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FEATURE ARTICLE - Environmental DNA (eDNA) for the management of marine living resources

eDNA promises to revolutionize the examination of biodiversity in the wild by allowing the detection of larger organisms without the need to sample them and in the marine environment where traditional sampling is difficult to carry out.
Published: 7 August 2020

​​​​​​​Through the dedication of many of its members, and the coordination by John Gilbey (eDNA ToR leader) the Working Group on Application of Genetics in Fisheries and Aquaculture (WGAGFA), currently chaired by Jann Martinsohn, has produced a non-technical overview of the rapidly developing eDNA field and relevant applications.

Developments in the field of genetics have transformed our understanding of the natural world. In a fisheries context, it has helped us identify species, define population structures, begin to understand the genetic basis of adaptive traits, and monitor adaptive population changes. Typically, such insights have been gained from the analysis of DNA obtained from tissue samples collected directly from individuals across a study area. Additionally, the analysis of DNA through metabarcoding from a bulk sample composed of a mixture of individuals of different zooplankton and/or macroinvertebrate species has enabled cost-effective and efficient biodiversity assessments. Recently, a new source of DNA is being used for analysis of macro species - so-called “environmental DNA” (eDNA), made up of DNA shed from individuals into the natural environment. Uptake of novel approaches using eDNA promises to revolutionize biodiversity monitoring by allowing the detection of larger organisms without the need to directly sample them, or of small/rare ones whose presence would not be otherwise picked up. This is of particular use in the marine environment where traditional sampling is often challenging.​

Management and monitoring

Ecosystem-based management increasingly demands regular ​​monitoring of the marine environment and its living resources. Progress with recent genetic technologies and their routine employment have provided powerful and reliable tools to address a diversity of issues spanning biosurveillance, biosecurity, conservation, ecosystem and biodiversity monitoring, and aquaculture and fisheries management.

What is eDNA?

eDNA is the genetic material released from an organism into its environment through physiological and mechanical processes. It persists in the environment for some time and can be collected for analysis. In the case of fish, eDNA stems from waste products, skin/tissue, scales, eggs and sperm, mucus, blood, and carcasses. In contrast to DNA extracted from tissue samples, or community DNA where DNA is extracted from whole organisms, eDNA does not require sampling the target organisms. ​

Collection and analysis

eDNA can be collected by simply sampling water in sterile containers. This is then passed through sterile filters with a mesh so fine it retains genetic material. The DNA retained in the filters is then extracted in the laboratory. Depending on the scope of the survey, these samples can be used to target a specific organism or a community as a whole, or both. In either case, extracted DNA is processed to produce a catalogue of different "DNA-profiles", that can be matched to the species they come from by using a reference database.

eDNA and traditional surveys

Environmental DNA and traditional survey methods complement, rather than replace, each other. Many studies have shown that eDNA may be faster and more cost-effective in assessing biodiversity and community composition. However, it is widely understood that eDNA cannot replace traditional methods when investigating behaviour, size, age class and maturity distribution. Significant developments have also been made to address quantitative aspect of eDNA in order to estimate biomass. Occasional taxonomic validation, especially in understudied systems, remains indispensable.

Fisheries Management

Fisheries management relies on accurate estimates of both stock distribution and abundance. eDNA can aid the former, while more research is needed to reliably use this tool for the latter. Using eDNA in fisheries management has the potential to enable non-invasive, less costly and faster monitoring of stocks, and may identify a greater diversity of the species by capturing organisms which can be under-represented in traditional surveys. At present, eDNA sampling-based approaches typically provide information on presence and diversity of targeted species, and can facilitate otherwise challenging monitoring. Research efforts are now focusing on improved precision of species abundance estimates based on eDNA; peer-reviewed studies are beginning to appear suggesting good concordance between eDNA and fish biomass.​

​Environmental Monitoring

eDNA analysis has many cost-effective applications for ecosystem monitoring. eDNA is particularly well suited for rapid detection of invasive species and those species that are under-estimated/under-represented using traditional sampling approaches. Given its relatively short life-span, eDNA is useful in giving a reliable snapshot of species present in a habitat at the time of sampling. That means, it is also useful for assessing small-scale migration of species of interest. Using eDNA, a composition of species living in the benthic or pelagic locations can be rapidly assessed and impacts due to anthropogenic influences such as fishery or aquaculture activities can thus be estimated and addressed.


How to
apply?

eDNA sampling can be readily integrated into existing monitoring programs. Particular attention to avoid sample contamination with DNA from other sources is a prerequisite, as well as the inclusion of sample replicates. The samples themselves are analysed in dedicated molecular laboratories, although a number of automated sequencing platforms are beginning to show potential for application directly in the field. The results provide novel complementary information to traditional surveys from a sample of seawater/sediment. 

eDNA investigations by ICES WGAGFA members

eDNA focused investigations are being undertaken by WGAGFA members in a number of areas of relevance to fisheries management and ecosystem monitoring.

A team under the lead of Naiara Rodriguez-Ezpeleta, Marine Research Division of AZTI Basque Research and Technology Alliance, recently tested the potential of eDNA metabarcoding to assess the fish community composition in a large marine area, such as the Bay of Biscay. The team compared eDNA metabarcoding-based biodiversity estimates with those derived from fishing trawl catches. They have related eDNA metabarcoding-based estimates with the known spatial distribution and ecological patterns of the species in the area. According to the authors, results support the notion that eDNA metabarcoding forbroad-scale marine fish diversity monitoring is valuable in the context of theimplementation of marine policy and legislation.
 
In England, Ilaria Coscia, University of Salford, routinely uses eDNA to monitor fish communities in estuaries and coastal habitats. In Scotland, Marine Scotland Science had recently developed a Strategy for development of DNA-based biomonitoring, with Iveta Matejusova leading on incorporation of eDNA into routine monitoring of diversity in marine protected areas (MPAs), including a variety of priority marine features (PMFs), as well as monitoring for presence of invasive species where eDNA has already demonstrated its ability to outcompete the traditional assessments.  
 

The Flanders research institute for agriculture, fisheries and food (ILVO) conducts research on stock management of flatfishes, and has under the supervision of Sofie Derycke been involved in the development of species specific digital droplet PCR assays to detect and quantify common sole, plaice and whiting and to better delineate spawning and nursery grounds of the flatfishes at a temporal and spatial scale in the North Sea region using eDNA.​

Conclusions

The benefits of using eDNA based approaches are numerous and can prove invaluable in monitoring marine environments. The field is relatively new, but developing at a fast pace, with new applications continuously being optimized, including the deployment of autonomous underwater vehicles (AUV).

At a time when the marine environment is under threat, eDNA-based techniques are a cost-effective resource to provide information to managers and policy-makers, and hence aid in the conservation and sustainable exploitation of aquatic living resources. ​

The Working Group on Application of Genetics in Fisheries and Aquaculture provides advice on methods to describe, conserve, and manage intra-specific biodiversity, focusing on the application of genetic and genomic analyses. The group's work on eDNA addresses Ecosystem science and Emerging techniques and technologies - two of ICES science priorities. Discover all seven interrelated science priorities and how our network will address them​ in our Science Plan: “Marine ecosystem and sustainability science for the 2020s and beyond”​.


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eDNA is the genetic material released from an organism into its environment​.

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FEATURE ARTICLE - Environmental DNA (eDNA) for the management of marine living resources

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