3 Biotech

, 7:171 | Cite as

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

  • Sumit Kumar Verma
  • Himanshi Singh
  • Prakash C. SharmaEmail author
Protocols and Methods


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.


Diverse soils DNA isolation Improved method Metagenomic DNA Tannery waste 



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

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.


  1. Amorim JH, Macena TNS, Lacerda-Junior GV, Rezende RP, Dias JCT, Brendel M, Cascardo JCM (2008) An improved extraction protocol for metagenomic DNA from a soil of the Brazilian Atlantic rainforest. Genet Mol Res 7:1226–1232CrossRefGoogle Scholar
  2. Bashir Y, Singh SP, Konwar BK (2014) Metagenomics: an application based perspective. Chin J Biol 2014:1–7CrossRefGoogle Scholar
  3. Devi SG, Fatima AA, Radha S, Arunraj R, Curtis WR, Ramya M (2015) A rapid and economical method for efficient DNA extraction from diverse soils suitable for metagenomic applications. PLoS ONE 10:e0132442CrossRefGoogle Scholar
  4. Fatima F, Pathak N, Rastogi VS (2014) An improved method for soil DNA extraction to study the microbial assortment within rhizospheric region. Mol Biol Int 2014:1–6CrossRefGoogle Scholar
  5. Gabor EM, de Vries EJ, Janssen DB (2003) Efficient recovery of environmental DNA for expression cloning by indirect extraction methods. FEMS Microbiol Ecol 44:153–163CrossRefGoogle Scholar
  6. Nair HP, Vincent H, Bhat SG (2014) Evaluation of five in situ lysis protocols for PCR amenable metagenomic DNA from mangrove soils. Biotechnol Rep 4:134–138CrossRefGoogle Scholar
  7. Rajendhran J, Gunasekaran P (2008) Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 26:576–590CrossRefGoogle Scholar
  8. Sharma PK, Caplash N, Kaur J (2007) An improved method for single step purification of metagenomic DNA. Mol Biotechnol 36:61–63CrossRefGoogle Scholar
  9. Siddhapura PK, Vanparia S, Purohit MK, Singh SP (2010) Comparative studies on the extraction of metagenomic DNA from the saline habitats of coastal Gujarat and Sambhar Lake, Rajasthan (India) in prospect of molecular diversity and search for novel biocatalysts. Int J Biol Macromol 47:375–379CrossRefGoogle Scholar
  10. Singh R, Devi T, Verma V, Rasool S (2014) Comparative studies on the extraction of metagenomic DNA from various soil and sediment samples of Jammu and Kashmir region in prospect for novel biocatalysts. IOSR J Environ Sci Toxicol Food Technol 8:46–56Google Scholar
  11. Steffan RJ, Goksoyr J, Bej AK, Atlas R (1988) Recovery of DNA from soils and sediments. Appl Environ Microbiol 54:2908–2915Google Scholar
  12. Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070–1074Google Scholar
  13. Urban M, Adamczak M (2008) Exploration of metagenomes for new enzymes useful in food biotechnology—a review. Polish J Food Nutr Sci 58:11–22Google Scholar
  14. Verma D, Satyanarayana T (2011) An improved protocol for DNA extraction from alkaline soil and sediment samples for constructing metagenomic libraries. Appl Biochem Biotechnol 165:454–464CrossRefGoogle Scholar
  15. Volossiouk T, Robb EJ, Nazar RN (1995) Direct DNA extraction for PCR-mediated assays of soil organisms. Appl Environ Microbiol 61:3972–3976Google Scholar
  16. Wilson DB (2009) Cellulases and biofuels. Curr Opin Biotechnol 20:295–299CrossRefGoogle Scholar
  17. Zhou J, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322Google Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityNew DelhiIndia

Personalised recommendations