A lab-made method for extracting DNA from soils

Abstract

Most soil biologists rely on proprietary commercial kits to extract soil DNA for sequencing projects, primarily for their ease of use. However, most of these kits lack procedural transparency which limits comparative long-term standardisation efforts. Here I demonstrate a new procedure that is well defined and yields results similar or superior to the PowerSoil and SoilMaster kits. The Laboratory Technique utilises bead-beating, a well-defined extraction buffer, ammonium acetate precipitation, isopropyl alcohol precipitation and purification through a Sephacryl 300-S HR gel filtration spin column. Based on Sybr Green assays the Laboratory Technique extracted on average 21% and 430% more DNA than the PowerSoil and SoilMaster kits respectively. Purity based on 260/280 nm spectrophotometric ratios averaged 1.94 for the Laboratory Technique and the PowerSoil procedure, and 1.35 for the SoilMaster kit. Correlation between community taxonomic structure analysis from DNA extracted by the Laboratory Technique and the PowerSoil procedure were in near complete agreement yielding an R2 of 0.99 at the level of phyla and 0.97 at the level of genera. Overall, the Laboratory Technique is an attractive alternative in terms of yield, purity, transparency, cost and potential for long-term standardisation.