1. Meta-analyses of eDNA literature
Our meta-analyses showed that filter pore size, water temperature,
target gene, and water source could influence eDNA degradation, not as
individual parameters but in conjunction. We focused on three
substantial interactions that were included in almost all supported
models. Firstly, the interaction between filter pore size and water
temperature influenced eDNA decay rates (Figure 1). Considering that a
larger pore size filter can selectively collect eDNA particles in larger
size fractions, our result implied that higher water temperature could
accelerate the degradation of eDNA in larger size fractions by a greater
degree than that in smaller size fractions. However, it is unlikely that
smaller-sized eDNA itself is less affected by higher
temperature-mediated degradation, and its apparent persistence can be
increased by the inflow of eDNA from larger to smaller size fractions,
as described in Jo et al. (2019b). Organic matter in water, including
eDNA, is degraded by microbes and extra-cellular enzymes in the
environment for uptake, and their activities are promoted by moderately
high temperatures (less than 50°C) (Price & Sowers, 2004; Nielsen et
al., 2007; Arnosti, 2014; Strickler et al., 2015). During the
degradation processes, aqueous eDNA in larger size fractions, such as
intra-cellular DNA, is believed to flow into smaller size fractions,
such as extra-cellular DNA. This suggests that water temperature does
not uniformly influence the apparent degradation of eDNA among the
different size fractions, and the effect of temperature on eDNA
degradation might be buffered in smaller-sized eDNA particles. Thus, the
effect of temperature on eDNA degradation would be smaller when using a
smaller pore size filter and collecting eDNA particles at various size
fractions.
Secondly, the interaction between the target gene (nuclear or
mitochondrial) and water temperature influenced the eDNA decay rates;
higher water temperature could accelerate the degradation of nuclear
eDNA by a greater extent when compared with mitochondrial DNA (Figure
2). This may be attributed to the difference in the protection conferred
to the DNA molecules against the attack of extra-cellular enzymes in the
environment by the outer nuclear and mitochondrial membranes. In
contrast to mitochondrial DNA, which is surrounded by a non-porous outer
membrane (Ernster & Schatz, 1981), nuclear DNA is enclosed in a porous
membrane (45-50 nm in diameter; Fahrenkrog & Aebi, 2003), rendering it
more susceptible to environmental extra-cellular enzymes, and thus, more
likely be degraded by a greater degree at higher temperatures (Price &
Sowers, 2004; Strickler et al., 2015). However, these results should be
interpreted with caution, because the number of nuclear eDNA decay rate
constants (n = 17) included was considerably lower than that of
mitochondrial eDNA decay rate constants (n = 89). It is necessary to
estimate nuclear eDNA decay rates in various environmental and
experimental conditions in the future, which would enable a more robust
comparison of eDNA degradation between nuclear and mitochondria DNA.
Thirdly, the interaction between the target gene and water source
influenced the eDNA decay rates (Figure 3). Although the effects of
water source on eDNA degradation differed between nuclear and
mitochondrial DNA, it was evident that eDNA degradation was suppressed
in artificial waters, such as tap water and DW, when compared to that in
natural waters. Eichmiller et al. (2016) compared the degradation of
common carp (Cyprinus carpio ) eDNA in natural waters with
different trophic states, and found that eDNA decay rates in well water
were lower than those in eutrophic and oligotrophic waters, which could
be attributed to the lower microbial activity in the former. Our results
were generally consistent with those of Eichmiller et al. (2016). Using
tap water and DW as water sources can lead to underestimation of eDNA
persistence in the natural environment. Moreover, no significant
difference could be observed in the eDNA decay rates between freshwater
and seawater. The difference in eDNA persistence between freshwater and
seawater has previously been reported; some studies indicated faster
eDNA degradation in seawater than in freshwater (Thomsen et al., 2012;
Sassoubre et al., 2016), whereas Collins et al. (2018) showed that eDNA
degradation was higher in terrestrially-influenced inshore waters than
in ocean-influenced offshore environments. Marine systems are generally
characterized by higher salinity and ionic content, higher pH, and more
stable temperatures when compared with freshwater systems, which can
promote DNA preservation in water (Okabe & Shimazu, 2007; Schulz &
Childers, 2011; Collins et al., 2018). However, the direct effects of
microbial abundance and composition and other physicochemical parameters
of water were not included in our meta-analyses. Thus, greater
variations in eDNA decay rates in seawater when compared with artificial
water and freshwater observed in our meta-analyses might partly be
explained by such microbial and physicochemical conditions. The effects
of various nutrient salts and microbial activities on eDNA persistence
and differences in the eDNA degradation processes between freshwater and
seawater systems require further investigation.
The interaction between filter pore size and water source influenced the
eDNA decay rates in some supported models; however, its effect was
relatively smaller when compared with those of the interactions
discussed above (Table 2). The water source might affect the apparently
longer persistence of smaller-sized eDNA described previously. Although
no linear regressions were statistically significant (Figure S1;P > 0.05), the increase in eDNA decay rates with
larger filter pore sizes appeared to be greater in seawater than in
artificial water, which might also be attributed to the differences in
microbial activities among the different water sources.
Contrary to these four factors, model selection in the present study did
not strongly support the effects of DNA fragment size and its
interactions with other variables on the eDNA decay rate (Table 2),
which may be due to the potential bias of DNA fragment sizes in the eDNA
studies included in the meta-analysis. Only three studies have
previously estimated eDNA decay rates in water targeting longer DNA
fragments (>200 bp) (aqueous eDNA; Jo et al. 2017; Weltz et
al., 2017; Bylemans et al., 2018), and there was no consensus on the
relationship between eDNA degradation and DNA fragment size among these
studies. Although our additional meta-analysis, which targeted only
shorter DNA fragments (70 to 190 bp), supported rapid eDNA degradation
in longer DNA fragments, as suggested by Jo et al. (2017) and Wei et al.
(2018), the analysis might be considered slightly arbitrary, and thus,
the validity of the result would need to be tested in the future.
Interactions between DNA fragment size and other factors may become
evident when more information is available on eDNA persistence and
degradation at different fragment sizes.