The effect of tides on nearshore environmental DNA.

Ryan P Kelly,Emily Jacobs-Palmer,Ramón Gallego

doi:10.7717/peerj.4521

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.

Highlights

As environmental DNA becomes an increasingly important tool in ecological research (Sigsgaard et al, 2016; Deiner et al, 2017), it is critical to understand how techniques for eDNA collection and analysis perform under real-world conditions (Port et al, 2016)
Most efforts to quantify the behavior of eDNA in the field have taken the form of quantitative PCR studies, in which the concentration of a particular template DNA is measured over space or time
To evaluate the spatial and temporal turnover between eDNA communities, we first apportioned the observed variation in COI Bray-Curtis dissimilarities among tides, sampling sites, sampling events within a site, biological replicates, and technical replicates (PCR replicates from the same bottle of water)

Summary

Introduction

As environmental DNA (eDNA) becomes an increasingly important tool in ecological research (Sigsgaard et al, 2016; Deiner et al, 2017), it is critical to understand how techniques for eDNA collection and analysis perform under real-world conditions (Port et al, 2016). We must characterize the spatial and temporal resolution of amplicon-sequencing studies in order to confidently identify ecological patterns in the field (O’Donnell et al, 2017); like any sampling technique, eDNA can reveal a phenomenon only where the effects of that phenomenon are sufficiently large to be detected above background variation (e.g., among replicates or time points). Most efforts to quantify the behavior of eDNA in the field have taken the form of quantitative PCR (qPCR) studies, in which the concentration of a particular template DNA is measured over space or time. The precise findings vary by setting and details of the molecular assay employed, even with highly sensitive qPCR, the distance from its source that eDNA can reliably be detected appears to be small, on the order of 10 – 1000m.

Methods

Results

Discussion

Conclusion