Illumina-Based Analysis of Bulk and Rhizosphere Soil Bacterial Communities in Paddy Fields Under Mixed Heavy Metal Contamination

There is an increasing concern about rice (Oryza sativa L.) soil microbiomes under the influence of mixed heavy metal contamination. We used the high-throughput Illumina MiSeq sequencing approach to explore the bacterial diversity and community composition of soils in four paddy fields, exhibiting four degrees of mixed heavy metal (Cd, Pb and Zn) pollution, and examined the effects of these metals on the bacterial communities. Our results showed that up to 2 104 to 4 359 bacterial operational taxonomic units (OTUs) were found in the bulk and rhizosphere soils of the paddy fields, with the dominant bacterial phyla (greater than 1% of the overall community) including Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes and Nitrospirae. A number of rare and candidate bacterial groups were also detected, and Saprospirales, HOC36, SC-I-84 and Anaerospora were rarely detected in rice paddy soils. Venn diagram analysis showed that 174 bacterial OTUs were shared among the bulk soils with four pollution degrees. Rice rhizosphere soils displayed higher bacterial diversity indices (ACE and Chao 1) and more unique OTUs than bulk soils. Total Cd and Zn in the soils were significantly negatively correlated with ACE and Chao 1, respectively, and the Mantel test suggested that total Pb, total Zn, pH, total nitrogen and total phosphorus significantly affected the community structure. Overall, these results provided baseline data for the bacterial communities in bulk and rhizosphere soils of paddy fields contaminated with mixed heavy metals.