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.
Extraction kit, Paddy soil, Clayey soil, PCR-DGGE, Microbial community
© The Author(s) 2014. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License which permits unrestricted use, sharing, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.