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Comparison of Performance and Efficiency of Four Methods to Extract Genomic Dna From Oil Contaminated Soils in Southwestern of Iran Publisher



Basim Y1 ; Mohebali G2 ; Jorfi S1 ; Nabizadeh R3 ; Ghadiri A4 ; Moghadam MA1 ; Soleymani F5 ; Fard NJH1
Authors
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Authors Affiliations
  1. 1. Environmental Technologies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
  2. 2. Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
  3. 3. Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
  4. 4. Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
  5. 5. Gene Research Company, Karaj, Iran

Source: Journal of Environmental Health Science and Engineering Published:2020


Abstract

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. © 2020, Springer Nature Switzerland AG.
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