Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil.
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 A 260/A 230 and A 260/A 280 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.
Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom, Chosun University, Gwangju, 61452, Republic of Korea.
Mathur Nadarajan
MN
Kathiravan
Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom, Chosun University, Gwangju, 61452, Republic of Korea.
Geun Ho
GH
Gim
Department of Energy Convergence, Chosun University, Gwangju, 61452, Republic of Korea.
Jaewon
J
Ryu
Bio Control Research Institute, JBF, Jeonnam, 516-944, Republic of Korea.
Pyung Il
PI
Kim
Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
Chul Won
CW
Lee
Department of Environmental Engineering and Pioneer Research Center for Controlling of Harmful Algal Bloom, Chosun University, Gwangju, 61452, Republic of Korea. swkim@chosun.ac.kr.
Si Wouk
SW
Kim
D000383:Agriculture; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification*; D056186:Metagenomics / Q000379:methods*; D059013:Microbial Consortia / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S; D012988:Soil Microbiology
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
DNA extraction purification; metagenomics; microbial community DNA; soil texture