SeaDNA - Assessing marine biodiversity and structure using environmental DNA: from groundtruthing to food web structure and stability

Lead Research Organisation: British Antarctic Survey


DNA evidence has revolutionised our understanding of the natural world. It has helped us to appreciate how species are related to one other, how environmental change can lead to species divergence and how individual populations become adapted through evolutionary processes to their local environments. It has also been particularly useful in quantifying the diversity of species in communities of microorganisms that cannot readily be seen and assessed using standard microscopy.

Importantly, DNA in the natural environment can also be used in a "forensic" manner. Traces of DNA from skin, blood, faeces or mucous can be used to identify which species have recently been present in the local environment. Given recent developments in DNA sequencing technology, this "environmental DNA" (eDNA) promises to revolutionise the way we probe biodiversity in our environment, particularly in marine environments that can be very difficult to sample reliably. Traditionally we have used specialist grabs and nets to survey species larger than microbes in marine communities. However, sampling free eDNA in surrounding water is potentially faster, less expensive and less destructive than such gears. Use of trace eDNA also holds potential to identify species that are not reliably sampled in the environment, either because they are rare, small, or adept at avoiding nets and grabs.

The utility of eDNA as a tool for sampling aquatic environments has been mostly tested in freshwater systems, and there are only a handful of studies that have tested the approach in the marine environment. Thus, there is a need to further evaluate the potential using a combination of laboratory experiments and field surveys. As an important first stage, we need to establish how long eDNA from fish and invertebrates persists in the marine environment before it is broken down beyond the point of detectability. This will tell us how well an eDNA-derived species list reflects the species community at the sampling site. We will conduct a set of laboratory experiments that will enable us to quantify the rate of eDNA break-down, and identify main environmental variables that influence this rate of decay. We will then aim to develop the laboratory and field methods needed to reliably detect DNA from these species groups, before testing these methods in experimental communities that we will assemble in laboratory aquaria.

An important stage in testing the ability of eDNA to be used as a tool in surveying and monitoring marine species is to survey the natural environment using both traditional methods (e.g. nets), and eDNA methods. We will do this in two UK marine habitats that are important for fisheries, conservation and environmental monitoring, namely estuaries and inshore shelf seas. We will also do this in an open ocean habitat, the Southern Ocean, which is an important habitat for fisheries and oceanic megafauna such as whales. We will directly compare data from eDNA methods to those from traditional methods to ask if eDNA accurately captures the fish and invertebrate communities, and if the method has the added ability to inform us on the presence of species that are typically rare or difficult to sample, some of which may be new to science.

Finally, we will use the eDNA derived species lists to reconstruct the food webs present in our sampling locations. We will use these data to test how stable marine communities are over space and time, and how environmental variables such as temperature affect their composition and stability. The results of these analyses will provide insight into the role of eDNA in helping us to understand how future climate change may affect fished species.

Planned Impact

The main beneficiaries will be:
1) Governmental Biodiversity/Conservation/Environmental Agencies & NGOs. The development of robust marine eDNA profiles could prove to be a powerful tool in biodiversity discovery, long-term monitoring and evaluation of the success of conservation and management initiatives. In addition to drawing on the wealth of contacts that the project team have with environmental agencies to seek knowledge exchange opportunities, we aim to use the existing Environment Agency-led "Environmental DNA network" as a forum for discussion and sharing of results.
2) Fisheries management organisations. Organisations such as DEFRA, CEFAS, Marine Scotland and the Marine Management Organisation have shown interest in scientific advances that can support enhancements to fisheries management and marine environmental monitoring. The project has strong potential to clarify the role that environmental DNA could have in the spatial and temporal mapping of target fished species, and the resilience of the food webs upon which they rely. We aim to share knowledge primarily through regular meeting exchanges, including the SEAFISH "Common Language Group" which includes representatives from NGOs, Fishermen Associations, Retailers, Consumer Groups and Scientists. This will ensure that a very broad base of stakeholders will be aware of the project tasks and achievements.
3) The General Public. We will play to the considerable interest that the general public have in marine life, and how new technologies can be used in species discovery, monitoring, conservation and exploitation. We will communicate specific research findings using institutional press offices while coordinating with the NERC communications team. We will use events such as National Science Week, the Manchester Science Festival and Bristol Festival of Nature to engage at the local level within our respective cities. We will generate and maintain a blog throughout the project, with an attached twitter account, which will give updates on project activities. All project researchers will contribute to the blog through short posts, photos, videos, news items and travel/meeting reports. We also aim to create a documentary, using existing links between project researchers and the science film making community, which will be accessible via websites of the project partners.


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Description 1. Southern Ocean water sampling by BAS and eDNA profiling at the University of Bristol revealed that using large volumes (10s of Litres) of seawater filtered through liquid filter cartridges offers a more practical method to obtain eDNA signals of larger animals/vertebrates than the smaller (<1L) volumes typically used with sterivex filters for water assessments.
2. Laboratory based proof of concept tests at BAS revealed that: a) Small (3cm by 3cm) squares of muslin cloth or 'Hybond N' paper can be used to capture low quantities of eDNA from seawater and these eDNA 'patches' could be attached to sea gliders for remote eDNA sampling. b) In addition to standard ethanol preservatives, a novel mixture of RNAlater with the anti-bacterial agent benzalkonium chloride can be used as a preservative eDNA in for seawater. These preservative solutions can be used for remote time series eDNA sampling in moorings.
3. Data from the Southern Ocean reveal dominance of different pelagic species at different depths, and for some of them an association with certain key planktonic invertebrates. In this case, also, eDNA data provide additional information on what can be termed 'molecular by-catch', by detecting several important species of marine mammals and sea birds. DNA metabarcoding of lanternfish stomach contents, paired with visual identification and stable isotope analysis, allow for a redefinition of the trophic niche of these important species, by showing a much more diverse food spectrum, and in particular a far greater importance of gelatinous carnivore zooplankton in the diet of lanternfishes.
Exploitation Route eDNA technology is rapidly advancing and our studies will have a wide commercial interest should they confirm that species diversity in the open ocean can be determined from water samples alone. Nevertheless, this research is at an early stage and it is too soon to entertain commercial development.
Sectors Agriculture, Food and Drink,Environment

Description We have consistently engaged with the UK DNA Working Group (now represented under the UK EOF: in order to translate evidence from 'SeaDNA' into practical solutions for marine environmental monitoring. For instance, SeaDNA members participated in a DNA-focused "marine benthic monitoring workshop" organised by the JNCC in Manchester, Feb 25-26; and also attended the UK DNA WG Steering Committee group at the NHM, London, March 11th.
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Education,Environment
Impact Types Policy & public services

Title Epi- and mesopelagic mesozooplankton depth-discrete distribution and abundance across Polar Frontal Zone in Southern Ocean Atlantic sector (Version 1.0) [Data set] 
Description Mesozooplankton were collected with a MOCNESS net system during the oceanographic cruise JR16003 (Dec 2016 to Jan 2017). The MOCNESS comprised 9 separate nets which opened in sequence such that the closing of one net opened the next; net 1 was open during the descent of the net to its maximum depth (1000 m) while the remaining 8 depths opened at regular intervals during the reascent to the surface. All catches were immediately preserved in 4% buffered formaldehyde. Identification of taxa was performed by the Morski Institute (Poland). Specimens were categorised to the lowest possible taxonomic level, which, in some cases, encompassed developmental stages but, in other cases, was limited to higher order taxa. Each taxa was enumerated to determine abundance in units of individuals m-3. The dataset allows examination of the distribution and abundance of these species across Polar Frontal Zone in Southern Ocean Atlantic sector. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact This dataset accompanies genetic information with which to validate the eDNA approach to determining foodweb structure in the marine environment. The eDNA technique has a great deal of potential to open up new avenues of research with regards our understanding of the structure and function of marine foodwebs. 
Description Collaboration with ADAS Ltd on developing eDNA sampling techniques for krill 
Organisation ADAS
Country United Kingdom 
Sector Private 
PI Contribution We contributed significantly during the initial stages of the collaboration by providing raw material for analysis: Antarctic and Ice krill DNA samples and Southern Ocean water samples. Furthermore, we developed the molecular markers (suites of species specific PCR primers) that form the basis of the analysis methods that ADAS employs. Since then we have contributed by assisting with results interpretation and planning for subsequent analyses.
Collaborator Contribution ADAS UK contributed by extracting eDNA from Southern Ocean water samples and by analysing the extracts obtained using qPCR methods with the PCR primers we developed. They assessed standard methods as used in their commercial operations assessing freshwater samples for Great Crested Newts, and they also explored other approaches better suited for Ocean water samples.
Impact This is a multidisciplinary project between ecologist and geneticists. Development of the techniques is still ongoing and the collaboration remains active.
Start Year 2015