Development and application of eDNA tools to assess the structure and function of coastal sea ecosystems (MARINe-DNA)

Lead Research Organisation: Marine Biological Association
Department Name: CPR Survey


This NERC highlight topic focuses on the use of eDNA as a new tool for 21st century ecology. Environmental DNA (eDNA) is defined in the call as 'free DNA present outside of any organism'. The aim of the call is to address the current knowledge gaps in the application of eDNA approaches to help understand community biodiversity and dynamics of ecosystem functioning.

We will conduct a proof-of-concept investigation at Station L4, an exemplar coastal ocean ecosystem, and natural laboratory, in the English Channel off Plymouth, UK. Starting with a hydrodynamic model to spatially and temporally define the ecosystem (how large is the natural laboratory?) the project will then be split into three experimental phases:

1) eDNA methodological validation (developing the tools);

2) 18-month temporal pelagic survey (testing the tools); and

3) Comprehensive data analysis and model assimilation (did the tools work, what did they tell us, and are they useful?)

Using a wide range of expertise from 4 different institutions (PML, MBA, NOC, and U.Exeter), we will investigate a spatially defined region, from estuarine to coastal, benthic to pelagic; and at a range of temporal resolutions building on NERC National Capability sampling regimes and biosensor deployment. E-metagenetic and e-metagenomic data (individual genes to whole genomes) will be used to answer cross-cutting science questions utilising current physicochemical and biological information collected in parallel at this important coastal site.

Results from this project will provide a methodological template for the use of eDNA and remote eDNA biosensors in aquatic ecosystems. Downstream data will significantly advance our understanding of persistence of eDNA, and its potential impact on informing models of ecosystem functioning.

Products of this research will have wider implications for the use of this tool on fisheries assessments, fish pathogen detection, conservation biology, environmental risk management (e.g. toxic algae blooms, human pathogens, ballast water regulations), with the wider aim of supporting biodiversity and nature's services through NERC's strategic pillar of "Managing environmental change".

Planned Impact

Products of this research will have implications for a wide range of stakeholders interested in the use of this tool on fisheries assessments, aquaculture pathogen detection, conservation biology, environmental risk management (e.g. toxic algae blooms, human pathogens, ballast water regulations), with the wider aim of supporting biodiversity and nature's services through NERC's strategic pillar of "Managing environmental change" and the EU's Marine Strategy Framework Directive (MSFD) Good Environmental Status (GES) key Biodiversity Maintenance descriptor 1.

We plan to hold a stakeholder workshop in the first year of the project with the aim of:
1) Explaining the science behind the SeA-tools;
2) evaluating the needs of the stakeholder community; and
3) determining an individualised roadmap of engagement with each stakeholder group.

Exploiting strong institutional relationships and strategic alliances, we plan to engage: DEFRA (MSFD implementation); CEFAS (fisheries assessments); IMO Joint Group of Experts on the Scientific Aspects of Marine Environmental Protection - GESAMP (ballast water); Census of Marine Life (Biodiversity); European Centre for Environment and Human Health (human pathogens); British Ecological Society (conservation biology); and the Marine Management Organisation - MMO (marine sustainability and policy). As part of our final SeA-DNA project workshop we will invite stakeholders to assess results and investigate future implementation plans for use of these new tools.

Our research is strongly stakeholder driven in that maintenance of biodiversity is a key objective in the EU MSFD, indeed it is the first of the GES descriptors in the Directive. In addition, our project specifically addresses GES Descriptors: 4 (Elements of food webs ensure long-term abundance and reproduction); 6 (Sea floor integrity ensures the functioning of the ecosystem); and 7 (Permanent alteration of hydrographical conditions does not adversely affect the ecosystem). Application of eDNA tools, including sensitive and specific molecular detection methods and in situ sensor development, could advance MSFD implementation. We will discuss utilising our SeA-DNA project data with DEFRA, to help with implementation of GES Descriptors 1, 4, 6 & 7 of MSFD. The aim will be to establish SeA-DNA tools as widely accepted biodiversity benchmarks for the MSFD.

In addition to typical science society meetings (ISME; ASLO, BES), we plan to disseminate our results to the widest possible audiences. For example, we will aim to organise a session linked to one of the forthcoming ICES Annual Science Conferences. The session could be used to provide transparent and useful guidance to policymakers and stakeholders dealing with provision of biodiversity advice and baselines.

We plan to provide the PML Communications Group with a more thorough background of this complex science area to enable them to maximise potential for widespread coverage by embedding a communicator in our science regime.

By years 3 & 4, the aim will be for the PML Communications Group to have helped establish a social network presence for our activities (Twitter feeds, Facebook); produce a video for potential use by TV for any newsworthy articles that come out of our research (BBC Focus and video/podcasts accessible through the PML YouTube channel and website); and generate written material for articles to be published in popular science magazines, e.g. Planet Earth, Marine Scientist and the Marine Biologist. In addition, we will endeavour to influence science policy through awareness raising with key policymakers and also by engaging with the Parliamentary Office of Science & Technology to develop a relevant POST-Note to hold a discussion meeting on 'Role of Genomic Tools in Biodiversity Assessments'.
Description • An assessment of the cost (both financial and scientific effort) of each eDNA method has been conducted and recommendations made for implementation for progression to the fieldwork campaign.
• Bioinformatic pipelines for downstream analysis of amplicon data for 18S and 16S rRNA have been established and tested.
• A high resolution implementation of the unstructured grid hydrodynamic model FVCOM-ERSEM for the target sampling area of the project (Plymouth coastal region) has been developed.
• An experiment to assess the longevity of eDNA (carp DNA) in sediments was conducted. This showed a rapid reduction in eDNA concentration (97 % in 5 days), but it took 42 days before no eDNA could be detected. Samples from within Atilla virens burrow structures show the eDNA is transported down through the burrow and at times was at a higher concentration than the surface.
Exploitation Route Our findings will contribute to the next stage of the project field campaign. Ultimately, results from the method development and method costs will be used by industry or agencies interested in screening for rare or unusual organisms in the marine environment.
Sectors Agriculture, Food and Drink,Environment,Leisure Activities, including Sports, Recreation and Tourism

Description Presentation at POGO Annual Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The talk was very well received and sparked questions and advice on future activities for GACS and future eDNA initiatives

POGO remains a keen supporter of the GACS partnership and there is the opportunity for future capacity building funded by their Fellowships.
Year(s) Of Engagement Activity 2017