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.
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”.
