Title |
Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil |
Author |
Mathur Nadarajan Kathiravan1, Geun Ho Gim1, Jaewon Ryu2, Pyung Il Kim3, Chul Won Lee4, and Si Wouk Kim1* |
Address |
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 Korea |
Bibliography |
Journal of Microbiology, 53(11),767-775, 2015,
|
DOI |
10.1007/s12275-015-5454-0
|
Key Words |
microbial community DNA, metagenomics, soil
texture, DNA extraction purification |
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. |