Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil

Mathur Nadarajan Kathiravan; Geun Ho Gim; Jaewon Ryu; Pyung Il Kim; Chul Won Lee; Si Wouk Kim

doi:10.1007/s12275-015-5454-0

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Research Support, Non-U.S. Gov't
Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil: Mathur Nadarajan Kathiravan ¹, Geun Ho Gim ¹, Jaewon Ryu ², Pyung Il Kim ³, Chul Won Lee ⁴, Si Wouk Kim ¹; Journal of Microbiology 2015;53(11):767-775
DOI: https://doi.org/10.1007/s12275-015-5454-0
Published online: October 28, 2015

¹Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom, Chosun University, Gwangju 61452, Republic of Korea, ²Department of Energy Convergence, Chosun University, Gwangju 61452, Republic of Korea, ³Bio Control Research Institute, JBF, Jeonnam 516-944, Republic of Korea, ⁴Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea¹Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom, Chosun University, Gwangju 61452, Republic of Korea, ²Department of Energy Convergence, Chosun University, Gwangju 61452, Republic of Korea, ³Bio Control Research Institute, JBF, Jeonnam 516-944, Republic of Korea, ⁴Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea

Corresponding author: Si Wouk Kim , Tel: +82-62-230-6649,

Received: 8 September 2015 • Revised: 2 October 2015 • Accepted: 2 October 2015

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Abstract

In this study, novel DNA extraction and purification methods were developed to obtain high-quantity and reliable quality DNA from the microbial community of agricultural yellow loess soil samples. The efficiencies of five different soil DNAextraction protocols were evaluated on the basis of DNA yield, quality and DNA shearing. Our suggested extraction
method
, which used CTAB, EDTA and cell membrane lytic enzymes in the extraction followed by DNA precipitation using isopropanol, yielded a maximum DNA content of 42.28 ± 5.59 μg/g soil. In addition, among the five different purification protocols, the acid-treated polyvinyl polypyrrolidone (PVPP) spin column purification method yielded high-quality DNA and recovered 91% of DNA from the crude DNA. Spectrophotometry revealed that the ultraviolet A260/A230 and A260/A280 absorbance ratios of the purified DNA were 1.82 ± 0.03 and 1.94 ± 0.05, respectively. PCR-based 16S rRNA amplification showed clear bands at ~1.5 kb with acid-treated PVPP–purified DNA templates. In conclusion, our suggested extraction and purification protocols can be used to recover high concentration, high purity, and high-molecular-weight DNA from clay and silica-rich agricultural soil samples.

Keywords: microbial community DNA; metagenomics; soil texture; DNA extraction purification

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Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil

J. Microbiol. 2015;53(11):767-775. Published online October 28, 2015

DOI: https://doi.org/10.1007/s12275-015-5454-0

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