This week we discussed a paper by Diaz (2020) detailing a pilot study on extracting eDNA from suspended particulate matter (SPM). The paper made me appreciate the complexities surrounding field sampling in a project like this and we felt that there were many field related details that the research didn’t directly address. For example, my group discussed how the quantity and quality of SPM may differ depending on the shape and flow of the river, and how it could be difficult to determine the actual origin of the eDNA due to transport of the SPM. We also discussed how difficult it can be to take a sample really close to the bottom without resuspending any sediment and causing contamination. Resuspension can occur from weights on the bottom of equipment, drones, or uncareful divers so it is important to consider the sample collection method.
I think it is important to remember that this paper was more for proof of concept than specifically eDNA detailed oriented which is why we found some of their methods insufficient. Personally I was a little surprised that they didn’t address the issue of contamination in their samples in their discussion, as they had both bacterial contamination and zebrafish cross contamination. They seem to justify not addressing these points of contamination because they were aware of where they were coming from, but there still seems to be an issue with their sterilization protocols. I would have appreciated them addressing them to ensure that future studies are not contaminated. I was particularly aware and focused on this aspect of the paper because last week I ran a PCR that resulted in a contaminated negative control. This made me analyze all of my steps in the lab that day to try to pinpoint where contamination may have occurred and it made me realize why molecular scientists are so paranoid about contamination!
Overall I learned a lot from this paper and think that it shows there is great potential for using SPM in eDNA studies. I also really liked Alex’s suggestion to integrate both SPM and water samples into research to gather data on both fine and broad scales, as well as further validate the effectiveness of both approaches .