The effect of tides on nearshore environmental DNA

Abstract

Organisms of all kinds leave genetic traces in their environments, and in recent years, sequencing this environmental DNA (eDNA) has become a tractable means of surveying many species using water, air, or soil samples. The technique is beginning to become a core tool for ecologists, environmental scientists, and biologists of many kinds, but the temporal resolution of eDNA sampling is often unclear, limiting the ecological interpretations of the resulting datasets. Here, in a temporally and spatially replicated field study using ca. 330bp of eukaryotic COI mtDNA as a marker, we find that nearshore organismal communities are largely consistent across tides. Our findings suggest that nearshore eDNA tends to be endogenous to the site and water mass sampled, rather changing systematically as waters change over during the tidal cycle. However, where water-mass characteristics change, we find that the eDNA communities change in concert, again suggesting a close association between the habitat sampled and the eDNA community recovered.

Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

“…When the main source of eDNA would rapidly sink out of the water column, for example, potentially in the case of feces, the eDNA distribution range would probably be much smaller. Indeed, limited distribution ranges of eDNA were measured by Kelly, Gallego, and Jacobs‐Palmer () for near‐shore eDNA from benthic and planktonic taxa, and by Murakami et al () for eDNA of caged fish in a marine environment. Within our sample area, the eDNA community composition including small species that were not caught in the fykes showed significant differences among locations.…”

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

“…All sampling methods are subject to methodological limitations, and different sampling methods will capture different subsets of biodiversity (Kelly et al, ; Shelton et al, ). Like more traditional survey methods, eDNA metabarcoding has a certain level of taxonomic selectivity, which may be the result of primer bias.…”

“…Studies targeting marine eukaryotic community diversity have, as of yet, been scarce (Cowart, Murphy, & Cheng, ; Deagle et al, ; Djurhuus et al, ; Drummond et al, ; Günther, Knebelsberger, Neumann, Laakmann, & Martínez Arbizu, ; Kelly, Gallego, & Jacobs‐Palmer, ; Villarino et al, ); the majority of these have relied on ribosomal markers, such as 18S (de Vargas et al, ; Guardiola et al, ; Lindeque et al, ), 16S (Kelly et al, ), and 12S (Miya et al, ), but due to their relatively conserved sequences, it is often impossible to distinguish taxa at the species, genus, or even family level (Tang et al, ), which represents a significant limitation to the evaluation of community changes and the biological and/or environmental mechanisms responsible for these changes (Mackas & Beaugrand, ).…”

Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

“…Encouragingly, Harper et al () demonstrated that Triturus cristatus (great crested newt) detection via metabarcoding with no threshold is equivalent to qPCR with a stringent detection threshold. eDNA metabarcoding has also been applied to large‐scale investigations of spatial or temporal variation in marine and freshwater communities, with some studies indicating that communities can be distinguished from 100 m to 2 km due to stream discharge or tidal patterns (Civade et al, ; Kelly, Gallego, & Jacobs‐Palmer, ; Li, Evans, et al, ; O’Donnell et al, ; Port et al, ).…”