The effect of activity, energy use, and species identity on environmental DNA shedding of freshwater fish

Abstract

The quantitative measurement of eDNA form field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed. In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which exhibited lower activity and higher energy use. Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

“…We also thank two reviewers for their extensive and constructive feedback on the original manuscript. This manuscript has been uploaded as preprint to bioRxiv https://doi.org/10.1101/2020.10.28.359653 (Thalinger et al, 2020).…”

How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs?

“…Importantly, variability sources exist in the recovered biodiversity estimates which are poorly understood (Bessey et al., 2020; Juhel et al., 2020; Rourke et al., 2021; Thalinger et al., 2021). Detection rates and resultant variability in biodiversity estimates depend on eDNA (a) origin (source of an organism's genetic material shed into its environment), (b) state (forms of eDNA), (c) transport (e.g., through diffusion, flocculation or settling, currents or biological transport which can vary according to the depth), and (d) fate (how eDNA degrades and decays) (Barnes & Turner, 2016; Harrison et al., 2019; Thalinger et al., 2021) with DNA particles best preserved in cold and alkaline waters with low exposure to solar radiation (Moyer et al., 2014; Pilliod et al., 2014; Strickler et al., 2015; but see Mächler et al., 2018). As a result, marine eDNA residence time is shorter than in freshwater and ranges from a few hours to a few days (Collins et al., 2018).…”

Intraspecific genetic variability and diurnal activity affect environmental DNA detection in Japanese eel

“…A positive correlation between eDNA concentration and fish activity has been reported in seven freshwater fishes [ 35 ]. In the present study, eDNA concentration and activity were also positively correlated.…”

“…Individual differences, such as metabolic rate, stress conditions, life stage, and physiological or behavioral status, have been reported to potentially influence eDNA emission rates in salamanders [ 34 ]. Furthermore, Thalinger et al [ 35 ] observed a positive correlation between eDNA detection and fish activity in seven fish species in freshwater.…”