Figure 2: (a) Fish eDNA decay in relation to temperature. Data for marine and freshwater fish were included. The natural logarithm of the decay constant k is plotted against the reciprocal values of the temperature expressed in Kelvin [1/T], analogous to the temperature dependence of reaction rates presented in the Arrhenius equation. (b) eDNA data from amphibians, fish and crustaceans in relation to water pH. eDNA half-life (in hours) is plotted against pH of water where the organisms were present. Data were extracted from46,47,51and visualized using the R package ggplot2 v3.3.3.
Lastly, microbial abundance and activity are expected to play an important role in animal and plant eDNA decay in water (6and references therein). While studies have been performed on soil and sediments52–55, no systematic experiment has been conducted to determine the relative importance of abiotic versus biotic DNA degradation in water. Several studies have suggested higher microbial activity contributes to the faster DNA degradation observed at higher temperatures43,46,56,57, which appears to be supported by a mesocosm experiment that examined the influence of microbial activity on fish eDNA degradation. However, the experiment did not control bacterial abundance independently of temperature or time58. Another study examining bacterial abundance in relation to eDNA used radio-labelling as opposed to PCR amplification of natural seawater samples7, thus results are based on total eDNA as opposed to animal and/or plant eDNA. Bacteria are known to graze on DNA for nutrients in aquatic ecosystems through extracellular enzymes and ectoenzymes (e.g., nucleases on the surface of their cells that hydrolyse DNA11,15). Active DNA degrading enzymes have been found in filtered water fractions containing bacteria, cyanobacteria, algae, fungi, and single- and multicellular plankton animals, but some enzyme types (e.g., 5’-nucleotidase) have only been found on the surface of bacteria cells59. Another study employed antibiotics to decrease bacterial loads and found that antibiotics decreased eDNA decay rates to smaller values than measured under higher bacterial loads in untreated samples45, suggesting that microbial decay is the main driver. However in both of these studies, there was no control without bacteria to determine the relative importance of abiotic reactions. If enzymes secreted by cells are the main driver of hydrolysis of DNA, the subsequent nutrient utilization (N and P) by microbial cells is a plausible mechanism for the shorter decay rates (hours to days) observed for animal eDNA in natural water compared to abiotic reactions which occur over much longer timescales (Box 1)7. This would lead to environment-specific rates of eDNA decay requiring an understanding of both N and P limitation, and the parameters that control eDNA state (discussed in the “State conversion processes” section).