Integrating high-throughput sequencing and metagenome analysis to reveal the characteristic and resistance mechanism of microbial community in metal contaminated sediments

Some metallic tailings from closed mines were scattered in upstream of the Miyun Reservoir, Beijing, threatening the ecological environment of rivers due to trace metals. The Liuli River, one of the main rivers affected, was investigated as a typical model in this work. In this study, we selected eight sites to assess interactions among the various geochemical factors especially between trace metals and sediment microbiota. Random forest predicted that low concentrations of Cu, Cd, Cr and Ni (lower than 61.8 mg/kg, 3.2 mg/kg, 173.2 mg/kg and 34.1 mg/kg, respectively) were able to enhance community diversity but generally, trace metals contamination impaired microbial diversity. Environmental factor correlation analysis showed that As, pH and available P were the major factors that shifted the distribution of the microbial communities. Metagenome sequencing revealed that Proteobacteria harbored the vast majority of heavy metal resistance genes followed by Actinobacteria and Bacteroidetes. Metal tolerance of Proteobacteria were achieved by exportation of metals by the corresponding transporters, by pumps and ion channels, or by their reduction via redox reactions. In addition, Proteobacteria harbored a greater ability to repair DNA damage via DNA recombination. [Display omitted] •The microbial mechanisms of adaptation to heavy metals in sediments was investigated.•Low concentrations of Cu, Cd, Cr, Zn, Pb and Ni were able to enhance biodiversity.•As, pH and AP were the main factors shaping microbial community distribution.•Proteobacteria contained many genes related to DNA repair and heavy-metal resistance.