1
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Saranholi BH, França FM, Vogler AP, Barlow J, Vaz de Mello FZ, Maldaner ME, Carvalho E, Gestich CC, Howes B, Banks-Leite C, Galetti PM. Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics. Mol Ecol Resour 2024; 24:e13961. [PMID: 38646932 DOI: 10.1111/1755-0998.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/16/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.
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Affiliation(s)
- Bruno H Saranholi
- Department of Life Sciences, Imperial College London, Ascot, UK
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Filipe M França
- School of Biological Sciences, University of Bristol, Bristol, UK
- Graduate Program in Ecology, Biological Sciences Institute, Federal University of Pará, Belém, Pará, Brazil
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Fernando Z Vaz de Mello
- Departamento de Biologia e Zoologia, Universidade Federal de Mato Grosso, Instituto de Biociências, Cuiabá, MT, Brazil
| | - Maria E Maldaner
- Programa de Pós-Graduação Em Ecologia e Conservação da Biodiversidade (PPGECB), Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Edrielly Carvalho
- Programa de Pós-Graduação Em Entomologia, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Carla C Gestich
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Benjamin Howes
- Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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2
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Wang S, Wu D, Song Y, Wang T, Fan S, Wu E, Chen N, Xia W, Xu MN, Chen Z, Wen J, Zhang Y, Mo L, Xiang L. Application of environmental DNA metabarcoding to identify fish community characteristics in subtropical river systems. Ecol Evol 2024; 14:e11214. [PMID: 38725828 PMCID: PMC11079634 DOI: 10.1002/ece3.11214] [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: 08/04/2023] [Revised: 02/28/2024] [Accepted: 03/15/2024] [Indexed: 05/12/2024] Open
Abstract
Fish are vital in river ecosystems; however, traditional investigations of fish usually cause ecological damage. Extracting DNA from aquatic environments and identifying DNA sequences offer an alternative, noninvasive approach for detecting fish species. In this study, the effects of environmental DNA (eDNA), coupled with PCR and next-generation sequencing, and electrofishing for identifying fish community composition and diversity were compared. In three subtropical rivers of southern China, fish specimens and eDNA in water were collected along the longitudinal (upstream-downstream) gradient of the rivers. Both fish population parameters, including species abundance and biomass, and eDNA OTU richness grouped 38 sampling sites into eight spatial zones with significant differences in local fish community composition. Compared with order-/family-level grouping, genus-/species-level grouping could more accurately reveal the differences between upstream zones I-III, midstream zones IV-V, and downstream zones VI-VIII. From the headwaters to the estuary, two environmental gradients significantly influenced the longitudinal distribution of the fish species, including the first gradient composed of habitat and physical water parameters and the second gradient composed of chemical water parameters. The high regression coefficient of alpha diversity between eDNA and electrofishing methods as well as the accurate identification of dominant, alien, and biomarker species in each spatial zone indicated that eDNA could characterize fish community attributes at a level similar to that of traditional approaches. Overall, our results demonstrated that eDNA metabarcoding can be used as an effective tool for revealing fish composition and diversity, which is important for using the eDNA technique in aquatic field monitoring.
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Affiliation(s)
- Sai Wang
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Dong‐Hai Wu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
- College of Ecology and EnvironmentHainan UniversityHaikouChina
| | - Yong‐Duo Song
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Tuan‐Tuan Wang
- College of Ecology and EnvironmentHainan UniversityHaikouChina
- Key Laboratory of Agro‐Forestry Environmental Processes and Ecological Regulation of Hainan ProvinceHainan UniversityHaikouChina
| | - Shi‐Di Fan
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - En‐Ni Wu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Nan‐Lin Chen
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Wen‐Tong Xia
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Min N. Xu
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
| | - Zhong‐Bing Chen
- Department of Applied·Ecology, Faculty of Environmental SciencesCzech University of Life Sciences PraguePraha‐SuchdolCzech Republic
| | - Jing Wen
- State Key Laboratory of Marine Resource Utilization in South China SeaHainan UniversityHaikouChina
- Hainan Qingxiao Environmental Testing Co., Ltd.SanyaChina
- Hainan Qianchao Ecological Technology Co., Ltd.SanyaChina
| | - Yang Zhang
- Shenzhen Guanghuiyuan Environment Water Co., Ltd.ShenzhenChina
| | - Ling Mo
- Hainan Research Academy of Environmental SciencesHaikouChina
| | - Lei Xiang
- Department of EcologyJinan UniversityGuangzhouChina
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3
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Kawaguchi M, Aoki H, Kamo H, Miura K, Hiruta Y, Simizu S, Citterio D. Simplified capture, extraction, and amplification of cellular DNA from water samples. ANAL SCI 2024; 40:501-510. [PMID: 38142247 DOI: 10.1007/s44211-023-00482-7] [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: 10/28/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
DNA analysis in water samples is attracting attention in various fields. However, conventional methods for DNA analysis require a work-intensive and time-consuming sample pre-treatment. In this study, a simplified pre-treatment method for analyzing DNA in water samples was evaluated. The process consists of filtration, DNA extraction, and amplification, which can be achieved within a short time. In the filtration process, two types of filters, firstly a tissue paper (Kimwipe) and then a glass filter (GF/F), were used in sequence. The first large pore size filter enabled a reduction in filtration time by removing large particulate matter impurities present in river water matrix. Cells spiked into 1 L of river water were recovered at more than 90% within approximately 5 min filtration time. Also, DNA was extracted from the captured cells directly on the surface of the filter in only 5 min. Thus, DNA collection and extraction from a water sample can be completed within about 10 min. Furthermore, PCR amplification was performed directly from DNA-attached filter sections, which greatly reduced the number of required pre-treatment steps. Finally, we succeeded in establishing a simple and fast on-site pre-treatment system by using a hand-driven syringe filtration method. This pre-treatment system is expected to offer the possibility for the future establishment of a rapid and easy DNA analysis method applicable to various types of water samples.
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Affiliation(s)
- Mai Kawaguchi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Hiroshi Aoki
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Hiroki Kamo
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kazuki Miura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Hiruta
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Daniel Citterio
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
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4
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Zhang L, Zhou W, Jiao M, Xie T, Xie M, Li H, Suo A, Yue W, Ding D, He W. Use of passive sampling in environmental DNA metabarcoding technology: Monitoring of fish diversity in the Jiangmen coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168298. [PMID: 37939943 DOI: 10.1016/j.scitotenv.2023.168298] [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: 04/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
Environmental DNA (eDNA) metabarcoding technology is proving to be the most up-to-date and promising method for monitoring marine fish diversity. Fish eDNA is usually collected on a filter membrane after the filtration of water. Not only does this require the use of specialized equipment, but the amount of filtered water needed is also difficult to meet. The recently proposed passive eDNA collection method can expand the sampling scale, providing new perspectives for monitoring marine biodiversity. The role of collection methods in eDNA surveys, however, remains unclear. In this study, a low-cost custom framework with two types of filter membrane materials was used to conduct passive submersion samplings at the north and south ends of Shangchuan Island, Jiangmen, China. After defined periods of submersion, the filter membranes were recovered and eDNA extracted. Metabarcoding techniques were applied to detect fish species information in the eDNA samples. A total of 106 marine fish species from 27 orders, 53 families, and 92 genera, including one cartilaginous fish, were identified in the samples. The majority of fish detected by active filtration were also found in the passively collected samples, within the same location. Both sampling methods, therefore, showed similar species richness. Passive sampling was effective in identifying fish species diversity and provided a higher spatial resolution owing to the sample replicates. Passive sampling was also more sensitive in detecting species that differ significantly in abundance (biomarkers) between different sampling depths. When active filtration is not possible, or when large-scale sampling is the purpose of the study, passive sampling methods certainly provide a promising alternative. The findings of our study provide guidance for fish surveys and continuous bio-stereoscopic monitoring in coastal waters.
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Affiliation(s)
- Li Zhang
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiguo Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Mengyu Jiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mujiao Xie
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Hanying Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anning Suo
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Weizhong Yue
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Dewen Ding
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 51145, China
| | - Weihong He
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
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5
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Shen Y, Zhang Y, Cheng R, Wang W, Duan C, Liu Z, Chen Q, Li Y, Wang M, Luo Y. Diversity and spatiotemporal dynamics of fish communities in the Chongqing section of the upper Yangtze River based on eDNA metabarcoding. Ecol Evol 2023; 13:e10681. [PMID: 37953986 PMCID: PMC10636638 DOI: 10.1002/ece3.10681] [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: 12/27/2022] [Revised: 09/28/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Fish diversity plays a critical role in maintaining the balance of water ecosystems, especially in the Chongqing section of the National Nature Reserve for Rare and Endemic Fishes in the upper Yangtze River, which serves as an important habitat for rare and endemic fish, as well as an important channel for the replenishment of fishery resources in the Three Gorges Reservoir. Under a 10-year ban on fishing in the Yangtze River basin, we investigate fish diversity and seasonal variation in the Reserve by using environmental DNA (eDNA) metabarcoding. We found fishes belonging to 85 genera, 24 families, and 8 orders in the Reserve. A comparison of eDNA metabarcoding results with the diversity of a recent fish catch revealed that eDNA metabarcoding not only enables rapid and efficient fish monitoring but also has a high sensitivity. Furthermore, the study demonstrates that eDNA metabarcoding can be used as a tool for monitoring seasonal variations of fish composition in freshwater ecosystems. The alpha and beta diversity analysis both showed compositional differences in the fish community in accordance with seasonal variations. In addition, changes in eDNA relative sequence abundance and the detection of fish species at different sampling sites may reflect shifts in habitat use and distribution. Thus, we provide detailed seasonal data on fish diversity in the Chongqing section of the Reserve. This will contribute to conservation and to the understanding of fish diversity and community dynamics in the Chongqing section of the Reserve.
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Affiliation(s)
- Yanjun Shen
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yufeng Zhang
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Ruli Cheng
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Wei Wang
- Chongqing Rare and Endemic Fish National Nature Reserve Management OfficeChongqingChina
| | - Cong Duan
- Chongqing Rare and Endemic Fish National Nature Reserve Management OfficeChongqingChina
| | - Zhihao Liu
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Qiliang Chen
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yingwen Li
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Meng Wang
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
| | - Yang Luo
- Laboratory of Water Ecological Health and Environmental Safety, School of Life SciencesChongqing Normal UniversityChongqingChina
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6
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Saranholi BH, Rodriguez-Castro KG, Carvalho CS, Chahad-Ehlers S, Gestich CC, Andrade SCS, Freitas PD, Galetti PM. Comparing iDNA from mosquitoes and flies to survey mammals in a semi-controlled Neotropical area. Mol Ecol Resour 2023; 23:1790-1799. [PMID: 37535317 DOI: 10.1111/1755-0998.13851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 06/10/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
Ingested-derived DNA (iDNA) from insects represents a powerful tool for assessing vertebrate diversity because insects are easy to sample, have a diverse diet and are widely distributed. Because of these advantages, the use of iDNA for detecting mammals has gained increasing attention. Here we aimed to compare the effectiveness of mosquitoes and flies to detect mammals with a small sampling effort in a semi-controlled area, a zoo that houses native and non-native species. We compared mosquitoes and flies regarding the number of mammal species detected, the amount of mammal sequence reads recovered, and the flight distance range for detecting mammals. We also verified if the combination of two mini-barcodes (12SrRNA and 16SrRNA) would perform better than either mini-barcode alone to inform local mammal biodiversity from iDNA. To capture mosquitoes and flies, we distributed insect traps in eight sampling points during 5 days. We identified 43 Operational Taxonomic Units from 10 orders, from the iDNA of 17 mosquitoes and 46 flies. There was no difference in the number of species recovered per individual insect between mosquitoes and flies, but the number of flies captured was higher, resulting in more mammal species recovered by flies. Eight species were recorded exclusively by mosquitoes and 20 by flies, suggesting that using both samplers would allow a more comprehensive screening of the biodiversity. The maximum distance recorded was 337 m for flies and 289 m for mosquitoes, but the average range distance did not differ between insect groups. Our assay proved to be efficient for mammal detection, considering the high number of species detected with a reduced sampling effort.
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Affiliation(s)
- Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Karen G Rodriguez-Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Facultad Ciencias Básicas e Ingeniería, Universidad de los Llanos, Villavicencio, Colombia
| | - Carolina S Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Instituto Tecnológico Vale, Belém, Brazil
| | - Samira Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carla C Gestich
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Sónia C S Andrade
- Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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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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McColl-Gausden EF, Weeks AR, Coleman R, Song S, Tingley R. Using hierarchical models to compare the sensitivity of metabarcoding and qPCR for eDNA detection. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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9
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Yan H, Chen S, Liu X, Cheng Z, Schmidt BV, He W, Cheng F, Xie S. Investigations of Fish Assemblages Using Two Methods in Three Terminal Reservoirs of the East Route of South-to-North Water Transfer Project, China. Animals (Basel) 2023; 13:ani13101614. [PMID: 37238044 DOI: 10.3390/ani13101614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The terminal reservoirs of water transfer projects directly supply water for domestic, agricultural, and industrial applications, and the water quality of these reservoirs produce crucial effects on the achievement of project targets. Typically, fish assemblages are monitored as indicators of reservoir water quality, and can also be regulated for its improvement. In the present study, we compared traditional fish landing (TFL) and environmental DNA (eDNA) metabarcoding methods for monitoring fish assemblages in three terminal reservoirs of the East Route of the South-to-North Water Transfer Project, China. Results of TFL and eDNA showed similar assemblage structures and patterns of diversity and spatial distribution with obvious differences in fish composition across three examined reservoirs. Demersal and small fish were dominant in all reservoirs. In addition, a strong association between water transfer distance and assemblages and distribution of non-native fish was found. Our findings highlight the necessity of the fish assemblage monitoring and managing for water quality and revealed the impact of water diversion distance on the structure of fish assemblages and dispersal of alien species along the water transfer project.
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Affiliation(s)
- Huiguo Yan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University, Chongqing 400715, China
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Sibao Chen
- Changjiang Institute of Survey Planning Design and Research, Key Laboratory of Changjiang Regulation and Protection of Ministry of Water Resources, Wuhan 430010, China
| | - Xia Liu
- Shandong Main Line Co., Ltd. of East Route of South-to-North Water Transfer Project, Jinan 250013, China
| | - Zhenhao Cheng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Bjorn Victor Schmidt
- Department of Biological and Environmental Sciences, Texas A&M University, Commerce, TX 77843, USA
| | - Wenping He
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), College of Fisheries, Southwest University, Chongqing 400715, China
| | - Fei Cheng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Songguang Xie
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, China
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10
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Pragmatic applications of DNA barcoding markers in identification of fish species – a review. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
DNA barcoding and mini barcoding involve Cytochrome Oxidase Subunit I (COI) gene in mitochondrial genome and is used for accurate identification of species and biodiversity. The basic goal of the current study is to develop a complete reference database of fishes. It also evaluates the applicability of COI gene to identify fish at the species level with other aspects i.e., as Kimura 2 parameter (K2P) distance. The mean observed length of the sequence was ranging between 500 to 700 base pairs for fish species in DNA barcoding and 80 to 650 base pairs for DNA mini barcoding. This method describes the status of known to unknown samples but it also facilitates the detection of previously un-sampled species at distinct level. So, mini-barcoding is a method focuses on the analysis of short-length DNA markers has been demonstrated to be effective for species identification of processed food containing degraded DNA. While DNA meta-barcoding refers to the automated identification of multiple species from a single bulk sample. The may contain entire organisms or a single environmental sample containing degraded DNA. Despite DNA barcoding, mini barcoding and meta-barcoding are efficient methods for species identification which are helpful in conservation and proper management of biodiversity. It aids researchers to take an account of genetic as well as evolutionary relationships by collecting their morphological, distributional and molecular data. Overall, this paper discusses DNA barcoding technology and how it has been used to various fish species, as well as its universality, adaptability, and novel approach to DNA-based species identification.
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11
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Barbosa J, Asselman J, Janssen CR. Synthesizing the impact of sea-dumped munition and related chemicals on humans and the environment. MARINE POLLUTION BULLETIN 2023; 187:114601. [PMID: 36652858 DOI: 10.1016/j.marpolbul.2023.114601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Marine environments are globally impacted by vast quantities of munition disposed following both World Wars. Dumped munitions contain conventional explosives, chemicals warfare agents as well as a variety of metals. Field monitoring studies around marine dumpsites report the presence of munition constituents in water and sediment samples. The growing interest and developments in the ocean as a new economic frontier underline the need to remediate existing dumpsites. Here, we provide a comprehensive assessment of the magnitude and potential risks associated with marine munition dumpsites. An overview of the global distribution of dumpsites identifying the most impacted areas is provided, followed by the currently available data on the detection of munition constituents in environmental samples and evidence of their toxic potential to human and environmental health. Finally, existing data gaps are identified and future research needs promoting better understanding of the impact of the dumped material on the marine environment suggested.
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Affiliation(s)
- João Barbosa
- Laboratory for Environmental Toxicology and Aquatic Ecology, GhEnToxLab, Ghent University, Belgium; Blue Growth Research Lab, Ghent University, Bluebridge, Wetenschapspark 1, 8400 Ostend, Belgium.
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Bluebridge, Wetenschapspark 1, 8400 Ostend, Belgium
| | - Colin R Janssen
- Laboratory for Environmental Toxicology and Aquatic Ecology, GhEnToxLab, Ghent University, Belgium; Blue Growth Research Lab, Ghent University, Bluebridge, Wetenschapspark 1, 8400 Ostend, Belgium
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12
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Mahon AR, Grey EK, Jerde CL. Integrating invasive species risk assessment into environmental DNA metabarcoding reference libraries. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2730. [PMID: 36054696 PMCID: PMC10078450 DOI: 10.1002/eap.2730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 05/12/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) metabarcoding has shown promise as a tool for estimating biodiversity and early detection of invasive species. In aquatic systems, advantages of this method include the ability to concurrently monitor biodiversity and detect incipient invasions simply through the collection and analysis of water samples. However, depending on the molecular markers chosen for a given study, reference libraries containing target sequences from present species may limit the usefulness of eDNA metabarcoding. To explore the extent of this issue and how it may be resolved to aid biodiversity and invasive species early detection goals, we focus on fishes in the well-studied Laurentian Great Lakes region. First, we provide a synthesis of species currently known from the region and of non-indigenous species identified as threats by international, national, regional, and introduction pathway-specific fish risk assessments. With these species lists, we then evaluate 23 primer pairs commonly used in fish eDNA metabarcoding with available databases of sequence coverage and species specificity. Finally, we identify established and potentially invasive non-indigenous fish that should be prioritized for genetic sequencing to ensure robust eDNA metabarcoding for the region. Our results should increase confidence in using eDNA metabarcoding for fisheries conservation and management in the Great Lakes region and help prioritize reference sequencing efforts. The ultimate utility of eDNA metabarcoding approaches will come when conservation management of existing fish communities is integrated with early detection efforts for invasive species surveillance to assess total fish biodiversity.
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Affiliation(s)
- Andrew R. Mahon
- Department of BiologyCentral Michigan UniversityMount PleasantMichiganUSA
| | - Erin K. Grey
- School of Biology and Ecology and Maine Center for Genetics in the EnvironmentUniversity of MaineOronoMaineUSA
| | - Christopher L. Jerde
- Marine Science InstituteUniversity of California Santa BarbaraSanta BarbaraCaliforniaUSA
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13
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Environmental DNA (eDNA): Powerful Technique for Biodiversity Conservation. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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URycki DR, Bassiouni M, Good SP, Crump BC, Li B. The streamwater microbiome encodes hydrologic data across scales. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157911. [PMID: 35944633 DOI: 10.1016/j.scitotenv.2022.157911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/15/2022] [Accepted: 08/04/2022] [Indexed: 05/20/2023]
Abstract
Many fundamental questions in hydrology remain unanswered due to the limited information that can be extracted from existing data sources. Microbial communities constitute a novel type of environmental data, as they are comprised of many thousands of taxonomically and functionally diverse groups known to respond to both biotic and abiotic environmental factors. As such, these microscale communities reflect a range of macroscale conditions and characteristics, some of which also drive hydrologic regimes. Here, we assess the extent to which streamwater microbial communities (as characterized by 16S gene amplicon sequence abundance) encode information about catchment hydrology across scales. We analyzed 64 summer streamwater DNA samples collected from subcatchments within the Willamette, Deschutes, and John Day river basins in Oregon, USA, which range 0.03-29,000 km2 in area and 343-2334 mm/year of precipitation. We applied information theory to quantify the breadth and depth of information about common hydrologic metrics encoded within microbial taxa. Of the 256 microbial taxa that spanned all three watersheds, we found 9.6 % (24.5/256) of taxa, on average, shared information with a given hydrologic metric, with a median 15.6 % (range = 12.4-49.2 %) reduction in uncertainty of that metric based on knowledge of the microbial biogeography. All of the hydrologic metrics we assessed, including daily discharge at different time lags, mean monthly discharge, and seasonal high and low flow durations were encoded within the microbial community. Summer microbial taxa shared the most information with winter mean flows. Our study demonstrates quantifiable relationships between streamwater microbial taxa and hydrologic metrics at different scales, likely resulting from the integration of multiple overlapping drivers of each. Streamwater microbial communities are rich sources of information that may contribute fresh insight to unresolved hydrologic questions.
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Affiliation(s)
- Dawn R URycki
- Water Resources Graduate Program, Oregon State University, USA; Department of Biological and Ecological Engineering, Oregon State University, USA; Department of Civil Engineering, University of Colorado Denver, USA.
| | - Maoya Bassiouni
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Sweden; Department of Environmental Science, Policy, and Management, University of California Berkeley, USA
| | - Stephen P Good
- Water Resources Graduate Program, Oregon State University, USA; Department of Biological and Ecological Engineering, Oregon State University, USA
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, USA
| | - Bonan Li
- Water Resources Graduate Program, Oregon State University, USA; Department of Biological and Ecological Engineering, Oregon State University, USA; Department of Biological and Agricultural Engineering, University of Arkansas, USA
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15
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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16
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Barco A, Kullmann B, Knebelsberger T, Sarrazin V, Kuhs V, Kreutle A, Pusch C, Thiel R. Detection of fish species from marine protected areas of the North Sea using environmental DNA. JOURNAL OF FISH BIOLOGY 2022; 101:722-727. [PMID: 35598112 DOI: 10.1111/jfb.15111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
This report describe the first application of environmental DNA-metabarcoding approach for the assessment of fish species diversity in two marine protected areas of the North Sea: the Doggerbank and the Sylt Outer Reef. We collected 64 water samples and detected 24 fish species. We discuss qualitative differences between MPAs and compare the results with those obtained from bottom-trawl surveys in the same areas. We found three additional species to those documented in the same year with trawls, including the critically endangered European eel.
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Affiliation(s)
| | - Björn Kullmann
- State Research Centre for Agriculture and Fisheries Mecklenburg-Vorpommern, Institute of Fisheries, Rostock, Germany
| | | | - Victoria Sarrazin
- University of Hamburg, Department of Biology, Biodiversity Research, Hamburg, Germany
| | - Vanessa Kuhs
- Leibniz Institute for the Analysis of Biodiversity Change, Centre for Taxonomy and Morphology, Zoological Museum, Hamburg, Germany
| | - Axel Kreutle
- Federal Agency for Nature Conservation (BfN), Island of Vilm, Putbus (Lauterbach), Germany
| | - Christian Pusch
- Federal Agency for Nature Conservation (BfN), Island of Vilm, Putbus (Lauterbach), Germany
| | - Ralf Thiel
- University of Hamburg, Department of Biology, Biodiversity Research, Hamburg, Germany
- Leibniz Institute for the Analysis of Biodiversity Change, Centre for Taxonomy and Morphology, Zoological Museum, Hamburg, Germany
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17
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Golpour A, Šmejkal M, Čech M, dos Santos RA, Souza AT, Jůza T, Martínez C, Bartoň D, Vašek M, Draštík V, Kolařík T, Kočvara L, Říha M, Peterka J, Blabolil P. Similarities and Differences in Fish Community Composition Accessed by Electrofishing, Gill Netting, Seining, Trawling, and Water eDNA Metabarcoding in Temperate Reservoirs. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.913279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is difficult to understand the composition and diversity of biological communities in complex and heterogeneous environments using traditional sampling methods. Recently, developments in environmental DNA metabarcoding have emerged as a powerful, non-invasive method for comprehensive community characterization and biodiversity monitoring in different types of aquatic ecosystems. In this study, water eDNA targeting fish (wf-eDNA) and four traditional fish sampling methods (electrofishing, gill netting, seining, trawling) were compared to evaluate the reliability and efficiency of wf-eDNA (vertebrate mitochondrial 12S ribosomal RNA (rRNA) as an alternative approach to assess the diversity and composition of freshwater fish communities. The results of wf-eDNA showed a consistency between the traditional sampling methods regarding species detection. However, some fish species detected using wf-eDNA assay were not detected using traditional sampling methods and vice versa. Comparison of wf-eDNA and traditional sampling methods revealed spatial homogeneity in fish community composition in all reservoirs. Ordination analysis showed that the wf-eDNA approach covers all traditional sampling methods and occupies an intermediate position. In addition, based on the Shannon diversity index, we found that in one reservoir the wf-eDNA method yielded similar fish community diversity to traditional sampling methods. However, in other reservoirs, the calculated Shannon diversity index of the wf-eDNA method was significantly higher than traditional sampling methods. In general, significant positive correlations were found between the wf-eDNA method and almost all traditional sampling methods. We conclude that wf-eDNA seems to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater ichthyofauna.
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18
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Jeunen GJ, Lipinskaya T, Gajduchenko H, Golovenchik V, Moroz M, Rizevsky V, Semenchenko V, Gemmell NJ. Environmental DNA (eDNA) metabarcoding surveys show evidence of non-indigenous freshwater species invasion to new parts of Eastern Europe. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.e68575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e. an ichthyological, hydrobiological and eDNA survey, whereby DNA was extracted from 500 ml surface water samples and amplified with two 16S rDNA primer assays targeting the fish and macroinvertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous benthic macroinvertebrates were detected by traditional surveys, while seven NISeDNA signals were picked up, including four fish, one aquatic and two benthic macroinvertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey might be attributed to: (i) preferential amplification of aquatic over benthic macroinvertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximise the probability of early detection of non-native organisms.
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19
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Ionescu D, Bizic M, Karnatak R, Musseau CL, Onandia G, Kasada M, Berger SA, Nejstgaard JC, Ryo M, Lischeid G, Gessner MO, Wollrab S, Grossart H. From microbes to mammals: Pond biodiversity homogenization across different land‐use types in an agricultural landscape. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- D. Ionescu
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Bizic
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - R. Karnatak
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - C. L. Musseau
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Biology, Chemistry, Pharmacy, Institute of Biology Free University of Berlin Germany
| | - G. Onandia
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. Kasada
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
| | - S. A. Berger
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - J. C. Nejstgaard
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - M. Ryo
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
- Brandenburg University of Technology Cottbus–Senftenberg Cottbus Germany
| | - G. Lischeid
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - M. O. Gessner
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Department of Ecology Berlin Institute of Technology (TU Berlin) Berlin Germany
| | - S. Wollrab
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - H.‐P. Grossart
- Leibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB) Stechlin & Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
- Institute of Biochemistry and Biology Potsdam University Potsdam Germany
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20
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Bernos TA, Jeffries KM, Mandrak NE. Aquatic invasive species specialists’ perceptions on the importance of genetic tools and concepts to inform management. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02758-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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21
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Keck F, Blackman RC, Bossart R, Brantschen J, Couton M, Hürlemann S, Kirschner D, Locher N, Zhang H, Altermatt F. Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Mol Ecol 2022; 31:1820-1835. [PMID: 35075700 PMCID: PMC9303474 DOI: 10.1111/mec.16364] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.
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Affiliation(s)
- François Keck
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Rosetta C Blackman
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Raphael Bossart
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Marjorie Couton
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Samuel Hürlemann
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Dominik Kirschner
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental System Science, ETH Zürich, Universitätstr. 16, 8092, Zürich, Switzerland.,Landscape Ecology, Land Change Science, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Nadine Locher
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Heng Zhang
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
| | - Florian Altermatt
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.,Research Priority Programme Global Change and Biodiversity (URPP-GCB), University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
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22
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Drake LE, Cuff JP, Young RE, Marchbank A, Chadwick EA, Symondson WOC. An assessment of minimum sequence copy thresholds for identifying and reducing the prevalence of artefacts in dietary metabarcoding data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Jordan P. Cuff
- School of Biosciences Cardiff University Cardiff UK
- Rothamsted Insect Survey, Rothamsted Research West Common Harpenden UK
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23
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Peterson GS, Hoffman JC, Trebitz AS, Hatzenbuhler CI, Myers JT, Ross JE, Okum SL, Pilgrim EM. Early detection monitoring for non-indigenous fishes; comparison of survey approaches during two species introductions in a Great Lakes port. Biol Invasions 2021; 24:463-478. [PMID: 35356708 PMCID: PMC8958937 DOI: 10.1007/s10530-021-02655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Assessing relative performance of different sampling methods used for early detection monitoring (EDM) is a critical step in understanding the likelihood of detecting new non-indigenous species (NIS) in an environment of interest. EDM performance metrics are typically based on the probability of detecting established NIS or rare indigenous species; however, detection probability estimates for these proxies may not accurately reflect survey effectiveness for newly introduced NIS. We used data from three different EDM survey approaches that varied by targeted life-stage (adult-juvenile versus ichthyoplankton), media (physical fish versus environmental DNA), and taxonomic method (morphology-based versus DNA-based taxonomy) to explore relative detection sensitivity for recently introduced white bass (Morone chrysops) and gizzard shad (Dorosoma cepedianum) in the Port of Duluth-Superior, a NIS introduction hot spot within the Laurentian Great Lakes. Detection efficiency, measured by the effort (number of samples) required to achieve 95% probability of detection, differed by EDM approach and species. Also, the relative sensitivity (detection rate) of each survey approach differed by species. For both species, detection in surveys using DNA-based taxonomy was generally as good or better than the adult-juvenile survey using morphology-based taxonomy. While both species appear to have been detected at early stages of invasion, white bass were likely present up to 5 years prior to initial detection, whereas gizzard shad may have been detected in the first year of introduction. We conclude that using complimentary sampling methods can help to balance the strengths and weaknesses of each approach and provide more reliable early detection of new invaders.
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Affiliation(s)
- Greg S. Peterson
- Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Joel C. Hoffman
- Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Anett S. Trebitz
- Center for Computational Toxicology and Ecology, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Chelsea I. Hatzenbuhler
- SpecPro Professional Services, Contractor To US Environmental Protection Agency, 6201 Congdon Blvd, Duluth, MN 55804, USA
| | - Jared T. Myers
- US Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, 2800 Lakeshore Drive E, Ashland, WI 54806, USA
| | - Jason E. Ross
- US Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, 2800 Lakeshore Drive E, Ashland, WI 54806, USA
| | - Sara L. Okum
- Pegasus Professional Services, Contractor To US Environmental Protection Agency, 26 Martin Luther King Dr, Cincinnati, OH 45268, USA
| | - Erik M. Pilgrim
- Center for Environmental Measurement and Modeling, Watershed and Ecosystem Characterization Division, US Environmental Protection Agency, 26 Martin Luther King Dr, Cincinnati, OH 45268, USA
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24
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Cantera I, Decotte JB, Dejean T, Murienne J, Vigouroux R, Valentini A, Brosse S. Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach. Mol Ecol Resour 2021; 22:1274-1283. [PMID: 34724352 DOI: 10.1111/1755-0998.13544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022]
Abstract
Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA. Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species-rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species. eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with increasing distance between sites. The distance decay of similarity derived from eDNA was similar and even more pronounced than that obtained with capture-based methods (gill-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species. Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provides a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture-based methods, which describes fish fauna over a few hundred metres.
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Affiliation(s)
- Isabel Cantera
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III Paul Sabatier, Toulouse, France
| | | | - Tony Dejean
- Vigilife, Le Bourget-du-Lac, France.,Spygen, Le Bourget-du-Lac, France
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut, Hydreco, Kourou Cedex, French Guiana
| | | | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III Paul Sabatier, Toulouse, France
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25
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Fernandez S, Miller DL, Holman LE, Gittenberger A, Ardura A, Rius M, Mirimin L. Environmental DNA sampling protocols for the surveillance of marine non-indigenous species in Irish coastal waters. MARINE POLLUTION BULLETIN 2021; 172:112893. [PMID: 34464822 DOI: 10.1016/j.marpolbul.2021.112893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Understanding the spread and distribution of Non-Indigenous Species (NIS) is key when implementing legislation to maintain good ecosystem health. Environmental DNA (eDNA) has shown great potential to detect aquatic organisms in a rapid and cost-effective way, however their applicability to new environments must be validated prior to their implementation. Here, we tested different field sampling methods in combination with eDNA metabarcoding to develop a tool to detect NIS. Large and small volumes of seawater were filtered, in addition to the collection of sediment and horizontal tow net samples at 12 locations across four distinct geographic areas in Ireland. The biggest dissimilarity in the species recovered was found between sediment and town net samples. Tow nets showed to be the most efficient. A total of 357 taxa were identified, including 16 NIS. Fine mesh tow nets were identified as the most cost-efficient for large-scale monitoring and surveillance of NIS.
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Affiliation(s)
- Sara Fernandez
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland.
| | - Dulaney L Miller
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
| | - Luke E Holman
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom
| | - Arjan Gittenberger
- GiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, the Netherlands; Department of Marine Zoology, Naturalis Biodiversity Center, Pesthuislaan 7, 2333 BA Leiden, the Netherlands
| | - Alba Ardura
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Marc Rius
- School of Ocean and Earth Science, National Oceanography Centre, European Way, Southampton SO14 3ZH, University of Southampton, United Kingdom; Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Dublin Road, H91 T8NW Galway, Ireland; Galway-Mayo Institute of Technology, School of Science and Computing, Department of Natural Sciences, Dublin Road, H91 T8NW Galway, Ireland
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26
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Leontidou K, Vokou D, Sandionigi A, Bruno A, Lazarina M, De Groeve J, Li M, Varotto C, Girardi M, Casiraghi M, Cristofori A. Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps). Sci Rep 2021; 11:18226. [PMID: 34521917 PMCID: PMC8440677 DOI: 10.1038/s41598-021-97619-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/02/2021] [Indexed: 01/28/2023] Open
Abstract
Monitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.
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Affiliation(s)
- Kleopatra Leontidou
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy. .,Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Despoina Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anna Sandionigi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonia Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Johannes De Groeve
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy.,Department of Geography, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
| | - Matteo Girardi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonella Cristofori
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
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27
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de Santana CD, Parenti LR, Dillman CB, Coddington JA, Bastos DA, Baldwin CC, Zuanon J, Torrente-Vilara G, Covain R, Menezes NA, Datovo A, Sado T, Miya M. The critical role of natural history museums in advancing eDNA for biodiversity studies: a case study with Amazonian fishes. Sci Rep 2021; 11:18159. [PMID: 34518574 PMCID: PMC8438044 DOI: 10.1038/s41598-021-97128-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
Ichthyological surveys have traditionally been conducted using whole-specimen, capture-based sampling with varied but conventional fishing gear. Recently, environmental DNA (eDNA) metabarcoding has emerged as a complementary, and possible alternative, approach to whole-specimen methodologies. In the tropics, where much of the diversity remains undescribed, vast reaches continue unexplored, and anthropogenic activities are constant threats; there have been few eDNA attempts for ichthyological inventories. We tested the discriminatory power of eDNA using MiFish primers with existing public reference libraries and compared this with capture-based methods in two distinct ecosystems in the megadiverse Amazon basin. In our study, eDNA provided an accurate snapshot of the fishes at higher taxonomic levels and corroborated its effectiveness to detect specialized fish assemblages. Some flaws in fish metabarcoding studies are routine issues addressed in natural history museums. Thus, by expanding their archives and adopting a series of initiatives linking collection-based research, training and outreach, natural history museums can enable the effective use of eDNA to survey Earth's hotspots of biodiversity before taxa go extinct. Our project surveying poorly explored rivers and using DNA vouchered archives to build metabarcoding libraries for Neotropical fishes can serve as a model of this protocol.
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Affiliation(s)
- C David de Santana
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.
| | - Lynne R Parenti
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Casey B Dillman
- Cornell University Museum of Vertebrates, Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Douglas A Bastos
- Programa de Pós-Graduação em Ciências Biológicas (BADPI), Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil
| | - Carole C Baldwin
- Division of Fishes, Department of Vertebrate Zoology, MRC 159, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Jansen Zuanon
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Gislene Torrente-Vilara
- Instituto do Mar, Universidade Federal de São Paulo, Campus Baixada Santista, Santos, São Paulo, Brazil
| | - Raphaël Covain
- Museum of Natural History, Department of Herpetology and Ichthyology, route de Malagnou 1, PO Box 6434, 1211, Geneva 6, Switzerland
| | - Naércio A Menezes
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - Aléssio Datovo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Av. Nazaré, 481, São Paulo, SP, 04263-000, Brazil
| | - T Sado
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
| | - M Miya
- Natural History Museum and Institute, Chuo-ku, Chiba, 260-8682, Japan
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28
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Xu CCY, Ramsay C, Cowan M, Dehghani M, Lasko P, Barrett RDH. Transgenes of genetically modified animals detected non-invasively via environmental DNA. PLoS One 2021; 16:e0249439. [PMID: 34437552 PMCID: PMC8389434 DOI: 10.1371/journal.pone.0249439] [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: 03/14/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
We demonstrate that simple, non-invasive environmental DNA (eDNA) methods can detect transgenes of genetically modified (GM) animals from terrestrial and aquatic sources in invertebrate and vertebrate systems. We detected transgenic fragments between 82–234 bp through targeted PCR amplification of environmental DNA extracted from food media of GM fruit flies (Drosophila melanogaster), feces, urine, and saliva of GM laboratory mice (Mus musculus), and aquarium water of GM tetra fish (Gymnocorymbus ternetzi). With rapidly growing accessibility of genome-editing technologies such as CRISPR, the prevalence and diversity of GM animals will increase dramatically. GM animals have already been released into the wild with more releases planned in the future. eDNA methods have the potential to address the critical need for sensitive, accurate, and cost-effective detection and monitoring of GM animals and their transgenes in nature.
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Affiliation(s)
- Charles C. Y. Xu
- Redpath Museum, McGill University, Montreal, Quebec, Canada
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | - Claire Ramsay
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), McGill University, Montreal, Quebec, Canada
| | | | - Paul Lasko
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Rowan D. H. Barrett
- Redpath Museum, McGill University, Montreal, Quebec, Canada
- Department of Biology, McGill University, Montreal, Quebec, Canada
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29
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Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding. Sci Rep 2021; 11:15763. [PMID: 34344957 PMCID: PMC8333312 DOI: 10.1038/s41598-021-95360-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.
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30
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Pukk L, Kanefsky J, Heathman AL, Weise EM, Nathan LR, Herbst SJ, Sard NM, Scribner KT, Robinson JD. eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13370] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Lilian Pukk
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
| | - Jeannette Kanefsky
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
| | - Amanda L. Heathman
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
| | - Ellen M. Weise
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
| | - Lucas R. Nathan
- Michigan Department of Natural Resources‐Fisheries Division Lansing MI USA
| | - Seth J. Herbst
- Michigan Department of Natural Resources‐Fisheries Division Lansing MI USA
| | - Nicholas M. Sard
- Biological Sciences Department State University of New York Oswego Oswego NY USA
| | - Kim T. Scribner
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
- Department of Integrative Biology Michigan State University East Lansing MI USA
| | - John D. Robinson
- Department of Fisheries and Wildlife Michigan State University East Lansing MI USA
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31
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Shu L, Ludwig A, Peng Z. Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks. Ecol Evol 2021; 11:8281-8294. [PMID: 34188886 PMCID: PMC8216916 DOI: 10.1002/ece3.7658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/25/2021] [Accepted: 04/19/2021] [Indexed: 11/10/2022] Open
Abstract
Environmental DNA (eDNA) techniques refer to utilizing the organisms' DNA extracted from environment samples to genetically identify target species without capturing actual organisms. eDNA metabarcoding via high-throughput sequencing can simultaneously detect multiple fish species from a single water sample, which is a powerful tool for the qualitative detection and quantitative estimates of multiple fish species. However, sequence counts obtained from eDNA metabarcoding may be influenced by many factors, of which primer bias is one of the foremost causes of methodological error. The performance of 18 primer pairs for COI, cytb, 12S rRNA, and 16S rRNA mitochondrial genes, which are all frequently used in fish eDNA metabarcoding, were evaluated in the current study. The ribosomal gene markers performed better than the protein-coding gene markers during in silico screening, resulting in higher taxonomic coverage and appropriate barcode lengths. Four primer pairs-AcMDB07, MiFish-U, Ve16S1, and Ve16S3-designed for various regions of the 12S and 16S rRNA genes were screened for tank metabarcoding in a case study targeting six freshwater fish species. The four primer pairs were able to accurately detect all six species in different tanks, while only MiFish-U, Ve16S1, and Ve16S3 revealed a significant positive relationship between species biomass and read count for the pooled tank data. The positive relationship could not be found in all species within the tanks. Additionally, primer efficiency differed depending on the species while primer preferential species varied in different fish assemblages. This case study supports the potential for eDNA metabarcoding to assess species diversity in natural ecosystems and provides an alternative strategy to evaluate the performance of candidate primers before application of eDNA metabarcoding in natural ecosystems.
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Affiliation(s)
- Lu Shu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Arne Ludwig
- Department of Evolutionary GeneticsLeibniz‐Institute for Zoo and Wildlife ResearchBerlinGermany
- Albrecht Daniel Thaer‐InstituteFaculty of Life SciencesHumboldt University BerlinBerlinGermany
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
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32
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Blackman RC, Osathanunkul M, Brantschen J, Di Muri C, Harper LR, Mächler E, Hänfling B, Altermatt F. Mapping biodiversity hotspots of fish communities in subtropical streams through environmental DNA. Sci Rep 2021; 11:10375. [PMID: 33990677 PMCID: PMC8121892 DOI: 10.1038/s41598-021-89942-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/05/2021] [Indexed: 11/15/2022] Open
Abstract
Large tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site sampling campaign across the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. The clusters not only accurately matched the topology of the river network, but also revealed distinct groups of sites enabling informed conservation measures. Our study reveals novel opportunities of large-scale monitoring via eDNA to identify relevant areas within whole river catchments for conservation and habitat protection.
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Affiliation(s)
- Rosetta C Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland. .,Research Priority Programme Global Change and Biodiversity (URPP GCB), University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
| | - Maslin Osathanunkul
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Research Centre in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland
| | - Cristina Di Muri
- Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Lynsey R Harper
- Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Elvira Mächler
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland.,Department for Infectious Diseases and Pathobiology, Vetsuisse Faculty, Centre for Fish and Wildlife Health, University of Bern, Länggassstrasse 122, 3012, Bern, Switzerland
| | - Bernd Hänfling
- Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland. .,Research Priority Programme Global Change and Biodiversity (URPP GCB), University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
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33
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Wang Y, Chen K, Gao J, Wang M, Dong J, Xie Y, Giesy JP, Jin X, Wang B. Environmental DNA of preservative ethanol performed better than water samples in detecting macroinvertebrate diversity using metabarcoding. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Yu Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Kai Chen
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Jin Gao
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Meng Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Jie Dong
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Yuwei Xie
- Toxicology Centre University of Saskatchewan Saskatoon Saskatchewan Canada
| | - John P. Giesy
- Toxicology Centre University of Saskatchewan Saskatoon Saskatchewan Canada
- Department of Veterinary Biomedical Sciences University of Saskatchewan Saskatoon Saskatchewan Canada
- Department of Environmental Sciences Baylor University Waco Texas USA
| | - Xiaowei Jin
- China National Environmental Monitoring Centre Beijing China
| | - Beixin Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
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34
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Euclide PT, Lor Y, Spear MJ, Tajjioui T, Vander Zanden J, Larson WA, Amberg JJ. Environmental DNA metabarcoding as a tool for biodiversity assessment and monitoring: reconstructing established fish communities of north‐temperate lakes and rivers. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13253] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
| | - Yer Lor
- U.S. Geological Survey Upper Midwest Environmental Sciences Center WI USA
| | - Michael J. Spear
- Center for Limnology University of Wisconsin‐Madison Madison WI USA
| | - Tariq Tajjioui
- U.S. Geological Survey Upper Midwest Environmental Sciences Center WI USA
| | | | - Wesley A. Larson
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
- U.S. Geological Survey Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
| | - Jon J. Amberg
- U.S. Geological Survey Upper Midwest Environmental Sciences Center WI USA
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35
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Cornman RS, McKenna JE, Fike JA. Composition and distribution of fish environmental DNA in an Adirondack watershed. PeerJ 2021; 9:e10539. [PMID: 33680576 PMCID: PMC7919543 DOI: 10.7717/peerj.10539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/19/2020] [Indexed: 11/24/2022] Open
Abstract
Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.
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Affiliation(s)
- Robert S Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - James E McKenna
- U.S. Geological Survey, Great Lakes Science Center, Cortland, NY, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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Wang S, Yan Z, Hänfling B, Zheng X, Wang P, Fan J, Li J. Methodology of fish eDNA and its applications in ecology and environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142622. [PMID: 33059148 DOI: 10.1016/j.scitotenv.2020.142622] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/09/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Fish environmental DNA (eDNA) studies have made substantial progress during the past decade, and significant advances in monitoring fishes have been gained by taking advantage of this technology. Although a number of reviews concerning eDNA are available and some recent fish eDNA reviews focused on fisheries or standard method have been published, a systematic review of methodology of fish eDNA and its applications in ecology and environment has not yet been published. To our knowledge, this is the first review of fish eDNA for solving ecological and environmental issues. First, the most comprehensive literature analysis of fish eDNA was presented and analyzed. Then, we systematically discuss the relevant experiments and analyses of fish eDNA, and infers that standard workflow is on the way to consensus. We additionally provide reference sequence databases and the primers used to amplify the reference sequences or detecting fish eDNA. The abiotic and biotic conditions affecting fish eDNA persistence are also summarized in a schematic diagram. Subsequently, we focus on the major achievements of fish eDNA in ecology and environment. We additionally highlight the exciting new tools, including in situ autonomous monitoring devices, CRISPR nucleic acid detection technology, and meta-omics technology for fish eDNA detection in future. Ultimately, methodology of fish eDNA will provide a wholly new paradigm for conservation actions of fishes, ecological and environmental management at a global scale.
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Affiliation(s)
- Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Bernd Hänfling
- School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jianlong Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan 570228, China
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Rathinasamy V, Tran L, Swan J, Kelley J, Hosking C, Williamson G, Knowles M, Elliott T, Rawlin G, Spithill TW, Beddoe T. Towards understanding the liver fluke transmission dynamics on farms: Detection of liver fluke transmitting snail and liver fluke-specific environmental DNA in water samples from an irrigated dairy farm in Southeast Australia. Vet Parasitol 2021; 291:109373. [PMID: 33578197 DOI: 10.1016/j.vetpar.2021.109373] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 12/27/2022]
Abstract
Livestock production around the world is impacted by liver fluke (Fasciola spp.) infection resulting in serious economic losses to the beef, dairy and sheep industries with significant losses of about $90 million per annum in Australia. Triclabendazole (TCBZ) is the most effective anthelmintic treatment available to control liver fluke infections; however, the widespread emergence of TCBZ resistance in livestock threatens liver fluke control. Alternative control measures to lower exposure of livestock to liver fluke infection would help to preserve the usefulness of current anthelmintic treatments. Environmental DNA (eDNA) based identification of liver fluke and the intermediate snail host in the water bodies is a robust method to assess the risk of liver fluke infection on farms. In this study, we used a multiplex quantitative PCR assay of water samples to detect and quantify eDNA of Fasciola hepatica (F. hepatica) and Austropeplea tomentosa (A. tomentosa), a crucial intermediate snail host for liver fluke transmission in South-east Australia. Water samples were collected from an irrigation channel for a period of 7 months in 2016 (February, March, May, September, October, November and December) at a dairy farm located at Maffra, Victoria, South-east Australia. Using an effective eDNA extraction method, the multiplex qPCR assay allows for the independent but simultaneous detection of eDNA released from liver fluke life stages and snails using specific primers and a probe targeting the ITS-2 region of the liver fluke and snail, respectively, with minimal inhibition from contaminants in field collected water samples. The sensitivity of this assay to detect eDNA of liver fluke and snails was observed to be 14 fg and 50 fg, respectively, in the presence of field collected water samples. Differential levels of liver fluke and snail specific eDNA in water were observed at the time points analysed in this study. The successful detection of eDNA specific to liver fluke and snails from the field collected water samples provides a precedent for the use of this method as a monitoring tool to determine the prevalence of liver fluke and liver fluke-transmitting snails in irrigation regions. Further, this method has the enormous potential to allow an assessment of the liver fluke transmission zones on farms and to inform the application of effective control strategies.
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Affiliation(s)
- Vignesh Rathinasamy
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia
| | - Lily Tran
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia
| | - Jaclyn Swan
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia
| | - Jane Kelley
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia
| | - Chris Hosking
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia
| | - Genevieve Williamson
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia
| | - Michaela Knowles
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia
| | - Timothy Elliott
- Invetus, Armidale Research Centre, Armidale, New South Wales, Australia
| | - Grant Rawlin
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia; Department of Jobs, Precincts and Regions, Bundoora, Vic, Australia
| | - Terry W Spithill
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia.
| | - Travis Beddoe
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic, Australia; Centre for AgriBioscience, La Trobe University, Bundoora, Vic, Australia.
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Milhau T, Valentini A, Poulet N, Roset N, Jean P, Gaboriaud C, Dejean T. Seasonal dynamics of riverine fish communities using eDNA. JOURNAL OF FISH BIOLOGY 2021; 98:387-398. [PMID: 31674010 DOI: 10.1111/jfb.14190] [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: 05/23/2019] [Accepted: 10/30/2019] [Indexed: 05/23/2023]
Abstract
As fish communities are a major concern in rivers ecosystems, we investigated if their environmental (e)DNA signals vary according to the sampling period or hydromorphological conditions. Three rivers were studied over a year using eDNA metabarcoding approach. The majority of the species (c. 80%) were detected all year round in two rivers having similar hydromorphological conditions, whereas in the river affected by an upstream lake waterflow, more species were detected sporadically (42%). For all the rivers, in more than 98% of the occasional detections, the reads abundance represented <0.4% of the total reads per site and per sampling session. Even if the majority of the fish communities remained similar over the year for each of the three rivers, specific seasonal patterns were observed. We studied if the waterflow or the reproduction period had an effect on the observed dynamics. Waterflow, which influences eDNA downstream transportation, had a global influence in taxonomic richness, while the fishes' reproductive period had only an influence on certain species. Our results may help selecting the best sampling strategy according to research objectives. To study fish communities at local scale, seasons of low waterflow periods are recommended. This particularly helps to restraint effects of external eDNA coming from connections with other aquatic environment (tributaries, lakes, wetlands, sewage effluents, etc.). To obtain a more integrative overview of the fish community living in a river basin, high waterflow or breeding seasons are preferable for enhancing species detection probability, especially for rare species.
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Affiliation(s)
| | | | - Nicolas Poulet
- Haute Garonne, French National Agency for Biodiversity, Pôle Écohydraulique, Toulouse, France
| | - Nicolas Roset
- Rhône, French National Agency for Biodiversity, Bron, France
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Lafferty KD, Garcia-Vedrenne AE, McLaughlin JP, Childress JN, Morse MF, Jerde CL. At Palmyra Atoll, the fish-community environmental DNA signal changes across habitats but not with tides. JOURNAL OF FISH BIOLOGY 2021; 98:415-425. [PMID: 32441343 PMCID: PMC9300262 DOI: 10.1111/jfb.14403] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/24/2020] [Accepted: 05/20/2020] [Indexed: 05/24/2023]
Abstract
At Palmyra Atoll, the environmental DNA (eDNA) signal on tidal sand flats was associated with fish biomass density and captured 98%-100% of the expected species diversity there. Although eDNA spilled over across habitats, species associated with reef habitat contributed more eDNA to reef sites than to sand-flat sites, and species associated with sand-flat habitat contributed more eDNA to sand-flat sites than to reef sites. Tides did not disrupt the sand-flat habitat signal. At least 25 samples give a coverage >97.5% at this diverse, tropical, marine system.
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Affiliation(s)
- Kevin D. Lafferty
- Western Ecological Research Center, U.S. Geological Survey, Reston, Virginia
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, California
| | - Ana E. Garcia-Vedrenne
- Ecology, Evolution and Marine Biology, University of California, Los Angeles, Los Angeles, California
| | - John P. McLaughlin
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, California
| | - Jasmine N. Childress
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, California
| | - Marisa F. Morse
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, California
| | - Christopher L. Jerde
- Marine Science Institute, University of California, Santa Barbara, Santa Barbara, California
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40
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Jerde CL. Can we manage fisheries with the inherent uncertainty from eDNA? JOURNAL OF FISH BIOLOGY 2021; 98:341-353. [PMID: 31769024 DOI: 10.1111/jfb.14218] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material in the water and hence to infer the species' physical presence. However, fisheries managers face making decisions with risk and uncertainty when eDNA indicates a fish is present but traditional methods fail to capture the fish. In comparison with traditional methods such as nets, electrofishing and piscicides, eDNA approaches have more sources of underlying error that could give rise to false positives. This has resulted in some managers to question whether eDNA can be used to make management decisions because there is no fish in hand. As a relatively new approach, the methods and techniques have quickly evolved to improve confidence in eDNA. By evaluating an eDNA based research programmes through the pattern of the eDNA signal, assay design, experimental design, quality assurance and quality control checks, data analyses and concurrent search for fish using traditional gears, the evidence for fish presence can be evaluated to build confidence in the eDNA approach. The benefits for fisheries management from adopting an eDNA approach are numerous but include cost effectiveness, broader geographic coverage of habitat occupancy, early detection of invasive species, non-lethal stock assessments, exploration of previously inaccessible aquatic environments and discovery of new species hidden beneath the water's surface. At a time when global freshwater and marine fisheries are facing growing threats from over-harvest, pollution and climate change, we anticipate that growing confidence in eDNA will overcome the inherent uncertainty of not having a fish in hand and will empower the informed management actions necessary to protect and restore our fisheries.
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Affiliation(s)
- Christopher L Jerde
- Marine Science Institute, University of California, Santa Barbara, California, USA
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41
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Varotto C, Pindo M, Bertoni E, Casarotto C, Camin F, Girardi M, Maggi V, Cristofori A. A pilot study of eDNA metabarcoding to estimate plant biodiversity by an alpine glacier core (Adamello glacier, North Italy). Sci Rep 2021; 11:1208. [PMID: 33441696 PMCID: PMC7807053 DOI: 10.1038/s41598-020-79738-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/13/2020] [Indexed: 11/09/2022] Open
Abstract
Current biodiversity loss is a major concern and thus biodiversity assessment of modern ecosystems is compelling and needs to be contextualized on a longer timescale. High Throughput Sequencing (HTS) is progressively becoming a major source of data on biodiversity time series. In this multi proxy study, we tested, for the first time, the potential of HTS to estimate plant biodiversity archived in the surface layers of a temperate alpine glacier, amplifying the trnL barcode for vascular plants from eDNA of firn samples. A 573 cm long core was drilled by the Adamello glacier and cut into sections; produced samples were analyzed for physical properties, stable isotope ratio, and plant biodiversity by eDNA metabarcoding and conventional light microscopy analysis. Results highlighted the presence of pollen and plant remains within the distinct layers of snow, firn and ice. While stable isotope ratio showed a scarcely informative pattern, DNA metabarcoding described distinct plant species composition among the different samples, with a broad taxonomic representation of the biodiversity of the catchment area and a high-ranking resolution. New knowledge on climate and plant biodiversity changes of large catchment areas can be obtained by this novel approach, relevant for future estimates of climate change effects.
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Affiliation(s)
- Claudio Varotto
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | | | | | - Federica Camin
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | - Matteo Girardi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy
| | - Valter Maggi
- Earth and Environmental Sciences, University of Milano Bicocca, Milan, Italy
| | - Antonella Cristofori
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, TN, Italy.
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Sigsgaard EE, Olsen K, Hansen MDD, Hansen OLP, Høye TT, Svenning JC, Thomsen PF. Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages. Mol Ecol 2020; 30:3374-3389. [PMID: 33205529 PMCID: PMC8359373 DOI: 10.1111/mec.15734] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 11/02/2020] [Indexed: 01/03/2023]
Abstract
Insects and other terrestrial invertebrates are declining in species richness and abundance. This includes the invertebrates associated with herbivore dung, which have been negatively affected by grazing abandonment and the progressive loss of large herbivores since the Late Pleistocene. Importantly, traditional monitoring of these invertebrates is time‐consuming and requires considerable taxonomic expertise, which is becoming increasingly scarce. In this study, we investigated the potential of environmental DNA (eDNA) metabarcoding of cow dung samples for biomonitoring of dung‐associated invertebrates. From eight cowpats we recovered eDNA from 12 orders, 29 families, and at least 54 species of invertebrates (mostly insects), representing several functional groups. Furthermore, species compositions differed between the three sampled habitats of dry grassland, meadow, and forest. These differences were in accordance with the species’ ecology; for instance, several species known to be associated with humid conditions or lower temperatures were found only in the forest habitat. We discuss potential caveats of the method, as well as directions for future study and perspectives for implementation in research and monitoring.
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Affiliation(s)
| | - Kent Olsen
- Natural History Museum Aarhus, Aarhus, Denmark
| | | | - Oskar Liset Pryds Hansen
- Department of Biology, Aarhus University, Aarhus, Denmark.,Natural History Museum Aarhus, Aarhus, Denmark
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West KM, Richards ZT, Harvey ES, Susac R, Grealy A, Bunce M. Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia. Sci Rep 2020; 10:21479. [PMID: 33293686 PMCID: PMC7722930 DOI: 10.1038/s41598-020-78525-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.
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Affiliation(s)
- Katrina M West
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Euan S Harvey
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Robert Susac
- Western Australian Speleological Group, Nedlands, WA, 6909, Australia
| | - Alicia Grealy
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Environmental Protection Authority, 215 Lambton Quay, Wellington, 6011, New Zealand
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McColl-Gausden EF, Weeks AR, Coleman RA, Robinson KL, Song S, Raadik TA, Tingley R. Multispecies models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams. Mol Ecol 2020; 30:3111-3126. [PMID: 32966639 DOI: 10.1111/mec.15644] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022]
Abstract
Environmental DNA (eDNA) sampling can provide accurate, cost-effective, landscape-level data on species distributions. Previous studies have compared the sensitivity of eDNA sampling to traditional sampling methods for single species, but similar comparative studies on multispecies eDNA metabarcoding are rare. Using hierarchical site occupancy detection models, we examined whether key choices associated with eDNA metabarcoding (primer selection, low-abundance read filtering and the number of positive water samples used to classify a species as present at a site) affect the sensitivity of metabarcoding, relative to backpack electrofishing for fish in freshwater streams. Under all scenarios (teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering thresholds; one or two positive samples required to classify species as present), we found that eDNA metabarcoding is, on average, more sensitive than electrofishing. Combining vertebrate and teleostei markers resulted in higher detection probabilities relative to the use of either marker in isolation. Increasing the threshold used to filter low-abundance reads decreased species detection probabilities but did not change our overall finding that eDNA metabarcoding was more sensitive than electrofishing. Using a threshold of two positive water samples (out of five) to classify a species as present typically had negligible effects on detection probabilities compared to using one positive water sample. Our findings demonstrate that eDNA metabarcoding is generally more sensitive than electrofishing for conducting fish surveys in freshwater streams, and that this outcome is not sensitive to methodological decisions associated with metabarcoding.
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Affiliation(s)
| | - Andrew R Weeks
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia.,cesar Pty Ltd, Parkville, VIC, Australia
| | | | - Katie L Robinson
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Sue Song
- cesar Pty Ltd, Parkville, VIC, Australia
| | - Tarmo A Raadik
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, VIC, Australia
| | - Reid Tingley
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
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Qu C, Stewart KA, Clemente-Carvalho R, Zheng J, Wang Y, Gong C, Ma L, Zhao J, Lougheed SC. Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding. Sci Rep 2020; 10:16715. [PMID: 33028872 PMCID: PMC7542144 DOI: 10.1038/s41598-020-73648-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 09/09/2020] [Indexed: 12/16/2022] Open
Abstract
Using environmental DNA (eDNA) metabarcoding, we compared fish diversity in two distinct water bodies within the Yangtze River Basin with known populations of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis; YFP): the Tian-e-Zhou Reserve and Poyang Lake. We aimed to create a fish surveying tool for use in the Yangtze River Basin, while also gaining a better understanding of the prey distribution and diversity within two of the remaining strongholds of YFP. 16S rRNA universal primers were developed to amplify fish eDNA. After high-throughput sequencing and stringent data filtering, we identified a total of 75 fish species (6 orders, 9 families, 57 genera) across seasons and regions. Nine of the 75 fish species were among the 28 known YFP prey species, three of which were detected in all water samples. Our eDNA metabarcoding identified many species that had been previously captured using traditional netting practices, but also numerous species not previously collected in these water bodies. Fish diversity was higher in Poyang Lake than in Tian-e-Zhou Reserve, as well as higher in the spring than in summer. These methods provide a broadly applicable tool to quantify fish diversity and distributions throughout the Yangtze River Basin, and to inform conservation strategies of YFP.
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Affiliation(s)
- Chanjuan Qu
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China.,Department of Biology, Queen's University, Kingston, ON, Canada
| | - Kathryn A Stewart
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Jinsong Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology of Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yuxiang Wang
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Cheng Gong
- Administrative Office of Hubei Yangtze Tian'eZhou Baiji National Natural Reserve, Shishou, Hubei, China
| | - Limin Ma
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Jianfu Zhao
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
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McElroy ME, Dressler TL, Titcomb GC, Wilson EA, Deiner K, Dudley TL, Eliason EJ, Evans NT, Gaines SD, Lafferty KD, Lamberti GA, Li Y, Lodge DM, Love MS, Mahon AR, Pfrender ME, Renshaw MA, Selkoe KA, Jerde CL. Calibrating Environmental DNA Metabarcoding to Conventional Surveys for Measuring Fish Species Richness. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00276] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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47
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Zhu WB, Zhao CL, Liao CL, Zou B, Xu D, Zhu W, Zhao T, Jiang JP. Spatial and temporal patterns of amphibian species richness on Tianping Mountain, Hunan Province, China. Zool Res 2020; 41:182-187. [PMID: 31957371 PMCID: PMC7109012 DOI: 10.24272/j.issn.2095-8137.2020.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Wen-Bo Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Lin Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan 637009, China
| | - Chun-Lin Liao
- National Nature Reserve of Badagongshan, Sangzhi, Hunan 427100, China
| | - Bei Zou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China
| | - Dan Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China.,College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Wei Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China
| | - Tian Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China. E-mail:
| | - Jian-Ping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation, Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China. E-mail:
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48
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Furlan EM, Davis J, Duncan RP. Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes. Mol Ecol Resour 2020; 20:1259-1276. [PMID: 32310337 DOI: 10.1111/1755-0998.13170] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 12/18/2022]
Abstract
Environmental DNA (eDNA) metabarcoding surveys enable rapid, noninvasive identification of taxa from trace samples with wide-ranging applications from characterizing local biodiversity to identifying food-web interactions. However, the technique is prone to error from two major sources: (a) contamination through foreign DNA entering the workflow, and (b) misidentification of DNA within the workflow. Both types of error have the potential to obscure true taxon presence or to increase taxonomic richness by incorrectly identifying taxa as present at sample sites, but multiple error sources can remain unaccounted for in metabarcoding studies. Here, we use data from an eDNA metabarcoding study designed to detect vertebrate species at waterholes in Australia's arid zone to illustrate where and how in the workflow errors can arise, and how to mitigate those errors. We detected the DNA of 36 taxa spanning 34 families, 19 orders and five vertebrate classes in water samples from waterholes, demonstrating the potential for eDNA metabarcoding surveys to provide rapid, noninvasive detection in remote locations, and to widely sample taxonomic diversity from aquatic through to terrestrial taxa. However, we initially identified 152 taxa in the samples, meaning there were many false positive detections. We identified the sources of these errors, allowing us to design a stepwise process to detect and remove error, and provide a template to minimize similar errors that are likely to arise in other metabarcoding studies. Our findings suggest eDNA metabarcoding surveys need to be carefully conducted and screened for errors to ensure their accuracy.
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Affiliation(s)
- Elise M Furlan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Jenny Davis
- Research Institute for Environment and Livelihoods, College of Engineering, IT and Environment, Charles Darwin University, Casuarina, NT, Australia
| | - Richard P Duncan
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
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49
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Fraija‐Fernández N, Bouquieaux M, Rey A, Mendibil I, Cotano U, Irigoien X, Santos M, Rodríguez‐Ezpeleta N. Marine water environmental DNA metabarcoding provides a comprehensive fish diversity assessment and reveals spatial patterns in a large oceanic area. Ecol Evol 2020; 10:7560-7584. [PMID: 32760549 PMCID: PMC7391350 DOI: 10.1002/ece3.6482] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/20/2020] [Accepted: 05/23/2020] [Indexed: 01/05/2023] Open
Abstract
Current methods for monitoring marine fish (including bony fishes and elasmobranchs) diversity mostly rely on trawling surveys, which are invasive, costly, and time-consuming. Moreover, these methods are selective, targeting a subset of species at the time, and can be inaccessible to certain areas. Here, we used environmental DNA (eDNA), the DNA present in the water column as part of shed cells, tissues, or mucus, to provide comprehensive information about fish diversity in a large marine area. Further, eDNA results were compared to the fish diversity obtained in pelagic trawls. A total of 44 5 L-water samples were collected onboard a wide-scale oceanographic survey covering about 120,000 square kilometers in Northeast Atlantic Ocean. A short region of the 12S rRNA gene was amplified and sequenced through metabarcoding generating almost 3.5 million quality-filtered reads. Trawl and eDNA samples resulted in the same most abundant species (European anchovy, European pilchard, Atlantic mackerel, and blue whiting), but eDNA metabarcoding resulted in more detected bony fish and elasmobranch species (116) than trawling (16). Although an overall correlation between fishes biomass and number of reads was observed, some species deviated from the common trend, which could be explained by inherent biases of each of the methods. Species distribution patterns inferred from eDNA metabarcoding data coincided with current ecological knowledge of the species, suggesting that eDNA has the potential to draw sound ecological conclusions that can contribute to fish surveillance programs. Our results support eDNA metabarcoding for broad-scale marine fish diversity monitoring in the context of Directives such as the Common Fisheries Policy or the Marine Strategy Framework Directive.
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Affiliation(s)
| | | | - Anaïs Rey
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)SukarrietaSpain
| | - Iñaki Mendibil
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)SukarrietaSpain
| | - Unai Cotano
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
| | - Xabier Irigoien
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
- IKERBASQUEBasque Foundation for ScienceBilbaoSpain
| | - María Santos
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
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50
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Delrieu‐Trottin E, Durand J, Limmon G, Sukmono T, Kadarusman, Sugeha HY, Chen W, Busson F, Borsa P, Dahruddin H, Sauri S, Fitriana Y, Zein MSA, Hocdé R, Pouyaud L, Keith P, Wowor D, Steinke D, Hanner R, Hubert N. Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods. Evol Appl 2020; 13:1451-1467. [PMID: 32684969 PMCID: PMC7359824 DOI: 10.1111/eva.12926] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/25/2022] Open
Abstract
DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.
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Affiliation(s)
- Erwan Delrieu‐Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- Museum für NaturkundeLeibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Jean‐Dominique Durand
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER)Université de MontpellierMontpellier CedexFrance
| | - Gino Limmon
- Maritime and Marine Science Center of ExcellenceUniversitas PattimuraAmbonIndonesia
| | - Tedjo Sukmono
- Department of BiologyUniversitas JambiJambiIndonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan SorongKota SorongIndonesia
| | - Hagi Yulia Sugeha
- Research Center for OceanographyIndonesian Institute of SciencesJakartaIndonesia
| | - Wei‐Jen Chen
- Institute of OceanographyNational Taiwan UniversityTaipeiTaiwan
| | - Frédéric Busson
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN)Muséum National d’Histoire NaturelleParis CedexFrance
| | - Philippe Borsa
- UMR 250 ENTROPIE (IRD, UR, UNC, CNRS, IFREMER), Centre IRD‐OccitanieMontpellierFrance
| | - Hadi Dahruddin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Sopian Sauri
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Yuli Fitriana
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | | | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER)Université de MontpellierMontpellier CedexFrance
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
| | - Philippe Keith
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN)Muséum National d’Histoire NaturelleParis CedexFrance
| | - Daisy Wowor
- Division of ZoologyResearch Center for BiologyIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Dirk Steinke
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Robert Hanner
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE)Université de MontpellierMontpellier CedexFrance
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