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

Lead Research Organisation: National Oceanography Centre
Department Name: Science and Technology

Abstract

Summary

SeA-DNA: Development and application of eDNA tools to assess the structure and function of coastal sea ecosystems.

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

Impact Summary

SeA-DNA: Development and application of eDNA tools to assess the structure and function of coastal sea ecosystems.

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

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Related Projects

Project Reference Relationship Related To Start End Award Value
NE/N006496/1 01/12/2015 31/10/2019 £236,313
NE/N006496/2 Transfer NE/N006496/1 01/11/2019 30/11/2020 £16,322
 
Description We have proved the concept of an automated eDNA sampling device and have a draft manuscript, patent and have done a market assessment.

We have developed new eDNA assays targeting harmful algae and demonstrated detection on a handheld genetic sensor.

We have found the ideal preservative for eDNA from filtered marine samples.

We have collected eDNA samples over a diel cycle and the analyses of these samples is ongoing.
Exploitation Route We anticipate that these devices will have a range of applications, based on the market assessment, from oceanography to waste water epidemiology.
Sectors Aerospace, Defence and Marine,Environment,Healthcare

 
Description (iAtlantic) - Integrated Assessment of Atlantic Marine Ecosystems in Space and Time
Amount € 10,803,099 (EUR)
Funding ID 818123 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 05/2019 
End 05/2023
 
Description Atlantic Ecosystems Assessment, Forecasting & Sustainability
Amount € 12,000,000 (EUR)
Funding ID 862923 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 05/2020 
End 05/2024
 
Description Marine Sensor Proof of Concept August 2017
Amount £140,000 (GBP)
Funding ID NE/R012318/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 03/2018 
End 03/2021
 
Title Design, development and testing of a Marine Autonomous Plankton Sampler 
Description The Marine Autonomous Plankton Sampler autonomously filters and preserves marine microbes and eDNA for 'omics' analyses. It can stop filtration based on pressure across the filter membrane (to prevent clogging) or filtration time (for rapid preservation for RNA analyses). It is capable of filtering 50 samples per deployment, in its current configuration. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact We have collected 200 samples from a 10 day cruise without complications, and will complete Quality Control on those samples this month and will soon have a draft manuscript. The benchtop device has undergone optimisation and a submersible version is being manufactured for deployment this year. 
 
Title Development of a rapid assay for quantification of the harmful alga Alexandrium within minutes 
Description A novel isothermal RPA assay was developed and successfully run on a miniaturised device that controls temperature with optical detection of DNA probes, for point-of-sample gene quantification. This device and assay detected Alexandrium within minutes and faster than our quantitative PCR assays on the bench (the standard way to count genes). This result on a field-deployable device saves time and money, allowing near-real-time bloom evaluation. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact We anticipate that this method can be used at aquaculutre facilities or other environments where Hamful algae monitoring. 
 
Title Preservation of qPCR reagents for a Lab-on-a-Chip biosensor 
Description We have developed two methods of robust preservation of qPCR reagents on an in-house lab-on-a-chip biosensor, using lyophilisation and encapsulation in pullulan. These methods require the stabilization of reagents, which are preserved over time, then hydrated upon the addition of purified aqueous DNA template. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Early qPCR results are promising, with lyophilization maintaining stability for 5 weeks and pullulan preservation for at least 4 weeks. The miniaturized Lab-on-a-Chip molecular detection device was not developed for quantitative PCR. This development has greatly expanded the versatility and potential user base for the device. 
 
Title quantification of the diagnostic neurotoxin synthesis gene in a harmful algae species 
Description The gene responsible for domoic acid (neurotoxin) synthesis in Pseudonitzschia was recently discovered (late 2018). We developed a qPCR assay targeting this gene and it showed specificity to Pseudonitzschia (without amplifying other harmful algae) and it was quantifiable across a 10^0 - 10^7 cell equivalents dynamic range. This assay will be employed to understand domoic acid production during shifts in nutrient environnents with cultured representatives. 
Type Of Material Technology assay or reagent 
Year Produced 2020 
Provided To Others? No  
Impact While this is a brand new method, we anticipate that it has utility across research groups to learn about environmental factors controlling the production of this neurotoxin. We will soon test its performance in marine environments using environmental samples. 
 
Description Evaluation of eDNA methodologies for holistic (ecosystem-level) biodiversity assessments 
Organisation University of Southampton
Country United Kingdom 
Sector Academic/University 
PI Contribution Sharing of students and research projects, contribution to manuscripts and proposals.
Collaborator Contribution Sharing of students and research projects, contribution to manuscripts and proposals.
Impact We have 1 manuscript in prep and another in review, and we've written 4 proposals together (1 pending).
Start Year 2017
 
Description POGO eDNA conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact PIs Wilson and Robidart planned and co-convened a POGO International Virtual Conference on the use of Environmental DNA (eDNA) in Marine Environments: Opportunities and Challenges, with 800+ participants from 69 countries, on 30 Nov - 4 Dec. This workshop converged on a shared vision for autonomous surveillance of DNA in the ocean and capacity building on eDNA methodologies.
Year(s) Of Engagement Activity 2020
URL https://pogo-ocean.org/capacity-development/activity-related-workshop/environmental-dna-edna-marine-...