Rhizosphere microbes influence wogonoside accumulation in perennial Scutellaria baicalensis

Dried roots of Scutellaria baicalensis Georgi are an acclaimed traditional Chinese medicine, and wogonoside content is a key indicator used to evaluate S. baicalensis quality. Rather than rising linearly with cultivation years, S. baicalensis quality initially increases and then declines. However, little is known regarding the dynamic variations in S. baicalensis rhizosphere microorganisms under long-term cultivation and underlying mechanisms of their effects on wogonoside formation and accumulation. The aim of this study was to investigate the roles of soil nutrients and rhizosphere microbes on S. baicalensis quality across different cultivation years (1–4 years). The wogonoside content (25.14 mg g^-1) was highest in the biennial S. baicalensis and then decreased following long-term cultivation. Most soil nutrients (available nitrogen, available phosphorus, available iron, available manganese, and available zinc) were reduced significantly as cultivation years increased. Time also affected rhizosphere bacterial community structure significantly, driving it toward deterministic process (i.e., β-nearest taxon index < -2). Available manganese and exchangeable calcium indirectly affected wogonoside formation and accumulation. Wogonoside inhibition was driven by the reduction in rhizosphere bacterial diversity, which significantly increased the relative abundance of beta-glucosidase and decreased the relative abundance of phenylalanine ammonialyase. The rhizosphere microenvironment was altered under long-term cultivation, thereby shaping rhizosphere bacterial community, reducing the community diversity, and ultimately inhibiting wogonoside formation and accumulation. Our findings may aid in understanding of the mechanisms and reasons for the reduction in S. baicalensis quality under long-term cultivation from the perspective of soil nutrients and microorganisms, which may theoretically support the future artificial cultivation and management of Chinese medicinal plants.