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

Abstract

Genetic material (short DNA fragments) left behind by species in nonliving components of the environment (e.g. soil, sediment, or water) is defined as environmental DNA (eDNA). This DNA has been previously described as particulate DNA and has been used to detect and describe microbial communities in marine sediments since the mid-1980's and phytoplankton communities in the water column since the early-1990's. More recently, eDNA has been used to monitor invasive or endangered vertebrate and invertebrate species. While there is a steady increase in the applicability of eDNA as a monitoring tool, a variety of eDNA applications are emerging in fields such as forensics, population and community ecology, and taxonomy. This review provides scientist with an understanding of the methods underlying eDNA detection as well as applications, key methodological considerations, and emerging areas of interest for its use in ecology and conservation of freshwater and marine environments. Rev. Biol. Trop. 62 (4): 1273-1284. Epub 2014 December 01.Key words: environmental DNA (eDNA), detection probability, occupancy models, persistence, metabarcode, minibarcode.In order to understand distributions, patterns, and abundances for populations or species, the collection (detection) and identification of individuals from their physical origins must be undertaken. Thus, species detection is fundamental to scientific disciplines such as phylogenetics, conservation biology, and ecology. However, species detection is sometimes extremely difficult especially in marine and aquatic environments where organisms have complex life cycles, and direct observation of early development stages is almost impossible (Ficetola, Miaud, Pompanon, & Taberlet, 2008). Species detection in these environments has been conducted using traditional direct observation methods (visual or acoustic) (Thomsen et al., 2012a). Nonetheless, traditional detection methods can have logistic limitations, be time consuming, expensive, and in some cases, harmful to the environment (e.g., marine bottom trawls, electrofishing and rotenone poisoning) (Thomsen et al., 2012b). The advent of novel molecular and forensic methods have provided innovative tools for detecting marine and aquatic organisms that may circumvent the aforementioned limitations (Darling & Blum, 2007;valentini, Pompano, & Taberlet, 2009;Lodge et al., 2012).One such tool is the detection of an organism's environmental DNA (eDNA). 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 d...

A framework for estimating the sensitivity of eDNA surveys

“…The data from some studies imply a relatively homogeneous distribution of DNA (Thomsen et al . ; Díaz‐Ferguson & Moyer ) while others imply a more heterogeneous distribution (Turner et al . , ; Nathan et al .…”

The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries

“…A promising means to improve our understanding of the complex interactions and dynamics of eDNA in marine systems is to incorporate oceanographic modelling on eDNA transport and detection. Combining oceanographic modelling with eDNA persistence rates can allow researchers to back‐track the most likely spatial origin of eDNA and hereby improve the ability to interpret data (Díaz‐Ferguson & Moyer, ; Kelly, Port, Yamahara, Martone, et al., ). A good outset can be to use rare sessile marine organisms (that constitute eDNA sources in known locations) as models, before trying to assess the dispersion patterns of eDNA from free‐moving organisms, such as fish.…”

The ecology of environmental DNA and implications for conservation genetics

“…Today, diverse fields of biological and environmental study use DNA to detect various taxa across many different types of environments, including forensics (van Oorschot et al 2010), fecal pollution tracking (Caldwell et al 2011), paleogenetics (Pedersen et al 2015), and environmental biosafety (Nielsen et al 2007). Detection and analysis of eDNA have been the topic of several recent literature reviews (Blanchet 2012;Díaz-Ferguson and Moyer 2014;Rees et al 2014b;Bohmann et al 2014), including one focused on the conservation biology implications of eDNA (Thomsen and Willerslev 2015). However, the present review uniquely examines the conservation applications of eDNA through a lens we call ''the ecology of eDNA.'…”