Introduction
Organisms release their DNA molecules into their surroundings, which are
termed as environmental DNA (eDNA) (Levy-Booth et al., 2007; Nielsen et
al., 2007; Taberlet et al., 2012). The analysis of eDNA has recently
been applied to monitor the abundance and composition of
macro-organisms, such as fish and amphibians (Ficetola et al., 2008;
Minamoto et al., 2012; Bohmann et al., 2014; Deiner et al., 2017; Jo et
al., 2020a). Detection of eDNA in water samples does not involve any
damage to the target species and their habitats, thus enabling
non-invasive and cost-effective monitoring of species in aquatic
environments, contrary to traditional monitoring methods such as
capturing and observing (Darling & Mahon, 2011). However, the
characteristics and dynamics of eDNA are not yet completely understood,
and thus, the spatiotemporal scale of eDNA signals at a given sampling
time and location is not certain, which can result in false-positive or
false-negative detection of eDNA in natural environments (Darling &
Mahon, 2011; Hansen et al., 2018; Beng & Corlett, 2020).
To determine the spatiotemporal scale of eDNA signals and accurately
estimate species presence/absence and abundance in the environment,
understanding the processes of eDNA persistence and degradation is
important. Aqueous eDNA is detectable from days to weeks (Barnes &
Turner, 2016; Collins et al., 2018), depending on various environmental
factors. For example, moderately high temperature (Strickler et al.,
2015; Eichmiler et al., 2016; Lance et al., 2017; Jo et al., 2020b) and
low pH (Strickler et al., 2015; Lance et al, 2017; Seymour et al., 2018)
accelerate eDNA degradation. In addition, eDNA decay rates are higher in
environments with higher species biomass density (Bylemans et al., 2018;
Jo et al., 2019a). These abiotic and biotic factors contribute to the
increase in microbial activities and abundance in water, thus indirectly
affecting eDNA degradation (Strickler et al., 2015). Moreover, eDNA
decay rates were found to be different between the trophic states of
studied lakes, and were negatively correlated with the dissolved organic
carbon (DOC) concentrations (Eichmiller et al., 2016). This may be
attributed to the binding of DNA molecules to humic substances,
protecting eDNA from enzymatic degradation.
However, apart from the effects of such environmental conditions, little
is known about the influence of the physiochemical and molecular states
of eDNA on its persistence and degradation. Fish eDNA has been detected
at various size fractions (<0.2 µm to >180 µm in
diameter; Turner et al., 2014; Jo et al., 2019b) in water, suggesting
that eDNA is present as various states and cellular structures, from
larger-sized and intra-cellular DNA (e.g., cell and tissue fragments) to
smaller-sized and extra-cellular DNA (e.g., organelles and dissolved
DNA). Enzymatic and chemical degradation of DNA molecules in the
environment depends on the presence of cellular membranes around the DNA
molecules, and thus, the persistence of eDNA is likely to be linked to
its state. In addition, eDNA persistence may be different depending on
the target genetic regions. Recent studies have suggested that eDNA
decay rates may vary between mitochondrial and nuclear DNA (Bylemans et
al., 2018; Moushomi et al., 2019; Jo et al., 2020b). Moreover, studies
comparing eDNA degradation between different target DNA fragment lengths
(i.e. PCR amplification length) have yielded inconsistent conclusions;
Jo et al. (2017) and Wei et al. (2018) reported higher eDNA decay rates
for longer DNA fragments, whereas Bylemans et al. (2018) did not observe
any difference in the eDNA decay rates of different DNA fragment sizes.
Notably, Jo et al. (2020c) reported that selective collection of
larger-sized eDNA using a larger pore size filter increased the ratio of
long to short eDNA concentrations and altered the ratio of nuclear to
mitochondrial eDNA concentrations; however, such reports linking eDNA
state to its persistence are scarce.
Although our understanding of the relationship between eDNA state and
persistence is currently limited, this relationship can be inferred by
integrating previous findings of eDNA persistence and degradation. Here,
we used meta-analyses to examine the relationship between eDNA states
and persistence. We extracted data on filter pore size, DNA fragment
size, target gene, and environmental parameters from previous studies
estimating first-order eDNA decay rate constants, and investigated the
influence of these factors on eDNA degradation. By assembling and
integrating the results of previous eDNA studies, our meta-analyses
revealed the hitherto unknown relationships between eDNA state and
persistence, which could not have been observed in the individual
studies. Furthermore, we assessed the validity of the findings of the
meta-analyses by re-analysing the dataset from a previous tank
experiment (Jo et al., 2019b).