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Background  Endophytic fungi influence the quality and quantity of the medicinal plant’s bioactive compounds through specific fungus-host interactions. Nevertheless, due to the paucity of information, the composition of endophytic fungal communities and the mechanism by which effective ingredients regulate endophytic fungal communities in roots remains unclear.    Methods  In this study, we collected root and soil samples (depth range: 0–20, 20–40, and 40–60 cm) of three  Glycyrrhiza  species ( Glycyrrhiza uralensis ,  Glycyrrhiza inflata,  and  Glycyrrhiza glabra ). Glycyrrhizic acid and liquiritin content were determined using high-performance liquid chromatography (HPLC), and total flavonoid content was determined using ultraviolet spectrophotometry. High-throughput sequencing technology was employed to explore the composition and diversity of the endophytic fungal community in different root segments of three  Glycyrrhiza  species. Furthermore, soil samples were subjected to physicochemical analyses.    Results  We observed that the liquiritin content was not affected by the root depth (0–20 cm, 20–40 cm, and 40–60 cm). Still, it was significantly affected by the  Glycyrrhiza  species ( Glycyrrhiza uralensis, Glycyrrhiza inflata, Glycyrrhiza glabra ) ( P  < 0.05). In  Glycyrrhiza  root, a total of eight phyla and 140 genera were annotated so far, out of which Ascomycota and Basidiomycota phyla, and the  Fusarium ,  Paraphoma,  and  Helminthosporium  genera were found to be significantly dominant. Spearman correlation analysis revealed that liquiritin content was accountable for the differences in the diversity of the endophytic fungal community. Furthermore, distance-based redundancy analysis (db-RDA) showed that physicochemical properties of the soil (available potassium and ammonium nitrogen) and the root factors (liquiritin and water content) were the main contributing factors for the variations in the overall structure of the endophytic fungal community. Our results showed that the effective ingredients of  Glycyrrhiza  root and physicochemical properties of the soil regulated the endophytic fungal community composition and medicinal licorice diversity.

Differences in the endophytic fungal community and effective ingredients in root of three Glycyrrhiza species in Xinjiang, China