Isopropanol precipitation method for collecting fish environmental DNA

Abstract

The environmental DNA (eDNA) method has been used to estimate the distributions of aquatic species, and both ethanol precipitation and filtration-based methods are commonly employed to capture eDNA from sampled water. Although filtration-based methods can capture more eDNA than that by ethanol precipitation, by processing larger volumes of water (e.g., 1 L vs. 15 mL), ethanol precipitation can immediately preserve eDNA on site and ease downstream processing, which are especially advantageous for eDNA studies conducted with limited resources, such as electric equipment, labor, and time. However, the ethanol precipitation method is limited by small volume of water that can be processed (i.e., 15 mL in a reaction volume of 50 mL). As an alternative, isopropanol could potentially be used to increase the volume of sample water processed, since lower volumes of isopropanol are required for precipitation. Therefore, in the present study, we compared the copy numbers of carp eDNA captured using isopropanol and ethanol precipitation in both mesocosm and field experiments. In both cases, we found that isopropanol precipitation recovered double the amount of eDNA recovered by ethanol precipitation, when the reaction volumes were equal. Therefore, isopropanol precipitation is a superior option for eDNA capture when surveys are conducted under resourcelimited conditions.