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

Abstract

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'.

Publications

10 25 50
publication icon
Batten S (2019) A Global Plankton Diversity Monitoring Program in Frontiers in Marine Science

 
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.
• The Marine Autonomous Plankton Sampler (MAPS- an eDNA autosampler) was deployed on the quayside pontoon at the National Oceanography Centre Southampton, sampling water from the harbour for eDNA. It sampled 500ml of seawater every 2 hours for 76 hours total, and preserved each sample with RLT+ buffer (which had highest recovery of eDNA in initial preservative trials). These samples are being extracted and will be sequenced by16S and 18S rRNA metabarcoding.
• Additional preservative testing was carried out alongside MAPS sampling in Southampton on 14/11/19. RNAlater, DNAShield, RLT+ buffer and Nucleic Acid Preservative (NAP) were all added to filtered material in order to find the best preservative for eDNA recovery (yield and quality) for MAPS-preserved samples relative to flash-frozen samples.
• Modelling of dissolved DNA movement at Station L4 (Western English Channel) has provided insight into potential sources, but also how dynamic water sources are at this site. Due to tidal movement, water samples taken hours apart would be expected to contain a completely different dDNA profile.
• Analysis of eDNA within the benthos shows sediments to be dominated by deposition of microphytobenthos in spring, followed by subsequent succession of microdecomposer taxa. A manuscript is in preparation.
• All (non-autonomous) fieldwork has now been completed at Station L4 (Western English Channel), both in terms of eDNA method development and subsequent application through a two year time-series assessment. Sample processing and metabarcode sequencing are also complete, with preliminary sequence analysis finished.
• MBA performed eDNA extraction from 552 seawater time-series samples collected from Station L4 over 19 years between 1999 and 2018. Samples sequenced for Fungi ITS metabarcoding. Datawill allow us to conduct an indepth time series analysis of microbial biodiversity during this period (ongoing).
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 Applied Genomics 
Organisation Applied Genomics
Country United Kingdom 
Sector Private 
PI Contribution We proved expertise and exchanged ideas on the application of eDNA tools in the environment.
Collaborator Contribution They provided access to industry partners and we entered into a joint project with on the used of new sampling technologies in the Marine Environment.
Impact Development of eDNA sampling tools for commercial use in the marine environment.
Start Year 2018
 
Description International Task Force on Biological Observations in the Ocean 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Strategic Task Force to investigate and advocate for upcoming technologies for global ocean observing. Task force part of an initiative supported by Partnership for the Observation of the Global Ocean (POGO)
Year(s) Of Engagement Activity 2017,2018,2019,2020,2021
URL https://pogo-ocean.org/
 
Description Planned and co-convened International Virtual Conference on the use of Environmental DNA (eDNA) in Marine Environments: Opportunities and Challenges 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 800+ participants from 69 countries, on 30 Nov - 4 Dec 2020. This workshop converged on a shared vision for autonomous surveillance of DNA in the ocean and capacity building on eDNA methodologies, which we will propose as an Ocean Decade programme.
Year(s) Of Engagement Activity 2020
URL https://pogo-ocean.org/capacity-development/activity-related-workshop/environmental-dna-edna-marine-...
 
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
URL http://www.ocean-partners.org/pogo-18
 
Description Presentation to the Southwest Marine Ecosystems Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Wilson W (2018) MARINeDNA: A forensic approach for detecting marine biodiversity. South West Marine Ecosystems Conference, Plymouth, April 2018.
Year(s) Of Engagement Activity 2018
 
Description Workshop on use of eDNA tools on the Continuous Plankton Recorder (CPR) Survey 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact An international workshop to to develop and produce a framework for the enhancement of global Continuous Plankton Survey (CPR) operations with the specific objective of developing the CPR as a platform for collecting samples for nucleic acid (DNA/RNA) analyses.
Year(s) Of Engagement Activity 2019
URL https://mailchi.mp/bb10672c00a2/pogo-newsletter-issue-39-february-2020?e=7467b872c0#mctoc18