Optimizing Environmental DNA Storage: Comparing DNA Recovery between Low Binding and Standard Polypropylene Plastic Tubes using Quantitative PCR

Abstract:

Environmental DNA (eDNA) is a molecular tool that utilizes trace amounts of DNA left behind in a habitat from an organism to derive genetic information. Advantages of eDNA over traditional sampling methods, such as dip netting and trapping, include being less expensive, non-invasive, does not require organism handling, as well as not having to rely on species identification expertise. Therefore, eDNA could be the preferred tool for detecting rare, imperiled species. Although eDNA is a powerful technique, it is relatively new to the field of molecular ecology and lacks a standardized protocol within the literature. The lack of standardization exemplifies limitations of eDNA by resulting in DNA detections that are heavily dependent on the methodology used for sample analyses. Standard polypropylene tubes could be inhibiting our ability to detect target DNA. This is caused by DNA binding to polypropylene tubes, potentially resulting in false-negatives. Low binding polypropylene tubes are manufactured to prevent DNA from adhering to the plastic. A reduction in DNA binding to the tube could decrease false-negative results. Our study compares standard polypropylene and low binding tubes for storing aqueous eDNA samples by assessing the amount of DNA recovered from Ambystoma bishopi, an endangered species commonly known as the Reticulated flatwoods salamander, through quantitative PCR.