Journal of Pure and Applied MicrobiologyVol. 8 No. Special Edition Nov. 2014

Comparison of Genomic DNA Extraction Commercial Kits Based on Clayey and Paddy Soils

Peng Li1,2†, Xuefeng Su1,2†, Jinbin Wang1,2, Shifang Yang1,2, Guogan Wu1,2, Meifeng Lin1,2, Kai Zhao1,2, Carlos Bezuidenhout3 and Xueming Tang1,2*

1Biotech Research Institute of Shanghai Academy of Agricultural Sciences, 2Shanghai Key Laboratory of Agricultural Genetics and Breeding, 3Unit for Environmental Sciences and Management, North-West University, South Africa.

Received on 26 March 2014 and accepted on 15 June 2014

 

ABSTRACT

In this study, the relative efficacy of three commercial DNA extraction kits (the ISOIL for Beads Beating kit (IS), the FastDNA® SPIN Kit for Soil (FD) and the ExtroSpin® Soil Kit (ES)) were evaluated. Further, PCR-DGGE technique was assessed for its feasibility in detecting differences in clayey and paddy soils bacterial fingerprint profiles. Sufficient amounts of DNA could be successfully extracted from the clayey and paddy soils using both IS and FD kits, while it failed to extract detectable amount of DNA by the ES kit. PCR products of bacterial 16S rRNA genes were achieved by all three kits. Results showed that higher amounts of DNA and bacterial diversity in DGGE fingerprints were obtained by the IS and FD kits than by the ES kit. The IS and FD kits were appropriate for DNA extraction, displaying no significant differences in experimental results. When time and cost were considered, the FD kit contributed in cost by about two-fold reduction compared with the IS kit. In summary, the FD kit was the most cost-effective and time-efficient technique to extract DNA from the clayey and paddy soils.

Keywords : Extraction kit, Paddy soil, Clayey soil, PCR-DGGE, Microbial community.