Objective  Endophytic microbes of Pinellia ternata and rhizosphere microbial communities in the habitat soils in Guizhou as affected by the environmental conditions were analyzed.

  Methods   High throughput sequencing to identify the endophytic and rhizosphere microbiota in P. ternata and soils of the wild, large-scale cultivated, and intercropped P. ternata plants grew in Guizhou was conducted. Microbial diversity, species, relationships, and enzyme activities as well as functional microflora were analyzed. Bioinformatics was employed to decipher the ecological relationship between the plant and its habitat.

  Results   The environmental, physiochemical, and enzymatic conditions on the land where P. ternata plants were grown in the wild or under cultivation varied significantly. For instance, the organic matter content and acidity were high in the cultivated plots, but the enzyme activity was high in the soil of virgin forest. In the plants, Rhizobium, Pseudomonas, Bacillus, and Bradyrhizobium were the dominant endophytic bacteria genera, whereas Campylospora, Neocosmospora,Rhizoctonia, Fusarium, Dactylonectria, unclassified genera of Xylariales order, etc. were found to be the dominant fungi genera. In the rhizosphere soil, abundant dominant microbial species regularly aggregated and were affected by the environmental factors and planting method. For example, 10 dominant bacteria genera and 13 fungi genera significantly correlated with the physicochemical properties and/or enzyme activity of the soil they inhabited. In general, the endophytic microbes in the plants were more sensitive to the environmental factors than those in the rhizosphere soil. And they could be synergistic as well as antagonistic to one another, but the rhizosphere community tended to be stable. Aside from the unclassified and unknown genera, the dominant endophytic bacteria were mostly considered beneficial for the plant.

  Conclusion  The microbial community in the soil could be improved by adjusting pH and applying microbial fertilizers. The endophytic microbes of P. ternate including Rhizobia,Pseudomonas, Bacillus, Agrobacterium, Trichoderma, and Metarhizium anisopliae could be used to enhance plant growth ushering in the development of a pharmaceutical industry based on the medicinal material.