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Blackman RC, Carraro L, Keck F, Altermatt F. Measuring the state of aquatic environments using eDNA-upscaling spatial resolution of biotic indices. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230121. [PMID: 38705183 PMCID: PMC11070250 DOI: 10.1098/rstb.2023.0121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/10/2023] [Indexed: 05/07/2024] Open
Abstract
Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Rosetta C. Blackman
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
| | - Luca Carraro
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
| | - François Keck
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, Zürich 8057, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf 8600, Switzerland
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McIntosh AR, Greig HS, Warburton HJ, Tonkin JD, Febria CM. Ecosystem-size relationships of river populations and communities. Trends Ecol Evol 2024; 39:571-584. [PMID: 38388323 DOI: 10.1016/j.tree.2024.01.010] [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: 08/02/2023] [Revised: 12/05/2023] [Accepted: 01/25/2024] [Indexed: 02/24/2024]
Abstract
Knowledge of ecosystem-size influences on river populations and communities is integral to the balancing of human and environmental needs for water. The multiple dimensions of dendritic river networks complicate understanding of ecosystem-size influences, but could be resolved by the development of scaling relationships. We highlight the importance of physical constraints limiting predator body sizes, movements, and population sizes in small rivers, and where river contraction limits space or creates stressful conditions affecting community stability and food webs. Investigations of the scaling and contingency of these processes will be insightful because of the underlying generality and scale independence of such relationships. Doing so will also pinpoint damaging water-management practices and identify which aspects of river size can be most usefully manipulated in river restoration.
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Affiliation(s)
- Angus R McIntosh
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
| | - Hamish S Greig
- School of Biology and Ecology, University of Maine, Orono, ME, USA; Rocky Mountain Biological Laboratory, Gothic, CO, USA
| | - Helen J Warburton
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; New Zealand's Biological Heritage National Science Challenge, Lincoln, New Zealand
| | - Jonathan D Tonkin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Te Pūnaha Matatini Centre of Research Excellence, University of Canterbury, Christchurch, New Zealand; Bioprotection Aotearoa Centre of Research Excellence, University of Canterbury, Christchurch, New Zealand
| | - Catherine M Febria
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada
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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [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: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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