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.

Computational analysis of LexA regulons in Cyanobacteria

Background

The transcription factor LexA plays an important role in the SOS response in Escherichia coli and many other bacterial species studied. Although the lexA gene is encoded in almost every bacterial group with a wide range of evolutionary distances, its precise functions in each group/species are largely unknown. More recently, it has been shown that lexA genes in two cyanobacterial genomes Nostoc sp. PCC 7120 and Synechocystis sp. PCC 6803 might have distinct functions other than the regulation of the SOS response. To gain a general understanding of the functions of LexA and its evolution in cyanobacteria, we conducted the current study.

Results

Our analysis indicates that six of 33 sequenced cyanobacterial genomes do not harbor a lexA gene although they all encode the key SOS response genes, suggesting that LexA is not an indispensable transcription factor in these cyanobacteria, and that their SOS responses might be regulated by different mechanisms. Our phylogenetic analysis suggests that lexA was lost during the course of evolution in these six cyanobacterial genomes. For the 26 cyanobacterial genomes that encode a lexA gene, we have predicted their LexA-binding sites and regulons using an efficient binding site/regulon prediction algorithm that we developed previously. Our results show that LexA in most of these 26 genomes might still function as the transcriptional regulator of the SOS response genes as seen in E. coli and other organisms. Interestingly, putative LexA-binding sites were also found in some genomes for some key genes involved in a variety of other biological processes including photosynthesis, drug resistance, etc., suggesting that there is crosstalk between the SOS response and these biological processes. In particular, LexA in both Synechocystis sp. PCC6803 and Gloeobacter violaceus PCC7421 has largely diverged from those in other cyanobacteria in the sequence level. It is likely that LexA is no longer a regulator of the SOS response in Synechocystis sp. PCC6803.

Conclusions

In most cyanobacterial genomes that we analyzed, LexA appears to function as the transcriptional regulator of the key SOS response genes. There are possible couplings between the SOS response and other biological processes. In some cyanobacteria, LexA has adapted distinct functions, and might no longer be a regulator of the SOS response system. In some other cyanobacteria, lexA appears to have been lost during the course of evolution. The loss of lexA in these genomes might lead to the degradation of its binding sites.