Metagenomic profiling of rhizosphere microbiota shaping medicinal quality in Angelica sinensis

This study investigates the impact and underlying mechanisms of rhizosphere microorganisms on the quality of Angelica sinensis in its geoherb region. Through extensive field experiments, the dynamic changes in rhizosphere microbes, rhizosphere soil metabolism, and medicinal components of A. sinensis under different cultivation practices and growth status were systematically examined. The results revealed that root dipping treatment significantly reduced the early bolting rate of A. sinensis by 48.3% compared to non-root dipping treatment, and notably influenced the expression of the alpha-linolenic acid metabolic pathway in rhizosphere soil metabolism. Furthermore, the transplantation of rhizosphere microbiota following root dipping treatment substantially increased the yield of A. sinensis by 101.1%, and significantly enhanced the contents of 3 medicinal components as well as polysaccharides. Moreover, the diversity of the rhizosphere microbial community significantly increased following the transplantation of rhizosphere microbiota after root dipping treatment. This transplantation led to the formation of a stable beneficial microbial community in the rhizosphere of A. sinensis, which notably improved the metabolic environment of the rhizosphere soil. Further experiments underscored the indispensable role of rhizosphere microorganisms in the formation of A. sinensis quality. The removal of rhizosphere microorganisms resulted in hindered growth, a sharp increase in early bolting rates, and a significant reduction in medicinal component levels. Comparative analysis between normal and early bolting A. sinensis showed that the content of medicinal components and rhizosphere microbial diversity were significantly lower in early bolting plants, with the enrichment of pathogenic bacteria negatively correlating with A. sinensis quality and growth indices. Based on microbial transplantation experiments, we theoretically identified 14 core microbial driving factors that consistently promote growth before and after rhizosphere microbiota transplantation. Practically, we screened 4 functional growth-promoting bacteria and constructed synthetic microbial communities (AngGrow4). Pot experiments demonstrated that Bacillus subtilis NF6 and AngGrow4 could serve as potential growth-promoting candidates for developing microbial fertilizers for A. sinensis. This study comprehensively reveals the critical role of rhizosphere microorganisms in shaping the quality of A. sinensis in its geoherb region, laying the foundation for addressing production challenges and promoting the development of efficient, stable, and environmentally friendly biofertilizers.