fundamentals of eDNA

Julia, Sharon, and Grayson presented their paper (Diaz et al. 2020) this week which was a proof of concept study revolving around extracting eDNA from suspended particulate matter (SPM). I have a lot of questions regarding this paper in terms of their methods, along with contamination of bacteria and the species Danio rerio. Their collection methods using the sedimentation boxes are questionable to me because they do not necessarily measure SPM, but rather are monitoring re-suspended sediment as well as the particulate matter. Discussion in the class revolved around how, even with Niskin bottles, sediment often can find its way into samples through bumping along the bottom, tides, strong currents, or even wave action that re-suspend sediments. However, the aim of this study was not to measure the sediment that was re-suspended, but rather they aimed to look at SPM, which needed better defining in the introduction. I am still unsure as to what classifies as SPM, but in my mind it does not include sediment that has re-entered the water column.

In addition to my opinions regarding the definition of SPM and the collection methods, I questioned the contamination that was found in the study. It seems as though this is a reoccurring problem with MiFish primers, which makes me think there could be issues revolving around the primer design. The authors of this paper hinted that there could be contamination from the environment they work in as Danio rerio is a common study species in their laboratory, and there could be bacteria contamination just by what is floating around in the air. I am not sure what can be done about this, but maybe creating reagents in a fume hood, or conducting lab processes in a fume hood can eliminate some of these problems. It was an interesting study, with some applications to my own work, my topic species, white sharks, swim close to the bottom in most cases, so I am anticipating most of their eDNA will likely be found near the bottom of the water column. I plan on paying attention to possibilities of suspended sediment more closely now, but I am not necessarily worried about this form of contamination amplification, as I am designing species specific primers as opposed to the MiFish metabarcoding primers.