Understanding the ecological relevance of eDNA in freshwater lotic ecosystems
Lead Research Organisation:
University of Birmingham
Department Name: Sch of Biosciences
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.
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.
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
Derelle R
(2020)
Broccoli: Combining Phylogenetic and Network Analyses for Orthology Assignment.
in Molecular biology and evolution
Eastwood N
(2022)
The Time Machine framework: monitoring and prediction of biodiversity loss.
in Trends in ecology & evolution
Eastwood N
(2023)
100 years of anthropogenic impact causes changes in freshwater functional biodiversity.
in eLife
Eastwood N
(2024)
Single metabarcoding multiplex captures community-level freshwater biodiversity and beyond
in Environmental DNA
Seymour M
(2020)
Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks
in Science of The Total Environment
Zhou J
(2023)
100 years of anthropogenic impact causes changes in freshwater functional biodiversity
in eLife
Description | Invited Expert: International workshop on advanced chemical safety assessment technologies |
Geographic Reach | National |
Policy Influence Type | Membership of a guideline committee |
Impact | Professor John Colbourne was invited to the Joint Meeting of Analytical Toxicology and Computational Toxicology Committee (Chinese Society of Toxicology) and International Workshop on Advanced Chemical Safety Assessment Technologies to provide guidance on the establishment of a new Society for Computational and Systems Toxicology and to align Chinese interests in environmental health protection research with those of the international Environment Care Consortium, which University of Birmingham leads. |
Description | NERC: Short course in Environmentmental Omics |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | A NERC funded short course to guide genomics and metabolomics research applied to environmental sciences. This annual training course highlights a multi-omics (system biology) approach to research in environmental sciences. It trains PhD students and early career postdoctoral scientists to investigate how gene function and metabolism are influenced by environmental conditions while accounting for variation that exists within and among natural populations. The course is built on the paradigm that this multidisciplinary research field encompassing ecology, evolution, toxicology, biostatistics and informatics will most effectively grow by training early career environmental scientists to properly design comprehensive, large-scale, Next Generation Sequencing and Metabolomics experiments enabled by drastically increased sample-throughput and lower costs. Most importantly, the challenges of manipulating and analysing population-level omics (big) data must be addressed. The course provided a significant introduction and much hands-on training experience so that participants can initiate their own environmental omics study and network with others in the field to launch Environmental Scientist careers in academia and industry. Case studies using multi-omics data sets collected at the University of Birmingham are provided so that students can gain practical experience of analysing and integrating multi-omics data. Daphnia is used for training because of its growing use as a model system in the environmental sciences and for improving environmental health protection, yet the skills learned during the course are applicable to all study systems with mature genomics and metabolomics resources. |
Description | Alan Turing Fellowship |
Amount | £162,577 (GBP) |
Organisation | Alan Turing Institute |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2019 |
End | 10/2021 |
Description | GLOBAL CHALLENGE RESEARCH FUND (Gnatwork), Validating Nanopore Sequencing Technology for Front-Line Pathogen-Vector Complex Studies, |
Amount | £100,000 (GBP) |
Organisation | The Pirbright Institute |
Sector | Academic/University |
Country | United Kingdom |
Start | 03/2019 |
End | 02/2020 |
Description | International Collaboration Awards for Research Professors |
Amount | £369,000 (GBP) |
Funding ID | IC160121 |
Organisation | The Royal Society |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 12/2016 |
End | 11/2021 |
Description | Gene Expression Profiling Essays for Precision Environmental Health |
Organisation | BioClavis Ltd |
Country | United Kingdom |
Sector | Private |
PI Contribution | An Overarching Collaboration Agreement is being executed to encourage the R&D of Gene Expression Profiling assays between BioClavis Ltd and the University of Birmingham drawing upon complementary expertise in the development of a platform towards the application of biomarkers of environmental health hazards, by specifically pursuing collaborative research with Professors John Colbourne and Mark Viant and members of the Environmental Omics group within the College of Life and Environmental Sciences. University of Birmingham is contributing knowledge and expertise around the use of Daphnia as an environmental health indicator species. |
Collaborator Contribution | BioClavis Ltd is contributing technological expertise and specific technology called Tempo-Seq that is owned by the company to explore its utility at environmental health monitoring. |
Impact | Thus far, there has been a transfer of materials and the creation of exploratory data. |
Start Year | 2019 |
Description | Joint Laboratory for Environmental Health Research |
Organisation | China Jiliang University |
Country | China |
Sector | Academic/University |
PI Contribution | An Overarching Collaboration Agreement was signed towards a Joint Laboratory for Environmental Health Research that will encourage the development of the relationship between Jiliang and Birmingham and will facilitate collaborative grant proposals and jointly funded research collaborations in the area of environmental health research leading to the application of precision toxicology for pollution interventions. Our research team contributes multi-omics expertise and data science in the use of indicator model species Daphnia as a biological indicator of environmental conditions that threaten human and ecosystem health |
Collaborator Contribution | China Jiliang University contributes expertise in analytical chemistry, specifically in the targeted and non-targeted detection of pollutants such as pesticides and industrial chemicals. The combination of chemistry with molecular biology is expected to deliver greater certainty between pollution and its environmental health consequences. |
Impact | The planned activities are primarily around China-UK funding opportunities including a first grant proposal to the China National Science Foundation and shared PhD students between our College of Life and Environmental Sciences and their Institute of Environmental and Health Sciences. |
Start Year | 2020 |
Description | 20th Congress of the Iberian Association of Limnology (AIL-2020) and III Ibero-American Congress of Limnology (CIL-2020) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | A keynote address was given by Luisa Orsini. |
Year(s) Of Engagement Activity | 2020 |
URL | https://limnologia2020.com/en |
Description | BBC Radio 5-live interview |
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 | BBC Radio interview to improve public understanding of the goals of COP26 and its role in preserving biodiversity |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.bbc.co.uk/sounds/play/live:bbc_radio_five_live |
Description | BBC Radio CWR |
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 | BBC Radio interview to improve public understanding of the goals of COP26 and its role in preserving biodiversity |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.bbc.co.uk/sounds/play/live:bbc_radio_coventry_warwickshire |
Description | Interview by BBC WM Radio |
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 | BBC Radio interview to improve public understanding of the goals of COP26 and its role in preserving biodiversity |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.bbc.co.uk/programmes/p09ydqcf |
Description | Interview: Inspiring women in 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 | In March 2019, Dr Orsini was interviewed in occasion of the Woman day - social media coverage 'Inspiring women in science' |
Year(s) Of Engagement Activity | 2019 |
Description | Interview: World Water Day, Water for all |
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 | In February 2019, Dr Orsini was interviewed in occasion of the World Water Day-Water for all organized by the Birmingham Water Council to increase awareness about water challenges https://youtu.be/A9gnFOGCSQ4. The interview has to this day had 419 views. |
Year(s) Of Engagement Activity | 2019 |
URL | https://youtu.be/A9gnFOGCSQ4 |
Description | Podcast 'Brilliant minds working at the Turing' |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | promoting biodiversity and AI science to colleagues and the generla public |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.turing.ac.uk/people/spotlights/luisa-orsini |
Description | Radio Global interview |
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 | increase awareness on climate change matters |
Year(s) Of Engagement Activity | 2021 |
Description | Research Event: Birmingham Strikes Back |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | In November 2019 the Star Wars Research Event - "Birmingham Strikes Back" organized by the University of Birmingham in which Dr Orsini was an invited speaker reached 11,000 views, 193 comments and 32 shares. The science podcast and the lecture described the process of long-term evolution using Daphnia as a model species, using parallels to Han Solo frozen in carbonite. If you missed #birminghamstrikesback, you can view it again on the UoB Facebook channel https://facebook.com/unibirmingham/); https://www.facebook.com/unibirmingham/videos/2507829439303910. |
Year(s) Of Engagement Activity | 2019 |
URL | https://www.birmingham.ac.uk/university/colleges/socsci/events/future-fest/events/birmingham-strikes... |
Description | University College London |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Centre for Biodiversity and Environment Research, University College London, London, UK |
Year(s) Of Engagement Activity | 2017 |
Description | World Water Day - Water for all |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Media (as a channel to the public) |
Results and Impact | Dr Luisa Orsini was interview for media campaign to bring awareness to water resource issues, organized by the Birmingham Water Council. |
Year(s) Of Engagement Activity | 2019 |
Description | interview BBC Radio Hereford & Worcester |
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 | BBC Radio interview to improve public understanding of the goals of COP26 and its role in preserving biodiversity |
Year(s) Of Engagement Activity | 2021 |
URL | https://uk.radio.net/s/cheshiresoundsradio |
Description | panellist Queen Baton Relay event on women in STEMM |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Third sector organisations |
Results and Impact | UK-India Women in STEMM' organised by the British High Commission in India as part of the Queen's Baton Relay and build-up to the Commonwealth games |
Year(s) Of Engagement Activity | 2022 |