Methods to maximise recovery of environmental DNA from water samples

One of the key requirements for eDNA methods to be used routinely is that there are standardised methodologies for all steps in the process. This is an example of one of our earlier projects where we developed such a standardised approach for eDNA extracted from water samples, which is now a widely cited and used study.

Since eDNA analysis often deals with small quantities of short and degraded DNA fragments, methods that maximise eDNA recovery are required to increase detectability. This study conducted a range of rigorous experiments at different stages of the analysis of eDNA from water samples in order to determine which combinations of methods gave the best recovery rate for DNA. Using the Oriental weatherloach (Misgurnus anguillicaudatus) as a study species, we showed that various combinations of DNA capture, preservation and extraction methods can significantly affect DNA yield.

Specifically we showed that;

• Filtration using cellulose nitrate filter paper preserved in ethanol or stored in a -20°C freezer and extracted with the Qiagen DNeasy kit outperformed other combinations in terms of cost and efficiency of DNA recovery.
• We recommend to filter water samples within 24hours but if this is not possible, our results suggest that refrigeration may be a better option than freezing for short-term storage (i.e., 3–5 days).

This information is useful in designing eDNA detection of low-density invasive or threatened species, where small variations in DNA recovery can signify the difference between detection success or failure.