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A comparison of methods for total community DNA preservation and extraction from various thermal environments

  • Original Paper
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

The widespread use of molecular techniques in studying microbial communities has greatly enhanced our understanding of microbial diversity and function in the natural environment and contributed to an explosion of novel commercially viable enzymes. One of the most promising environments for detecting novel processes, enzymes, and microbial diversity is hot springs. We examined potential biases introduced by DNA preservation and extraction methods by comparing the quality, quantity, and diversity of environmental DNA samples preserved and extracted by commonly used methods. We included samples from sites representing the spectrum of environmental conditions that are found in Yellowstone National Park thermal features. Samples preserved in a non-toxic sucrose lysis buffer (SLB), along with a variation of a standard DNA extraction method using CTAB resulted in higher quality and quantity DNA than the other preservation and extraction methods tested here. Richness determined using DGGE revealed that there was some variation within replicates of a sample, but no statistical difference among the methods. However, the sucrose lysis buffer preserved samples extracted by the CTAB method were 15–43% more diverse than the other treatments.

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Acknowledgments

We are grateful for the comments and input by Robert Sinsabaugh and Diana Northup who kindly reviewed an earlier version of the manuscript. This work was supported by NSF Biodiversity Surveys and Inventories grant 02-06773 to CTV.

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  1. Department of Biology, University of New Mexico, Albuquerque, NM, USA

    Kendra R. Mitchell & Cristina D. Takacs-Vesbach

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  1. Kendra R. Mitchell
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  2. Cristina D. Takacs-Vesbach
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Correspondence to Cristina D. Takacs-Vesbach.

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Mitchell, K.R., Takacs-Vesbach, C.D. A comparison of methods for total community DNA preservation and extraction from various thermal environments. J Ind Microbiol Biotechnol 35, 1139–1147 (2008). https://doi.org/10.1007/s10295-008-0393-y

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  • DOI: https://doi.org/10.1007/s10295-008-0393-y

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