Introduction
DNA extracted from the environment is referred to as environmental DNA
(eDNA), which is usually degraded (Taberlet et al., 2012,
Taberlet & al, 2018). Environmental DNA that is extracted from
freshwater samples may originate from feces, urine, skin, and excreted
tissue and can be free, cellular or particle-bound (e.g. Levy-Boothet al., 2007; Pietramellara et al., 2009). Although it is
often highly degraded, it is possible to PCR amplify small fragments of
eDNA such that even species that occur at low abundances can be detected
from, for instance, water samples (Dejean et al., 2011; Dejeanet al., 2012; Jerde et al., 2011). Among others, Thomsenet al., (2012a) and Katano et al., (2017) have shown that
eDNA can therefore be used to quantitatively monitor the occurrence of
various freshwater organisms.
Physical, chemical and biological degradation, e.g. by DNases and
microbial activity, is known to compromise amplification (Levy-Boothet al., 2007; Shapiro 2008). Several studies show that under
controlled conditions eDNA in aquatic environments is degraded beyond
detectability within a week (Dejean et al., 2011; Takaharaet al., 2012; Thomsen et al., 2012a; Thomsen et
al., 2012b; Eichmiller et al., 2016) and that a positive
relationship exists between the abundance of target organisms and eDNA
concentration (Dejean et al., 2011; Takahara et al., 2012;
Thomsen et al., 2012a). Maruyama & al. (2014) report degradation
rates of fish eDNA in freshwater of up to 10% per hour and found a
strong correlation with the developmental stage of the target organisms.
The authors state that quantitative eDNA data from the field should
therefore be corrected to control for post-sampling degradation. To
better understand the relationship between target organism abundance,
field eDNA degradation rate, and developmental state, more data should
be gathered on factors that influence degradation of and the ability to
detect eDNA. Insight in the limits of eDNA detection is essential to
prevent false negatives (Darling & Mahon 2011). Known factors that
affect DNA degradation are water temperature (e.g. Dupray et al.,1997; Lindahl 1993; Palmer et al., 1993; Takahara et al.,2012; Eichmiller et al., 2016; Tsuji et al., 2017), UV
level (Strickler et al., 2015) and DNA-consuming microorganisms
(Finkel & Kolter 2001; Alvarez et al., 1996; Dupray et
al., 1997). Other factors that influence the rate of decay or the
detectability of eDNA may be water conductivity and pH (Thomsen et
al., 2012a; Strickler et al., 2015), as well as the presence of
organic matter (Saeki et al., 2011).
Here, we study the effect of organic matter (hereafter referred to as
OM) and pH on eDNA degradation and detection efficiency in an aquarium
experiment using common freshwater shrimp (Gammarus pulex L.,
Amphipoda) as model species and DNA source. We hypothesize that both
survival and accumulation of eDNA would be affected by pH and OM.
Furthermore we test whether extracellular DNA responds differently to pH
and OM compared to eDNA released by dying shrimps. In addition, we test
the level of PCR inhibition in all aquariums and whether it is affected
by pH and OM.