fundamentals of eDNA

The paper “Aquatic suspended particulate matter as a source of eDNA for fish metabarcoding” (Diaz et al., 2020) addressed a pilot study that was conducted to determine whether suspended particulate matter (SPM) could be used for eDNA extractions. This paper brought up a few interesting aspects of the potential of eDNA from SPM, however, there were a few key conclusions they made which I felt was lacking some data and would be interested in seeing more data-driven validation behind them in the future.

The concept of using SPM seems very logical - it has been previously shown that sediment-eDNA degrades slower than eDNA from water, so for long term studies collecting samples that somewhat turn into sediment samples as they are being collected would make sense that the eDNA may last longer. This is also an interesting application of SPM when thinking of long term studies, such as the UN Global Oceans 2020 goal of implementing more eDNA in long term monitoring studies. By using instruments already being implemented for other analyses, this would allow us to integrate eDNA sampling into other monitoring programs more easily and potentially accelerate the process by which eDNA monitoring is incorporated into these programs. As they mentioned in the paper, sediment traps also allow for a more long-term visual of the organisms in the water in comparison to the “snap-shot” that collecting water for eDNA provides. When applying this to long term monitoring, this has some benefits - such as the more broad picture you may be capturing - but also some potential drawbacks, as the samples they used in this study were pooled monthly samples for an entire year. This does not necessarily provide the same resolution as multiple fish surveys over the course of the year, and in order to truly compare the effectiveness of these methods, I would be interested in seeing the sediment traps analyzed for eDNA at a smaller scale than one year. The authors also compared the total DNA yield from their extractions to previous extraction from water samples, claiming that they had a higher DNA yield compared to water samples. However, it does not seem like they conducted their own water samples for this comparison, and only compared it to previous work on water and sediment extractions. I would be interested in seeing a more direct comparison, where they sampled the water more regularly from a similar area for a year, then pooled those extracts together and sequenced the results.

On the whole, I do think that extracting eDNA from SPM would be beneficial for applying eDNA to conservation management, however, there are factors that need to be considered that may not be when collecting water eDNA samples. Temperature of the water where you are sampling may degrade the eDNA faster since it is sitting in the water longer than an eDNA water sample (despite being in the sediment traps), so knowing how long it takes for the eDNA to degrade will be vital for coming to relevant conclusions. Alongside this, being diligent about where these traps are placed will be vital to the success of the eDNA collection, especially in marine environments, addressing questions such as how fast is the current, what direction is it moving in, and if there is anything upstream that may alter the DNA recovery over time? Overall I think this paper addresses a new way of thinking about eDNA and SPM going hand-in-hand, and it will be interesting how these practices are applied in the future.