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Cook LSJ, Briscoe AG, Fonseca VG, Boenigk J, Woodward G, Bass D. Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment. Trends Microbiol 2025; 33:48-65. [PMID: 39164135 DOI: 10.1016/j.tim.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 08/22/2024]
Abstract
Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.
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Affiliation(s)
- Lauren S J Cook
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Andrew G Briscoe
- Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; NatureMetrics, Surrey Research Park, Guildford GU2 7HJ, UK
| | - Vera G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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Guerin AJ, Weise AM, Chu JWF, Wilcox MA, Greene ES, Therriault TW. High-resolution freshwater dissolved calcium and pH data layers for Canada and the United States. Sci Data 2024; 11:370. [PMID: 38605078 PMCID: PMC11009242 DOI: 10.1038/s41597-024-03165-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Freshwater ecosystems are biologically important habitats that provide many ecosystem services. Calcium concentration and pH are two key variables that are linked to multiple chemical processes in these environments, influence the biology of organisms from diverse taxa, and can be important factors affecting the distribution of native and non-native species. However, it can be challenging to obtain high-resolution data for these variables at regional and national scales. To address this data gap, water quality data for lakes and rivers in Canada and the continental USA were compiled and used to generate high-resolution (10 × 10 km) interpolated raster layers, after comparing multiple spatial interpolation approaches. This is the first time that such data have been made available at this scale and resolution, providing a valuable resource for research, including projects evaluating risks from environmental change, pollution, and invasive species. This will aid the development of conservation and management strategies for these vital habitats.
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Affiliation(s)
- Andrew J Guerin
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, 850 route de la mer, PO Box 1000, Mont Joli, Quebec, G5H 3Z4, Canada.
| | - Andréa M Weise
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, 850 route de la mer, PO Box 1000, Mont Joli, Quebec, G5H 3Z4, Canada.
| | - Jackson W F Chu
- Pacific Science Enterprise Centre, Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, British Columbia, V7V 1N6, Canada
| | - Mark A Wilcox
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Erin Sowerby Greene
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada
| | - Thomas W Therriault
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, British Columbia, V9T 6N7, Canada
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Liu L, Dobson B, Mijic A. Water quality management at a critical checkpoint by coordinated multi-catchment urban-rural load allocation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 340:117979. [PMID: 37094387 DOI: 10.1016/j.jenvman.2023.117979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/01/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Improving river water quality at critical checkpoints, defined as locations with significant impacts on water use, to satisfy regulation standards is an important goal of sustainable catchment management. Challenges remain in investigating pollution hotspots, designing efficient target reduction, and evaluating management performance. To address these challenges, we develop a systems approach for water quality management that integrates natural physical processes with human activities and their environmental impacts. In this approach, we firstly expand the concepts of headroom (amount under a permitted value) and excess (amount exceeding a permit) onto the source, spatial, and temporal domains for water quality management. We evaluate system-wide pollution contributions by simulating physical processes in a semi-distributed integrated representation using the CatchWat-SD model. We apply the model to the Upper Thames River basin and validate it using available monitoring data. We then incorporate the evaluated headroom-excess into a coordinated load allocation to enhance the efficiency and feasibility of interventions. Load allocation scenarios where headroom-excess is coordinated at different domains are generated and simulated. Finally, we evaluate the performance of these scenarios using multi-criteria metrics to demonstrate the advantages of headroom-excess coordination. Results show that urban sources, downstream sub-catchments, and dry season flows are associated with excess, thus, enabling managers to identify which cases (pollution sources, locations, and times) to focus load reductions towards. The more a load allocation strategy coordinates headroom-excess across domains, the more target reduction is allocated to the cases with excess, and the better performance it obtains in all the criteria. The study emphasises the need to incorporate headroom-excess in load allocation, which helps to improve systems-level water quality performance more efficiently. The approach can be further expanded to water quality management at multiple checkpoints for sustainable management of regional water systems.
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Affiliation(s)
- Leyang Liu
- Department of Civil and Environmental Engineering, Imperial College London, London, UK.
| | - Barnaby Dobson
- Department of Civil and Environmental Engineering, Imperial College London, London, UK
| | - Ana Mijic
- Department of Civil and Environmental Engineering, Imperial College London, London, UK
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Liu L, Dobson B, Mijic A. Optimisation of urban-rural nature-based solutions for integrated catchment water management. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 329:117045. [PMID: 36549055 DOI: 10.1016/j.jenvman.2022.117045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/22/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Nature-based solutions (NBS) have co-benefits for water availability, water quality, and flood management. However, searching for optimal integrated urban-rural NBS planning to maximise co-benefits at a catchment scale is still limited by fragmented evaluation. This study develops an integrated urban-rural NBS planning optimisation framework based on the CatchWat-SD model, which is developed to simulate a multi-catchment integrated water cycle in the Norfolk region, UK. Three rural (runoff attenuation features, regenerative farming, floodplain) and two urban (urban green space, constructed wastewater wetlands) NBS interventions are integrated into the model at a range of implementation scales. A many-objective optimisation problem with seven water management objectives to account for flow, quality and cost indicators is formulated, and the NSGAII algorithm is adopted to search for optimal NBS portfolios. Results show that rural NBS have more significant impacts across the catchment, which increase with the scale of implementation. Integrated urban-rural NBS planning can improve water availability, water quality, and flood management simultaneously, though trade-offs exist between different objectives. Runoff attenuation features and floodplains provide the greatest benefits for water availability. Regenerative farming is most effective for water quality and flood management, though it decreases water availability by up to 15% because it retains more water in the soil. Phosphorus levels are best reduced by expansion of urban green space to decrease loading on combined sewer systems, though this trades off against water availability, flood, nitrogen and suspended solids. The proposed framework enables spatial prioritisation of NBS, which may ultimately guide multi-stakeholder decision-making, bridging the urban-rural divide in catchment water management.
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Affiliation(s)
- Leyang Liu
- Department of Civil and Environmental Engineering, Imperial College London, London, United Kingdom.
| | - Barnaby Dobson
- Department of Civil and Environmental Engineering, Imperial College London, London, United Kingdom
| | - Ana Mijic
- Department of Civil and Environmental Engineering, Imperial College London, London, United Kingdom
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