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.