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Background Pinellia ternata  (Thunb.) Breit. is a commonly used herb in traditional Chinese medicine, and the main raw material of various Chinese patent medicines. Continuous cropping obstacle (CCO) is the main factor leading to the decline of crop yields and quality. Methods Metagenomics sequencing technology was used to analyze the microbial community and functional genes of continuous cropping (CC) and control (CK) soils of  P. ternata . In addition, differences in physicochemical properties, enzyme activities, microbial community composition and the abundance of functional genes in CC and CK were evaluated, as well as the relationship between these factors and CCO. Results Results indicated that CC of  P. ternata  led to the decline of rhizosphere soil pH, nutrient imbalance and enzyme activity reduction. Metagenomic analysis indicted that CC also changed the composition of the microbial community, causing an increase in the relative abundance of pathogenic microorganisms such as  Fusarium ,  Klebsiella oxytoca  and  Pectobacterium carotovorum  in the  P. ternata  rhizosphere. The relative abundance of potentially beneficial  Burkholderia  and  Bradyrhizobium  was recorded to decrease. Results also showed that there were considerable differences in CC and CK about the abundances of functional genes related to soil enzymes and the degradation of  P. ternata  allelochemicals, as well as the microbial groups which they belong. These results clarified the effects of CC on the microbial community structure and functional genes of soil. In addition,  Burkholderia  and  Bradyrhizobium  might play important roles in enhancing soil fertility and reducing the toxicity of phenolic acids in rhizosphere soil. Conclusions CC of  P. ternata  changed the physicochemical properties, microbial community and functional genes of rhizosphere soil.  Burkholderia  and  Bradyrhizobium  for enhancing soil fertility and reducing the toxicity of phenolic acids might be potentially beneficial. These results provide theoretical guidance for bioremediation of CCO soil of  P. ternata  and other staple crops. Graphic abstract

chemical and biological technologies in agriculture

Effects of continuous cropping of Pinellia ternata (Thunb.) Breit. on soil physicochemical properties, enzyme activities, microbial communities and functional genes