fundamentals of eDNA

This week we discussed two different studies. The first by Deiner et al. (2015) explored whether different eDNA sample capture and extraction methods affected the detection rates for various species. They compared two different capture methods and three different DNA extraction protocols using samples from two different freshwater sites. They found differences in results between sample capture and extraction methods. This paper brought up the importance of doing a pilot study and tests to ensure that you are utilizing the optimal methods for your target organism(s). Additionally, it is important to remain consistent in your methodology throughout your study in order to compare between all samples in the study.

We discussed the following questions related to the study by Deiner et al. (2015): • What do you use (other than literature) to decide which extraction method is best for your research? Which factors hold the most value to you when deciding an extraction technique? Time, labor, cost, and ability to positively detect your target organisms. • What are some things that are important to include in team discussions for standardizing protocols? Making sure you are selecting methods that are optimized the best that they can be for everyone’s target organisms and ensuring everyone is following the protocols correctly. • What is the benefit of higher DNA yields? There are certain thresholds for sequencing, samples with higher yields are more useful (can always be diluted), and potential for detection of your target (especially if it is a rare organism).

The second paper we discussed this week was by Foote et al. (2012), which discussed using water samples to detect marine mammals. In this study, the authors were testing whether or not they could detect marine mammals using eDNA. They included both a control (sea pen with harbor porpoises) and natural seawater samples from several different sites. What stood out to me about this paper is the fact that they were using such small sample volumes via the precipitation method for detection of marine species in the ocean. Although, the precipitation method is useful for detecting extracellular DNA, which can inform you of more recent presence since that is the type of DNA that degrades first. I did like the fact that they were pairing acoustic detection with the eDNA work.

We discussed the following questions related to the study by Deiner et al. (2015): • What was the rationale for conducting this experiment with the methods they used? • Were there any questionable methods in this paper? If so, what were they? Small sample volumes, and problems with acoustic detection equipment. • How would you have changed the methods in this paper? Switch to filtration method to get larger sample volumes. • How have sampling methods for this type of target (rare single species) changed since this paper? Most studies now seem to use filtration method.