An Effective Method for Extracting DNA from Contaminated Soil Due to Industrial Waste

Recently, labor accidents caused by toxic gas production such as H ₂S and CH₄ have happened at some waste disposal sites and illegal dumping sites in Japan. The gas production has been known to be end products of bacterial respiration. In order to investigate a microbial flora in industrial waste contaminated soil by a DNA-based detection method, we developed a simple DNA extraction method. The method is based on lysis with sodium dodecyl sulfate(SDS)and a high concentration (4.0 mg/ml) of lysozyme at room temperature. DNA yields increased according to the concentration of lysozyme (0 ∼ 2 mg/ml), although the cell lysis occurred at comparable efficiency independent of the lysozyme concentration. Interestingly, bovine serum albumin and insulin (4 mg/ml) also contributed high DNA yields. This suggests proteins play an important role at high concentration on a DNA extraction process, presumably by suppressing DNA degradation or adsorption. DNA yields from three contaminated soil samples at 0.3, 1.5 and 3 m in depth by using our method were significantly higher than those extracted by using a widely-used conventional method which did not contain lysozyme. A novel and simple DNA extraction method using high concentration of protein was established for a DNA-based detection method of microbial flora in soil.