16S rRNA sequencing and Targeted Metabolomics Analyses Reveal Rhizosphere Microbial Diversity and Flavonoids Dynamics in Scutellaria baicalensis Georgi

Abstract Aims Scutellaria baicalensis Georgi is a commonly used bulk Chinese medicinal material in China. Clinically, it is often divided into Ziqin and Kuqin respectively into medicine, and herbal research and pharmacological studies have shown that Ziqin and Kuqin have different effects. Therefore, we collected the HuangQin and its rhizosphere soils at different growth periods to explore the influence of soil microorganisms on flavonoid synthesis in HuangQin. Methods In this study, high-throughput sequencing and the UPLC-MS/MS-based metabolomics method were used to sequencing 16S rRNA sequencing and metabolic analysis of HuangQin rhizosphere soil samples and HuangQin, respectively. Results The results showed that the number of OTUs for the four years were 7594, 10227, 10280, and 9796, respectively. And with prolonged cultivation, the abundance of Pseudarthrobacter, Achromobacter and other beneficial bacteria gradually decreased. A total of 552 secondary metabolites were identified in the metabolome. Correlation analysis of soil physicochemical properties and differential microorganisms showed that Pseudarthrobacter was significantly correlated with TN, AN, AK, and NH₄⁺-N, Nocardioides exhibited a notable correlation with TN and AK, as well as a significant association with AN and pH, and there is a significant correlation between Haliangium and AP. Conclusion This study showed that soil physicochemical properties and soil microorganisms would affect the accumulation of flavonoids in S. baicalensis, which provided an important basis for improving the quality of S. baicalensis through reasonable fertilization and precise microbiota management.