Community Structure and Metabolomics

Abstract

Codonopsis pilosula is an important medicinal plant in China. Continuous cropping of C. pilosula affects crop quality and yield. However, comprehensive research on the impacts of continuous cropping on soil properties, microbial community structures, and soil metabolites is lacking. This study involved collecting rhizosphere soil samples from C. pilosula monocropped for 1 to 4 years to analyze variations in soil properties, microbial community structure, and metabolites across different continuous-cropping years (CCYs) through metabolomic and microbiomic analyses. Significant variations in the soil properties were observed; total phosphorus (TP) and available potassium (AK) in the rhizosphere soil increased with the number of CCYs, and pH declined. The microbial community structure significantly changed with continuous cropping. Overall, the soil bacterial diversity decreased with increasing CCY. The abundances of Proteobacteria and Firmicutes significantly decreased with increasing CCY, whereas the abundance of Acidobacteria significantly increased. The fungal diversity tended to decrease, with an increase in the abundance of beneficial Basidiomycota and an increase in potentially pathogenic Rozellomycota. Metabolomic analysis revealed 101 metabolites and significant changes in lipid compounds, organic acids, phenols, and carbohydrates. Notably, autotoxic substances such as 2,6-di-tert-butylphenol accumulated with increasing CCY. The results indicated that the main factors causing continuous-cropping obstacles in C. pilosula were soil nutrient imbalance and autotoxic substance accumulation. Continuous cropping of C. pilosula significantly altered the microbial community structure and metabolomic profile of rhizosphere soils. Effective management practices are needed to mitigate soil acidification, nutrient imbalances, and autotoxic substance accumulation during continuous cropping. Future research should focus on integrated soil management strategies to maintain soil health and crop productivity in C. pilosula continuous-cropping systems.