Study of the Correlation Between Endophyte Abundances and Metabolite Levels in Different Parts of the Tissue of Cultivated and Wild Arnebia euchroma (Royle) Johnst. Based on Microbiome Analysis and Metabolomics

<i>Arnebia euchroma</i> (Royle) Johnst. has high medicinal and economic value, but in recent years, wild resources of this species have been depleted and the quality of artificially cultivated <i>A. euchroma</i> has been poor. The endophyte community of medicinal plants is rich, serving as an internal resource that promotes the growth of medicinal plants and the accumulation of secondary metabolites, and has important potential application value in improving the quality of medicinal materials. <i>A. euchroma</i> cultivars and wild varieties contain abundant endophyte communities and metabolites in different tissues. However, the relationships between <i>A. euchroma</i> endophytes and metabolites with different growth patterns and different tissue sites remain unclear. In this study, microbiome analysis and metabolomics were used to analyze the diversity of endophytes in the root and leaf tissues of cultivated and wild <i>A. euchroma</i> and their correlations with metabolites. The results revealed that the diversity of endophytes in <i>A. euchroma</i> was different from that in wild <i>A. euchroma</i> and that there was tissue specificity among different tissues. A species composition analysis revealed that the dominant endophytic fungi belonged to Ascomycota and Basidiomycota, and the dominant endophytic bacteria belonged to Proteobacteria and Cyanobacteria. A total of 248 metabolites, including quinones, flavonoids, alkaloids, organic acids, sugars, amino acids, coumarins, sterols, terpenoids, polyphenols, fatty ketones, and their derivatives, were identified in positive ion mode via LC-MS/MS. According to their different growth patterns and associated tissue parts, 9 differentially abundant metabolites were screened between AEZ-L (cultivated leaf tissue of <i>A. euchroma</i>) and AEY-L (wild leaf tissue of <i>A. euchroma</i>), 6 differentially abundant metabolites were screened between AEZ-R (cultivated root tissue of <i>A. euchroma</i>) and AEY-R (wild root tissue of <i>A. euchroma</i>), and 104 differentially abundant metabolites were screened between AEZ-R and AEZ-L. Eighty-two differentially abundant metabolites were screened between AEY-R and AEY-L. The contents of eight naphthoquinones in AEZ-R and AEY-R were determined via HPLC. The contents of <i>β,β'</i>-dimethylacrylylakanin in wild <i>A. euchroma</i> were greater than those in cultivated <i>A. euchroma</i>. A correlation analysis revealed that the dominant endophytes in the four groups were significantly correlated with a variety of metabolites, and the eight naphthoquinones in the root tissue were also significantly correlated with the dominant endophytes. The diversity of the <i>A. euchroma</i> endophyte community differed across different growth patterns and different tissue parts. There were significant differences in the relative contents of <i>A. euchroma</i> metabolites in different tissues. A correlation analysis verified the correlation between <i>A. euchroma</i> endophytes and metabolites.