Effects of Temperature and Trophic State on Degradation of Environmental DNA in Lake Water

Abstract

Degradation of environmental DNA (eDNA) in aquatic habitats can affect the interpretation of eDNA data and the ability to detect aquatic organisms. The effect of temperature and trophic state on the decay of Common Carp (Cyprinus carpio) eDNA was evaluated using lake water microcosms and quantitative PCR for a Common Carp-specific genetic marker in two experiments. The first experiment tested the effect of temperature on Common Carp eDNA decay. Common Carp eDNA exhibited exponential decay that increased with temperature. The slowest decay rate was observed at 5 °C, with a T90 value (time to 90% reduction from initial concentration) of 6.6 days, as opposed to ∼1 day at higher temperatures. In a second experiment, decay was compared across waters from lakes of different trophic states. In this experiment, Common Carp eDNA exhibited biphasic exponential decay, characterized by rapid decay for 3-8 days followed by slow decay. Decay rate was slowest in dystrophic water and fastest in oligotrophic water, and decay rate was negatively correlated to dissolved organic carbon concentration. The overall rapid decay of eDNA and the effects of temperature and water quality should be considered in protocols for water sample storage and field sampling design.

Attracting Common Carp to a bait site with food reveals strong positive relationships between fish density, feeding activity, environmental DNA, and sex pheromone release that could be used in invasive fish management

“…Other behaviors may have similar effects on eDNA, especially spawning (Erickson et al., 2016). Finally, while our finding that eDNA rapidly dissipated within just 5 m reinforces our previous results (Eichmiller et al., 2014) as well as numerous laboratory studies (Barnes & Turner, 2016; Eichmiller et al., 2016; Lance et al., 2017; Turner et al., 2014) which describe rapid decay and binding; further research is needed to precisely estimate degradation rates and the many factors that likely influence it in natural waters, especially in rivers.…”

“…Filtration equipment was decontaminated between samples using a 10‐min soak in 10% bleach, followed by liberal rinsing with distilled water. Extraction and quantitative PCR techniques were performed as previously described by Eichmiller, Best, and Sorensen (2016). Briefly, prior to extraction, filters containing water or sediment samples were sliced into 1 mm × 3 mm pieces using a sterile razor blade.…”

“…Quantitative PCR was performed as previously described (Eichmiller et al., 2016) using a qPCR marker specific for Common Carp that targets mtDNA cytochrome oxidase b gene. Triplicate negative PCR controls and copies of standards were included in each qPCR reaction plate, as previously described (Eichmiller et al., 2016).…”

“…Triplicate negative PCR controls and copies of standards were included in each qPCR reaction plate, as previously described (Eichmiller et al., 2016). Each water sample had three analytical replicates (i.e., each extracted water sample was run in three different PCR reactions and results were averaged).…”

Using Environmental DNA to Improve Species Distribution Models for Freshwater Invaders

“…Small-scale freshwater lentic bodies provide an excellent opportunity to study eDNA characteristics related to degradation, which can affect successful detectability of species. Recent studies have tried to underline degradation rates in correlation to abiotic factors, such as, (i) most effective water stratum for eDNA detection (Moyer et al, 2014), (ii) pH, UV-B (Strickler et al, 2015), (iii) effects of temperature on eDNA degradation (Strickler et al, 2015;Eichmiller et al, 2016), and (iv) temporal effects (Dejean et al, 2011). Freshwater lotic bodies can provide important information due to their longitudinal downstream dynamics, such as, (i) eDNA persistence in the environment Wilcox et al, 2016), (ii) residence time of eDNA , and (iii) the ecology of eDNA (Barnes and Turner, 2016).…”