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Li M, Cheng X, Li S, Li B, Ma L, Chen X. Human activities strengthen the influence of deterministic processes in the mechanisms of fish community assembly in tropical rivers of Yunnan, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122131. [PMID: 39121627 DOI: 10.1016/j.jenvman.2024.122131] [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: 12/21/2023] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Human-induced global alterations have worsened the severe decrease in fish biodiversity in rivers. To successfully reduce the pace of reduction in fish diversity, it is crucial to prioritize the understanding of how human activities impact the processes that shape and maintain fish diversity. Traditional fish survey methods are based on catch collection and morphological identification, which is often time-consuming and ineffective. Hence, these methods are inadequate for conducting thorough and detailed large-scale surveys of fish ecology. The rapid progress in molecular biology techniques has transformed environmental DNA (eDNA) technique into a highly promising method for studying fish ecology. In this work, we conducted the first systematic study of fish diversity and its formation and maintenance mechanism in the Xishuangbanna section of the Lancang River using eDNA metabarcoding. The eDNA metabarcoding detected a total of 159 species of freshwater fishes spanning 13 orders, 34 families, and 99 genera. The fishes in the order cypriniformes were shown to be overwhelmingly dominant. At different intensities of anthropogenic activity, we found differences in fish community composition and assembly. The analysis of the Sloan's neutral community model fitting revealed that stochastic processes were the dominant factor in the shaping of fish communities in the Xishuangbanna section of the Lancang River. We have further confirmed this result by using the phylogenetic normalized stochasticity ratio. Furthermore, our findings indicate that as human activities get more intense, the influence of stochastic processes on the shaping of fish communities decreases, while the influence of deterministic processes eventually becomes more prominent. Finally, we discovered that salinity positively correlated with fish community changes in the high-intensity anthropogenic sample sites, but all environmental factors had little effect on fish community changes in the low-intensity and moderate-intensity anthropogenic sample sites. Our study not only validated the potential application of eDNA metabarcoding for monitoring fish diversity in tropical rivers, but also revealed how fish communities respond to human activities. This knowledge will serve as a solid foundation for the protection of fish resources in tropical rivers.
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Affiliation(s)
- Miao Li
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Naypyitaw 05282, Myanmar; Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation, Mengla, 666303, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaopeng Cheng
- Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Bo Li
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Naypyitaw 05282, Myanmar; Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation, Mengla, 666303, China
| | - Li Ma
- Cave Fish Development and Evolution Research Group, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xiaoyong Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Naypyitaw 05282, Myanmar; Yunnan International Joint Laboratory of Southeast Asia Biodiversity Conservation, Mengla, 666303, China.
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Li Z, Zhao W, Jiang Y, Wen Y, Li M, Liu L, Zou K. New insights into biologic interpretation of bioinformatic pipelines for fish eDNA metabarcoding: A case study in Pearl River estuary. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122136. [PMID: 39128344 DOI: 10.1016/j.jenvman.2024.122136] [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: 01/26/2024] [Revised: 05/31/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Environmental DNA (eDNA) metabarcoding is an emerging tool for monitoring biological communities in aquatic ecosystems. The selection of bioinformatic pipelines significantly impacts the results of biodiversity assessments. However, there is currently no consensus on the appropriate bioinformatic pipelines for fish community analysis in eDNA metabarcoding. In this study, we compared three bioinformatic pipelines (Uparse, DADA2, and UNOISE3) using real and mock (constructed with 15/30 known fish) communities to investigate the differences in biological interpretation during the data analysis process in eDNA metabarcoding. Performance evaluation and diversity analyses revealed that the choice of bioinformatic pipeline could impact the biological results of metabarcoding experiments. Among the three pipelines, the operational taxonomic units (OTU)-based pipeline (Uparse) showed the best performance (sensitivity: 0.6250 ± 0.0166; compositional similarity: 0.4000 ± 0.0571), the highest richness (25-102) and minimal inter-group differences in alpha diversity. It suggested the OTU-based pipeline possessed superior capability in fish diversity monitoring compared to ASV/ZOTU-based pipeline. Additionally, the Bray-Curtis distance matrix achieved the highest discriminative effect in the PCoA (43.3%-53.89%) and inter-group analysis (P < 0.01), indicating it was better at distinguishing compositional differences or specific genera of fish community at different sampling sites than other distance matrices. These findings provide new insights into fish community monitoring through eDNA metabarcoding in estuarine environments.
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Affiliation(s)
- Zhuoying Li
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Wencheng Zhao
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yun Jiang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yongjing Wen
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Min Li
- Key Laboratory for Sustainable Utilization of Open-sea Fishery, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
| | - Li Liu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China.
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Van Driessche C, Everts T, Neyrinck S, Halfmaerten D, Verschelde P, Breine J, Bonte D, Brys R. Environmental DNA metabarcoding reflects spatiotemporal fish community shifts in the Scheldt estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173242. [PMID: 38763188 DOI: 10.1016/j.scitotenv.2024.173242] [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: 01/03/2024] [Revised: 03/28/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Estuarine ecosystems face increasing anthropogenic pressures, necessitating effective monitoring methods to mitigate their impacts on the biodiversity they harbour. The use of environmental DNA (eDNA) based detection methods is increasingly recognized as a promising tool to complement other, potentially invasive monitoring techniques. Integrating such eDNA analyses into monitoring frameworks for large ecosystems is still challenging and requires a deeper understanding of the scale and resolution at which eDNA patterns may offer insights in species presence and community composition space and time. The Scheldt estuary, characterized by its diverse habitats and complex currents, is one of the largest Western European tidal river systems. Until now, it remains challenging to obtain accurate information on fish communities living in and migrating through this ecosystem, consequently confining our knowledge to specific locations. To explore the potential of eDNA based monitoring, we simultaneously combine stow net fishing with eDNA metabarcoding, to assess spatiotemporal shifts in the Scheldt estuary's fish communities. In total, we detected 71 fish species in the estuary using eDNA metabarcoding, partly overlapping with historic fish community data gathered at the different study locations and in contrast to only 42 species using stow net fishing during the same survey period. Community compositions found by both detection methods varied among sampling locations, driven by a clear correlation to the salinity gradient. Limited effects of sampling depth and tide were observed on the eDNA metabarcoding data, allowing a significant reduction of the eDNA sampling effort for future eDNA fish monitoring campaigns in this study system. Our results further demonstrate that seasonal shifts in fish species occurrence can be detected using eDNA metabarcoding. Combining eDNA metabarcoding and stow net fishing further enhances our understanding of this vital waterway's diverse fish populations, allowing a higher resolution and more efficient monitoring strategy.
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Affiliation(s)
- Charlotte Van Driessche
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium; Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium.
| | - Teun Everts
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium; KU Leuven, Department of Biology, Plant Conservation and Population Biology, Leuven, Belgium
| | - Sabrina Neyrinck
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - David Halfmaerten
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Pieter Verschelde
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Jan Breine
- Research Institute for Nature and Forest (INBO), Linkebeek, Belgium
| | - Dries Bonte
- Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium
| | - Rein Brys
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
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Wang C, Ma Z, Cao K, Wang X, Xi R, Jiang T, Yang R, Xing Y. Species diversity of fish at the Wuzhizhou Island, South China Sea, based on environmental DNA. Biodivers Data J 2024; 12:e127120. [PMID: 38912114 PMCID: PMC11193053 DOI: 10.3897/bdj.12.e127120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
Background Wuzhizhou Island (WZZ) is located in Haitang Bay in the northern region of Sanya, Hainan Island. The sea area surrounding WZZ represents a typical tropical marine ecosystem, characterised by diverse and complex habitats. Therefore, there is a rich variety of marine fish species at WZZ. The marine ecosystem of WZZ was seriously destroyed initially in the 1970s-1980s and recovered in the 1990s, then constructed as the first national tropical marine ranch demonstration area of China in 2019. As fish is an important high trophic vertebrate in the marine ecosystem, understanding the composition and distribution of fish species could help us to recognise the status of the ecosystem of WZZ and supply scientific data for construction of the national marine ranch demonstration area. This study used eDNA technology to investigate the composition of fish community surrounding WZZ and provided a scientific basis for realising and protecting the marine ecosystem of the South China Sea. New information The WZZ is an offshore island in the South China Sea, harbouring abundant marine fish resources. Although previous research investigated fish species of WZZ, the data were, however, still incomplete due to limitation of sampling methods and survey seasons. In this study, we intended to take advantage of eDNA and supplement data of fish species at WZZ as much as possible. Based on eDNA, this study provided the data on 188 fish species (including nine undetermined species denoted by genus sp.) belonging to 17 orders, 63 families and 124 genera and they were the more comprehensive records of fish species surrounding WZZ. In addition, the information on Molecular Operational Taxonomic Units (MOTUs) for taxon identification was also provided, aiming to contribute to the establishment of a specific eDNA taxon database for fish of the South China Sea. This study included two datasets, which were occurrences of fish taxa at WZZ, as well as MOTUs sequences and geographical coordinate information of sampling sites. The "fish taxon occurrences" dataset presented records on taxonomic, distribution and habitat conditions of 188 fish species detected using eDNA, as well as the latitude and longitude information of the sampling sites, the "MOTUs information" dataset provided the MOTUs sequences, source of sequences, abundance of sequences for 188 fish species, also included the species matched in NCBI and the best NCBI BLAST sequence similarity.
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Affiliation(s)
- Chongzhao Wang
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572024, ChinaHainan Fisheries Innovation Research Institute, Chinese Academy of Fishery SciencesSanya 572024China
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityShanghai 201306China
| | - Zhenhua Ma
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, ChinaTropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesSanya 572018China
| | - Kun Cao
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572024, ChinaHainan Fisheries Innovation Research Institute, Chinese Academy of Fishery SciencesSanya 572024China
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
| | - Xin Wang
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityShanghai 201306China
| | - Rui Xi
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityShanghai 201306China
| | - Ting Jiang
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityShanghai 201306China
| | - Rui Yang
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
- Tropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Sanya 572018, ChinaTropical Aquaculture Research and Development Center, South China Sea Fisheries Research Institute, Chinese Academy of Fishery SciencesSanya 572018China
| | - Yingchun Xing
- Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572024, ChinaHainan Fisheries Innovation Research Institute, Chinese Academy of Fishery SciencesSanya 572024China
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
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5
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Cheng R, Zhou X, Zhang Y, Li Q, Zhang J, Luo Y, Chen Q, Liu Z, Li Y, Shen Y. eDNA reveals spatial homogenization of fish diversity in a mountain river affected by a reservoir cascade. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 361:121248. [PMID: 38820798 DOI: 10.1016/j.jenvman.2024.121248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 05/05/2024] [Accepted: 05/25/2024] [Indexed: 06/02/2024]
Abstract
One of the main reasons for the decline in global freshwater biodiversity can be attributed to alterations in hydrological conditions resulting from dam construction. However, the majority of current research has focused on single or limited numbers of dams. Here, we carried out a seasonal fish survey, using environmental DNA (eDNA) method, on the Wujiang River mainstream (Tributaries of the Yangtze River, China) to investigate the impact of large-scale cascade hydropower development on changes in fish diversity patterns. eDNA survey revealed that native fish species have decreased in contrast to alien fish. There was also a shift in fish community structure, with declines of the dominant rheophilic fish species, an increase of the small-size fish species, and homogenization of species composition across reservoirs. Additionally, environmental factors, such as temperature, dissolved oxygen and reservoir age, had a significant effect on fish community diversity. This study provides basic information for the evaluation of the impact of cascade developments on fish diversity patterns.
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Affiliation(s)
- Ruli Cheng
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Xinxin Zhou
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yufeng Zhang
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Qinghua Li
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Jiaming Zhang
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yang Luo
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Qiliang Chen
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Zhihao Liu
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yingwen Li
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China
| | - Yanjun Shen
- Laboratory of Water Ecological Health and Environmental Safety, Chongqing Key Laboratory of Conservation and Utilization of Freshwater Fishes, Animal Biology Key Laboratory of Chongqing Education Commission, Chongqing Normal University, Chongqing, 401331, China.
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6
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Perry WB, Seymour M, Orsini L, Jâms IB, Milner N, Edwards F, Harvey R, de Bruyn M, Bista I, Walsh K, Emmett B, Blackman R, Altermatt F, Lawson Handley L, Mächler E, Deiner K, Bik HM, Carvalho G, Colbourne J, Cosby BJ, Durance I, Creer S. An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding. Nat Commun 2024; 15:4372. [PMID: 38782932 PMCID: PMC11116482 DOI: 10.1038/s41467-024-48640-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20-35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
- Water Research Institute, Cardiff University, Cardiff, CF10 3AX, UK.
| | | | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ifan Bryn Jâms
- Water Research Institute, Cardiff University, Cardiff, CF10 3AX, UK
| | - Nigel Milner
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - François Edwards
- APEM Ltd, A17 Embankment Business Park, Heaton Mersey, Manchester, SK4 3GN, UK
| | - Rachel Harvey
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor, LL57 2UW, UK
| | - Mark de Bruyn
- Australian Research Centre for Human Evolution, School of Environment and Science, Griffith University, Queensland, 4111, Australia
| | - Iliana Bista
- LOEWE Centre for Translational Biodiversity Genomics, 60325, Frankfurt, Germany
- Senckenberg Research Institute, 60325, Frankfurt, Germany
- Naturalis Biodiversity Center, Darwinweg 2, 2333, Leiden, Netherlands
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kerry Walsh
- Environment Agency, Horizon House, Deanery Road, Bristol, BS1 5AH, UK
| | - Bridget Emmett
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor, LL57 2UW, UK
| | - Rosetta Blackman
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Evolutionary Biology Group (@EvoHull), Department of Biological and Marine Sciences, University of Hull (UoH), Cottingham Road, Hull, HU6 7RX, UK
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Lori Lawson Handley
- Evolutionary Biology Group (@EvoHull), Department of Biological and Marine Sciences, University of Hull (UoH), Cottingham Road, Hull, HU6 7RX, UK
| | - Elvira Mächler
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Kristy Deiner
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zurich, Zurich, Switzerland
| | - Holly M Bik
- Department of Marine Sciences and Institute of Bioinformatics, University of Georgia, Georgia, USA
| | - Gary Carvalho
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - John Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Bernard Jack Cosby
- Centre for Ecology & Hydrology, Environment Centre Wales, Bangor, LL57 2UW, UK
| | - Isabelle Durance
- Water Research Institute, Cardiff University, Cardiff, CF10 3AX, UK
| | - Simon Creer
- Molecular Ecology and Evolution at Bangor (MEEB), School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
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7
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Jaquier M, Albouy C, Bach W, Waldock C, Marques V, Maire E, Juhel JB, Andrello M, Valentini A, Manel S, Dejean T, Mouillot D, Pellissier L. Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands. Ecol Evol 2024; 14:e11337. [PMID: 38766310 PMCID: PMC11099785 DOI: 10.1002/ece3.11337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/23/2024] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
Islands have been used as model systems to study ecological and evolutionary processes, and they provide an ideal set-up for validating new biodiversity monitoring methods. The application of environmental DNA metabarcoding for monitoring marine biodiversity requires an understanding of the spatial scale of the eDNA signal, which is best tested in island systems. Here, we investigated the variation in Actinopterygii and Elasmobranchii species composition recovered from eDNA metabarcoding along a gradient of distance-to-reef in four of the five French Scattered Islands in the Western Indian Ocean. We collected surface water samples at an increasing distance from reefs (0 m, 250 m, 500 m, 750 m). We used a metabarcoding protocol based on the 'teleo' primers to target marine reef fishes and classified taxa according to their habitat types (benthic or pelagic). We investigated the effect of distance-to-reef on β diversity variation using generalised linear mixed models and estimated species-specific distance-to-reef effects using a model-based approach for community data. Environmental DNA metabarcoding analyses recovered distinct fish species compositions across the four inventoried islands and variations along the distance-to-reef gradient. The analysis of β-diversity variation showed significant taxa turnover between the eDNA samples on and away from the reefs. In agreement with a spatially localised signal from eDNA, benthic species were distributed closer to the reef than pelagic ones. Our findings demonstrate that the combination of eDNA inventories and spatial modelling can provide insights into species habitat preferences related to distance-to-reef gradients at a small scale. As such, eDNA can not only recover large compositional differences among islands but also help understand habitat selection and distribution of marine species at a finer spatial scale.
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Affiliation(s)
- Mélissa Jaquier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Camille Albouy
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Wilhelmine Bach
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Conor Waldock
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Virginie Marques
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
- CEFE, Univ. Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | - Eva Maire
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
- Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Marco Andrello
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | | | - Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
| | | | - David Mouillot
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRDMontpellierFrance
- Institut Universitaire de FranceParisFrance
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
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8
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Nakai M, Masumoto T, Asaeda T, Rahman M. Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA. PLoS One 2024; 19:e0301197. [PMID: 38557776 PMCID: PMC10984549 DOI: 10.1371/journal.pone.0301197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.
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Affiliation(s)
- Masahiko Nakai
- Japan International Consultants for Transportation Co., Ltd, Tokyo, Japan
| | - Taku Masumoto
- Energy Planning Department, East Japan Railway Company, Tokyo, Japan
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9
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Jiang W, Guo M, Yu J, Fan C, Yang M, Pang X. Variations of the fungal microbiome in Corydalis Rhizoma with different collection areas, processing methods, and storage conditions. Food Res Int 2024; 180:114045. [PMID: 38395573 DOI: 10.1016/j.foodres.2024.114045] [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: 11/19/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Corydalis Rhizoma (CR, Yanhusuo in Chinese) has been widely used as an analgesic in herbal medicine and functional food. Cases of fungal and mycotoxin contamination in CR have been reported. In this study, the composition and diversity of fungal microbiome in CR samples from four herbal markets and two processing methods were investigated by DNA metabarcoding. Variations of the fungal microbiome in CR during cold and conventional storage were monitored. Results showed that Aspergillus was the dominant genus and saprotroph was the dominant trophic mode. Six potential toxigenic fungi, namely, Aspergillus fumigatus, Aspergillus ostianus, Aspergillus terreus, Penicillium citrinum, Penicillium oxalicum, and Trichothecium roseum, were detected. Differences in fungal composition and diversity among various groups based on collection areas and processing methods were also observed. Moreover, the relative abundance of dominant genera in CR samples stored at different temperatures was significantly different and changed with storage time. This study is the first to reveal the influence of collection areas, processing methods, and storage conditions on the fungal microbiome in CR, which was expected to provide a basis for control strategies of fungal contamination in the industrial chain of CR.
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Affiliation(s)
- Wenjun Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Mengyue Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jingsheng Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Chune Fan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Meihua Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xiaohui Pang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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10
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Li Z, Li F, Qin S, Guo F, Wang S, Zhang Y. Environmental DNA biomonitoring reveals the human impacts on native and non-native fish communities in subtropical river systems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119595. [PMID: 37979384 DOI: 10.1016/j.jenvman.2023.119595] [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: 07/30/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023]
Abstract
Subtropical rivers are one of the hotspots of global biodiversity, facing increased risks of fish diversity changes and species extinction. However, until now, human impacts on native and non-native fish communities in subtropical rivers still lack sufficient effort. Here, we used the environmental DNA (eDNA) approach to investigate fish communities in the Dongjiang River of southeast China, a typical subtropical river, and explored the effects of regional land use and local water pollution on fish taxonomic and functional diversity. Our data showed that 90 species or genera of native fish and 15 species or genera of non-native fish were detected by the eDNA approach, and there was over 85% overlap between eDNA datasets and historical records. The taxonomic and functional diversity of all, native and non-native fish communities showed consistent spatial patterns, that is, the upstream of the tributary was significantly higher than that of the mainstream and downstream. Land use and water pollution such as COD and TP were the determinants in shaping the spatial structure of fish communities, and water pollution explained 31.56%, 29.88%, and 27.80% of the structural variation in all, native and non-native fish communities, respectively. The Shannon diversity and functional richness of native fish showed a significant downward trend driven by COD (pShannon = 0.0374; pfunctional = 0.0215) and land use (pShannon = 0.0159; pfunctional = 0.0441), but they did not have significant impacts on non-native fish communities. Overall, this study emphasizes the inconsistent response of native and non-native fish communities to human impacts in subtropical rivers, and managers need to develop strategies tailored to specific fish species to effectively protect water security and rivers.
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Affiliation(s)
- Zhen Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Feilong Li
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Shan Qin
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Fen Guo
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yuan Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China
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11
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Duarte S, Simões L, Costa FO. Current status and topical issues on the use of eDNA-based targeted detection of rare animal species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166675. [PMID: 37647964 DOI: 10.1016/j.scitotenv.2023.166675] [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: 06/13/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luara Simões
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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12
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Allan EA, Kelly RP, D'Agnese ER, Garber-Yonts MN, Shaffer MR, Gold ZJ, Shelton AO. Quantifying impacts of an environmental intervention using environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2914. [PMID: 37641194 DOI: 10.1002/eap.2914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/12/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023]
Abstract
Environmental laws around the world require some version of an environmental-impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon-sequencing-also called metabarcoding-of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental-impact analysis for development projects. Here, we analyze an 18-month time series of water samples taken before, during, and after two culvert removals in a salmonid-bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species-specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court-mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental-impact reporting using eDNA that is widely applicable in environments worldwide.
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Affiliation(s)
| | - Ryan P Kelly
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Erin R D'Agnese
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Maya N Garber-Yonts
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Megan R Shaffer
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Zachary J Gold
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Andrew O Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
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13
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Lines R, Juggernauth M, Peverley G, Keating J, Simpson T, Mousavi-Derazmahalleh M, Bunce M, Berry TE, Taysom A, Bernardino AF, Whittle P. A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106239. [PMID: 37926039 DOI: 10.1016/j.marenvres.2023.106239] [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: 07/01/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
Seawater contains a wealth of genetic information, representing the biodiversity of numerous species residing within a particular marine habitat. Environmental DNA (eDNA) metabarcoding offers a cost effective, non-destructive method for large scale monitoring of environments, as diverse taxonomic groups are detected using metabarcoding assays. A large-scale eDNA monitoring program of marine vertebrates was conducted across three sampling seasons (Spring 2018, Autumn 2019; Spring 2019) in coastal waters of Brazil. The program was designed to investigate eDNA as a testing method for long term monitoring of marine vertebrates following the Fundão tailings dam failure in November 2015. While no baseline samples were available prior to the dam failure there is still value in profiling the taxa that use the impacted area and the trajectory of recovery. A total of 40 sites were sampled around the mouths of eight river systems, covering approximately 500 km of coastline. Metabarcoding assays targeting the mitochondrial genes 16S rRNA and COI were used to detect fish, marine mammals and elasmobranchs. We detected temporal differences between seasons and spatial differences between rivers/estuaries sampled. Overall, the largest eDNA survey in Brazil to date revealed 69 families from Class Actinopterygii (fish), 15 species from Class Chondrichthyes (sharks and rays), 4 species of marine and estuarine mammals and 23 species of conservation significance including 2 species of endangered dolphin. Our large-scale study reinforces the value eDNA metabarcoding can bring when monitoring the biodiversity of coastal environments and demonstrates the importance of collection of time-stamped environmental samples to better understand the impacts of anthropogenic activities.
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Affiliation(s)
- Rose Lines
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia.
| | | | - Georgia Peverley
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia
| | | | - Tiffany Simpson
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Mahsa Mousavi-Derazmahalleh
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Michael Bunce
- Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Tina E Berry
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia
| | | | - Angelo F Bernardino
- Grupo de Ecologia Bentônica, Universidade Federal do Espirito Santo, Vitória, ES, Brazil
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14
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Corral-Lou A, Doadrio I. Environmental DNA metabarcoding of water samples as a tool for monitoring Iberian freshwater fish composition. PLoS One 2023; 18:e0283088. [PMID: 37903086 PMCID: PMC10615313 DOI: 10.1371/journal.pone.0283088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/01/2023] [Indexed: 11/01/2023] Open
Abstract
Environmental DNA (eDNA) metabarcoding has been increasingly used to monitor the community assemblages of a wide variety of organisms. Here, we test the efficacy of eDNA metabarcoding to assess the composition of Iberian freshwater fishes, one of the most endangered groups of vertebrates in Spain. For this purpose, we sampled 12 sampling sites throughout one of Spain's largest basins, the Duero, which is home to approximately 70% of the genera and 30% of the primary freshwater fish in Spain. We sampled these sampling sites in the summer by using electrofishing, a traditional sampling method, and eDNA metabarcoding of river water samples using the mitochondrial 12S rRNA gene (12S) as a marker. We also resampled four of these sampling sites in autumn by eDNA. We compared the results obtained through eDNA metabarcoding with those of electrofishing surveys (ones conducted for the present study and past ones) and assessed the suitability of 12S as an eDNA metabarcoding marker for this group of freshwater fishes. We found that the 12S fragment, analysed for 25 Iberian species, showed sufficient taxonomic resolution to be useful for eDNA approaches, and even showed population-level differences in the studied populations across the tissue samples for Achondrostoma arcasii. In most cases, a greater number of species was detected through eDNA metabarcoding than through electrofishing. Based on our results, eDNA metabarcoding is a powerful tool to study the freshwater fish composition in the Iberian Peninsula and to unmask cryptic diversity. However, we highlight the need to generate a local genetic database for 12S gene for such studies and to interpret the results with caution when studying only mitochondrial DNA. Finally, our survey shows that the high detection sensitivity of eDNA metabarcoding and the non-invasiveness of this method allows it to act as a detection system for species of low abundance, such as early invasive species or species in population decline, two key aspects of conservation management of Spanish freshwater fishes.
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Affiliation(s)
- Andrea Corral-Lou
- Biodiversity and Evolutionary Biology Department, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, Madrid, Spain
- Consultores en Biología de la Conservación S.L., Daoiz, Madrid, Spain
| | - Ignacio Doadrio
- Biodiversity and Evolutionary Biology Department, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, Madrid, Spain
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15
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Teixeira DF, Hilário HO, Santos GB, Carvalho DC. DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent. Ecol Evol 2023; 13:e10649. [PMID: 37869433 PMCID: PMC10587807 DOI: 10.1002/ece3.10649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of ichthyoplankton is paramount to understanding fish assemblages' reproductive dynamics. DNA metabarcoding has been applied as a rapid, cost-effective, and accurate taxonomy tool, allowing the identification of multiple individuals simultaneously. However, there remain significant challenges when using DNA metabarcoding, such as molecular marker choice according to the taxonomic resolution and length of the fragment to be sequenced, primer bias, incomplete reference databases, and qualitative inference incongruences. Here, 30 ichthyoplankton pools collected from a Neotropical river were identified at a molecular level using DNA metabarcoding to compare the resolution, sensibility, specificity, and relative read abundance (RRA) recovery of three molecular markers: the standard COI fragment (650 pb, with each end analyzed individually) and two short 12S rRNA genes markers (≅200 bp - NeoFish and MiFish markers). The combined use of the three markers increased the genera detection rates by 25%-87.5%, allowing an increased taxonomic coverage and robust taxonomic identification of complex Neotropical ichthyoplankton communities. RRA is marker-dependent, indicating caution is still needed while inferring species abundance based on DNA metabarcoding data when using PCR-dependent protocols.
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Affiliation(s)
- Daniel Fonseca Teixeira
- Post‐Graduate Program in Vertebrate BiologyPontifical Catholic University of Minas Gerais, PUC MinasBelo HorizonteBrazil
- Post‐Graduate Program in GeneticsFederal University of Minas GeraisBelo HorizonteBrazil
| | - Heron Oliveira Hilário
- Post‐Graduate Program in Vertebrate BiologyPontifical Catholic University of Minas Gerais, PUC MinasBelo HorizonteBrazil
| | - Gilmar Bastos Santos
- Post‐Graduate Program in Vertebrate BiologyPontifical Catholic University of Minas Gerais, PUC MinasBelo HorizonteBrazil
| | - Daniel Cardoso Carvalho
- Post‐Graduate Program in Vertebrate BiologyPontifical Catholic University of Minas Gerais, PUC MinasBelo HorizonteBrazil
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16
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Zhang M, Zou Y, Xiao S, Hou J. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects. MARINE POLLUTION BULLETIN 2023; 194:115430. [PMID: 37647798 DOI: 10.1016/j.marpolbul.2023.115430] [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: 04/23/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.
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Affiliation(s)
- Miaolian Zhang
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yingtong Zou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Xiao
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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17
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Carvalho DC, Leal CG. Steps forward in biomonitoring 2.0: eDNA Metabarcoding and community-level modelling allow the assessment of complex drivers of Neotropical fish diversity. GLOBAL CHANGE BIOLOGY 2023; 29:1688-1690. [PMID: 36635221 DOI: 10.1111/gcb.16596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/19/2022] [Accepted: 01/08/2023] [Indexed: 05/28/2023]
Affiliation(s)
- Daniel C Carvalho
- Conservation Genetics Lab, Postgraduate Program in Vertebrate Biology, Pontifícal Catholic University of Minas Gerais (PUC Minas), Belo Horizonte, Brazil
| | - Cecília G Leal
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
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18
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Huang S, Yoshitake K, Watabe S, Asakawa S. Environmental DNA study on aquatic ecosystem monitoring and management: Recent advances and prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116310. [PMID: 36261997 DOI: 10.1016/j.jenvman.2022.116310] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Environmental DNA (eDNA) is organismal DNA that can be detected in the environment and is derived from cellular material of organisms shed into aquatic or terrestrial environments. It can be sampled and monitored using molecular methods, which is important for the early detection of invasive and native species as well as the discovery of rare and cryptic species. While few reviews have summarized the latest findings on eDNA for most aquatic animal categories in the aquatic ecosystem, especially for aquatic eDNA processing and application. In the present review, we first performed a bibliometric network analysis of eDNA studies on aquatic animals. Subsequently, we summarized the abiotic and biotic factors affecting aquatic eDNA occurrence. We also systematically discussed the relevant experiments and analyses of aquatic eDNA from various aquatic organisms, including fish, molluscans, crustaceans, amphibians, and reptiles. Subsequently, we discussed the major achievements of eDNA application in studies on the aquatic ecosystem and environment. The application of eDNA will provide an entirely new paradigm for biodiversity conservation, environment monitoring, and aquatic species management at a global scale.
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Affiliation(s)
- Songqian Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 200120, China; Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa, 252-0313, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan.
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19
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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20
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Xi R, Gao W, Wang X, Xing Y. Species diversity of coral reef fishes around the West Island of Sanya City, South China Sea, based on environmental DNA. Biodivers Data J 2022; 10:e89685. [PMID: 36761609 PMCID: PMC9836608 DOI: 10.3897/bdj.10.e89685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/27/2022] [Indexed: 11/12/2022] Open
Abstract
Background West Island is the second largest island in the Hainan Province, China and its surrounding sea area has a well-preserved coral reef ecosystem and high species diversity of coral reef fishes. Undoubtedly, coral reef fishes and coral reefs have complex symbiotic relationships and fish species diversity should reflect the healthy status of coral reef ecosystems. Environmental DNA (eDNA) is a useful and sensitive tool to detect fish species and causes less environmental damage than traditional fish survey methods. This paper investigated coral reef fish species of West Island, Hainan Province, China, based on eDNA and provided scientific data for understanding and protection of the coral reef ecosystem of the South China Sea. New information The sea area surrounding West Island is the most important component of the coral reef ecosystem in the northern part of the South China Sea, which is also an essential part of the largest National Coral Reef Reserve in China. However, complete data of fish species distributed in this region have been a long-term gap. This study provides information on 41 fish species belonging to 28 genera, 16 families and three orders in this sea area and is the first complete record of coral reef fishes surrounding the West Island. In addition, the information of Molecular Operational Taxonomic Units (MOTUs) for taxon identification were also provided and it could contribute to building specific eDNA taxonomy database of coral reef fishes of the South China Sea. The study includes three datasets, with aspects of fish taxon-occurrences, MOTUs sequences and information of environmental indicators surrounding West Island, Hainan Province, China. The "fish taxon occurrences" dataset presents records involving taxonomic, distribution, habitat condition, latitude and longitude of 41 coral reef fish species detected, based on eDNA, the "MOTUs sequences" dataset provides MOTUs sequences and their abundance of 31 species detected and the "information of environmental indicators" dataset presents records of transparency, temperature, water pressure, dissolved oxygen, electrical conductivity, hydrogen and redox potential measured from five sampling localities.
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Affiliation(s)
- Rui Xi
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityShanghai 201306China,Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
| | - Wanru Gao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityShanghai 201306China,Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
| | - Xin Wang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, ChinaNational Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean UniversityShanghai 201306China,Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China
| | - Yingchun Xing
- Resource and Environmental Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, ChinaResource and Environmental Research Center, Chinese Academy of Fishery SciencesBeijing 100141China,Hainan Fisheries Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572024, ChinaHainan Fisheries Innovation Research Institute, Chinese Academy of Fishery SciencesSanya 572024China
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21
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Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary. PLoS One 2022; 17:e0266720. [PMID: 35714082 PMCID: PMC9205523 DOI: 10.1371/journal.pone.0266720] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 03/26/2022] [Indexed: 12/21/2022] Open
Abstract
Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.
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22
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Pawlowski J, Bruce K, Panksep K, Aguirre FI, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa FO, Danovaro R, Dell'Anno A, Duarte S, Eisendle U, Ferrari BJD, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman JK, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151783. [PMID: 34801504 DOI: 10.1016/j.scitotenv.2021.151783] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/06/2021] [Accepted: 11/14/2021] [Indexed: 06/13/2023]
Abstract
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.
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Affiliation(s)
- J Pawlowski
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - K Bruce
- NatureMetrics Ltd, CABI Site, Bakeham Lane, Egham TW20 9TY, UK
| | - K Panksep
- Institute of Technology, University of Tartu, Tartu 50411, Estonia; Chair of Hydrobiology and Fishery, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia; Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Estonia
| | - F I Aguirre
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - S Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy
| | - L Apothéloz-Perret-Gentil
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Baussant
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Bouchez
- INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - L Carugati
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - K Cermakova
- ID-Gene Ecodiagnostics, 1202 Geneva, Switzerland
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland; NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | - C Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - F O Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - R Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - A Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, Ancona 60131, Italy
| | - S Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - U Eisendle
- University of Salzburg, Dept. of Biosciences, 5020 Salzburg, Austria
| | - B J D Ferrari
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - F Frontalini
- Department of Pure and Applied Sciences, Urbino University, Urbino, Italy
| | - L Frühe
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - A Haegerbaeumer
- Bielefeld University, Animal Ecology, 33615 Bielefeld, Germany
| | - V Kisand
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - A Krolicka
- Norwegian Research Center AS, NORCE Environment, Marine Ecology Group, Mekjarvik 12, 4070 Randaberg, Norway
| | - A Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - F Leese
- University of Duisburg-Essen, Faculty of Biology, Aquatic Ecosystem Research, Germany
| | - F Lejzerowicz
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - E Lyautey
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - I Maček
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - M Sagova-Marečková
- Czech University of Life Sciences, Dept. of Microbiology, Nutrition and Dietetics, Prague, Czech Republic
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - X Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand; Institute of Marine Science, University of Auckland, Warkworth 0941, New Zealand
| | - T Stoeck
- Technische Universität Kaiserslautern, Ecology Group, D-67663 Kaiserslautern, Germany
| | - R Vivien
- Swiss Centre for Applied Ecotoxicology (Ecotox Centre), EPFL ENAC IIE-GE, 1015 Lausanne, Switzerland
| | - A Weigand
- National Museum of Natural History Luxembourg, 25 Rue Münster, L-2160 Luxembourg, Luxembourg
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Monterotondo, Rome, Italy.
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23
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Mariac C, Duponchelle F, Miranda G, Ramallo C, Wallace R, Tarifa G, Garcia-Davila C, Ortega H, Pinto J, Renno JF. Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA. PLoS One 2022; 17:e0262357. [PMID: 34982802 PMCID: PMC8726463 DOI: 10.1371/journal.pone.0262357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
To date, more than 2400 valid fish species have been recorded in the Amazon basin. However, some regions remain poorly documented. This is the case in the Beni basin and in particular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlapping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species compositions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the different hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possible to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a baseline for future studies, including on other Andean tributaries.
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Affiliation(s)
- Cédric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- * E-mail:
| | - Fabrice Duponchelle
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Guido Miranda
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Camila Ramallo
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Robert Wallace
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Gabriel Tarifa
- Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia
| | - Carmen Garcia-Davila
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
- Instituto de Investigaciones de la Amazonía Peruana (IIAP), Laboratorio de Biología y Genética Molecular (LBGM), Iquitos, Perú
| | - Hernán Ortega
- Departamento de Ictiología, Museo de Historia Natural, Universidad Nacional Mayor San Marcos, Lima, Peru
| | - Julio Pinto
- Unidad de Limnología, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Jean-François Renno
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France
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24
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Broadhurst HA, Gregory LM, Bleakley EK, Perkins JC, Lavin JV, Bolton P, Browett SS, Howe CV, Singleton N, Tansley D, Sales NG, McDevitt AD. Mapping differences in mammalian distributions and diversity using environmental DNA from rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149724. [PMID: 34467903 DOI: 10.1016/j.scitotenv.2021.149724] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Finding more efficient ways to monitor and estimate the diversity of mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. Here, we first focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding two rivers in southeastern England. Community diversity and composition was then assessed based on species richness and β-diversity, with differences between communities partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. eDNA metabarcoding detected 25 wild mammal species from five orders, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorphs) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.
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Affiliation(s)
- Holly A Broadhurst
- School of Science, Engineering and Environment, University of Salford, UK
| | - Luke M Gregory
- School of Science, Engineering and Environment, University of Salford, UK
| | - Emma K Bleakley
- School of Science, Engineering and Environment, University of Salford, UK
| | - Joseph C Perkins
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenna V Lavin
- School of Science, Engineering and Environment, University of Salford, UK
| | - Polly Bolton
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, UK; School of Science and Computing, Waterford Institute of Technology, Waterford, Ireland
| | - Claire V Howe
- Natural England, Horizon House, Deanery Road, Bristol, UK
| | - Natalie Singleton
- Essex Wildlife Trust, Abbotts Hall Farm, Great Wigborough, Colchester, UK
| | - Darren Tansley
- Essex Wildlife Trust, Abbotts Hall Farm, Great Wigborough, Colchester, UK
| | | | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, UK.
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25
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Marques V, Castagné P, Polanco A, Borrero-Pérez GH, Hocdé R, Guérin PÉ, Juhel JB, Velez L, Loiseau N, Letessier TB, Bessudo S, Valentini A, Dejean T, Mouillot D, Pellissier L, Villéger S. Use of environmental DNA in assessment of fish functional and phylogenetic diversity. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1944-1956. [PMID: 34224158 DOI: 10.1111/cobi.13802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/19/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
Assessing the impact of global changes and protection effectiveness is a key step in monitoring marine fishes. Most traditional census methods are demanding or destructive. Nondisturbing and nonlethal approaches based on video and environmental DNA are alternatives to underwater visual census or fishing. However, their ability to detect multiple biodiversity factors beyond traditional taxonomic diversity is still unknown. For bony fishes and elasmobranchs, we compared the performance of eDNA metabarcoding and long-term remote video to assess species' phylogenetic and functional diversity. We used 10 eDNA samples from 30 L of water each and 25 hr of underwater videos over 4 days on Malpelo Island (pacific coast of Colombia), a remote marine protected area. Metabarcoding of eDNA detected 66% more molecular operational taxonomic units (MOTUs) than species on video. We found 66 and 43 functional entities with a single eDNA marker and videos, respectively, and higher functional richness for eDNA than videos. Despite gaps in genetic reference databases, eDNA also detected a higher fish phylogenetic diversity than videos; accumulation curves showed how 1 eDNA transect detected as much phylogenetic diversity as 25 hr of video. Environmental DNA metabarcoding can be used to affordably, efficiently, and accurately census biodiversity factors in marine systems. Although taxonomic assignments are still limited by species coverage in genetic reference databases, use of MOTUs highlights the potential of eDNA metabarcoding once reference databases have expanded.
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Affiliation(s)
- Virginie Marques
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valery Montpellier 3, Montpellier, France
| | - Paul Castagné
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Andréa Polanco
- Instituto de Investigaciones Marinas y Costeras-INVEMAR, Colombia, Museo de Historia Natural Marina de Colombia (MHNMC), Programa de Biodiversidad y Ecosistemas Marinos, Santa Marta, Colombia
| | - Giomar Helena Borrero-Pérez
- Instituto de Investigaciones Marinas y Costeras-INVEMAR, Colombia, Museo de Historia Natural Marina de Colombia (MHNMC), Programa de Biodiversidad y Ecosistemas Marinos, Santa Marta, Colombia
| | - Régis Hocdé
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Pierre-Édouard Guérin
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valery Montpellier 3, Montpellier, France
| | | | - Laure Velez
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Nicolas Loiseau
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Sandra Bessudo
- Fundación Malpelo y Otros Ecosistemas Marinos, Bogotá, Colombia
| | | | | | - David Mouillot
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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26
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Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world. Sci Rep 2021; 11:23167. [PMID: 34848787 PMCID: PMC8632987 DOI: 10.1038/s41598-021-02593-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022] Open
Abstract
The Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.
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Polanco F. A, Mutis Martinezguerra M, Marques V, Villa‐Navarro F, Borrero Pérez GH, Cheutin M, Dejean T, Hocdé R, Juhel J, Maire E, Manel S, Spescha M, Valentini A, Mouillot D, Albouy C, Pellissier L. Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA. Biotropica 2021. [DOI: 10.1111/btp.13009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Andrea Polanco F.
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Virginie Marques
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | - Francisco Villa‐Navarro
- Grupo de Investigación en Zoología Facultad de Ciencias Universidad del Tolima Ibagué Colombia
| | - Giomar Helena Borrero Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR, Santa Marta, Colombia, Programa de Biodiversidad y Ecosistemas MarinosMuseo de Historia Natural Marina de Colombia (MHNMC Santa Marta Colombia)
| | - Marie‐Charlotte Cheutin
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | | | - Régis Hocdé
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
| | | | - Eva Maire
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Stéphanie Manel
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
- CEFE Univ. Montpellier CNRS EPHE‐PSL University IRD Univ. Paul Valéry Montpellier Montpellier France
| | - Manuel Spescha
- Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
| | | | - David Mouillot
- MARBEC CNRS Ifremer IRD Univ. Montpellier Montpellier France
| | - Camille Albouy
- IFREMER Unité Écologie et Modèles pour l’Halieutique Nantes cedex 3 France
| | - Loïc Pellissier
- Landscape Ecology Department of Environmental Systems Science Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
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Ji F, Yan L, Yan S, Qin T, Shen J, Zha J. Estimating aquatic plant diversity and distribution in rivers from Jingjinji region, China, using environmental DNA metabarcoding and a traditional survey method. ENVIRONMENTAL RESEARCH 2021; 199:111348. [PMID: 34029550 DOI: 10.1016/j.envres.2021.111348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
Traditional survey methods (TSMs) are difficult to use to perform a census of aquatic plant diversity completely in river ecosystems, and improved aquatic plant community monitoring programs are becoming increasingly crucial with a continuous decline in diversity. Although environmental DNA (eDNA) metabarcoding has been applied successfully to assess aquatic biodiversity, limited work has been reported regarding aquatic plant diversity in rivers. In this study, the efficiency of eDNA to estimate the aquatic plant diversity and spatial distribution of rivers from the Jingjinji (JJJ) region was evaluated by comparing results obtained by the TSM. Based on a combination of the two methods, 157 aquatic plant species, including 24 hydrophytes, 61 amphibious plants, and 72 mesophytes, were identified. The spatial patterns in species richness and abundance by eDNA exhibited agreement with the TSM results with a gradual decline from the mountain area (MA) to the agricultural area (AA) and then to the urban area (UA). Compared to the TSM, eDNA identified a significantly greater number of species per site (p < 0.01) and obtained a significantly higher abundance in hydrophytes (p < 0.01), supplementing the unavailable abundance data from the TSM. Furthermore, the aquatic plant assemblages from the different areas were discriminated well using eDNA (p < 0.05), but they were better discriminated by the TSM (p < 0.01). Thus, our study provides more detailed data on aquatic plant diversity in rivers from the JJJ region, which is essential for biodiversity conservation. Our findings also highlight that eDNA can be reliable for evaluating aquatic plant diversity and has the potential to respond to landscape heterogeneity in river ecosystems.
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Affiliation(s)
- Fenfen Ji
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Liang Yan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Saihong Yan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianlong Qin
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China
| | - Jianzhong Shen
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, College of Fisheries, Huazhong Agriculture University, Wuhan, 430070, China.
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Burian A, Mauvisseau Q, Bulling M, Domisch S, Qian S, Sweet M. Improving the reliability of eDNA data interpretation. Mol Ecol Resour 2021; 21:1422-1433. [PMID: 33655639 DOI: 10.1111/1755-0998.13367] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 01/07/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023]
Abstract
Global declines in biodiversity highlight the need to effectively monitor the density and distribution of threatened species. In recent years, molecular survey methods detecting DNA released by target-species into their environment (eDNA) have been rapidly on the rise. Despite providing new, cost-effective tools for conservation, eDNA-based methods are prone to errors. Best field and laboratory practices can mitigate some, but the risks of errors cannot be eliminated and need to be accounted for. Here, we synthesize recent advances in data processing tools that increase the reliability of interpretations drawn from eDNA data. We review advances in occupancy models to consider spatial data-structures and simultaneously assess rates of false positive and negative results. Further, we introduce process-based models and the integration of metabarcoding data as complementing approaches to increase the reliability of target-species assessments. These tools will be most effective when capitalizing on multi-source data sets collating eDNA with classical survey and citizen-science approaches, paving the way for more robust decision-making processes in conservation planning.
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Affiliation(s)
- Alfred Burian
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK.,Marine Ecology Department, Lurio University, Nampula, Mozambique.,Department of Computational Landscape Ecology, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Quentin Mauvisseau
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Mark Bulling
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
| | - Sami Domisch
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Song Qian
- Department of Environmental Sciences, University of Toledo, Toledo, OH, USA
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
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Tsukamoto Y, Yonezawa S, Katayama N, Isagi Y. Detection of Endangered Aquatic Plants in Rapid Streams Using Environmental DNA. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.622291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Podostemaceae are a eudicot family of plants that grow on rapid streams and waterfalls. Two genera and six species of this family are distributed in Japan, all of which are threatened with extinction. It is difficult to find these species from the river side and it takes much effort to investigate their distribution. In this study, we attempted to determine the presence and absence of the Podostemaceae species by environmental DNA (eDNA) metabarcoding. Four species of Podostemaceae were detected near four known habitats, and the detected species were in perfect agreement with the results of a past survey that was based on visual observation. The marker used in this study had sufficient resolution to distinguish all six Podostemaceae species distributed in Japan and detected multiple species growing in a site. These results show that eDNA metabarcoding can quickly detect rare aquatic plants that are difficult to find by visual observation and can provide important information regarding their conservation.
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Lozano Mojica JD, Caballero S. Applications of eDNA Metabarcoding for Vertebrate Diversity Studies in Northern Colombian Water Bodies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.617948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Environmental DNA metabarcoding is a tool with increasing use worldwide. The uses of such technology have been validated several times for diversity census, invasive species detection, and endangered/cryptic/elusive species detection and monitoring. With the help of this technology, water samples collected (n = 37) from several main river basins and other water bodies of the northern part of Colombia, including the Magdalena, Sinú, Atrato, and San Jorge river basins, were filtered and analyzed and processed using universal 12S primers for vertebrate fauna and NGS. Over 200 native taxa were detected, the majority of them being fish species but also including amphibia, reptiles, and several non-aquatic species of birds and mammals (around 78, 3, 2, 9, and 8%, respectively). Among the matches, vulnerable, and endangered species such as the catfish Pseudoplatystoma magdaleniatum and the Antillean manatee (Trichechus manatus) were detected. The manual revision of the data revealed some geographical incongruencies in classification. No invasive species were detected in the filters. This is, to our knowledge, the first time this technique is used in rivers of the country and this tool promises to bring advances in monitoring and conservation efforts, since its low cost and fast deployment allows for sampling in small periods of time, together with the fact that it can detect a wide range of species, allows for a new way of censing the vertebrate diversity in Colombia. Diversity analysis showed how the species identified using this method point to expected community structure although still much needs to be improved in rates of detection and genomic reference databases. This technique could be used in citizen science projects involving local communities in these regions.
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