Over the last decade, the use of eDNA-based detection to monitor aquatic
biodiversity in both marine and freshwater systems has rapidly
increased1.
The reproducibility of eDNA surveys relies on the assumption that the
DNA detected provides an accurate measure of presence of the local
community or targeted species at the respective point in time and
space2,3.
As many conservation and management strategies have now adopted
eDNA-based
surveys4,5,
it is urgent to understand the various processes that influence eDNA
persistence in aquatic systems so that accurate inferences of a species
presence can be made from the detection of its eDNA. Indeed, previous
studies highlighted that eDNA stability can vary in systems depending on
many parameters, including species-specific eDNA shedding rates,
seasonality, and environmental
conditions6–8.
When organisms shed DNA into the water column, this gives rise to
extra-organismal eDNA (i.e. DNA no longer associated with its organism
of origin) and can take the form of at least four
states9,10.
These four states include: dissolved DNA, DNA bound to the surfaces of
suspended
particles3,6,10,
and DNA still encapsulated in either a cell or an
organelle11.
What we currently lack is a robust understanding of how water chemistry
and other environmental parameters affect which eDNA state(s)
predominate in specific aquatic environments and how they persist.
The state-of-the-art is to extract eDNA from water and target a single
species or whole communities of species using a set of primers and
Polymerase Chain Reaction
(PCR)12.
However, the presence of eDNA in different states has implications for
data interpretation, as detection of species might be influenced by the
‘detectability’ of a specific state that is the result of both the
environmental parameters determining the state and the analytical
workflow (i.e., preservation, capture, extraction and detection methods)
used to isolate the DNA from the water column. Consequently, the
relative distribution of eDNA among the different states could affect
the probability of detection for a targeted species’ DNA. Therefore, the
currently unknown stabilities of eDNA in different states combined with
the lack of information on which eDNA states are being detected creates
large uncertainty for the spatial and temporal inferences that can be
made from extra-organismal eDNA
detection3,13.
To reduce this uncertainty, we require a better understanding of the
states that eDNA assumes, the processes converting eDNA between
different states, and the variations in state-dependent eDNA decay
rates.
In this perspective, we describe four principal states of eDNA that are
likely in aquatic environments. Based on the presumed chemical behaviour
of each state, we discuss how environmental parameters, such as
temperature, pH and suspended particles, may influence the conversion of
eDNA between states (e.g.,14).
We briefly review what is known about DNA decay, covered in detail
elsewhere3,12,13,
and summarize what has been observed from experimental studies on eDNA
decay in relation to the environmental parameters of temperature and pH.
We then present the results of a literature search to ascertain what
states of eDNA are likely being detected using single-species eDNA
assays. Lastly, we outline a number of analytic controls, which, if
used, will help to assess the loss of specific states from aquatic
samples and allow for post hoc observations about the state(s)
contributing to species detection. We close with suggestions for future
research that would help to fill knowledge gaps regarding the space and
time inference that can be made from extra-organismal eDNA species
detections.