Open AccessComparison of performance and efficiency of four methods to extract genomic DNA from oil contaminated soils in southwestern of Iran
Author(s) -
Yalda Basim,
Ghasemali Mohebali,
Sahand Jorfi,
Ramin Nabizadeh,
Ata Ghadiri,
Mehdi Ahmadi Moghadam,
Farid Soleymani
Publication year - 2020
Publication title -
journal of environmental health science and engineering
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.447
H-Index - 45
ISSN - 2052-336X
DOI - 10.1007/s40201-020-00474-z
Subject(s) - dna extraction , genomic dna , bioremediation , agarose gel electrophoresis , lysis buffer , extraction (chemistry) , metagenomics , chromatography , polymerase chain reaction , contamination , population , environmental remediation , biology , soil water , dna , bacteria , lysis , chemistry , microbiology and biotechnology , gene , biochemistry , genetics , ecology , demography , sociology
The wide spectrum of oil industry activities caused soil contaminants, as environmental concern in many areas of the world. Bioremediation of oily soils, as biological approach done by bacteria and fungi, is very important to eliminate this pollution. In this study four different metagenomic protocols for DNA extraction has been tested in order to sequence and identify the native bacterial species involved in remediation of oily soils. In this regard, 3 manual methods and a soil DNA extraction kit are used. In manual protocol, physical processes including the addition of silica beads and freezing samples by liquid nitrogen, chemical methods such as treating the lysozyme, and lysis buffer and proteinase K as biochemical methods were utilized for optimal extraction. Quality and quantity of the extracted DNA analyzed using Agarose gel electrophoresis and Picodrop respectively. Then, the 16S rdna gene of bacteria amplified through universal primer for preparing a genomic library by PCR. Results showed that the highest concentration and quality of extracted DNA was obtained by protocol D which was about 135 μg/ul and 260/230 = 2.2 respectively. Moreover, 500 bp fragment amplified perfectly by using DNA extracted through protocol D in the PCR test. Therefore, protocol D can be used as an appropriate and effective way in order to study the microbial population of oily soils using direct extraction of DNA.