Understanding the ecological relevance of eDNA in freshwater lotic ecosystems

Lead Research Organisation: NERC Centre for Ecology and Hydrology
Department Name: Soils and Land Use (Bangor)

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.
 
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
 
Title Overview of lifespan of lotic eDNA 
Description Dr. Mat Seymour features discussing the findings of Seymour et al. 2018 Communications Biology paper and demonstrates the eDNA sampling and analysis method. 
Type Of Art Film/Video/Animation 
Year Produced 2018 
Impact Good altimetric score for the paper. 
URL http://mefgl.bangor.ac.uk/news/dna-pinpoints-river-animals-in-the-here-and-now-35752
 
Title Singers at Royal Oak 
Description Singers at pub local to the artificial fumes sing songs about uplands and rivers to help communicate to the local community the research we are doing in their community. 
Type Of Art Performance (Music, Dance, Drama, etc) 
Year Produced 2016 
Impact Community more aware of research and supportive of the work. 
 
Description We have discovered the freshwater eDNA from multiple species lasts for a very short space of time (<43 hours) and is loss is accelerated under lower pH conditions, according to our WP1 mecocosm experiment.
Exploitation Route They contextualise the likely persistence and potential transit of freshwater eDNA in moving water systems, such as rivers.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Environment

URL https://www.nature.com/articles/s42003-017-0005-3
 
Description The DEFRA group have recently started a consultation to establish whether a Centre of Excellence needs to be established in the field of eDNA analysis in relation to environmental biomonitoring and ecosystem assessment. Welsh Government commissioned report on the use of eDNA in biodiversity assessment.
First Year Of Impact 2016
Sector Environment
Impact Types Policy & public services

 
Description FRESH CDT
Amount £2,100,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 10/2018 
End 09/2024
 
Description Freshwater macroinvertebrate barcoding 
Organisation Environment Agency
Country United Kingdom 
Sector Public 
PI Contribution Collecting and producing individual species with COI DNA barcodes for reference database building
Collaborator Contribution Producing individulal species with COI DNA barcodes for reference database building work ongoing and so no results yet
Impact Work ongoing
Start Year 2017
 
Description Freshwater macroinvertebrate barcoding 
Organisation Natural History Museum
Country United Kingdom 
Sector Public 
PI Contribution Collecting and producing individual species with COI DNA barcodes for reference database building
Collaborator Contribution Producing individulal species with COI DNA barcodes for reference database building work ongoing and so no results yet
Impact Work ongoing
Start Year 2017
 
Description LOFRESH global sampling 
Organisation Cornell University
Department Department of Ecology and Evolutionary Biology
Country United States 
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 
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 
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 UK co-representative for EU COST Action DNAquanet 
Organisation University Duisburg-Essen
Country Germany 
Sector Academic/University 
PI Contribution Attendance at DNAquanet meetings and workshops around the EU, networking
Collaborator Contribution Co-ordination of DNAquanet meetings and workshops around the EU, networking
Impact Knowledge exchange in field of DNA biomonitoring; Molecular genetics, environmental sciences
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 CEH Conwy Catchment Stakeholder Event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Professors Johnes, Jones and Evans gave presentations to a large group of stakeholder organisations as a CEH-led Stakeholder engagement event at the Glasdir Centre in Llanrwst, Conwy catchment on 16/06/2015. New links were made with local Natural Resources Wales staff and National Trust field officers.
Year(s) Of Engagement Activity 2015
 
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 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 Talk by Mat Seymour at UK DNA Working Group meeting, Salford, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk by Mat Seymour at UK DNA Working Group meeting, Salford, UK: overviewing the findings of WP1 of the NERC grant.
Year(s) Of Engagement Activity 2017
 
Description Talk by Mat Seymour at the Ecology without Borders conference, Ghent, Belgium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk by Mat Seymour at the Ecology without Borders conference, Ghent, Belgium, sparking questions and debates
Year(s) Of Engagement Activity 2017
 
Description Talk by Simon Creer at EU COST Action DNAquanet 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Overviewed the NERC grant and background to international audience at the inaugural DNAquanet meeting in University of Duiseburg, Essen, Spring 2017
Year(s) Of Engagement Activity 2017
 
Description University Press release 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Third sector organisations
Results and Impact Bangor University, in collaboration with broader LOFRESH team, constructed a press release to outline the major findings of our 2018 Communications Biology paper (altimetric score of 99), outlining the empirical life of eDNA in higher order lotic ecosystems. Press activity was sought, but instead substituted with a short video clip.
Year(s) Of Engagement Activity 2018
URL http://mefgl.bangor.ac.uk/news/dna-pinpoints-river-animals-in-the-here-and-now-35752