Evaluation of Some Potential Protocols to Extract DNA from Paddy Soil

Abstract

Isolation of DNA from environmental samples is a crucial step in microbial community analyses through molecular methods. The present study was conducted to evaluate a DNA extraction protocol from paddy soil with a comparison on quality, quantity and integrity of the isolated DNA and to determine the suitability of extracted DNA for downstream applications in microbial community analyses. Three protocols (i.e. PEG/NaCl, Mannitol/CTAB and Sodium Phosphate Buffer) used for the extraction of DNA from different types of soil were attempted on paddy soil. The quality and quantity of the extracted genomic DNA was quantified spectrophotometrically and integrity was checked by gel electrophoresis. The efficiency of DNA extraction by the three protocols was compared with a commercial soil DNA extraction kit (Norgen's Soil DNA Isolation Plus Kit). Further, quality of the extracted DNA for PCR amplification was assessed using universal primer pairs for bacteria and fungi. DNA extracted using PEG/NaCl method resulted in the highest DNA concentration, while the highest purity was recorded by the DNA extracted by Mannitol/CTAB method (A260/A280 = 1.61 and A260/A230 = 1.15). Expected PCR products targeting 16s rDNA and ITS regions were obtained from the DNA samples extracted by Mannitol/CTAB method. Therefore, Mannitol/CTAB method used in the present study is suitable to extract high-quality DNA from paddy soil for molecular microbial studies.