Correlation analysis of endophytic microbiota and shikonin accumulation in Arnebia euchroma (Royle) Johnst. across geographical origins

Background Arnebia euchroma (Royle) Johnst. is of high medicinal and economic value and is in expanding demand, but in recent years, the depletion of wild resources and the poor quality of artificially cultivated A. euchroma have exacerbated the supply demand imbalance. The rich endophytic community of medicinal plants is an endogenous driver that promotes the growth and secondary metabolite accumulation of medicinal plants, which has important potential application value in improving the quality of medicinal herbs. The content of active ingredients in the herbs of A. euchroma from different origins is variable; however, the studies affecting the quality of the herbs of A. euchroma are mostly focused on environmental factors, and the effects of endophytes, as endophytes residing inside the root tissues inside the root tissues of A. euchroma, on the quality of the herbs of A. euchroma have not yet been reported.Medthod High throughput sequencing technology combined with bioinformatics approaches was employed to analyze the diversity and compositional differences of endophytes in the root tissues of A. euchroma from different geographical regions. In combination with high performance liquid chromatography (HPLC) for the quantification of eight shikonin components, this study further investigated the correlation between endophytic communities and shikonin biosynthesis in A. euchroma.Results The endophytic communities in the root tissues of A. euchroma from different geographical origins are diverse, and endophytic bacteria are more abundant than endophytic fungi. The endophytic fungi Ascomycota and Basidiomycota and the endophytic bacteria Cyanobacteria and Proteobacteria were the dominant endophytes in each sample. There are differences in the diversity of endophytic communities, among which the differences in endophytic fungi are more significant. LefSe analysis revealed that the root tissues of A. euchroma with different contents of pharmacodynamic components contained different differential biomarkers. The functional predictions by FUNGuild and PICRUSt2 indicate that the endophytes in the root tissues of A. euchroma have diverse biological functions. In particular, endophytic bacteria are involved mainly in metabolic pathways. The contents of eight shikonin components in the samples from three geographical origins varied, indicating the specificity of the geographical origins for the quality of Arnebia Radix. Correlation analysis revealed that various endophytes have different effects on the accumulation of shikonin components in the root tissues of A. euchroma from different geographical origins. For example, genera such as Sphingomonas and Cadophora may be influencing factors for the differences in the quality of Arnebia Radix from different geographical origins.Conclusion This study revealed the composition, diversity, differences, and functions of endophytic communities in the root tissues of A. euchroma from different geographical origins. This study explained the differences in A. euchroma from different geographical origins from the perspective of the endophytic environment, analyzed the correlation between endophytes and shikonin components, and laid a foundation for further exploration of the role of endophytes in influencing the accumulation of secondary metabolites in the root tissues of A. euchroma. This study can provide a reference for the subsequent development and utilization of microbial resources.