Skip to main content
SpringerLink
Log in

An improved method for single step purification of metagenomic DNA

  • Original Paper
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

An improved method for purification of intact metagenomic DNA from soil has been developed using Q-Sepharose, which purified the DNA from phenolic and humic acid contaminants in a single step. The entire procedure for purification took only 45 min. A total of 81% of DNA was recovered after purification and there was 84% reduction in humic acid contents. The purified DNA was readily digested with restriction enzymes and can be further used for molecular applications.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Ward, D. M., Bateson, M. M., Weller, R., & Ruff-Roberts, A. L. (1992). Ribosomal RNA analysis of microorganism as occur in nature. Advances in Microbial Ecology, 12, 219–286.

    CAS  Google Scholar 

  2. Pace, N. R., Angert, E. R., Delong, E. F., Schmidt, T. M., & Wickham, O. S. (1993). New perspective on the natural microbial world. In: R. H. Baltz, B. D. Hegeman, & P. L. Skatrud (Eds.), Industrial microorganisms: Basic and applied molecular genetics (pp. 77–84). Washington: ASM.

    Google Scholar 

  3. More, M. I., Herrick, J. B., Silva, M. C., Ghiorse, W. C., & Madsen, E. L. (1994). Quantitative cell lysis of indigenous microorganisms and rapid extraction of DNA from sediments. Applied and Environmental Microbiology, 60, 1572–1580.

    PubMed  CAS  Google Scholar 

  4. Clegg, C. D., Ritz, K., & Griffith, B. S. (1997). Direct isolation of microbial community DNA from humified upland soils. Applied Microbiology, 25, 30–33.

    Article  CAS  Google Scholar 

  5. Luna, M. G., Anno, D. A., & Danovaro, R. (2006). DNA extraction procedure: A critical issue for bacterial diversity assessment in marine sediments. Environmental Microbiology, 8, 308–320.

    Article  PubMed  CAS  Google Scholar 

  6. Niemi, M. R., Heiskanen, I., Wallenius, K., & Lindström, K. (2001). Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. Journal of Microbiological Methods, 45, 155–165.

    Article  Google Scholar 

  7. Holben, W. E., Jansson, J. K., Chelm, B. K., & Tidje, J. M. (1988). DNA probe method for the detection of specific microorganisms in the soil community. Applied and Environmental Microbiology, 54, 703–711.

    PubMed  CAS  Google Scholar 

  8. Steffan, R. J., & Atlas, R. M. (1998). DNA amplification to enhance detection of genetically engineered bacteria in environmental samples. Applied and Environmental Microbiology, 54, 2185–2191.

    Google Scholar 

  9. Ranjan, R., Grover, A., Kapardar, R. K., & Sharma, R. (2005). Isolation of novel lipolytic genes from uncultured bacteria of pond water. Biochemical and Biophysical Research Communications, 335, 57–65.

    Article  PubMed  CAS  Google Scholar 

  10. Bertrand, H., Poly, F., Van, T. V., Lombard, N., Nalin, R., Vogel, T. M., & Simonet, P. (2005). High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction. Journal of Microbiological Methods, 62, 1–11.

    Article  PubMed  CAS  Google Scholar 

  11. Yeates, C., Gilling, M. R., Davison, A. D., Altaviilla, N., & Veal, D. A. (1998). Methods for microbial DNA extraction from soil for PCR amplification. Biological Procedures Online, 1, 40–47.

    Article  PubMed  Google Scholar 

  12. Roose-Amsaleg, C. L., Garnier-Sillam, E., & Harry, M. (2001). Extraction and purification of microbial DNA from soil and sediment samples. Applied Soil Ecology, 18, 47–60.

    Article  Google Scholar 

  13. Santosa, D. A. (2001). Rapid extraction and purification of environmental DNA for molecular cloning application and molecular diversity studies. Molecular Biotechnology, 17, 59–64.

    Article  PubMed  CAS  Google Scholar 

  14. Lakay, F. M., Botha, A., & Prior, B. A. (2006). Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils. Journal of Applied Microbiology, 100, 1365–1373.

    Google Scholar 

  15. Miller, D. N., Bryant, J. E., Madsen, E. L., & Ghiorse, W. C. (1999). Evaluation and optimization of DNA extraction and purification procedure for soil and sediments sample. Applied and Environmental Microbiology, 65, 4715–4724.

    PubMed  CAS  Google Scholar 

  16. Zhou, J., Bruns, M. A., & Tiedje, J. M. (1996). DNA recovery from soils of diverse composition. Applied and Environmental Microbiology, 62, 316–322.

    PubMed  CAS  Google Scholar 

  17. Wise, M. G., Mcarthur, J. V., & Shimkets L. J. (1997). Bacterial diversity of Carolina Bay as determined by 16S rRNA gene analysis: Confirmation of Novel Taxa. Applied and Environmental Microbiology, 63, 1505–1514.

    PubMed  CAS  Google Scholar 

  18. Holben, W. E, Jansson, J. K., Chelm B. K., & Tiedje, J. M. (1988). DNA probe method for the detection of specific microorganisms in the soil bacterial community. Applied and Environmental Microbiology, 54, 703–711.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biotechnology, Panjab University, Chandigarh, 160014, India

    Pushpender K. Sharma, Neena Capalash & Jagdeep Kaur

Authors
  1. Pushpender K. Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Neena Capalash
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jagdeep Kaur
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jagdeep Kaur.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sharma, P.K., Capalash, N. & Kaur, J. An improved method for single step purification of metagenomic DNA. Mol Biotechnol 36, 61–63 (2007). https://doi.org/10.1007/s12033-007-0015-3

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12033-007-0015-3

Keywords

Search

Navigation