Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Abstract

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

“…This is possible for example when faecal samples are collected from an animal's burrow or nest (see Table 1 for examples). Such predators can therefore provide minimum estimates of prey abundance, which unlocks wider applications in environmental science research (Lodge et al, 2012).…”

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

“…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).…”

“…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).…”

Ascidians as models for studying invasion success

“…Given such surveys are labor-intensive and time-consuming, environmental DNA (eDNA) in combination with high-throughput sequencing or microarrays represents a promising screening strategy for "dangerous" ascidians. More conveniently, such a strategy can be used to detect target species by sampling water from the areas of concern without ever detecting living animals (Lodge et al 2012;Thomsen et al 2012;Egan et al 2013). Moreover, these genetic techniques are very powerful at detecting species at low population abundance (Zhan et al 2013) and may be used to powerfully screen for all invasive ascidian species simultaneously as long as technical issues are well addressed (e.g., Zhan et al 2014a, b;Zhan and MacIsaac 2015).…”

“…In addition to effective policy and management solutions, developing practical antifouling technologies that can be used for commercial shipping, recreational boats, and aquaculture could reduce the scale of both primary and secondary introductions (e.g., Cahil et al 2012). Finally, future development and application of robust detection tools such as microarrays and highthroughput sequencing based on environmental DNA may greatly enhance the power of early detection of new infestations (Lodge et al 2012;Thomsen et al 2012;Egan et al 2013;Zhan et al 2013).…”