Identifying information needed to understand eDNA states, decay and implications for species detection
We have discussed four eDNA states (dissolved, particle-absorbed, intracellular, inter-organellar) from eukaryotic organisms that are likely to be present in aquatic environments. Processes responsible for conversion between states and eDNA decay are detailed and well understood. Studies of eDNA decay in natural and artificial aquatic systems to date provide evidence that environmental parameters affect DNA decay rates in water3. We have made the case that chemical reactions that cause eDNA decay are likely to be state-specific and decay rate constants are influenced by the physical and chemical properties of aquatic environments. Thus, the next step is to form a greater understanding of what states are present for analysis in natural systems.
With this in mind, a meta-analysis of published eDNA studies targeting single species was performed to assess whether we could ascertain what eDNA states are being analysed overall, and whether the detection of the species’ DNA from a specific environmental context could inform which eDNA state was present. We note that this literature review may potentially be biased by methodologies that resulted in a positive eDNA detection from water samples (as non-detections are less likely to be published). Details of the search and analysis are presented in the Supporting Information. Because of the chemical properties of eDNA states, we know that molecular purification protocols can select and potentially isolate different states from a water sample (e.g.,60). Thus, we focused our literature review on methods used to isolate eDNA from a water sample and infer what states were likely analysed. We also recorded what environmental parameters were co-measured at the time of sampling.
Our literature review of 74 peer-reviewed articles showed that most eDNA studies are broadly employing the same molecular methods for DNA capture (i.e., filtration) and extraction (i.e., enzyme and chemical) albeit in different combinations (Figure 3).