Variation in Rhizosphere Fungal Communities Is Associated with Flavonoid Accumulation in Wild and Cultivated Glycyrrhiza uralensis

Glycyrrhiza uralensis Fisch. is a valuable perennial medicinal legume with multiple pharmacological activities. G. uralensis from the Ordos Plateau is widely recognized for its high quality, with flavonoids serving as its primary bioactive components. However, substantial variation exists among cultivated populations in terms of quality, which limit the sustainable utilization of this medicinal plant. In this study, root tissues, rhizosphere soil, and bulk soil samples were collected from three wild (W1–W3) and two cultivated (C1–C2) populations of G. uralensis across the Ordos Plateau. Flavonoid metabolomics and fungal community analyses were integrated to investigate the relationship between rhizosphere fungi and flavonoid accumulation. The results showed that the cultivated C1 group exhibited higher liquiritin content and greater rhizosphere fungal diversity, suggesting that wild origin does not necessarily guarantee higher medicinal quality in G. uralensis. Thirteen differentially abundant fungal genera were significantly associated with flavonoid accumulation. Correlation analysis identified genus-specific associations between Alfaria, Alternaria, Botryotrichum, Fusarium, and Pseudogymnoascus and metabolites involved in the liquiritin biosynthetic pathway. These results revealed associations between the relative abundances of selected rhizosphere fungal genera and the contents of specific flavonoid metabolites in G. uralensis, and identified key fungal communities. This study provides candidate fungal taxa and testable hypotheses for future studies on the associations between rhizosphere fungi and flavonoid metabolism in G. uralensis.