Energy, Ecology and Environment

, Volume 3, Issue 2, pp 102–109 | Cite as

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

  • Jatindra N. Bhakta
  • Susmita Lahiri
  • Feroze A. Bhuiyna
  • Md. Rokunuzzaaman
  • Kouhei Ohonishi
  • Kozo Iwasaki
  • Bana B. Jana
Original Article


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.


Metal(loid) Resistant Metagenomics Bacterial diversity Environmental contamination Bioremediation 



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.

Compliance with ethical standards

Conflicts of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Joint Center on Global Change and Earth System Science of the University of Maryland and Beijing Normal University and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Jatindra N. Bhakta
    • 1
  • Susmita Lahiri
    • 1
  • Feroze A. Bhuiyna
    • 2
  • Md. Rokunuzzaaman
    • 2
  • Kouhei Ohonishi
    • 2
  • Kozo Iwasaki
    • 3
  • Bana B. Jana
    • 1
  1. 1.Department of Ecological Studies & International Centre for Ecological EngineeringUniversity of KalyaniKalyaniIndia
  2. 2.Research Institute of Molecular Genetics, Faculty of AgricultureKochi UniversityNankokuJapan
  3. 3.Life and Environmental Medical Science Cluster, Faculty of AgricultureUniversity of KochiNankokuJapan

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