High-throughput sequencing clarifies the spatial structures of microbial communities in cadmium-polluted rice soils

Abstract

Soil microbial communities are affected by environmental factors. Contamination with heavy metals such as cadmium (Cd) can decrease soil microbial species richness and substantially alter soil microbial species composition. Investigations of the microbial communities in Cd-contaminated soils are necessary to obtain data for soil bioremediation efforts. However, depth-associated variations in microbial community composition and structure in Cd-contaminated paddy soils are not well understood. Here, the effects of various degrees of long-term Cd pollution on soil microorganisms were investigated at different soil depths within the plough layer using 16S rRNA gene amplicon sequencing. We found that, in Cd-polluted soils, microbial communities were more similar between the surface soil and the underlying soil. In addition, microbial community richness and/or diversity were significantly reduced in the Cd-polluted underlying soil as compared with the non-polluted underlying soil. However, species richness in the surface layer was significantly greater in the mildly and severely Cd-polluted soils. The soil microbial communities in the same soil layer differed significantly between the non-polluted and polluted soils. Furthermore, Cd contamination affected the microbial communities of different soil layers differently. Soil pH had a synergistic effect on microbial community abundance and composition. The potential functions of the soil microbiota were mainly related to environmental processing, genetic processing, and metabolic pathways. Notably, our identification of the phyla that were differently abundant among sites with different levels of Cd pollution will provide experimental guidance for further explorations of the effects of Cd on soil microbes in natural environments. Our results not only demonstrate that long-term Cd pollution leads to a marked reduction in microbial richness and diversity in the underlying soil layer, but they also help to clarify how long-term heavy metal contamination affects the soil bacterial community.

Keywords: 16S rRNA amplicon sequencing; Bacterial community; Cadmium; Contaminated soil; Spatial profile.