The effect of tides on nearshore environmental DNA

Abstract

We can recover genetic information from organisms of all kinds using environmental sampling. 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. 313 bp of eukaryotic COI mtDNA as a marker, we find that nearshore organismal communities are largely consistent across tides. Our findings suggest that nearshore eDNA from both benthic and planktonic taxa tends to be endogenous to the site and water mass sampled, rather than changing with each tidal cycle. However, where physiochemical water mass characteristics change, we find that the relative contributions of a broad range of organisms to eDNA communities shift in concert.

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

“…It has previously been suggested that many animal lineages remain unsampled and/or unsequenced, potentially even harboring novel phyla (López-escardó et al, 2018;Nguyen et al, 2019). All sampling methods are subject to methodological limitations, and different sampling methods will capture different subsets of biodiversity (Kelly et al, 2017;Shelton et al, 2016). Like more traditional survey methods, eDNA metabarcoding has a certain level of taxonomic selectivity, which may be the result of primer bias.…”

“…as of yet, been scarce (Cowart, Murphy, & Cheng, 2017;Djurhuus et al, 2017;Drummond et al, 2015;Günther, Knebelsberger, Neumann, Laakmann, & Martínez Arbizu, 2018;Kelly, Gallego, & Jacobs-Palmer, 2017;Villarino et al, 2018); the majority of these have relied on ribosomal markers, such as 18S Guardiola et al, 2015;Lindeque et al, 2013), 16S , and 12S (Miya et al, 2015), 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, 2012), which represents a significant limitation to the evaluation of community changes and the biological and/or environmental mechanisms responsible for these changes (Mackas & Beaugrand, 2010).…”

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

“…Encouragingly, Harper et al (2018) 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 Kelly, Gallego, & Jacobs-Palmer, 2018;Li, Evans, et al, 2018;O'Donnell et al, 2017;Port et al, 2016).…”

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

“…To counteract the inclusion of these organisms into our analysis, we specifically excluded from the analysis any aeDNA from groups with no marine representatives, since our primary interest was to describe the in situ coral reef community. However, lateral mixing may still occur through local currents that transport DNA across reef habitats or sites (Kelly, Gallego, & Jacobs-Palmer, 2018). Moreover, we have presented data from just two sediment cores as a proof of concept; given the different patterns exhibited by PAN1 and PAN3, more replication at the level of cores should increase confidence in the strength of our approach.…”