Variations in DNA extraction efficiency among soil samples are an important issue for soil DNA-based analyses
of soil microorganisms. The objective of this study was to present a practical method for evaluating soil DNA extraction efficiency. Soil DNA extraction conditions were optimized for three Andosol samples (H, M, and L) collected from sloping fields with uneven surface soil distribution due to soil erosion. The recovery amount of lambda DNA added to soil prior to extraction was measured by real-time PCR to evaluate DNA extraction efficiency. While it was difficult to extract soil DNA from sample L among the three samples under the condition using a commercial kit combined with skim milk, soil DNA could be extracted from all three samples by using casein sodium instead of skim milk. The DNA extraction efficiencies of samples H, M, and L were 30.3%, 21.1%, and 0.001%, respectively, under the condition using skim milk, whereas they were 29.6%, 28.2%, and 22.6%, respectively, under the condition using casein sodium. The soil DNA yields corrected based on the extraction efficiencies under the latter condition were 24.2, 14.7, and 1.8 μg/g dry soil, respectively. The method presented in this study is expected to improve the accuracy of quantitative analyses of soil microorganisms, especially in soils with different DNA extraction efficiencies.
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