Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs
Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision‐making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technologi...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-07-01
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| Series: | Environmental DNA |
| Online Access: | https://doi.org/10.1002/edn3.430 |
| _version_ | 1797770513839292416 |
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| author | Florian Altermatt Luca Carraro Manuel Antonetti Camille Albouy Yan Zhang Arnaud Lyet Xiaowei Zhang Loïc Pellissier |
| author_facet | Florian Altermatt Luca Carraro Manuel Antonetti Camille Albouy Yan Zhang Arnaud Lyet Xiaowei Zhang Loïc Pellissier |
| author_sort | Florian Altermatt |
| collection | DOAJ |
| description | Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision‐making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and efficient recovery of biodiversity signals, but the rapid pace of technological development has meant that some important principles regarding sampling design, which are well established in traditional biodiversity inventories, have been neglected. Using a spatially explicit river flow model, we illustrate how sampling must be adjusted to the size of the watercourse to increase the quality of the biodiversity signal recovered. We additionally investigate the effect of sampling parameters (volume, number of sites, sequencing depth) on detection probability in an empirical data set. Based on traditional sampling principles, we propose that aquatic eDNA sampling replication and volume must be scaled to match the organisms' and ecosystems' properties to provide reliable biodiversity estimates. We present a generalizable conceptual equation describing sampling features as a function of the size of the ecosystem monitored, the abundance of target organisms, and the properties of the sequencing procedure. The aim of this formalization is to enhance the standardization of critical steps in the design of biodiversity inventory studies using eDNA. More robust sampling standards will generate more comparable biodiversity data from eDNA, which is necessary for the method's long‐term plausibility and comparability. |
| first_indexed | 2024-03-12T21:24:22Z |
| format | Article |
| id | doaj.art-2071e9837765460699c03b5bf8387f39 |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-03-12T21:24:22Z |
| publishDate | 2023-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-2071e9837765460699c03b5bf8387f392023-07-28T10:02:53ZengWileyEnvironmental DNA2637-49432023-07-015467168210.1002/edn3.430Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designsFlorian Altermatt0Luca Carraro1Manuel Antonetti2Camille Albouy3Yan Zhang4Arnaud Lyet5Xiaowei Zhang6Loïc Pellissier7Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich SwitzerlandDepartment of Evolutionary Biology and Environmental Studies University of Zürich Zürich SwitzerlandZHAW School of Life Sciences and Facility Management Institute of Natural Resource Sciences Wädenswil SwitzerlandEcosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science ETH Zürich Zürich SwitzerlandState Key Laboratory of Pollution Control & Resource Reuse, School of the Environment Nanjing University Nanjing ChinaWorld Wildlife Fund, Wildlife Conservation Team District of Columbia Washington USAState Key Laboratory of Pollution Control & Resource Reuse, School of the Environment Nanjing University Nanjing ChinaEcosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science ETH Zürich Zürich SwitzerlandAbstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision‐making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and efficient recovery of biodiversity signals, but the rapid pace of technological development has meant that some important principles regarding sampling design, which are well established in traditional biodiversity inventories, have been neglected. Using a spatially explicit river flow model, we illustrate how sampling must be adjusted to the size of the watercourse to increase the quality of the biodiversity signal recovered. We additionally investigate the effect of sampling parameters (volume, number of sites, sequencing depth) on detection probability in an empirical data set. Based on traditional sampling principles, we propose that aquatic eDNA sampling replication and volume must be scaled to match the organisms' and ecosystems' properties to provide reliable biodiversity estimates. We present a generalizable conceptual equation describing sampling features as a function of the size of the ecosystem monitored, the abundance of target organisms, and the properties of the sequencing procedure. The aim of this formalization is to enhance the standardization of critical steps in the design of biodiversity inventory studies using eDNA. More robust sampling standards will generate more comparable biodiversity data from eDNA, which is necessary for the method's long‐term plausibility and comparability.https://doi.org/10.1002/edn3.430 |
| spellingShingle | Florian Altermatt Luca Carraro Manuel Antonetti Camille Albouy Yan Zhang Arnaud Lyet Xiaowei Zhang Loïc Pellissier Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs Environmental DNA |
| title | Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs |
| title_full | Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs |
| title_fullStr | Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs |
| title_full_unstemmed | Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs |
| title_short | Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs |
| title_sort | quantifying biodiversity using edna from water bodies general principles and recommendations for sampling designs |
| url | https://doi.org/10.1002/edn3.430 |
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