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Extraction of the metagenomic DNA and assessment of the bacterial diversity from the petroleum-polluted sites

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Abstract

The assessment of the microbial diversity of the entire community of a given habitat requires the extraction of the total environmental DNA. Metagenomic investigations of a petroleum-polluted habitat have its unique challenges. The specific methods were developed for the extraction of high-quality metagenome in good quantity from the petroleum-polluted saline and non-saline sites in Gujarat (India). The soil samples were washed to remove the toxic, hazardous organic pollutants which might interfere with the recovery of the metagenomic DNA. The metagenomic DNA extraction results were encouraging with the mechanical bead beating, soft lysis, and combination of both. The extracted DNA was assessed for its purity and yield followed by its application in the amplification of the 16S rRNA region. The amplicons were used for judging the molecular diversity by the denaturing gradient gel electrophoresis (DGGE). The microbial diversity was also analyzed statistically by calculating various diversity indices and principal component analysis (PCA). The results on the metagenomic diversity of the bacterial population among the three cohorts based on the culture-independent technique exhibited significant difference among the PAH sites and Okha–Madhi and Porbandar Madhavpur habitats.

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Acknowledgments

Ms. Viral Akbari and Ms. Rupal Pandya are the recipients of the UGC-Meritorious Research Fellowship, sponsored by the UGC, New Delhi, India. We also acknowledge the support of the UGC, New Delhi by sanctioning the ‘Centre of Advance Studies’ to the Department of Biosciences, Saurashtra University. The financial and other supports by the Saurashtra University are also acknowledged.

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  1. Department of Biosciences, Saurashtra University, Rajkot, Gujarat, India, 360 005

    Viral G. Akbari, Rupal D. Pandya & Satya P. Singh

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  1. Viral G. Akbari
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  2. Rupal D. Pandya
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Correspondence to Satya P. Singh.

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Akbari, V.G., Pandya, R.D. & Singh, S.P. Extraction of the metagenomic DNA and assessment of the bacterial diversity from the petroleum-polluted sites. Environ Monit Assess 186, 6351–6362 (2014). https://doi.org/10.1007/s10661-014-3859-6

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