Reflection - Wk5
This week’s class covered ways to collect, store, and extract eDNA (environmental DNA). The group-led discussion furthered the conversations about these methods and covered two papers, one by Foote et al, “Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals”, and the other by Deiner et al, “Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA”.
We discussed methods and protocols for eDNA sampling and filtering (including in the field). One sampling method that I thought was super interesting is “passive” eDNA collection through natural sponges, which act like natural filters. For example, Mariani et al “obtained sponge samples from Mediterranean and Antarctic surveys, extracted total DNA from their tissues, and obtained tens of thousands of fish DNA reads via metabarcoding, which were able to clearly distinguish samples from the two regions” (p. R401). Two other interesting “passive” methods as described by a study conducted by Kirtane et al are through the use of “adsorbents, Montmorillonite Clay (MC) and Granular Activated Carbon (GAC).”
We covered the variety of ways to filter samples including the possibility for field filtering, such as positively through a syringe or via negative pressure through a hand pump. I knew of the electric suction pump used in the Maine-eDNA lab, but I was not aware of the other methods. Through this class I am also becoming more keenly aware of the importance of preventing sample contamination, especially if one is sampling in multiple, nearby locations. Thinking about these issues helps me understand the importance and value of control blank methods, which is something I did not do in my eDNA brook trout study. Oops.
Also, when we covered the extraction process and “lysing” the cell, the lecture was really helpful in understanding how tough certain organisms’ cellular structures are compared to other organisms. The images were especially helpful! For example, a diatom has a silica wall with two lipid membranes versus an animal cell which has two lipid membranes, but lacks an exterior wall. Knowing your organism’s cellular structure is key to choosing effective extraction strategy to facilitate the lysis process.