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An improved method suitable for isolation of high-quality metagenomic DNA from diverse soils

3 Biotech volume 7, Article number: 171 (2017) Cite this article

Abstract

Standardization of metagenomic DNA extraction protocol is a pre-requisite for a successful metagenomic study aiming to screen and exploit the variety of microorganisms inhabiting a particular soil environment. Six methods reported earlier were used for isolation of metagenomic DNA in the present study. These methods suffered with regard to either poor yield or quality of DNA. Therefore, we developed an improved method for isolation of high-molecular weight and good quality metagenomic DNA from different soil samples. Our protocol combines the enzymatic (lysozyme and proteinase K) and chemical (CTAB and CaCl2) strategies to ensure efficient cell lysis and use of PEG and isopropanol for precipitation of humic impurities-free DNA. Our improved method gave high yield of good quality metagenomic DNA from diverse soils collected from garden, domestic waste dumping site, cellulose waste dumping site, sewage site, and tannery waste site. The good quality of the metagenomic DNA was evident by spectrophotometry data, PCR amplification of 16S rRNA gene and restriction digestion.

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Acknowledgements

SKV thanks the University Grants Commission, Government of India for the award of a research fellowship.

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  1. University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India

    Sumit Kumar Verma, Himanshi Singh & Prakash C. Sharma

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  1. Sumit Kumar Verma
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  2. Himanshi Singh
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  3. Prakash C. Sharma
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Correspondence to Prakash C. Sharma.

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Verma, S.K., Singh, H. & Sharma, P.C. An improved method suitable for isolation of high-quality metagenomic DNA from diverse soils. 3 Biotech 7, 171 (2017). https://doi.org/10.1007/s13205-017-0847-x

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  • DOI: https://doi.org/10.1007/s13205-017-0847-x

Keywords

  • Diverse soils
  • DNA isolation
  • Improved method
  • Metagenomic DNA
  • Tannery waste