SeaDNA - Assessing marine biodiversity and structure using environmental DNA: from groundtruthing to food web structure and stability

Lead Research Organisation: University of Salford
Department Name: Sch of Environment & 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.

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.

Publications

10 25 50
 
Description We have produced five publications, and several more are in preparation.
All initial results demonstrate that 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.
Exploitation Route We are currently preparing several more publications to showcase all the project achievements.
We have also 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.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Leisure Activities, including Sports, Recreation and Tourism,Government, Democracy and Justice,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology

URL https://twitter.com/SeaDNAproject
 
Description 2020: 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. And also attended the UK DNA WG Steering Committee group at the NHM, London, March 11th. 2019: New developments: 1) Discussions with colleagues at Southampton, Bristol, NOCS, CEFAS and JNCC have led to the preparation of a Large Grant Outline bid (not successful). 2) Preliminary data generated through the collaboration with the NHM are leading to a new grant proposal (now awarded). 2016: The project is at n early phase, but meetings with CEFAS, Natural England, the Environment Agency, as well as a number of NGOs outside the UK, indicate that the project approaches and findings will have a significant impact on environmental monitoring activities and management planning potentially at a global scale. As a result of liaising with CEFAS, we developed a new project aimed at strengthening our understanding of efficacy of the eDNA approach to monitor and assess pelagic stocks, which was funded under the NERC-CASE initiative and will start in October 2018. We have also organised the 5th UK DNA Working Group Meeting in Salford (https://www.salford.ac.uk/events/event/2017/uk-dna-working-group), which catalysed further discussions and burgeoning collaborations between academics and stakeholders interested in putting eDNA approaches into practice.
First Year Of Impact 2016
Sector Agriculture, Food and Drink,Education,Environment,Leisure Activities, including Sports, Recreation and Tourism,Culture, Heritage, Museums and Collections
Impact Types Cultural,Societal,Economic,Policy & public services

 
Description NERC CASE
Amount £89,114 (GBP)
Funding ID NE/R007861/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 10/2018 
End 09/2022
 
Description Natural History Museum, London 
Organisation Natural History Museum
Country United Kingdom 
Sector Public 
PI Contribution We metabarcoded sponge samples, analysed data and drafted a manuscript for submission.
Collaborator Contribution Procurement of invaluable sponge tissue samples from the Mediterranean and Antarctica.
Impact A paper was published in 2019 (see relevant section). A grant proposal based on these ideas was submitted to the July 2019 NERC Standard Grant round, and this was recently awarded as NE/T007028/1.
Start Year 2018
 
Description University of La Reunion 
Organisation University of La Réunion
Country Réunion 
Sector Academic/University 
PI Contribution We are metabarcoding samples from coastal waters around La Reunion, in order to investigate shark diversity.
Collaborator Contribution Invaluable sampling activities from a remote tropical location.
Impact We are still generating data.
Start Year 2018
 
Description University of Palermo 
Organisation University of Palermo
Country Italy 
Sector Academic/University 
PI Contribution A network of researchers investigating fish biodiversity in 11 Mediterranean Marine Protected Areas, led by Prof. M. Milazzo from the University of Palermo, requested our team contribution to produce eDNA metabarcoding screening of the localities investigated by their project, using a range of 'traditional' methods, such as visual census and baited cameras.
Collaborator Contribution The partners carried out eDNA water sampling in 11 locations in Spain, France, Italy, Slovenia and Greece. They also sent a postdoctoral fellow to my lab to carry out most of the required lab work.
Impact We have completed the first draft manuscript from the project, which will be submitted in the coming weeks. An oral presentation was contributed to the FSBI SYmposium in HUll, July 2019, based on the above manuscript: "Integrated Biodiversity Assessment in Mediterranean Marine Protected Areas".
Start Year 2019
 
Description University of Rome 
Organisation University of Rome Tor Vergata
Department Department of Biology
Country Italy 
Sector Academic/University 
PI Contribution We have metabarcoded samples of "trawl slush" from survey vessels, in order to generate total biodiversity data.
Collaborator Contribution carried out sampling from Southern Italian continental shelf and slope.
Impact A manuscript has been submitted to the journal Frontiers in Ecology & the Environment, titled "All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment".
Start Year 2018
 
Description BBC radio 4 Inside Science 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Extensive interview about the use of DNA reads from a shrimp's stomach to monitor fish diversity in estuaries.
Year(s) Of Engagement Activity 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 National
Primary Audience Public/other audiences
Results and Impact - stand with demonstration materials for keen public.
- round-table discussion about the topic "can you study animals without seeing them"?
Year(s) Of Engagement Activity 2018
 
Description Radio Interview with the popular CBC science programme "Quirks and Quarks" 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Live interview with a popular science radio broadcast, explaining and discussing the "natural sampler DNA" approach.
Link here:
https://www.cbc.ca/radio/quirks/june-22-is-your-wi-fi-watching-you-dog-s-manipulative-eyebrows-darwin-s-finches-in-danger-and-more-1.5182752/a-research-assistant-named-spongebob-sea-sponges-collect-data-for-science-1.5182754
Year(s) Of Engagement Activity 2019
URL https://www.cbc.ca/radio/quirks/june-22-is-your-wi-fi-watching-you-dog-s-manipulative-eyebrows-darwi...