fundamentals of eDNA

This week, we discussed the proof of concept paper Diaz et al. 2020, but I felt it was a little sloppy in many aspects, which gave a feel of a paper more in line with the earlier days of eDNA. To be a little harsh, it felt more similar to my unpublished undergraduate eDNA work than a Scientific Reports paper.

While the idea of suspended particulate matter (SPM) as a source of eDNA is interesting, the paper made no attempt to examine what sort of temporal scale the recovered eDNA represents, even if the data correlates with conventional fish surveys. Can eDNA from SPM pick out spatio-temporal trends in community structure?

Where is the SPM coming from? How much is contemporary, and how much of it is coming from older resuspended sediment? What is the hydrological regime of the rivers in question like, and how might that affect SPM? In the earlier days of eDNA, we had a limited understanding of the importance of the ecology of eDNA, but now we know better, and as such the fact that these issues were not discussed is a little disappointing.

Some of my classmates pointed out that the collected sediment samples were likely to be for physicochemical studies, using sampling methods that are hardly optimal for eDNA, with eDNA merely being an opportunistic study subject. In addition, there was no explanation of why samples will pooled when they had month-level resolution to begin with. Why was the decision made to lose temporal resolution which could have been highly informative? While Scientific Reports papers are admittedly short, omitting such critical details of the methodology is unhelpful for researchers following in their footsteps.

As such, the main value of this paper is in identifying SPM as a potential source for follow up-studies, but it fails to clearly provide useful details about proper implementation and the potential caveats of such an approach. One can hope that the authors might be more thorough in any follow-up papers to come.

Therefore, it is heartening that my fellow classmates are exploring proof-of-concept approaches looking at the ecology of eDNA. Until we discussed the idea in class, I didn’t consider the possible extent of contamination from older sediment when conducting our usual Niskin bottle sampling methods, even though we did our best to minimise the risk via the use of equipment such as depth guns.

When it comes to my own project in the future, I will have to carefully consider the physicochemical and biological conditions affecting the ecology of eDNA at my sample sites, and how best to control for all these confounding factors. In addition, this study has reinforced the importance of documenting as much important information about experimental methodology as possible. Why were these decisions made? Why was this method chosen? It’s a rather daunting task, and may not always be practical, but it is best done whenever feasible in order to build a stronger scientific base for future researchers to follow.