Characterization of root-associated microbiota in medicinal plants Astragalus membranaceus and Astragalus mongholicus

Although the quality of herbal medicine is tightly associated with plant genotype and location, microbial traits of most herbs remain unclear. In this study, bacterial communities residing Astragali Radix, which is derived from Astragalus membranaceus and A. mongholicus roots, have been characterized by automated ribosomal intergenic spacer analysis (ARISA) and pyrosequencing of 16S rRNA amplicons. The samples were collected from four representive locations and differing in genotype and planting pattern. The spatial resolution study by ARISA firstly distinguished between the two anatomically-based parts, the periderm and secondary vascular tissue, demonstrating that microbial communities residing in the former were more diverse and clearly separated by host genotype and location as compared with those residing in the latter. Taxonomic coverage revealed that phyla of Proteobacteria, Planctomycetes and Bacteroidetes dominated the bacterial assemblages across the samples. The community diversity in A. mongholicus was more abundant than it was in A. membranaceus, especially A. mongholicus in Shanxi province of China. In addition, the conventional cultivation exerted consistently negative effects on microbiota complexity when compared with the planting pattern “imitating wild conditions”, which was regardless of the host genotype. With the focus on microbiota members in Shanxi, taxa associated with the genotype, geography and planting pattern were finally discriminated and used as indicators for the screening of endophytic bacteria that contain ACC deaminase. Taken together, microbiota should be an important trait of herbal medicines and the periderm should be a specialized niche for microbiota research in medicinal plants.