SeaDNA - Assessing marine biodiversity and structure using environmental DNA: from groundtruthing to food web structure and stability
Lead Research Organisation:
Imperial College London
Department Name: Life Sciences
Abstract
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.
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.
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.
Publications
Zhao L
(2016)
Weighting and indirect effects identify keystone species in food webs
in Ecology Letters
Donohue I
(2016)
Navigating the complexity of ecological stability.
in Ecology letters
Brose U
(2017)
Predicting the consequences of species loss using size-structured biodiversity approaches.
in Biological reviews of the Cambridge Philosophical Society
Collins RA
(2018)
Persistence of environmental DNA in marine systems.
in Communications biology
Brose U
(2019)
Predator traits determine food-web architecture across ecosystems.
in Nature ecology & evolution
Woodward G
(2021)
Using Food Webs and Metabolic Theory to Monitor, Model, and Manage Atlantic Salmon-A Keystone Species Under Threat
in Frontiers in Ecology and Evolution
López-López L
(2021)
Ecological Networks in the Scotia Sea: Structural Changes Across Latitude and Depth
in Ecosystems
O'Gorman EJ
(2022)
Machine learning ecological networks.
in Science (New York, N.Y.)
Eskuche-Keith P
(2023)
Trophic structuring of modularity alters energy flow through marine food webs
in Frontiers in Marine Science
Gupta A
(2023)
How many predator guts are required to predict trophic interactions?
in Food Webs
Description | Obtaining trace DNA from seawater allows us to infer the species that have recently been present in the area. We have optimised methods for extracting that DNA. We have also developed methods to assess the rate of environmental DNA degradation, which will allow us to interpret results showing the presence or absence of DNA belonging to species in the area. We have conducted a series of experiments to quantify the rate of degradation of environmental DNA in UK coastal seas, and discovered that DNA typically decays to undetectable levels after 2-3 days in UK waters. We have also quantified our ability to detect fish species in seawater using several different methods, and identified the most appropriate methods for both bony fishes and sharks/rays. We have sampled the DNA from both UK and Antarctic waters, and are currently exploring levels of species diversity in those samples, and comparing them to data obtained from conventional survey methods. We have successfully applied to the use of DNA evidence for quantifying the diet of Antarctic fish species, and have confirmed the importance of gelatinous zooplankton to their diets, which has previously been overlooked by researchers studying Antarctic food webs. |
Exploitation Route | The methods and resources developed (e.g. reference databases) can be adopted by other researchers working on marine environmental DNA. |
Sectors | Environment |
Description | Approaches used in the project have been incorporated into a policy briefing paper on next-generation management of Atlantic salmon. We have also presented work to the general public, through the NERC Into the Blue showcase event and through public outreach events at the Natural History Museum, London. We have consistently engaged with the UK DNA Working Group (now represented under the UK EOF: http://www.ukeof.org.uk/our-work/ukdna) in order to translate evidence from 'SeaDNA' into practical solutions for marine environmental monitoring. In particular, S. Mariani participated in a DNA-focused "marine benthic monitoring workshop" organised by the JNCC in Manchester (Feb 25-26 2019); attended the UK DNA WG Steering Committee group at the NHM, London (March 11th, 2019) and presented at the UK DNA Working Group conference NHM London (27th-28th Jan 2020). |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink,Environment,Culture, Heritage, Museums and Collections |
Impact Types | Cultural Societal Policy & public services |
Description | Grantham institute panel discussion |
Geographic Reach | National |
Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
Description | New Strategies to Sustainable Fisheries Management: A Case Study of Atlantic salmon |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
Description | A Novel Framework for Predicting Emerging Chemical Stressor Impacts in Complex Ecosystems |
Amount | £1,411,113 (GBP) |
Funding ID | NE/S000348/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 08/2018 |
End | 02/2023 |
Description | ARIES DTP studentship |
Amount | £90,000 (GBP) |
Organisation | United Kingdom Research and Innovation |
Department | Aries Doctoral Training Partnership |
Sector | Public |
Country | United Kingdom |
Start | 09/2020 |
End | 09/2024 |
Description | Atlantic salmon population forecasting and sustainability in Icelandic rivers |
Amount | £150,000 (GBP) |
Organisation | Fálkaþing ehf.. |
Sector | Private |
Country | Iceland |
Start | 01/2018 |
End | 09/2018 |
Description | Functionality and Ecological Connectivity of Man-Made Structures (FuECoMMS) |
Amount | £847,607 (GBP) |
Funding ID | NE/T010800/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 07/2020 |
End | 08/2024 |
Description | Impacts of environmental and anthropogenic stressors on North Sea food webs |
Amount | £90,000 (GBP) |
Organisation | Chinese Scholarship Council |
Sector | Charity/Non Profit |
Country | China |
Start | 09/2021 |
End | 09/2025 |
Description | Marine environmental DNA as a tool for monitoring fish stocks |
Amount | £120,000 (GBP) |
Organisation | University of Leeds |
Department | China Scholarship Council |
Sector | Academic/University |
Country | United Kingdom |
Start | 08/2018 |
End | 08/2022 |
Description | Match-funded PhD studentship |
Amount | £90,000 (GBP) |
Organisation | Centre For Environment, Fisheries And Aquaculture Science |
Sector | Public |
Country | United Kingdom |
Start | 09/2020 |
End | 09/2023 |
Description | NERC Large Grant |
Amount | £1,815,580 (GBP) |
Funding ID | NE/M020843/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 08/2015 |
End | 09/2019 |
Description | Predicting the Impacts of Global Environmental Change on Ecological Networks |
Amount | £840,297 (GBP) |
Funding ID | NE/Y001184/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 03/2024 |
End | 02/2027 |
Description | Pyramids of Life: Working with nature for a sustainable future |
Amount | £9,304 (GBP) |
Funding ID | NE/V016016/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 11/2021 |
End | 10/2024 |
Title | A generalised, dynamic DNA reference library for UK fishes |
Description | This repository hosts a comprehensive mitochondrial DNA reference library dataset for UK fish species, derived from the NCBI GenBank and Barcode of Life BOLD databases. The dataset includes freshwater and marine species, and can be used in a variety of applications from DNA barcoding of human food products using full COI barcodes, to metabarcoding of gut or environmental samples using fragments of 12S. The library will be updated with each new GenBank release. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | No |
Impact | The database provides the first comprehensive curated compilation of DNA barcode data for UK fish species. The database enables rapid and reliable assignment of environmental DNA sequences at the species-level. |
URL | https://github.com/boopsboops/reference-libraries |
Title | Pelagic trophic network in the Scotia Sea (2006-2009) |
Description | Among all possible interaction types, trophic interactions are easily observable and essential in terms of energy transfer, and thus binary networks have arisen as the most straightforward method to describe complex ecological communities. These food-web models also inform on the ecosystem dynamics and function, and the patterns arising from food web topology can be indicators for ecosystem stability. We present a comprehensive pelagic network for the Scotia Sea underpinned by surveys and dietary studies conducted in the Scotia Sea in the last century. Selection of the trophic links followed a protocol based on taxonomy and geographic location, and was further refined based on the consumer and resource depth ranges and their body size ratios. The resulting network consists on 228 nodes and 10880 links which represent the main trophic paths in the Scotia Sea ecosystem and can serve as a basis for ecosystem modelling in the Scotia Sea or comparison with other ecosystems. Funding was provided by NERC Highlight Topic grant NE/N005937/1 and NERC Fellowship NE/L011840/1. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | https://data.bas.ac.uk/full-record.php?id=GB/NERC/BAS/PDC/01407 |
Description | Murray Thompson |
Organisation | Centre For Environment, Fisheries And Aquaculture Science |
Country | United Kingdom |
Sector | Public |
PI Contribution | I approached Dr Murray Thompson about submitting a joint application for funding to Cefas and the University of Essex for a match-funded PhD studentship. We developed a project idea together, secured approval from our institutes, and are currently advertising for a PhD student (to start in October) |
Collaborator Contribution | Dr Thompson helped to develop the ideas, contributed to writing of the proposed project, and will also participate in the interview process for selecting a candidate in due course. |
Impact | Match-funding for a PhD student (50% from Cefas, 50% from University of Essex School of Life Sciences) |
Start Year | 2016 |
Description | Simeon Hill |
Organisation | British Antarctic Survey |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | I built on connections made with Dr Simeon Hill at BAS during my NERC Fellowship and NERC-funded SeaDNA project to apply to the ARIES DTP for a PhD studentship in collaboration with Dr Hill. We have just found out that we were successful with this funding application and our nominated student has accepted the award. |
Collaborator Contribution | Dr Simeon Hill helped to develop the ideas for the proposed project, contributed to writing of the application for funding, and participated in the interview process for selecting a candidate. Dr Hill also brought another collaborator from BAS on board, Dr Philip Hollyman, who will join the supervisory team for the project. |
Impact | UKRI funding for a PhD studentship (ARIES DTP) |
Start Year | 2018 |
Description | European Researchers Night "Planet 2.0" |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | SeaDNA project stand at the European Researchers Night "Planet 2.0" at the Natural History Museum London |
Year(s) Of Engagement Activity | 2018 |
Description | Interview with the Economist |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Interview with the economist on the effects of environmental change on fish stocks (Genner) |
Year(s) Of Engagement Activity | 2017 |
Description | NERC Into the Blue |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | The SeaDNA project maintained a stall at the Manchester NERC Into the Blue showcase event (25-29 October 2016). The team engaged with several hundred members of the general public, typically with discussion on the methods and applications of the research. |
Year(s) Of Engagement Activity | 2016 |
URL | http://intotheblue.nerc.ac.uk/manchester/ |
Description | Nature Live |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Nature Live "Traces in the Water" 14th October 2018. Two sessions of 30 minutes with a reduced audience (approx. 50 pp). An interactive talk featuring environmental DNA and the research being carried within the project seaDNA on biodiversity and ecosystems, with the participation of Laura Balcells and Lucía López-López. |
Year(s) Of Engagement Activity | 2018 |
Description | Nature Live at the Natural History Museum |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | An interactive talk at the Natural History Museum, London, featuring environmental DNA and the research being carried within the project seaDNA on biodiversity and ecosystems |
Year(s) Of Engagement Activity | 2018 |
Description | Planet 2.0 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | SeaDNA project stand at the European Researchers Night "Planet 2.0" at the Natural History Museum London, with the participation of Rupert, Eoin, Stefano, Laura and Lucía. The event was attended by over 3000 people. We also participated in the Dialogue Den during the event. In this activity, where the researcher met a small audience (4-6 pp) and discussed some aspects of the research, aimed at changing people attitudes towards science. |
Year(s) Of Engagement Activity | 2018 |
Description | RRS Discovery |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | As part of my role as a NERC 50th Anniversary Ambassador, I attended the mooring of the RRS Discovery in the Thames near Tower Bridge and promoted NERC science to members of the general public as part of a stall with the Centre for Ecology and Hydrology. |
Year(s) Of Engagement Activity | 2015 |
Description | Water Explorer Final |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | I presented tanks of freshwater pond organisms at the final of the Water Explorer competition, an initiative aimed at conserving water use at a national level through involvement by school children. I educated the school children that made the final and their teachers on the kinds of organisms that can be found in healthy freshwater bodies. I also got the opportunity to interact with environmental representatives from HSBC Bank and Global Action Plan, which is an independent charity committed to engaging people in practical solutions to environmental and social problems. |
Year(s) Of Engagement Activity | 2015 |