Analysis of endophyte diversity and its correlation with eight naphthoquinone metabolites in Arnebia euchroma grown for different cultivation years

Previous studies on Arnebia euchroma have focused on its physicochemical and pharmacological properties, and studies on the differences in metabolites in A. euchroma have also highlighted the effects of external environmental factors. In this study, we compared the differences in the diversity of endophytes in the interroot zone of A. euchroma grown for 14 years in HeJing County using high-throughput sequencing and analyzed their relationship with eight secondary metabolites, including alkannin, bate, bate dimethylacrylshikonin, deoxyshikonin, acetylshikonin, bate acetoxyisovaleryshikonin, bate hydroxyisovalerylshikonin, isobutyrylshikonin, and isovalerylshikonin. The results showed that the alpha diversity of endophytic fungal and bacterial amplicon sequence variants (ASVs) in A. euchroma tended to increase and decrease, respectively, with plant aging. The results of Spearman's correlation analysis found that bate,bate dimethylacrylshikonin had a promoting effect on an order of endophytic fungi: unclassified Auriculariales, endophytic bacteriophages of no-rank Chitinophagaceae, and Myxobacteria (P3OB42). In contrast, an inhibitory effect was observed on unclassified Ceratobasidiaceae. FUNGuild and PICRUSt2 predictive analyses showed that the dominant trophic modes of endophytic fungi in all samples were saprotrophic and pathotrophic, with the highest relative abundance in X4Z, while the main trophic mode of endophytic bacteria was metabolic. Our results help to elucidate the importance of plant-microbe interactions and provide key information about the role of endophytes in promoting the cultivation of A. euchroma and its important secondary metabolites. They also provide a reference for further research on the effects of differences in community composition of endophytes on the accumulation of medicinal compounds in A. euchroma and for the development of resources for its cultivation.