Shedding light on eDNA: neither natural levels of UV radiation nor the presence of a filter feeder affect eDNA-based detection of aquatic organisms

Abstract

The use of environmental DNA (eDNA) as a species detection tool is attracting attention from both scientific and applied fields, especially for detecting invasive or rare species. In order to use eDNA as an efficient and reliable tool, however, we need to understand its origin and state as well as factors affecting its degradation. Various biotic and abiotic environmental factors have been proposed to affect degradation of eDNA in aquatic environments and thus to influence detection rates of species. Here, we were interested in two of them, namely UV light, which can break down DNA, and the presence of filter feeders, which can remove DNA and DNA-bound particles. A few, mostly laboratory-based studies have found minor effects of UVB on the degradation of eDNA. Ultraviolet A radiation (UVA), however, has been neglected although it also causes DNA lesions and is 10- to 100-fold more prevalent than UVB when reaching the earth’s surface. Filter feeders are common in aquatic ecosystem, but their effects on eDNA has hitherto been ignored. We conducted a full-factorial aquatic mesocosm experiment under near-natural outdoor conditions manipulating UV radiation as well as the presence of Dreissena polymorpha, a strong filter feeder capable of filtering cells or organelles containing DNA. Surprisingly, we found that neither UV radiation nor the presence of the filter feeder affected eDNA-based detection rates of macroinvertebrates, even though the experiment took place in summer when UV radiation intensity and filtration activity is high for the chosen experimental site and conditions. These results, in combination with studies from marine or laboratory settings finding no effect of sunlight and its UV components on the detectability of eDNA, suggest that eDNA based species assessments could be relatively robust with respect to our two factors studied.

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

“…In our study, the very cold Arctic waters may further contribute to reducing DNA degradation, thus providing more time for dispersion over larger distances compared to what has been previously reported at more temperate latitudes (Jeunen et al, 2019). In contrast, given that sunlight is known to break down DNA in marine systems (El-Sayed, Van Dijken, & Gonzalez-Rodas, 1996), the prolonged daylight in the study sites at the time of sampling (up to 24 hr) may encourage DNA degradation (Mächler, Osathanunkul, & Altermatt, 2018). In contrast, given that sunlight is known to break down DNA in marine systems (El-Sayed, Van Dijken, & Gonzalez-Rodas, 1996), the prolonged daylight in the study sites at the time of sampling (up to 24 hr) may encourage DNA degradation (Mächler, Osathanunkul, & Altermatt, 2018).…”

“…This raises the hypothesis that spatial eDNA homogenization should be more important in the Arctic Ocean than more southern regions. In contrast, given that sunlight is known to break down DNA in marine systems (El-Sayed, Van Dijken, & Gonzalez-Rodas, 1996), the prolonged daylight in the study sites at the time of sampling (up to 24 hr) may encourage DNA degradation (Mächler, Osathanunkul, & Altermatt, 2018). However, a study by Andruszkiewicz, Sassoubre, and Boehm (2017) concluded that sunlight may not be the primary factor causing degradation of the fish DNA in their experiment and that degradation of the latter would depend more on the time elapsed since its shedding in the water.…”

Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes

“…cytosine deamination) and oxidation (Hawkins et al, 2016); thus, degradation of eDNA can be a limiting factor in such analyses (Pilliod et al, 2014). However, a recent study demonstrated that UV radiation does not negatively affect eDNA-based detection rates from water samples (Mächler, Osathanunkul, & Altermatt, 2018). Under optimal conditions, the stability of DNA in the environment facilitates the tracing of mammals in environmental samples for a considerable amount of time which may produce a bias in the accuracy of results (Dejean et al, 2011); however, in natural water bodies in the tropics, eDNA degrades within a comparably short amount of time, that is within a few days (Eichmiller, Best, & Sorensen, 2016)..…”

Assessing different components of diversity across a river network using eDNA

“…At each site, we sampled three times 250 ml of river water, each on a separate GF/F filter (pore size 0.7 μm, Whatman International Ltd., Maidstone, UK; for more details, see supplementary materials and Mächler, Osathanunkul, & Altermatt, 2018). We collected eDNA samples about 5-10 m upstream of the kicknet sampling to minimize cross-contamination.…”

“…We collected eDNA samples about 5-10 m upstream of the kicknet sampling to minimize cross-contamination. We directly sampled water with a disposable syringe out of the water body; for more detailed sampling procedure, see also Mächler et al (2018). Samples were stored in a Styrofoam box equipped with cooling elements until we came back from the field (no longer than 9 hr).…”