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Background and aims: Endophyte and rhizosphere soil microorganism are vital microbial environments of the plant, namely plant microenvironments. A robust understanding of the structural composition of the microbiome present in below-ground and above-ground communities has remained elusive. Schisandra sphenanthera Rehd. et Wils. is a kind of traditional Chinese Medicine (TCM) of Schisandra, which can protect the kidney and liver. Methods: In this study, high-throughput sequencing analysis is applied to unravel microbial communities in rhizosphere soil and different parts of wild S. sphenanthera, and the movement regularity of endophytes in plant tissues.Results: There are differences in microbial composition and diversity between rhizosphere soil and four parts of S. sphenanthera. Proteobacteria, Cyanobacteria, and Acidobacteria are main bacteria, Ascomycota and Basidiomycota are main fungi at phylum level of microbe in S. sphenanthera. There are 12 common bacterial genera and 11 common fungal genera in rhizosphere soil and different parts of S. sphenanthera. In addition, each of the four parts and rhizosphere soil have its own dominant communities, such as Achromobacter (stem and leaf) and Methylobacterium (leaf). OTUs clustering results indicate that the bacterial community of root is greatly influenced by rhizosphere soil, while the microbial community of stem and fruit are greatly affected by the microorganisms of leaf. Conclusions: Understanding the microbial community structure and diversity in rhizosphere soil and different parts of S. sphenanthera can provide basis for further study of host-microbial interactions of S. sphenanthera in phytoremediation, sustainable utilization, and secondary metabolite production.

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