Metagenomics reveals an interaction among rhizosphere microbial community, soil properties and active ingredients in a medicinal crop Panax notoginseng

This study aimed to examine the effects of intensive cultivation practices on the rhizosphere microecology of Panax notoginseng . Additionally, we sought to compare these practices with an understory cultivation model that was intended to mimic native growth conditions, with the objective of improving the quality of Radix Notoginseng. The total saponin and active ingredient content in both cultivation methods were quantified using high-performance liquid chromatography (HPLC). The nutrients of the rhizosphere soils associated with both cultivation methods (understory cultivated P. notoginseng rhizosphere soil [UCPS] and intensive cultivated P. notoginseng rhizosphere soil [ICPS]) were analyzed. The microbial communities present in UCPS and ICPS were characterized using metagenomic sequencing. The underground biomass accounted for 71.21% and 74.00% of the total biomass in understory cultivated P. notoginseng (UCPn) and intensively cultivated P. notoginseng (ICPn), respectively. The total saponin content in the main root of UCPn was found to be 109.24 ± 3.40 mg/g, compared to 91.31 ± 5.82 mg/g in ICPn. The concentration of medicinal ingredients (ginsenoside Rb1 + ginsenoside Rg1 + notoginsenoside R1) in UCPn was 10.83%, while ICPn exhibited a higher concentration of 13.39%. Microbial biomarkers identified in UCPS include Bradyrhizobium , Pseudomonas , and Paraburkholderia , which are associated with nitrogen cycling processes. In contrast, Variovorax and Sphingobium were predominant in ICPS, contributing to phosphorus metabolism. Rhizosphere soil microbial biomarkers influence soil carbon nutrition, which directly impacts the quality of UCPn. The quality of ICPn is primarily determined by phosphorus-related biomarkers, with indirect influences from carbon and nitrogen nutrition. • Reintroducing medicinal plants into understory cultivation is an effective strategy for sustainable agriculture • Understory cultivated Panax notoginseng is beneficial for the balance of rhizosphere microorganisms • Bioorganic carbon is the driving factors for the growth of Panax notoginseng • Understory cultivated Panax notoginseng improved the quality of Radix Notoginseng