Module 4 - eDNA Collection, Storage, and Extraction Methods
This week we discussed the study by Díaz et al. (2020), which discussed using suspended particulate matter (SPM) as a source of eDNA for detecting fish. In this study, they used sediment traps to collect their SPM. They used different methods for extraction and purification of DNA and found that the modified protocol for the Qiagen DNeasy PowerSoil Kit was the best overall (which was implemented for this study). The authors were able to detect 29 taxa across the 9 study sites (27 of which were able to be identified down to the species level).
This paper raised a lot of questions for me. Does suspended particulate matter attract DNA because SPM is often charged and/or made up of charged particles? Can DNA be preserved in aggregates and by particulate matter in the water column by protecting it from being eaten by microbes (which is often the case with certain nutrients)? How do you know the age of the DNA due to probable preservation of DNA in the SPM and sediment resuspension events (i.e. natural or human activity related)? Often times grazers and microbes will be attracted to sediment traps because they are essentially food concentrators for these organisms (some people apply antibacterial and antieukaryotic compounds to prevent degradation of collected SPM), could these organisms’ presence affect what and how much DNA is collected?
In the discussion, we reviewed our individual answers to the following questions: • Were their methods sufficient? How can they be improved? (i.e. Bacterial contamination? Pooling samples? Details (site locations)? Etc.? • Were their results convincing?