Expected decay processes
Chemical reactions of DNA may alter its size and modify its chemical structure, both of which determine its detectability in aquatic samples (Box 1). Chemical reactions include photochemical oxidation, abiotic hydrolysis, and enzymatically mediated hydrolysis (which we refer to as biological degradation since these enzymes are produced by living organisms). Both enzymatic and abiotic reactions cause hydrolytic cleavage of ester bonds in the backbone of DNA and result in the conversion of a longer DNA molecule into shorter molecules. Physical shearing of DNA molecules is also a potential mechanism, but these forces are unlikely in natural aquatic systems (Box 1). The importance of these reactions for using eDNA to infer species presence is that eventually these short molecules can no longer be detected using methods such as PCR. It is assumed that hydrolysis of eDNA can occur both intracellularly and extracellularly (Figure 1), thus affecting multiple eDNA states. Abiotic hydrolysis or photochemical oxidation are likely easier to predict (based on readily measurable chemical parameters such as solution pH and UV light irradiance) than enzymatic hydrolysis which requires more detailed information concerning type, abundance and activity of the enzymes, as well as the population dynamics of the microorganisms secreting these enzymes. Further, microbial activities (e.g., demand for phosphorus) are expected to be sample and time-specific and may require assessment when a water sample is collected7. Adsorption of nucleic acids to particle surfaces has been shown to stabilize these molecules by protecting it from hydrolytic enzymes in water38–41. Likewise, there is evidence that particle adsorbed DNA is protected from photochemical degradation42. Thus, once DNA is bound to surfaces of minerals, it is expected to be stabilized from degradation.