Understanding the ecological relevance of eDNA in freshwater lotic ecosystems

Lead Research Organisation: Bangor University
Department Name: Sch of Biological Sciences

Abstract

Understanding the impacts of environmental change and changing land use on biodiversity and how ecosystems work require comprehensive knowledge of communities and their ecology. Molecular biodiversity identification is emerging as a high throughput and cost effective alternative to traditional approaches and in particular, the analysis of environmental DNA (eDNA) provides an opportunity to measure biodiversity in space and time at unprecedented scales. Unlike DNA obtained through direct analysis of communities, eDNA refers to shed cells or free-DNA from organisms as they pass through an environment, or die and decay. eDNA is being applied for various uses such as identification and monitoring of endangered/invasive species and analysis of biodiversity. It is very clear that researchers can detect eDNA from a variety of natural environments and in particular, freshwater environments. However, understanding how those sources of eDNA relate to living biodiversity and associated ecological function in ecologically and socio-economically important river ecosystems is at the heart of the eDNA:LOFRESH proposal.
Focusing on a range of exemplar experimental semi-natural and natural freshwater catchment systems from local to national scales, we will (a.) improve understanding of the movement, and persistence of lotic eDNA, (b.) quantify the relationship between lotic eDNA and the in situ community using different combinations of genetic and genomic approaches, (c.) improve methodological approaches for eDNA data acquisition and interpreting eDNA data using novel ecological and phylogenetic algorithms, (e.) develop and test new models relating lotic eDNA to stream biodiversity and ecosystem function and their variation in response to land use pressures. Over a 4 year period, five work packages (WPs) will be delivered by the Universities of Bangor, Birmingham, Cardiff and the Centre for Ecology and Hydrology. In WP1, we will use artificial stream channels in a series of experiments to assess the effects of a range of physical and chemical drivers on the loss of lotic eDNA and to compare and contrast genetic and genomic approaches for assessing known sources of lotic eDNA. In WP2, we will test our experimental findings from WP1 by tracking natural lentic (i.e. lake) and experimentally introduced control lotic eDNA through the natural stream network of the intensely studied Conwy River research catchment in north Wales. WP2 will also assess relationships between observed lotic eDNA and the in situ community in selected tributaries of the Conwy displaying a range of physicochemical characteristics and experiencing different land use pressures. WP3 will sample lotic eDNA in coordination with an on-going national survey in Wales to up-scale the experimental and catchment-scale findings of WP1 and WP2 to the Welsh landscape and national scales. WP4 will provide informatics support, but specifically, develop workflows to identify species level diversity in eDNA datasets. Finally, in WP5 we will further test our model findings, by manipulating the experimental stream systems with emulated land use pressures, quantify the ecosystem functions of decomposition and food web structure and test linkages with eDNA signals. Effective engagement with a broad range of stakeholder groups (government, end-users, environmental agencies) and project partners (research institutions and academic partners specialising in eDNA, sequencing and informatics) will optimise impact and research synergies of potentially transformative science throughout the consortium network.

Planned Impact

The Impact Plan is based on engagement with Partners representing key stakeholders and end-users, and the national and international science community including all NERC eDNA projects. The principal policy areas where eDNA applications in freshwater ecosystems are likely to be greatest are the future development of Water Framework Directive (2000/60/EC), Habitats Directive (92/43/EEC), JNCC Biodiversity Action Plan for Rivers, and the Welsh Government's approach to Natural Resource Management as engendered by 'A Living Wales'. We have targeted impact at the sectors responsible for this and other similar applications. The plan aims to ensure that the excellence in science produced by the project has real impact on the community knowledge of eDNA, the next generation of monitoring and freshwater functional ecology (at the reach, catchment- and national scale) and for environmental management. Our programme of activity to better understand the needs of the different communities will evolve over the lifetime of the project. This will build on existing networks and joint initiatives thus efficiently increasing interaction and engagement with a broad set of academic activities and expertise and end-users. Impact will be ensured in the following ways:
Annual (potentially 6 monthly) stakeholder and end-user meetings shared with a range of other NERC/EPSRC projects focussed on land and water management will ensure inter-connectivity between a range of academic and end-user communities including the NERC Macronutrients Programme, BESS, Environmental Microbiology and Human Health and EPSRC Internet of the Wild. Briefings and presentations at a wide range of existing groups, projects and conferences the team are already actively engaged in, which involves Defra, EA, devolved administrations, NGOs and the water industry (incl. Catchment Management Forum and Modelling Platform funded by Defra, NERC, Scottish Government and EA; GB integrated monitoring through co-design of the next Countryside Survey; Defra DTCs Advisory Group). The project will contribute to a Conwy website and use of social media identified as useful by endusers.
Our letters of support from the Environment Agency, Natural Resources Wales, NERC Environmental 'Omics Centre (Cardiff University), CSIRO (Australia), EAWAG (Switzerland), Environmental Change Initiative at University of Notre Dame (USA), CNRS Laboratoire d'Ecologie Alpin (France), Beijing Genomics Institute (China), indicate the level of interest and ongoing engagement we have with a range of stakeholders, leading academic partners and end-users. Participation by the project partners at four annual meetings throughout the project will ensure that research outcomes will permeate rapidly through the global eDNA community and to associated stakeholders by extended networking. Links to academic beneficiaries to ensure maximum outcomes with respect to development of this field will be by attendance at eDNA events organised by the UK eDNA Working Group (Creer and de Bruyn are on the Steering Committee), attendance at relevant conferences and publishing in the peer reviewed literature.
Biodiversity and environmental change are high profile topics across broad sectors of society, resulting in a "biodiversity aware" general public. The strategy which addresses RCUK central definitions of impact: "demonstrable contribution to society...enhancing the quality of life, health and creative output" will enhance public engagement and communication regarding science and societal issues. Plans for engagement with schools and the general public include participation in Wales Gene Park and Bangor Science Festival events, the use of radio and other media for outreach (e.g. Science Café, NERC Planet Earth), in addition to presentation at University UCAS open days for students and parents. Regular scheduling of engagement activities by all project partners will be encouraged, and actively monitored on a quarterly basis by Bangor.

Publications


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Creer S (2017) Marine ecology: Genetics from a drop in the ocean in Nature Ecology & Evolution
Creer S (2016) The ecologist's field guide to sequence-based identification of biodiversity in Methods in Ecology and Evolution
 
Title Experimental eDNA video 
Description The film explains what is eDNA and how the Lofresh team collaborates 
Type Of Art Film/Video/Animation 
Year Produced 2017 
Impact This has just been developed but will be put on youtube and aims to inform the public 
URL https://vimeo.com/193605236
 
Description Biomonitoring marine macroinvertebrate communities
Amount £5,000 (GBP)
Organisation Natural England 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start  
 
Description Lamprey eDNA feasibility study
Amount £9,000 (GBP)
Organisation Scottish Natural Heritage 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start  
 
Description Marine eDNA South African research grant
Amount £60,000 (GBP)
Organisation Government of South Africa 
Sector Public
Country South Africa, Republic of
Start  
 
Description Santander Universities Research Mobility Awards
Amount £1,000 (GBP)
Organisation Santander Bank 
Sector Private
Country United States of America
Start 09/2016 
End 09/2017
 
Description LOFRESH global sampling 
Organisation Cornell University
Department Department of Ecology and Evolutionary Biology
Country United States of America 
Sector Academic/University 
PI Contribution Leaders and co-members of the collaboration providing methods and analytical expertise.
Collaborator Contribution Collaboration with external groups to coordinate sampling of lotic environments to complement work package 2 of the LOFRESH project.
Impact No outputs as of yet as the collaboration is slated to begin production mid 2017
Start Year 2017
 
Description LOFRESH global sampling 
Organisation Swiss Federal Institute of Aquatic Science and Technology
Country Switzerland, Swiss Confederation 
Sector Public 
PI Contribution Leaders and co-members of the collaboration providing methods and analytical expertise.
Collaborator Contribution Collaboration with external groups to coordinate sampling of lotic environments to complement work package 2 of the LOFRESH project.
Impact No outputs as of yet as the collaboration is slated to begin production mid 2017
Start Year 2017
 
Description LOFRESH global sampling 
Organisation University of Hull
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Leaders and co-members of the collaboration providing methods and analytical expertise.
Collaborator Contribution Collaboration with external groups to coordinate sampling of lotic environments to complement work package 2 of the LOFRESH project.
Impact No outputs as of yet as the collaboration is slated to begin production mid 2017
Start Year 2017
 
Description BBC Radio Wales Science Cafe program 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Podcast via the BBC
Year(s) Of Engagement Activity 2016
 
Description BES Aquatic macroecology group meeting. London, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Persistence of environmental DNA in experimental streams
Year(s) Of Engagement Activity 2016
 
Description BES annual meeting, Liverpool, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Persistence of environmental DNA in experimental river systems
Year(s) Of Engagement Activity 2016
 
Description DNA Working Group Meeting, Edinburgh, UK. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Persistence of environmental DNA in experimental river systems: implications for molecular biodiversity assessment
Year(s) Of Engagement Activity 2016
 
Description DNAqua-Net conference, Essen, Germany. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Ecological relevance of eDNA persistence
Year(s) Of Engagement Activity 2017
 
Description ESA Fort Lauderdale 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 Ecological Society of America International conference
Year(s) Of Engagement Activity 2016
 
Description Future Earth workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact The Future Earth cluster on "Global Biodiversity Monitoring, Prediction and Reporting" aims to provide a forum for interdisciplinary research activities and scientific questions associated with globally integrated monitoring and assessment of biodiversity (species, populations, traits). The purpose of the 2016 workshop on Global Biodiversity Assessment and Monitoring -Science, Data and Infrastructure Needs for IPBES and Beyond, was to reflect on monitoring of biodiversity at a global scale. Two papers were produced. One paper was provided to IPBES - Inter government panel on Biodiversity and Ecosystem Sustainability - to provide the science evidence and inform on gaps. One paper was published focused on freshwater ecosystems, the paper refers to both Duress and Lofresh.
Year(s) Of Engagement Activity 2016
URL http://biodiversitymonitoring.org
 
Description Invited talk to a Canadian network on aquatic biodiversity and ecosystem services 
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 Provide an overview of the Duress/Lofresh project to a Canadian programme engaged in a similar field of Biodiversity and an Ecosystem service sustainability in freshwaters. Compare and contrast, lessons learned from the Duress project and insights into the Lofresh project. NSERC CNAES is a national research network supported by NSERC's Strategic Network Grants program, which encourages large-scale, multidisciplinary, collaborative research projects that could improve Canada's economy, society and environment within the next decade. CNAES is a consortium of approximately 30 researchers from 11 universities, government, and industrial partners, plus many graduate students and post-doctoral researchers, that conduct research and training about aquatic ecosystems.
Year(s) Of Engagement Activity 2016
URL http://www.cnaes.ca
 
Description Manuscript featured on Molecular Ecologist blog: 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Featured article on Molecular Ecologist Blo (180 likes)
Year(s) Of Engagement Activity 2016
URL http://www.molecularecologist.com/2016/10/making-ecology-count-a-review-of-the-why-and-how-of-molecu...
 
Description Simon Creer featured in New Scientist article on eDNA 
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 Article featured in regular New Scientist magazine with global reach.
Year(s) Of Engagement Activity 2016
URL https://www.newscientist.com/article/mg23130811-500-dna-sequencing-turns-rivers-into-ecosystem-surve...
 
Description University of East Anglia, School of Biosciences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Invited Lecture
Year(s) Of Engagement Activity 2016