Objective   The microbial communities in rhizosphere and non-rhizosphere soils growing Paris polyphylla var. chinensis plants were analyzed and compared in the field as well as in laboratory.

  Method   The high throughput sequencing Illumina Miseq 2×300 bp was applied to sequence total DNA of the microbes in the soils. The LDA Effect Size analysis was used to examine the differences on selected microbial groups between the communities in the field and laboratory.

  Result   The microbial diversity in the soils of P. polyphylla was rich with 21 phyla, 33 classes, 52 orders, 89 families, and 160 genera identified. The Chao, Ace, Shannon, and Simpson indices on the soil samples indicated that the non-rhizosphere soil was more abundant and diverse than the rhizosphere soil. However, there were no significant differences between them on the phylum or family level. Among the differentially abundant groups, Chlorobia on the class level, Chlorobiales and Myxococcales on the order level, and Acinetobacter and Rudaea on the genus level were significantly lower in the rhizosphere.

  Conclusion  This study not only shows that Paris polyphylla var. chinensis non-rhizosphere soil bacterial communities have higher abundance and diversity, but also lays the foundation for further exploration of the soil microbial environment of Paris polyphylla var. chinensis.