Observed decay processes
In aquatic systems, the reactions expected to lead to DNA decay are likely further influenced by the state that eDNA assumes8. We conducted a literature search to evaluate what is known about eDNA decay processes based on temperature, pH and microbial activity. We collected data from previous literature reviews46,47and supplemented this with published studies that followed (see Table S1 and Figures S1-S2). Values for eDNA half-life in hours were directly extracted or calculated from the reported first order decay rate constant. Data from marine and freshwater organisms, namely fish, crustaceans, amphibians, and insects were included in our analysis, but see Figure 2B. Based on this literature review, exponential decay functions are increasingly fit to experimental DNA decay data showing that, independent of source organism, eDNA decay exhibits a pattern of first-order kinetics. Yet, some studies also demonstrate that a second-order (or biphasic) decay rate constant better describes the observed eDNA data48,49. As suggested by8, the need to fit a biphasic decay rate constant to observed experimental data may indicate that different rates may be associated with different eDNA states. However, because PCR detection of DNA cannot differentiate between states, the first order decay rate constant is likely an integrated estimate for eDNA decay across multiple states contributing to detection. The integrated estimate may be good if the question is “Was this species ever present in this ecosystem?” but integrating across states with unknown persistence times in the environment can decrease the accuracy of this inference if a finer temporal resolution of species presence is sought.
Studies to date (see Table S1) include both semi-natural or experimental aquatic systems but have thus far measured animal eDNA (especially fish), leaving much to be explored for what happens to plant and other animal eDNA in the water column. Broadly, observations are that animal eDNA rate constants of decay increase with increasing temperatures (>20ºC) but decrease with more basic (pH > 5.0) or alkaline solutions (pH > 9.0) (Figure 2a, b). Enzyme kinetics depend on the same parameters that affect abiotic DNA decay, for example, temperature, pH, UV-B light irradiation, and co-factors such as metal ions that either enhance or inhibit enzymatic activity50. Thus, we would expect these environmental parameters to be highly correlated with eDNA decay rates whether or not enzymes are involved. A single study has co-measured eDNA in different states (cell vs. dissolved DNA) and found differences in the decay rates between states for pond water but not salt water45. This suggests that water chemistry in different habitats may play a role in degradation of different states.