Mann Week5
The topic for this week was DNA extraction methods. Figuring out which extraction method to use is pretty daunting. It seems like every paper I read uses a different method AND finds different results. For example: Deiner et al. (2014) found that MO Bio’s Power Water kit does not detect eukaryotes as well as phenol-chloroform-isoamyl alcohol and Qiagen’s DNA easy kit when paired with water filtration. This is surprising because the Power Water kit was designed to be used by aquatic ecologists (or so I’ve been told). The confusion over which extraction method to use is very relevant to the eDNA program right now. There is a push to standardize the extraction method for all index sampling sites. Last I heard they settled on a Power Soil (or some variation of sediment/soil) extraction kit. It seems like choosing a one size fits all extraction kit for index sampling is not the best approach as we are collecting water in salt, fresh, and brackish water. Furthermore, Deiner et al. (2014) suggests that you should choose different extraction protocols depending on what you are trying to find. For example: they found that the Power Water kit was most effective at targeting procaryotes when paired with precipitation. All index samples will be used for three different PCR reactions- 16s for prokaryotes, 12s for invertebrates, and 18s for fish. Since we are shooting for the whole “tree of life” metabarcoding, shouldn’t we expect to use three different extraction methods that are best for certain primers?