SeaDNA - Assessing marine biodiversity and structure using environmental DNA: from groundtruthing to food web structure and stability
Lead Research Organisation:
University of Bristol
Department Name: Biological 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.
People |
ORCID iD |
Martin Genner (Principal Investigator) |
Publications
Collins R
(2019)
Non-specific amplification compromises environmental DNA metabarcoding with COI
in Methods in Ecology and Evolution
Collins R
(2022)
Reproduction influences seasonal eDNA variation in a temperate marine fish community
in Limnology and Oceanography Letters
Collins RA
(2021)
Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes.
in Journal of fish biology
Collins RA
(2018)
Persistence of environmental DNA in marine systems.
in Communications biology
Hastings RA
(2020)
Climate Change Drives Poleward Increases and Equatorward Declines in Marine Species.
in Current biology : CB
Liu Z
(2022)
Environmental DNA captures elasmobranch diversity in a temperate marine ecosystem
in Environmental DNA
López-López L
(2021)
Ecological Networks in the Scotia Sea: Structural Changes Across Latitude and Depth
in Ecosystems
Mariani S
(2021)
Estuarine molecular bycatch as a landscape-wide biomonitoring tool
in Biological Conservation
Description | Obtaining trace DNA from seawater allows us to infer the species that recently been present in the area. We have optimised methods of extracting that DNA. We have also developed methods assess the rate of environmental DNA degradation, that 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 in UK coastal seas, and discovered that typically DNA 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, explored levels of species diversity in those samples, and compared 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 jellyfish to their diets which has previously been overlooked by researchers studying Antarctic food webs. We have produced five publications, and several more are in preparation. Initial results demonstrate that once all publications are finalised, our goals will be achieved and in some cases surpassed. - Data from UK estuaries show that eDNA can detect between two to three times more number of fish species than netting techniques and also detect spatial and seasonal patterns that would not be apparent using traditional techniques. It also shows that a great deal of additional important faunal information can be obtained from the same data, especially pertaining to seabirds and mammals of conservation importance. - Data from the English Channel illustrate seasonal changes in fish assemblages and identify different habitat and life history related eDNA signatures. While the eDNA signatures correlate with trawl data for several species, we find that in others (such as sardines and plaice), eDNA peaks are associated with the spawning period, and hence gamete release. In other instances, differences in eDNA signatures between surface and bottom collections reflect the preferred habitat of the species (benthic/pelagic). - 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. -A key limitation regarding the use of environmental DNA for analyses is the availability or curated reference material. We have developed a new database of DNA markers of UK fishes, including novel sequences for large number of species obtained opportunistically by researchers undertaking fisheries surveys. |
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 | We have 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). The work seeded ideas for a new eDNA filtration method, which was designed and piloted in 2023, using BBSRC IAA funding. Using the new filter we are able to obtain on average 4x the quantity of eDNA with reduced fieldwork effort. |
First Year Of Impact | 2019 |
Sector | Environment |
Impact Types | Societal Policy & public services |
Description | Innovative data services for aquaculture, seismic resilience and drought adaptation in East Africa |
Amount | £809,141 (GBP) |
Funding ID | EP/T015462/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2019 |
End | 03/2022 |
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 |
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 | Data from: Non-specific amplification compromises environmental DNA metabarcoding with COI |
Description | 1. Metabarcoding extra-organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. However, choice of genetic marker and primer set is a critical consideration when designing experiments, especially so when developing community standards and legislative frameworks. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power, and predictable sequence variation, is the natural choice for many metabarcoding applications such as the bulk sequencing of invertebrates. However, the overall utility of COI for environmental sequencing of targeted taxonomic groups has yet to be fully scrutinised. 2. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve mitochondrial primer pairs from COI, cytochrome b, 12S and 16S, in terms of reference library coverage, taxonomic discriminatory power, and primer universality. We subsequently test in vitro three COI primer pairs and one 12S pair for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites in the English Channel and North Sea coast. 3. Our results show that for aqueous extra-organismal DNA at low template concentrations, both metazoan and fish-targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non-specific amplification of prokaryotic and non-target eukaryotic DNAs. 4. An ideal metabarcode would have an extensive reference library for which custom primer sets can be designed for either broad assessments of biodiversity or taxon specific surveys, but unfortunately, low primer specificity hinders the use of COI, while the paucity of reference sequences is problematic for 12S. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome-skimming existing tissue collections. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.b8f6s44 |
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 |
Title | Reproduction influences seasonal eDNA variation in a temperate marine fish community |
Description | All code and scripts required to reproduce the analysis of data in the paper. |
Type Of Material | Data analysis technique |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | Opportunity to better understand the factors that explain the amount of fish eDNA detectable in temperate shelf seas. |
URL | https://zenodo.org/record/6858158#.ZAnC8-zP2lM |
Title | Reproduction influences seasonal eDNA variation in a temperate marine fish community |
Description | Full data sets for the above-mentioned paper |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | Yes |
Impact | Understanding temporal variation of eDNA signatures in relation to fish life histories and reproduction |
URL | https://www.ncbi.nlm.nih.gov/sra/PRJNA725897 |
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 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 |