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

Abstract

The quantitative measurement of environmental DNA (eDNA) from 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 showed 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.

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

“…Yet, routine and widespread eDNA applications to marine ecosystems face multiple challenges (Hansen et al ., 2018) with variability introduced to biodiversity estimates from multiple sources that are still poorly understood (Bessey et al ., 2020; Juhel et al ., 2020; Rourke et al ., 2021; Thalinger et al ., 2021). For example, eDNA signals from source-species are weakened by the low biomass-to-water volume ratio and frequent movement of individuals (Moyer et al ., 2014).…”

“…Detection rates and resultant biodiversity estimates thus critically depend on eDNA (i) origin (source of an organism’s genetic material shed into its environment), (ii) state (forms of eDNA), (iii) transport (e.g. through diffusion, flocculation or settling, currents or biological transport which can vary according to the depth) and (iv) fate (how eDNA degrades and decays) (Barnes and Turner, 2016; Harrison, Sunday and Rogers, 2019; Thalinger et al ., 2021). Besides, water chemistry, salinity and temperature affect the persistence of DNA particles which are best preserved in cold and alkaline waters with low exposure to solar radiation (Moyer et al ., 2014; Pilliod et al ., 2014; Strickler, Fremier and Goldberg, 2015; but see Mächler, Osathanunkul and Altermatt, 2018).…”

Ontogeny of eDNA shedding during early development in Chinook Salmon (Oncorhynchus tshawytscha)

“…We did not assess larval activity in our study, and, therefore are unable to infer whether movement of newly hatched larvae may have been a contributing factor to the spike in DNA. However, positive relationships between eDNA shedding and fish activity have been observed (Thalinger et al, 2021), suggesting that both the hatching process and movement of newly hatched larvae could contribute to the pool of sampled eDNA.…”

A practical guide to DNA-based methods for biodiversity assessment

“…Behavioural factors interact with life-history and physiology to affect the amount of DNA released by a given species at any one time. Animals have been documented to release more eDNA when they are stressed, when they are active, and when they are warm (Jo et al 2019a, Thalinger et al 2021a).…”