Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils

Abstract

The direct extraction of DNA from different New Zealand soils using three simple and rapid methods has revealed that poor recovery of DNA during extraction was influenced by extraction procedure and also edaphic factors. Clay mineralogy and purification strategies required to remove compounds, such as humic acids that are inhibitory to DNA analysis, can significantly reduce yields and are dependant on soil type. The extraction methods were selected for a range of extraction intensities, and included the use of a direct lysis incubation (Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborne, A.M., Strike, P., Ritchie, D.A., 1992. Applied & Environmental Microbiology 58, 3413–3416), along with two bead mill homogenization-based methods of differing vigour (Berthelet, M., Whyte, L.G., Greer, C.W., 1996. FEMS Microbiology Letters 138, 17–22; Bornemanm J, Skroch, P.W., O'Sullivan, K.M., Palus, J.A., Rumjanek, N.G., Jansen, J.L., Nienhuis, J., Triplett, D.W., 1996. Applied & Environmental Microbiology 62, 1935–1943). The basis for assessing the quantity and quality of extracted DNA was suitability for polymerase chain reaction (PCR) since the analysis of soil DNA often relies on applying PCR to study soil microorganisms, or for tracking introduced organisms such as pathogens or genetically modified organisms (GMOs) applied to soil. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for studies where very low copy numbers of target genes are anticipated.