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Profiling of heavy metal(loid)-resistant bacterial community structure by metagenomic-DNA fingerprinting using PCR–DGGE for monitoring and bioremediation of contaminated environment

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Abstract

Frequent exposure of microbes to hazardous metalloids/heavy metals in contaminated environment results in the development of heavy metal(loid)-resistance properties. The study attempted to assess the profile of elevated arsenic (As), cadmium (Cd) and mercury (Hg)—resistant bacterial community structures of sludge (S1, India), sludge and sediment (S2 and S3, Japan) and sediment (S4, Vietnam) samples by metagenomic-DNA fingerprinting using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) for monitoring and bioremediation of hazardous metal(loid) contamination in environment. The results revealed that As-resistant bacteria were dominant compared to Cd- and Hg-resistant bacteria with higher species diversity (Lysinibacillus sp., Uncultured soil bacterium clone, Staphylococcus sciuri, Bacillus fastidiosus, Bacillus niacini, Clostridium sp. and Bacillus sp.) in S1 and S4 than that of S2 and S3 samples. The occurrence of dominant As-resistant bacteria may indicate arsenic contamination in the investigated coastal habitats of India, Japan and Vietnam. The As-, Cd- and Hg-resistant bacteria/bacterial consortiums showed appreciable uptake ability of respective metal(loid) (0.042–0.125 mg As/l, 0.696–0.726 mg Cd/l and 0.34–0.412 mg Hg/l). Therefore, it might be concluded that the profiling of metalloids/heavy metal-resistant bacterial community structure by metagenomic-DNA fingerprinting using PCR–DGGE could be used to explore high metal(loid)-resistant bacteria for applying in metal(loid) bioremediation and as an indicator for monitoring hazardous metal(loid) contamination in environment.

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Acknowledgements

Authors are grateful to Japan Society for the promotion of Science (JSPS) for sponsoring research fund and fellowship (FY2009 JSPS postdoctoral fellowship) to Dr. Bhakta to carry out the study. Authors are also especially grateful to Dr. J. K. Pittman for reviewing the manuscript.

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Authors and Affiliations

  1. Department of Ecological Studies & International Centre for Ecological Engineering, University of Kalyani, Kalyani, West Bengal, 741235, India

    Jatindra N. Bhakta, Susmita Lahiri & Bana B. Jana

  2. Research Institute of Molecular Genetics, Faculty of Agriculture, Kochi University, B200, Monobe, Nankoku, Kochi, 7838502, Japan

    Feroze A. Bhuiyna, Md. Rokunuzzaaman & Kouhei Ohonishi

  3. Life and Environmental Medical Science Cluster, Faculty of Agriculture, University of Kochi, B200, Monobe, Nankoku, Kochi, 783-8502, Japan

    Kozo Iwasaki

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  1. Jatindra N. Bhakta
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Correspondence to Jatindra N. Bhakta.

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Bhakta, J.N., Lahiri, S., Bhuiyna, F.A. et al. Profiling of heavy metal(loid)-resistant bacterial community structure by metagenomic-DNA fingerprinting using PCR–DGGE for monitoring and bioremediation of contaminated environment. Energ. Ecol. Environ. 3, 102–109 (2018). https://doi.org/10.1007/s40974-017-0079-2

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