Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals

Abstract

The exploitation of non-invasive samples has been widely used in genetic monitoring of terrestrial species. In aquatic ecosystems, non-invasive samples such as feces, shed hair or skin, are less accessible. However, the use of environmental DNA (eDNA) has recently been shown to be an effective tool for genetic monitoring of species presence in freshwater ecosystems. Detecting species in the marine environment using eDNA potentially offers a greater challenge due to the greater dilution, amount of mixing and salinity compared with most freshwater ecosystems. To determine the potential use of eDNA for genetic monitoring we used specific primers that amplify short mitochondrial DNA sequences to detect the presence of a marine mammal, the harbor porpoise, Phocoena phocoena, in a controlled environment and in natural marine locations. The reliability of the genetic detections was investigated by comparing with detections of harbor porpoise echolocation clicks by static acoustic monitoring devices. While we were able to consistently genetically detect the target species under controlled conditions, the results from natural locations were less consistent and detection by eDNA was less successful than acoustic detections. However, at one site we detected long-finned pilot whale, Globicephala melas, a species rarely sighted in the Baltic. Therefore, with optimization aimed towards processing larger volumes of seawater this method has the potential to compliment current visual and acoustic methods of species detection of marine mammals.

History, applications, methodological issues and perspectives for the use environmental DNA (eDNA) in marine and freshwater environments

“…Persistence estimates have been determined for different taxonomic groups: from 15 to 30 days for fresh water fishes (Dejean et al, 2011& Takahara et al, 2012a, 15 to 30 days for amphibians (Ficetola et al, 2008;Goldberg et al, 2011), 0.9 to 7 days for marine mammals (Foote et al, 2012), 21 days for mudsnails (Goldberg, Sepulveda, Ray, Baumgardt, & Waits, 2013), and 14 days for reptiles (Piaggio et al, 2013). In addition to density, size and life history features of the target taxa, eDNA persistence can be influenced by other biotic factors such as bacterial and fungal concentrations (Dejean et al, 2011).…”

“…Other abiotic factors related to the system that can also affect persistence include: stream flow, currents, tidal oscillations, type of sediment, and salinity (Corinaldesi, Beolchini, & Dell'Anno, 2008;Golberg et al, 2011;Barnes et al, 2014). For example, eDNA persistence in freshwater lentic systems has been shown to be as great as 30 days (Ficetola et al, 2008) while for marine systems (open and highly dynamic systems) it only averages approximately seven days (Foote et al, 2012;Thomsen et al, 2012b).…”

“…In freshwater systems, eDNA is usually homogeneously distributed and the successful use of this technology has been proven in a number of studies comprising a range of taxa Thomsen et al, 2012a). For marine systems, the detection of eDNA is possible but less reliable than in freshwater systems (Foote et al 2012;Jones, 2013). Despite the high density of marine biota, the vast volume of sea water in relation to biomass promotes eDNA dilution and dispersion.…”

“…This compounded by the dynamic nature of marine environments (e.g., strong tides, current system and oceanographic events) and the increased inhibition of subsequent molecular procedures due to the high salinity environments, make eDNA detection more challenging when compared to freshwater systems. Currently, eDNA studies conducted in the marine environment are limited to detection of fishes, marine mammals and microbial communities in temperate areas (venter et al 2004;Foote et al 2012;Thomsen et al 2012b;Kelly, Port, Yamahara, & Crowder, 2013). Despite of the success on eDNA detection of these taxa in the marine systems; scientists have to consider that eDNA degrades rapidly in seawater (less than seven days) and detection of marine species is considered to be local (Thomsen et al 2012b).…”

“…Defined as short DNA fragments that an organism leaves behind in non-living components of the ecosystem (i.e., water, air or sediments), eDNA is derived from either cellular DNA present in epithelial cells released by organisms to the environment through skin, urine, feces or mucus or extracellular DNA that is the DNA in the environment resulting from cell death and subsequent destruction of cell structure (Foote, Thomsen, Sveegaard, Wahlberg, Kielgast, Kyhn, Salling, Galatius, Orlando, & Gilbert, 2012;Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012a). Methodologically, eDNA detection requires the development of genetic markers specific to that target taxon or taxa.…”