Diversity and correlation of endophytic microbiota and Shikonin accumulation in Arnebia Euchroma roots across geographical origins

Arnebia euchroma(Royle) Johnst. is a high-value medicinal plant. Owing to depleted wild resources and inferior quality of artificially cultivated populations, it currently faces a supply-demand imbalance. As endogenous regulators of plant growth and secondary metabolism, endophytes may influence the quality of medicinal materials. However, their role in A. euchroma remains unreported, as existing studies have primarily focused on the impacts of environmental factors. High-throughput sequencing and bioinformatics were employed to analyze the community characteristics of endophytes in the roots of A. euchroma from different geographical origins. High-performance liquid chromatography (HPLC) was used to quantify 8 shikonin-like components, to investigate associations between endophytes and shikonin accumulation. The endophytic community structure of A. euchroma exhibited geographical variations. Beta diversity analysis revealed a high degree of heterogeneity in endophytic communities across different regions. Alpha diversity analysis showed that bacterial Simpson and Shannon indices were higher than those of fungi. Community composition analysis indicated that the dominant endophytic phyla in A. euchroma included Ascomycota/Basidiomycota (fungi) and Cyanobacteria/Proteobacteria (bacteria), with more significant compositional differences observed in fungi. LefSe analysis identified region-specific biomarkers, such as Tetracladium and Leptodophora in the ZS area. Functional predictions via FUNGuild and PICRUSt2 revealed diverse endophytic roles; notably, bacteria were involved in carbohydrate, amino acid, and energy metabolism. Shikonin content varied among geographical regions, exhibiting geographical specificity. Quantitative analysis of 8 shikonin-like components revealed differences in active constituent levels of A. euchroma from different regions. Correlation analysis indicated that multiple endophytic genera, including Sphingomonas and Cadophora, exhibited significant positive or negative associations with shikonin accumulation. This study elucidates the geographical variation characteristics, functional profiles of the endophytic community associated with A. euchroma, and its associations with shikonin-like components. It provides novel insights into the mechanisms by which endophytes regulate plant secondary metabolism and lays a foundation for the development and application of microbial resources.