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Duval E, Blanchet S, Quéméré E, Jacquin L, Veyssière C, Loot G. When does a parasite become a disease? eDNA unravels complex host-pathogen dynamics across environmental stress gradients in wild salmonid populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174367. [PMID: 38955267 DOI: 10.1016/j.scitotenv.2024.174367] [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: 05/09/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
Infectious diseases stem from disrupted interactions among hosts, parasites, and the environment. Both abiotic and biotic factors can influence infection outcomes by shaping the abundance of a parasite's infective stages, as well as the host's ability to fight infection. However, disentangling these mechanisms within natural ecosystems remains challenging. Here, combining environmental DNA analysis and niche modelling at a regional scale, we uncovered the biotic and abiotic drivers of an infectious disease of salmonid fish, triggered by the parasite Tetracapsuloides bryosalmonae. We found that the occurrence and abundance of the parasite in the water-i.e., the propagule pressure- were mainly correlated to the abundances of its two primary hosts, the bryozoan Fredericella sultana and the fish Salmo trutta, but poorly to local abiotic environmental stressors. In contrast, the occurrence and abundance of parasites within fish hosts-i.e., proxies for disease emergence-were closely linked to environmental stressors (water temperature, agricultural activities, dams), and to a lesser extent to parasite propagule pressure. These results suggest that pathogen distribution alone cannot predict the risk of disease in wildlife, and that local anthropogenic stressors may play a pivotal role in disease emergence among wild host populations, likely by modulating the hosts' immune response. Our study sheds light on the intricate interplay between biotic and abiotic factors in shaping pathogen distribution and raises concerns about the effects of global change on pathogen emergence.
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Affiliation(s)
- Eloïse Duval
- Bureau d'études Fish-Pass, 18 rue de la plaine, 35890 Laillé, France.
| | - Simon Blanchet
- CNRS, Station d'Écologie Théorique et Expérimentale du CNRS, UAR-2029, 2 route du CNRS, F-09200 Moulis, France.
| | - Erwan Quéméré
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, 65 rue de Saint Brieuc F-35042, Rennes, France
| | - Lisa Jacquin
- Université Toulouse III Paul Sabatier, CNRS, IRD, UMR-5300 CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), 118 route de Narbonne, F-31062 Toulouse, France; Institut Universitaire de France, Paris, France
| | - Charlotte Veyssière
- Université Toulouse III Paul Sabatier, CNRS, IRD, UMR-5300 CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), 118 route de Narbonne, F-31062 Toulouse, France
| | - Géraldine Loot
- Université Toulouse III Paul Sabatier, CNRS, IRD, UMR-5300 CRBE (Centre de Recherche sur la Biodiversité et l'Environnement), 118 route de Narbonne, F-31062 Toulouse, France; Institut Universitaire de France, Paris, France
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2
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Dumith MT, Santos AFGN. Use of trophic ecology of omnivorous fish and abiotic factors as supporting tools for assessing environmental impacts in a neotropical river. JOURNAL OF FISH BIOLOGY 2024; 104:780-796. [PMID: 37984817 DOI: 10.1111/jfb.15616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/19/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
The study of diet is one of the mechanisms by which competition for resources between species that cohabit in the same ecosystem can be inferred. Therefore, the relationships of the indices that measure specialization in the diet of fish species are necessary to characterize the nutritional quality of these populations and the ecosystem's environmental health. Three species of catfish were selected: one invasive (Clarias gariepinus) and two natives (Trachelyopterus striatulus and Rhamdia quelen), with similar distribution along the Guapi-Macacu River, in the Guapimirim Protection Area (Rio de Janeiro). Fifty-nine catfish of the three species were collected in total, along 32 collection points in the Guapi-Macacu River in two periods (dry and rainy) in 2018. Non-parametric statistics showed the partition of resources between species and the influence of abiotic factors (temperature, pH, transparency, and dissolved oxygen) contributing to the selection of available resources in the environment. Diet-related indices-repletion index (RI), condition factor (K), niche width, and trophic position (TP) of the specimens collected-contributed to measuring the nutritional status of each of these catfish species, showing that R. quelen has a relationship between RI and K, tending to absorb and metabolize nutrients faster than other species. In addition, the invasive species occupies a wide range of TPs compared to native species, confirming its feeding plasticity. On the contrary, T. striatulus needs large amounts of terrestrial insects to maintain its poor condition factor. Also, the RI showed direct influences of abiotic variables, with the temperature being the most prominent. Our results suggest that the invasive species can benefit from this environment that shows signs of environmental degradation.
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Affiliation(s)
- Michelle Torres Dumith
- Graduate Program in Ocean and Terrestrial Dynamics, Department of Geology, Geosciences Institute, Universidade Federal Fluminense, Niterói, Brazil
| | - Alejandra F G N Santos
- Department of Animal Science and Sustainable Social-Environmental Development, Universidade Federal Fluminense, Niterói, Brazil
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3
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Sun X, Guo N, Gao J, Xiao N. Using eDNA to survey amphibians: Methods, applications, and challenges. Biotechnol Bioeng 2024; 121:456-471. [PMID: 37986625 DOI: 10.1002/bit.28592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.
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Affiliation(s)
- Xiaoxuan Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Ningning Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jianan Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Collage of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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4
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Zhang H, Mächler E, Morsdorf F, Niklaus PA, Schaepman ME, Altermatt F. A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161365. [PMID: 36634788 DOI: 10.1016/j.scitotenv.2022.161365] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/06/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms and resources. Such land-water linkages integrate biodiversity across ecosystems and suggest a spatial association of aquatic and terrestrial biodiversity. However, knowledge about the extent of this spatial association is limited. By combining satellite remote sensing (RS) and environmental DNA (eDNA) extraction from river water across a 740-km2 mountainous catchment, we identify a characteristic spatial land-water fingerprint. Specifically, we find a spatial association of riverine eDNA diversity with RS spectral diversity of terrestrial ecosystems upstream, peaking at a 400 m distance yet still detectable up to a 2.0 km radius. Our findings show that biodiversity patterns in rivers can be linked to the functional diversity of surrounding terrestrial ecosystems and provide a dominant scale at which these linkages are strongest. Such spatially explicit information is necessary for a functional understanding of land-water linkages.
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Affiliation(s)
- Heng Zhang
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.
| | - Elvira Mächler
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Felix Morsdorf
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Michael E Schaepman
- Remote Sensing Laboratories, Department of Geography, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Aquatic Ecology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland.
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5
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Sanders M, Tardani R, Locher A, Geller K, Partridge CG. Development of Novel Early Detection Technology for Hemlock Woolly Adelgid, Adelges tsugae (Hemiptera: Adelgidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:168-180. [PMID: 36421054 PMCID: PMC9912136 DOI: 10.1093/jee/toac175] [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: 06/26/2022] [Indexed: 06/16/2023]
Abstract
Hemlock woolly adelgid (HWA), Adelges tsugae Annand, threatens hemlock forests throughout eastern North America. Management efforts focus on early detection of HWA to ensure rapid management responses to control and stop the spread of this pest. This study's goal was to identify an affordable, efficient trap to aid with airborne environmental DNA (eDNA) sampling approaches as an early monitoring tool for HWA. We initially compared HWA detection success between a standard sticky trap, commonly used for HWA monitoring, and trap designs potentially compatible with eDNA protocols (i.e., passive trap, funnel trap, and motorized trap). Passive, funnel, and motorized traps' estimated capture success probabilities compared to sticky traps were 0.87, 0.8, and 0.4, respectively. A secondary evaluation of a modified version of the motorized trap further assessed trap performance and determined the number of traps needed in a set area to efficiently detect HWA. By modifying the original motorized trap design, its estimated capture success probability increased to 0.67 compared to a sticky trap. Overall, the cumulative capture success over the 16-week sampling period for the motorized trap was 94% and 99% for the sticky trap. The number of traps did impact capture success, and trap elevation and distance to infested hemlocks influenced the number of adelgids captured per trap. As eDNA-based monitoring approaches continue to become incorporated into invasive species surveying, further refinement with these types of traps can be useful as an additional tool in the manager's toolbox.
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Affiliation(s)
| | - Renee Tardani
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
| | - Alexandra Locher
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Kathryn Geller
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
| | - Charlyn G Partridge
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
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6
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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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7
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Rangaswamy B, Ji CW, Kim WS, Park JW, Kim YJ, Kwak IS. Profiling Analysis of Filter Feeder Polypedilum (Chironomidae) Gut Contents Using eDNA Metabarcoding Following Contrasting Habitat Types-Weir and Stream. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10945. [PMID: 36078662 PMCID: PMC9517803 DOI: 10.3390/ijerph191710945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
We analyzed the dietary composition of Polypedilum larvae among two contrasting habitats (river and weir). Our approach was (i) to apply eDNA-based sampling to reveal the gut content of the chironomid larvae, (ii) the diversity of gut contents in the two aquatic habitats, and (iii) assessment of habitat sediment condition with the food sources in the gut. The most abundant food was Chlorophyta in the gut of the river (20%) and weir (39%) chironomids. The average ratio of fungi, protozoa, and zooplankton in river chironomids gut was 5.9%, 7.2%, and 3.8%, while it was found decreased to 1.2%, 2.5%, and 0.1% in weir chironomids. Aerobic fungi in river midge guts were 3.6% and 10.34% in SC and IS, while they were in the range of 0.34-2.58% in weir midges. The hierarchical clustering analysis showed a relationship of environmental factors with food contents. Abiotic factors (e.g., pH) in the river and weir habitats correlated the clustered pattern with phytoplankton and minor groups of fungi. This study could help understand the food source diversity in the chironomid and habitat environmental conditions by using eDNA metabarcoding as an effective tool to determine dietary composition.
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Affiliation(s)
- Boobal Rangaswamy
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
| | - Chang Woo Ji
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
| | - Won-Seok Kim
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Jae-Won Park
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Yong Jun Kim
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
| | - Ihn-Sil Kwak
- Fisheries Science Institute, Chonnam National University, Yeosu 59626, Korea
- Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea
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8
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Molik DC. met v1: expanding on old estimations of biodiversity from eDNA with a new database framework. Database (Oxford) 2022; 2022:6583522. [PMID: 35543254 PMCID: PMC9216496 DOI: 10.1093/database/baac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/10/2022] [Accepted: 04/28/2022] [Indexed: 11/14/2022]
Abstract
Abstract
A long-standing problem in environmental DNA has been the inability to compute across large number of datasets. Here we introduce an open-source software framework that can store a large number of environmental DNA datasets, as well as provide a platform for analysis, in an easily customizable way. We show the utility of such an approach by analyzing over 1400 arthropod metabarcode datasets. This article introduces a new software framework, met, which utilizes large numbers of metabarcode datasets to draw conclusions about patterns of diversity at large spatial scales. Given more accurate estimations on the distribution of variance in metabarcode datasets, this software framework could facilitate novel analyses that are outside the scope of currently available similar platforms.
Database URL https://osf.io/spb8v/
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Affiliation(s)
- David C Molik
- Navari Family Center for Digital Scholarship, Hesburgh Library, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
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9
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Evaluating eDNA for Use within Marine Environmental Impact Assessments. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this review, the use of environmental DNA (eDNA) within Environmental Impact Assessment (EIA) is evaluated. EIA documents provide information required by regulators to evaluate the potential impact of a development project. Currently eDNA is being incorporated into biodiversity assessments as a complementary method for detecting rare, endangered or invasive species. However, questions have been raised regarding the maturity of the field and the suitability of eDNA information as evidence for EIA. Several key issues are identified for eDNA information within a generic EIA framework for marine environments. First, it is challenging to define the sampling unit and optimal sampling strategy for eDNA with respect to the project area and potential impact receptor. Second, eDNA assay validation protocols are preliminary at this time. Third, there are statistical issues around the probability of obtaining both false positives (identification of taxa that are not present) and false negatives (non-detection of taxa that are present) in results. At a minimum, an EIA must quantify the uncertainty in presence/absence estimates by combining series of Bernoulli trials with ad hoc occupancy models. Finally, the fate and transport of DNA fragments is largely unknown in environmental systems. Shedding dynamics, biogeochemical and physical processes that influence DNA fragments must be better understood to be able to link an eDNA signal with the receptor’s state. The biggest challenge is that eDNA is a proxy for the receptor and not a direct measure of presence. Nonetheless, as more actors enter the field, technological solutions are likely to emerge for these issues. Environmental DNA already shows great promise for baseline descriptions of the presence of species surrounding a project and can aid in the identification of potential receptors for EIA monitoring using other methods.
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10
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Korbel KL, Greenfield P, Hose GC. Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150870. [PMID: 34627912 DOI: 10.1016/j.scitotenv.2021.150870] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.
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Affiliation(s)
- K L Korbel
- Department of Biological Sciences, Macquarie University, Australia.
| | | | - G C Hose
- Department of Biological Sciences, Macquarie University, Australia
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11
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Astuto MC, Di Nicola MR, Tarazona JV, Rortais A, Devos Y, Liem AKD, Kass GEN, Bastaki M, Schoonjans R, Maggiore A, Charles S, Ratier A, Lopes C, Gestin O, Robinson T, Williams A, Kramer N, Carnesecchi E, Dorne JLCM. In Silico Methods for Environmental Risk Assessment: Principles, Tiered Approaches, Applications, and Future Perspectives. Methods Mol Biol 2022; 2425:589-636. [PMID: 35188648 DOI: 10.1007/978-1-0716-1960-5_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This chapter aims to introduce the reader to the basic principles of environmental risk assessment of chemicals and highlights the usefulness of tiered approaches within weight of evidence approaches in relation to problem formulation i.e., data availability, time and resource availability. In silico models are then introduced and include quantitative structure-activity relationship (QSAR) models, which support filling data gaps when no chemical property or ecotoxicological data are available. In addition, biologically-based models can be applied in more data rich situations and these include generic or species-specific models such as toxicokinetic-toxicodynamic models, dynamic energy budget models, physiologically based models, and models for ecosystem hazard assessment i.e. species sensitivity distributions and ultimately for landscape assessment i.e. landscape-based modeling approaches. Throughout this chapter, particular attention is given to provide practical examples supporting the application of such in silico models in real-world settings. Future perspectives are discussed to address environmental risk assessment in a more holistic manner particularly for relevant complex questions, such as the risk assessment of multiple stressors and the development of harmonized approaches to ultimately quantify the relative contribution and impact of single chemicals, multiple chemicals and multiple stressors on living organisms.
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Affiliation(s)
| | | | | | - A Rortais
- European Food Safety Authority, Parma, Italy
| | - Yann Devos
- European Food Safety Authority, Parma, Italy
| | | | | | | | | | | | | | | | | | | | | | - Antony Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency (U.S. EPA), Research Triangle Park, NC, USA
| | - Nynke Kramer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Edoardo Carnesecchi
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
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12
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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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13
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Gold Z, Curd EE, Goodwin KD, Choi ES, Frable BW, Thompson AR, Walker HJ, Burton RS, Kacev D, Martz LD, Barber PH. Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem. Mol Ecol Resour 2021; 21:2546-2564. [PMID: 34235858 DOI: 10.1111/1755-0998.13450] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023]
Abstract
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Emma S Choi
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Benjamin W Frable
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Andrew R Thompson
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Harold J Walker
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Ronald S Burton
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Dovi Kacev
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Lucas D Martz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
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14
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Hirohara T, Tsuri K, Miyagawa K, Paine RTR, Yamanaka H. The Application of PMA (Propidium Monoazide) to Different Target Sequence Lengths of Zebrafish eDNA: A New Approach Aimed Toward Improving Environmental DNA Ecology and Biological Surveillance. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.632973] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Environmental DNA (eDNA) analysis has enabled more sensitive and efficient biological monitoring than traditional methods. However, since the target species is not directly observed, interpretation of results cannot preclude process Type I errors. Specifically, there may be a spatial or temporal gap between the target eDNA and the eDNA source in the sampled area. Moreover, eDNA surveillance lacks the ability to distinguish whether eDNA originated from a living or non-living source. This kind of Type I error is difficult to control for, in part, because the relationship between the state of eDNA (i.e., intracellular or extracellular) and the degradation rate is still unclear. Here, we applied PMA (Propidium monoazide) to eDNA analysis which enabled us to differentiate “intact cells” from “disrupted cells.” PMA is a dye that has a high affinity for double-stranded DNA and forms a covalent bond with double-stranded DNA and inhibits amplification of the bonded DNA molecules by PCR. Since PMA is impermeable to the cell membrane, DNA protected by an intact cell membrane can be selectively detected. In this study, we investigated the workability of PMA on vertebrate eDNA using zebrafish, Danio rerio. Aquarium water was incubated for 1 week to monitor the eDNA degradation process of both intracellular and extracellular eDNA. We developed ten species-specific quantitative PCR assays for D. rerio with different amplification lengths that enabled independent quantification of total eDNA (sum of intracellular and extracellular eDNA, commonly measured in other studies) and intracellular eDNA (DNA in intact cells) and allow for analyses of sequence length-dependent eDNA degradation in combination with PMA. We confirmed that PMA is effective at differentiating “intact” and “disrupted” fish cells. We found that total eDNA and intracellular eDNA have different degradation processes that are dependent on the length of target sequence. For future conservation efforts using eDNA analyses, it is necessary to increase the reliability of the analysis results. The research presented here provides new analysis tools that expand our understanding of the ecology of eDNA, so that more accurate and reliable conclusions can be determined.
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15
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eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Sci Rep 2021; 11:6820. [PMID: 33767219 PMCID: PMC7994446 DOI: 10.1038/s41598-021-85488-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/24/2021] [Indexed: 01/31/2023] Open
Abstract
With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.
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16
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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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17
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Brys R, Halfmaerten D, Neyrinck S, Mauvisseau Q, Auwerx J, Sweet M, Mergeay J. Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis). JOURNAL OF FISH BIOLOGY 2021; 98:399-414. [PMID: 32154579 DOI: 10.1111/jfb.14315] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/24/2019] [Accepted: 03/07/2020] [Indexed: 06/10/2023]
Abstract
The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)-based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA-based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl-1 , respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017-2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample-specific estimates of effective DNA quantity (Qe ) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false-negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.
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Affiliation(s)
- Rein Brys
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | | | - Sabrina Neyrinck
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Quentin Mauvisseau
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
- SureScreen Scientifics Ltd, Morley, UK
| | - Johan Auwerx
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
- SureScreen Scientifics Ltd, Morley, UK
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
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18
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Andres KJ, Sethi SA, Lodge DM, Andrés J. Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples. Mol Ecol 2021; 30:685-697. [PMID: 33433059 PMCID: PMC7898893 DOI: 10.1111/mec.15765] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022]
Abstract
Advances in environmental DNA (eDNA) methodologies have led to improvements in the ability to detect species and communities in aquatic environments, yet the majority of studies emphasize biological diversity at the species level by targeting variable sites within the mitochondrial genome. Here, we demonstrate that eDNA approaches also have the capacity to detect intraspecific diversity in the nuclear genome, allowing for assessments of population-level allele frequencies and estimates of the number of genetic contributors in an eDNA sample. Using a panel of microsatellite loci developed for the round goby (Neogobius melanostomus), we tested the similarity between eDNA-based and individual tissue-based estimates of allele frequencies from experimental mesocosms and in a field-based trial. Subsequently, we used a likelihood-based DNA mixture framework to estimate the number of unique genetic contributors in eDNA samples and in simulated mixtures of alleles. In both mesocosm and field samples, allele frequencies from eDNA were highly correlated with allele frequencies from genotyped round goby tissue samples, indicating nuclear markers can be reliably amplified from water samples. DNA mixture analyses were able to estimate the number of genetic contributors from mesocosm eDNA samples and simulated mixtures of DNA from up to 58 individuals, with the degree of positive or negative bias dependent on the filtering scheme of low-frequency alleles. With this study we document the application of eDNA and multiple amplicon-based methods to obtain intraspecific nuclear genetic information and estimate the absolute abundance of a species in eDNA samples. With proper validation, this approach has the potential to advance noninvasive survey methods to characterize populations and detect population-level genetic diversity.
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Affiliation(s)
- Kara J Andres
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Suresh A Sethi
- U.S. Geological Survey, New York Cooperative Fish and Wildlife Unit, Cornell University, Ithaca, NY, USA
| | - David M Lodge
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, USA
| | - Jose Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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19
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Brys R, Haegeman A, Halfmaerten D, Neyrinck S, Staelens A, Auwerx J, Ruttink T. Monitoring of spatiotemporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA. Mol Ecol 2020; 30:3097-3110. [PMID: 33222312 PMCID: PMC8359355 DOI: 10.1111/mec.15742] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/29/2020] [Accepted: 11/02/2020] [Indexed: 12/21/2022]
Abstract
To effectively monitor, manage and protect aquatic species and understand their interactions, knowledge of their spatiotemporal distribution is needed. In this study, we used a fine-scale spatiotemporal water sampling design, followed by environmental DNA (eDNA) 12S metabarcoding, to investigate occupancy patterns of a natural community of fish and amphibian species in a lentic system. In the same system, we experimentally estimated the spatial and temporal dispersion of eDNA by placing a community of different fish and amphibian species in cages at one side of the pond, creating a controlled point of eDNA emission. Analyses of this cage community revealed a sharp spatial decline in detection rates and relative eDNA quantities at a distance of 5-10 m from the source, depending on the species and its abundance. In addition, none of the caged species could be detected 1 week after removal from the system. This indicates high eDNA decay rates and limited spatial eDNA dispersal, facilitating high local resolution for monitoring spatial occupancy patterns of aquatic species. Remarkably, for seven of the nine cage species, the presence of a single individual could be detected by pooling water of subsamples taken across the whole water body, illustrating the high sensitivity of the eDNA sampling and detection method applied. Finally, our work demonstrated that a fine-scale sampling design in combination with eDNA metabarcoding can cover total biodiversity very precisely and allows the construction of consistent spatiotemporal patterns of relative abundance and local distribution of free-living fish and amphibian species in a lentic ecosystem.
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Affiliation(s)
- Rein Brys
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | | | - Sabrina Neyrinck
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Ariane Staelens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Johan Auwerx
- Research Institute for Nature and Forest, Linkebeek, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
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20
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Kusanke LM, Panteleit J, Stoll S, Korte E, Sünger E, Schulz R, Theissinger K. Detection of the endangered European weather loach ( Misgurnus fossilis) via water and sediment samples: Testing multiple eDNA workflows. Ecol Evol 2020; 10:8331-8344. [PMID: 32788983 PMCID: PMC7417210 DOI: 10.1002/ece3.6540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/02/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
The European weather loach (Misgurnus fossilis) is classified as highly endangered in several countries of Central Europe. Populations of M. fossilis are predominantly found in ditches with low water levels and thick sludge layers and are thus hard to detect using conventional fishing methods. Therefore, environmental DNA (eDNA) monitoring appears particularly relevant for this species. In previous studies, M. fossilis was surveyed following eDNA water sampling protocols, which were not optimized for this species. Therefore, we created two full factorial study designs to test six different eDNA workflows for sediment samples and twelve different workflows for water samples. We used qPCR to compare the threshold cycle (C t) values of the different workflows, which indicate the target DNA amount in the sample, and spectrophotometry to quantify and compare the total DNA amount inside the samples. We analyzed 96 water samples and 48 sediment samples from a pond with a known population of M. fossilis. We tested several method combinations for long-term sample preservation, DNA capture, and DNA extraction. Additionally, we analyzed the DNA yield of samples from a ditch with a natural M. fossilis population monthly over one year to determine the optimal sampling period. Our results showed that the long-term water preservation method commonly used for eDNA surveys of M. fossilis did not lead to optimal DNA yields, and we present a valid long-term sample preservation alternative. A cost-efficient high salt DNA extraction led to the highest target DNA yields and can be used for sediment and water samples. Furthermore, we were able to show that in a natural habitat of M. fossilis, total and target eDNA were higher between June and September, which implies that this period is favorable for eDNA sampling. Our results will help to improve the reliability of future eDNA surveys of M. fossilis.
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Affiliation(s)
| | | | - Stefan Stoll
- Umwelt‐Campus BirkenfeldHoppstädten‐WeiersbachGermany
| | - Egbert Korte
- Institut für Gewässer‐ und Auenökologie GbRGriesheimGermany
| | | | - Ralf Schulz
- Eusserthal Ecosystem Research StationUniversity of Koblenz‐LandauEusserthalGermany
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21
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Stratton C, Sepulveda AJ, Hoegh A. msocc: Fit and analyse computationally efficient multi‐scale occupancy models in
r. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13442] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christian Stratton
- Department of Mathematical Sciences Montana State University Bozeman MT USA
| | - Adam J. Sepulveda
- Northern Rocky Mountain Science CenterU.S. Geological Survey Bozeman MT USA
| | - Andrew Hoegh
- Department of Mathematical Sciences Montana State University Bozeman MT USA
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22
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Postaire BD, Bakker J, Gardiner J, Wiley TR, Chapman DD. Environmental DNA detection tracks established seasonal occurrence of blacktip sharks (Carcharhinus limbatus) in a semi-enclosed subtropical bay. Sci Rep 2020; 10:11847. [PMID: 32678294 PMCID: PMC7367289 DOI: 10.1038/s41598-020-68843-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/29/2020] [Indexed: 11/27/2022] Open
Abstract
The integration of eDNA analysis into the population assessment and monitoring of sharks could greatly improve temporal and spatial data used for management purposes. This study aimed to compare eDNA detection against well-established seasonal changes in blacktip shark (Carcharhinus limbatus) abundance in Terra Ceia Bay (FL, USA). We used a species-specific real-time PCR approach to detect C. limbatus eDNA in the bay on a near monthly basis from spring through mid-fall in 2018 and 2019. Previous studies have shown that C. limbatus give birth in the bay in early summer and immature sharks occur there until late fall, when decreasing water temperatures cause them to move offshore and southwards. Water samples (2 L) were collected (4–6 per month) and filtered in the field, with each then being subjected to real-time PCR. Carcharhinus limbatus ‘positive’ filters were significantly more commonly collected during the April-July sampling period than during the August-October sampling period. While following the predicted pattern, eDNA concentration was generally too low for accurate quantification. Our results show that C. limbatus eDNA detection follows known seasonal residency patterns consistently over 2 years of monitoring. Species-specific eDNA analysis using real-time PCR could therefore represent a cost-effective, scalable sampling tool to facilitate improved shark population monitoring in semi-enclosed marine habitats.
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Affiliation(s)
- Bautisse D Postaire
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL, 33181, USA.
| | - Judith Bakker
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL, 33181, USA
| | - Jayne Gardiner
- Division of Natural Sciences, New College of Florida, 5800 Bayshore Rd, Sarasota, FL, 34243, USA
| | - Tonya R Wiley
- Havenworth Coastal Conservation, 5120 Beacon Road, Palmetto, FL, 34221, USA
| | - Demian D Chapman
- Department of Biological Sciences, Florida International University, 3000 NE 151st Street, North Miami, FL, 33181, USA
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23
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Itakura H, Wakiya R, Sakata MK, Hsu HY, Chen SC, Yang CC, Huang YC, Han YS, Yamamoto S, Minamoto T. Estimations of Riverine Distribution, Abundance, and Biomass of Anguillid Eels in Japan and Taiwan Using Environmental DNA Analysis. Zool Stud 2020; 59:e17. [PMID: 33262841 PMCID: PMC7688404 DOI: 10.6620/zs.2020.59-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/21/2020] [Indexed: 11/18/2022]
Abstract
Although populations of anguillid eels have declined remarkably in recent decades, monitoring data on the spatial and temporal variation in their dynamics are often limited, particularly for tropical eel species. As there are often sympatries of multiple eel species in tropical rivers, identifying eel species based solely on morphological characteristics is challenging. Basin-scale surveys were conducted in rivers of southern Japan and northern Taiwan to investigate (1) whether the spatial distribution, abundance, and biomass of the tropical eel species, the giant mottled eel (Anguilla marmorata), can be monitored in rivers by comparing the results obtained from environmental DNA (eDNA) analysis with data from electrofishing and (2) the riverine distribution of the sympatric A. marmorata and the temperate eel species, the Japanese eel (Anguilla japonica), in this region using eDNA analysis. Although we found an much lower abundance of A. marmorata in the study region, we identified the eDNA of the species from all of the study sites (21 sites) where it was collected by electrofishing, in addition to 22 further study sites where it was not collected directly. This indicates that eDNA analysis has a greater sensitivity for detecting A. marmorata, making it a powerful tool for monitoring the spatial distribution of the species in rivers. We found a significant positive relationship between eDNA concentration and both the abundance and biomass of A. marmorata, and eDNA concentration seemed to better reflect the abundance of the species than did biomass. eDNA of both A. japonica and A. marmorata was identified from almost all rivers, indicating the sympatry of these species in this region, although the degree of sympatry differed between rivers. Though the eDNA concentration of A. japonica decreased significantly with increasing distance from the river mouth, no significant relationship was found for A. marmorata. This study is the first to demonstrate the potential usefulness of eDNA analysis for estimating the spatial distribution, abundance, and biomass of tropical eels in rivers and to further apply this method to investigate sympatry among anguillid species. eDNA analysis can help in obtaining data on the population dynamics of tropical eels, providing invaluable information for managing these species.
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Affiliation(s)
- Hikaru Itakura
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, 146 Williams St., Solomons, MD 20688, USA
- Graduate School of Science, Kobe University, 1-1 Rokkoudaichou, Nadaku, Kobe, Hyogo 657-8501, Japan
| | - Ryoshiro Wakiya
- Research and Development Initiative, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan. E-mail: (Wakiya)
| | - Masayuki K Sakata
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nadaku, Kobe, Hyogo 657-8501, Japan. E-mail: (Sakata); (Minamoto)
| | - Hsiang-Yi Hsu
- Institute of Fisheries Science, College of Life Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan. E-mail: (Hsu); (Chen); (Yang); (Huang); (Han)
| | - Shih-Chong Chen
- Institute of Fisheries Science, College of Life Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan. E-mail: (Hsu); (Chen); (Yang); (Huang); (Han)
| | - Chih-Chao Yang
- Institute of Fisheries Science, College of Life Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan. E-mail: (Hsu); (Chen); (Yang); (Huang); (Han)
| | - Yi-Cheng Huang
- Institute of Fisheries Science, College of Life Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan. E-mail: (Hsu); (Chen); (Yang); (Huang); (Han)
| | - Yu-San Han
- Institute of Fisheries Science, College of Life Science, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan. E-mail: (Hsu); (Chen); (Yang); (Huang); (Han)
| | - Satoshi Yamamoto
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan. E-mail: (Yamamoto)
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nadaku, Kobe, Hyogo 657-8501, Japan. E-mail: (Sakata); (Minamoto)
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24
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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25
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Shu L, Ludwig A, Peng Z. Standards for Methods Utilizing Environmental DNA for Detection of Fish Species. Genes (Basel) 2020; 11:E296. [PMID: 32168762 PMCID: PMC7140814 DOI: 10.3390/genes11030296] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/13/2020] [Accepted: 03/07/2020] [Indexed: 11/30/2022] Open
Abstract
Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.
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Affiliation(s)
- Lu Shu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China;
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China;
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Bedwell ME, Goldberg CS. Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems. Ecol Evol 2020; 10:1602-1612. [PMID: 32076537 PMCID: PMC7029092 DOI: 10.1002/ece3.6014] [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: 10/16/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/31/2022] Open
Abstract
The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow-legged frog (Rana sierrae) and the foothill yellow-legged frog (Rana boylii). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2-9.19X) in our protocol, from a probability of 0.51-0.85 per technical replicate. Lake sample volumes were limited by filter clogging, and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3-2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow-legged frog eDNA captured in streams ceased between 100 and 200 m, indicating that sampling at close intervals is important.
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Altermatt F, Little CJ, Mächler E, Wang S, Zhang X, Blackman RC. Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems. OIKOS 2020. [DOI: 10.1111/oik.06806] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Florian Altermatt
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Chelsea J. Little
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Elvira Mächler
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
| | - Shaopeng Wang
- Inst. of Ecology, College of Urban and Environmental Science, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking Univ. Beijing PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing Univ. Nanjing PR China
| | - Rosetta C. Blackman
- Eawag, Swiss Federal Inst. of Aquatic Science and Technology, Dept of Aquatic Ecology Überlandstrasse 133 CH‐8600 Dübendorf Switzerland
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstr. 190 CH‐8057 Zürich Switzerland
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Pochardt M, Allen JM, Hart T, Miller SDL, Yu DW, Levi T. Environmental DNA facilitates accurate, inexpensive, and multiyear population estimates of millions of anadromous fish. Mol Ecol Resour 2019; 20:457-467. [DOI: 10.1111/1755-0998.13123] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Meredith Pochardt
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
- Chilkoot Indian Association Haines AK USA
- Takshanuk Watershed Council Haines AK USA
| | - Jennifer M. Allen
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Ted Hart
- Chilkoot Indian Association Haines AK USA
| | - Sophie D. L. Miller
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
- School of Biological Sciences University of East Anglia Norwich UK
| | - Taal Levi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
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Capo E, Spong G, Norman S, Königsson H, Bartels P, Byström P. Droplet digital PCR assays for the quantification of brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) from environmental DNA collected in the water of mountain lakes. PLoS One 2019; 14:e0226638. [PMID: 31851707 PMCID: PMC6919618 DOI: 10.1371/journal.pone.0226638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/01/2019] [Indexed: 01/02/2023] Open
Abstract
Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populations by applying the droplet digital PCR (ddPCR) method to eDNA molecules extracted from water samples collected in 28 Swedish mountain lakes. Overall, contemporary fish CPUE (catch per unit effort) estimates from standardized survey gill nettings were not correlated to eDNA concentrations for either of the species. In addition, the measured environmental variables (e.g. dissolved organic carbon concentrations, temperature, and pH) appear to not influence water eDNA concentrations of the studied fish species. Detection probabilities via eDNA analysis showed moderate success (less than 70% for both species) while the presence of eDNA from Arctic char (in six lakes) and brown trout (in one lake) was also indicated in lakes where the species were not detected with the gillnetting method. Such findings highlight the limits of one or both methods to reliably detect fish species presence in natural systems. Additional analysis showed that the filtration of water samples through 1.2 μm glass fiber filters and 0.45 μm mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 μm enclosed polyethersulfone filters, probably due to differential efficiencies of DNA extraction. Altogether, this work showed the potentials and limits of the approach for the detection and the quantification of fish abundance in natural systems while providing new insights in the application of the ddPCR method applied to environmental DNA.
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Affiliation(s)
- Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden
| | - Sven Norman
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Helena Königsson
- Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden
| | - Pia Bartels
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Pär Byström
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
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Development and validation of rapid environmental DNA (eDNA) detection methods for bog turtle (Glyptemys muhlenbergii). PLoS One 2019; 14:e0222883. [PMID: 31725720 PMCID: PMC6855662 DOI: 10.1371/journal.pone.0222883] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/09/2019] [Indexed: 11/24/2022] Open
Abstract
Bog turtles (Glyptemys muhlenbergii) are listed as Species of Greatest Conservation Need (SGCN) for wildlife action plans in every state it occurs and multi-state efforts are underway to better characterize extant populations and prioritize restoration efforts. However, traditional sampling methods can be ineffective due to the turtle’s wetland habitat, small size, and burrowing nature. Molecular methods, such as qPCR, provide the ability to overcome this challenge by effectively quantifying minute amounts of turtle DNA left behind in its environment (eDNA). Developing such methods for bog turtles has proved difficult partly because of the high sequence similarity between bog turtles and closely-related, cohabitating species, most often wood turtles (Glyptemys insculpta). Additionally, substrates containing bog turtle eDNA are often rich in organics or other substances that frequently inhibit both DNA extraction and qPCR amplification. Here, we describe the development and validation of a qPCR assay, BT3, targeting the mitochondrial cytochrome oxidase I gene that correctly identifies bog turtles with 100% specificity and sensitivity when tested on 201 blood samples collected from six species over a wide geographic range. We also developed a full-process internal control employing a genetically modified strain of Caenorhabditis elegans to improve DNA extraction methods, limit false negative results due to qPCR inhibition, and measure total DNA recovery from each sample. Using the internal control, we found that DNA recovery varied by over an order of magnitude between samples and likely explains the lack of bog turtle detection in some cases. Methods presented herein are highly-specific and may offer a more cost effective, non-invasive tool to supplement bog turtle population assessments in the Eastern United States. Poor or differential DNA recovery, which remains unmeasured in the vast majority of eDNA studies, significantly reduced the ability to detect bog turtle in their natural environment.
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Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02102-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Erickson RA, Merkes CM, Mize EL. Sampling Designs for Landscape-level eDNA Monitoring Programs. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2019; 15:760-771. [PMID: 30963692 DOI: 10.1002/ieam.4155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/20/2018] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
Effective natural resources management requires accurate information about species distributions. Environmental DNA (eDNA) analysis is a commonly used method to determine species presence and distribution. However, when understanding eDNA-based distribution data, managers must contend with imperfect detection in collection samples and subsamples (i.e., molecular analyses) impacting their ability to detect species and estimate occurrence. Occurrence models can estimate 3 probabilities: occurrence, capture, and eDNA detection. However, most occurrence models do not. To quantify imperfect detection in rare versus common species, we examined multiple field capture and detection probabilities. We studied this with 3 objectives: Determine sample sizes required to detect eDNA given imperfect detection, determine sample sizes required to estimate eDNA capture parameters, and examine performance of a 3-level occurrence model. We found detecting eDNA in ≥1 sample at a site required ≤15 samples per site for common species, but detecting eDNA when looking for rare species required 45 to 90 samples per site. Our occurrence model recovered known parameters unless capture and detection probabilities were <0.2 where >100 samples per site and ≥8 molecular replicates were required. Our findings illustrate the importance of sample size and molecular replication for eDNA-based work. Integr Environ Assess Manag 2019;15:760-771. Published 2019. This article is a US Government work and is in the public domain in the USA.
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Affiliation(s)
- Richard A Erickson
- Upper Midwest Environmental Sciences Center, US Geological Survey, La Crosse, Wisconsin
| | - Christopher M Merkes
- Upper Midwest Environmental Sciences Center, US Geological Survey, La Crosse, Wisconsin
| | - Erica L Mize
- Whitney Genetics Laboratory, Midwest Fisheries Center, US Fish and Wildlife Service, Onalaska, Wisconsin
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Moushomi R, Wilgar G, Carvalho G, Creer S, Seymour M. Environmental DNA size sorting and degradation experiment indicates the state of Daphnia magna mitochondrial and nuclear eDNA is subcellular. Sci Rep 2019; 9:12500. [PMID: 31467341 PMCID: PMC6715800 DOI: 10.1038/s41598-019-48984-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/13/2019] [Indexed: 12/04/2022] Open
Abstract
Environmental DNA analysis has emerged as a key component of biodiversity and environmental monitoring. However, the state and fate of eDNA in natural environments is still poorly understood for many ecological systems. Here we assess the state and fate of eDNA derived from the water flea, Daphnia magna, using a full factorial mesocosm experiment. We measured the quantity and degradation of eDNA over a two month period across a range of filters differing in pore size (0, 0.2, 1 and 10 µm), which spans the range of eDNA source material including subcellular, cellular and tissue. We also used two primer sets targeting mitochondrial (COI) and nuclear (18S) genomic regions. Our findings demonstrated that eDNA was most prevalent in the effluent water, but also reliably detected on the 0.2 μm filter, suggesting subcellular material is the predominate state of eDNA. Temporal eDNA quantity dynamics followed an exponential decay function over the course of 6-17 days, demonstrating a predictable decline in eDNA concentration. Nuclear eDNA was more abundant than mitochondrial eDNA, which may be a result of greater primer affinity, or indicate greater availability of nuclear eDNA gene targets in the environment. In contrast to two previous size-sorting experiments, which utilizing fish eDNA, our findings suggest that the state of invertebrate eDNA is much smaller than previously suspected. Overall, our data suggest that the detection of eDNA greatly depends on our knowledge of the state and fate of eDNA, which differ among species, and likely across environmental conditions.
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Affiliation(s)
- Rashnat Moushomi
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Gregory Wilgar
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Mathew Seymour
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
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Investigating the distribution of the Yangtze finless porpoise in the Yangtze River using environmental DNA. PLoS One 2019; 14:e0221120. [PMID: 31398225 PMCID: PMC6688821 DOI: 10.1371/journal.pone.0221120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/30/2019] [Indexed: 11/19/2022] Open
Abstract
Determining the distribution of the Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) in the Yangtze River has to date relied on traditional visual and counting methods, but such field surveys are time-consuming and expensive. Analyses using environmental DNA (eDNA) to investigate the presence and range of endangered aquatic species have proven to be more economical and effective detection methods, and are a non-invasive approach to sampling. A challenge of relying on eDNA for YFP monitoring is that the Yangtze River is characterized by high turbidity and a strong current. Here, we used an eDNA-based approach to estimate the presence of YFP at 18 sites in the Yangtze River in August 2017 and at an additional 11 sites in January 2018. At each sampling site, we filtered six 1 L water samples with 5 µm pore size filter paper and quantified the amount of YFP eDNA in each water sample using quantitative real-time polymerase chain reaction (qPCR). In addition, YFP eDNA was successfully detected in locations where we visually observed YFP, as well as in locations where YFP were not observed directly. We found that our eDNA-based method had higher detection rates than traditional field survey methods. Although YFP was visually observed in the Yangtze River in winter, water samples collected during the summer contained significantly higher YFP eDNA than winter water samples. Our results demonstrate the potential effectiveness of eDNA detection methods in determining the distribution of YFP in the Yangtze River.
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Bischof JC, Diller KR. From Nanowarming to Thermoregulation: New Multiscale Applications of Bioheat Transfer. Annu Rev Biomed Eng 2019; 20:301-327. [PMID: 29865870 DOI: 10.1146/annurev-bioeng-071516-044532] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This review explores bioheat transfer applications at multiple scales from nanoparticle (NP) heating to whole-body thermoregulation. For instance, iron oxide nanoparticles are being used for nanowarming, which uniformly and quickly rewarms 50-80-mL (≤5-cm-diameter) vitrified systems by coupling with radio-frequency (RF) fields where standard convective warming fails. A modification of this approach can also be used to successfully rewarm cryopreserved fish embryos (∼0.8 mm diameter) by heating previously injected gold nanoparticles with millisecond pulsed laser irradiation where standard convective warming fails. Finally, laser-induced heating of gold nanoparticles can improve the sensitivity of lateral flow assays (LFAs) so that they are competitive with laboratory tests such as the enzyme-linked immunosorbent assay. This approach addresses the main weakness of LFAs, which are otherwise the cheapest, easiest, and fastest to use point-of-care diagnostic tests in the world. Body core temperature manipulation has now become possible through selective thermal stimulation (STS) approaches. For instance, simple and safe heating of selected areas of the skin surface can open arteriovenous anastomosis flow in glabrous skin when it is not already established, thereby creating a convenient and effective pathway to induce heat flow between the body core and environment. This has led to new applications of STS to increase or decrease core temperatures in humans and animals to assist in surgery (perioperative warming), to aid ischemic stress recovery (cooling), and even to enhance the quality of sleep. Together, these multiscale applications of nanoparticle heating and thermoregulation point to dramatic opportunities for translation and impact in these prophylactic, preservative, diagnostic, and therapeutic applications of bioheat transfer.
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Affiliation(s)
- John C Bischof
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA;
| | - Kenneth R Diller
- Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA;
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Valdez-Moreno M, Ivanova NV, Elías-Gutiérrez M, Pedersen SL, Bessonov K, Hebert PDN. Using eDNA to biomonitor the fish community in a tropical oligotrophic lake. PLoS One 2019; 14:e0215505. [PMID: 31009491 PMCID: PMC6476559 DOI: 10.1371/journal.pone.0215505] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/04/2019] [Indexed: 12/14/2022] Open
Abstract
Environmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish and tilapia. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184-187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM or S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, six fish species represent new records for the study area, while two require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods would enable its detection. In summary, we developed protocols that recovered eDNA from tropical oligotrophic aquatic ecosystems and confirmed their effectiveness in detecting fishes and diverse species of vertebrates.
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Affiliation(s)
| | - Natalia V. Ivanova
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | | | - Stephanie L. Pedersen
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Kyrylo Bessonov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, ON, Canada
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Orzechowski SCM, Frederick PC, Dorazio RM, Hunter ME. Environmental DNA sampling reveals high occupancy rates of invasive Burmese pythons at wading bird breeding aggregations in the central Everglades. PLoS One 2019; 14:e0213943. [PMID: 30970028 PMCID: PMC6457569 DOI: 10.1371/journal.pone.0213943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/04/2019] [Indexed: 11/18/2022] Open
Abstract
The Burmese python (Python bivittatus) is now established as a breeding population throughout south Florida, USA. However, the extent of the invasion, and the ecological impacts of this novel apex predator on animal communities are incompletely known, in large part because Burmese pythons (hereafter “pythons”) are extremely cryptic and there has been no efficient way to detect them. Pythons are recently confirmed nest predators of long-legged wading bird breeding colonies (orders Ciconiiformes and Pelecaniformes). Pythons can consume large quantities of prey and may not be recognized as predators by wading birds, therefore they could be a particular threat to colonies. To quantify python occupancy rates at tree islands where wading birds breed, we utilized environmental DNA (eDNA) analysis—a genetic tool which detects shed DNA in water samples and provides high detection probabilities. We fitted multi-scale Bayesian occupancy models to test the prediction that pythons occupy islands with wading bird colonies at higher rates compared to representative control islands containing no breeding birds. Our results suggest that pythons are widely distributed across the central Everglades in proximity to active wading bird colonies. In support of our prediction that pythons are attracted to colonies, site-level python eDNA occupancy rates were higher at wading bird colonies (ψ = 0.88, 95% credible interval [0.59–1.00]) than at the control islands (ψ = 0.42 [0.16–0.80]) in April through June (n = 15 colony-control pairs). We found our water temperature proxy (time of day) to be informative of detection probability, in accordance with other studies demonstrating an effect of temperature on eDNA degradation in occupied samples. Individual sample concentrations ranged from 0.26 to 38.29 copies/μL and we generally detected higher concentrations of python eDNA in colony sites. Continued monitoring of wading bird colonies is warranted to determine the effect pythons are having on populations and investigate putative management activities.
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Affiliation(s)
- Sophia C. M. Orzechowski
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Peter C. Frederick
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, Florida, United States of America
| | - Robert M. Dorazio
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, United States of America
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, Florida, United States of America
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Deutschmann B, Müller AK, Hollert H, Brinkmann M. Assessing the fate of brown trout (Salmo trutta) environmental DNA in a natural stream using a sensitive and specific dual-labelled probe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:321-327. [PMID: 30471600 DOI: 10.1016/j.scitotenv.2018.11.247] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
Environmental DNA (eDNA) analysis in the aquatic environment has emerged as a promising tool for diagnosis of the ecological status in comprehensive monitoring strategies and might become useful in context of the European Water Framework Directive (WFD) and other legislations to derive stressor-specific indicators. Despite many studies having made significant progress for the future use of eDNA in terms of ecosystem composition and detection of invasive/rare species in inland waters, much remains unknown about the transport and fate of eDNA under natural environmental conditions. We designed a specific dual-labelled probe to detect brown trout (Salmo trutta, L.) eDNA and used the probe to describe the fate of eDNA released from an aquaculture facility into the low mountain range stream Wehebach, Germany. The probe was shown to be specific to brown trout, as ponds housing rainbow trout (Oncorhynchus mykiss) did not test positive. Even though we observed different strengths of eDNA signals for three ponds containing different brown trout quantities, no significant correlation was found between biomass (kg/L) and eDNA quantity. Our results indicate that the release of DNA from brown trout might be life stage and/or age-dependent. The effluents of the aquaculture facility were a source of high levels of eDNA which resulted in the greatest abundance of brown trout eDNA directly downstream of the facility. Despite the natural occurrence of brown trout in the Wehebach, as shown by ecological investigations conducted by authorities of the federal state of North Rhine-Westphalia (Germany) and personal observations, we observed a significant decrease of relative abundance of eDNA in the Wehebach within the first 1.5 km downstream of the aquaculture. Our results suggest that concentrations of eDNA in running waters rapidly decrease under natural conditions due to dilution and degradation processes, which might have important implications for the utility of eDNA in environmental research.
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Affiliation(s)
- Björn Deutschmann
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Anne-Kathrin Müller
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Henner Hollert
- Department of Ecosystem Analysis, Institute for Environmental Research, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany; College of Resources and Environmental Science, Chongqing University, Chongqing, China; College of Environmental Science, Engineering and State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China.
| | - Markus Brinkmann
- School of Environment and Sustainability (SENS), University of Saskatchewan, Saskatoon, SK, Canada; Global Institute for Water Security (GIWS), University of Saskatchewan, Saskatoon, SK, Canada; Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
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Qu C, Stewart KA. Evaluating monitoring options for conservation: comparing traditional and environmental DNA tools for a critically endangered mammal. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2019; 106:9. [PMID: 30778682 DOI: 10.1007/s00114-019-1605-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/06/2018] [Accepted: 01/30/2019] [Indexed: 11/28/2022]
Abstract
While conservation management has made tremendous strides to date, deciding where, when and how to invest limited monitoring budgets is a central concern for impactful decision-making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring at unprecedented scales, in part, due to time, and presumably cost, of methodological efficiency. Genetic approaches vary from conventional PCR (cPCR; species presence), to metabarcoding (community structure), and qPCR (relative DNA abundance, detection sensitivity). Knowing when to employ these techniques over traditional protocols could enable practitioners to make more informed choices concerning data collection. Using 12 species-specific primers designed for cPCR, eDNA analysis of the Yangtze finless porpoise (YFP; Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these primers for use in qPCR. We tested repeatability and sensitivity to detect YFP eDNA and subsequently compared the cost of traditional (visual and capture) sampling to eDNA tools. Our results suggest cPCR as the least expensive sampling option but the lack of PCR sensitivity suggests it may not be the most robust method for this taxon, predominately useful as a supplementary tool or with large expected populations. Alternatively, qPCR remained less expensive than traditional surveys, representing a highly repeatable and sensitive method for this behaviorally elusive species. Cost comparisons of surveying practices have scarcely been discussed; however, given budgetary constraints particularly for developing countries with limited local oversight but high endemism, we encourage managers to carefully consider the trade-offs among accuracy, cost, coverage, and speed for biodiversity monitoring.
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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, People's Republic of China
| | - Kathryn A Stewart
- State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, People's Republic of China. .,Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, Amsterdam, Netherlands.
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Jo T, Murakami H, Yamamoto S, Masuda R, Minamoto T. Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution. Ecol Evol 2019; 9:1135-1146. [PMID: 30805147 PMCID: PMC6374661 DOI: 10.1002/ece3.4802] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/22/2022] Open
Abstract
Environmental DNA (eDNA) analysis has successfully detected organisms in various aquatic environments. However, there is little basic information on eDNA, including the eDNA shedding and degradation processes. This study focused on water temperature and fish biomass and showed that eDNA shedding, degradation, and size distribution varied depending on water temperature and fish biomass. The tank experiments consisted of four temperature levels and three fish biomass levels. The total eDNA and size-fractioned eDNA from Japanese Jack Mackerels (Trachurus japonicus) were quantified before and after removing the fish. The results showed that the eDNA shedding rate increased at higher water temperature and larger fish biomass, and the eDNA decay rate also increased at higher temperature and fish biomass. In addition, the small-sized eDNA fractions were proportionally larger at higher temperatures, and these proportions varied among fish biomass. After removing the fish from the tanks, the percentage of eDNA temporally decreased when the eDNA size fraction was >10 µm, while the smaller size fractions increased. These results have the potential to make the use of eDNA analysis more widespread in the future.
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Affiliation(s)
- Toshiaki Jo
- Graduate School of Human Development and EnvironmentKobe UniversityKobe CityJapan
| | | | - Satoshi Yamamoto
- Graduate School of Human Development and EnvironmentKobe UniversityKobe CityJapan
- Department of Zoology, Graduate School of ScienceKyoto UniversityKyotoJapan
| | - Reiji Masuda
- Maizuru Fisheries Research StationKyoto UniversityKyotoJapan
| | - Toshifumi Minamoto
- Graduate School of Human Development and EnvironmentKobe UniversityKobe CityJapan
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Bracken FSA, Rooney SM, Kelly‐Quinn M, King JJ, Carlsson J. Identifying spawning sites and other critical habitat in lotic systems using eDNA "snapshots": A case study using the sea lamprey Petromyzon marinus L. Ecol Evol 2019; 9:553-567. [PMID: 30680136 PMCID: PMC6342126 DOI: 10.1002/ece3.4777] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/17/2018] [Accepted: 11/19/2018] [Indexed: 12/04/2022] Open
Abstract
Many aquatic species of conservation concern exist at low densities and are inherently difficult to detect or monitor using conventional methods. However, the introduction of environmental (e)DNA has recently transformed our ability to detect these species and enables effective deployment of limited conservation resources. Identifying areas for breeding, as well as the ecological distribution of species, is vital to the survival or recovery of a conservation species (i.e., areas of critical habitat). In many species, spawning events are associated with a higher relative abundance of DNA released within an aquatic system (i.e., gametes, skin cells etc.), making this the ideal time to monitor these species using eDNA techniques. This study aims to examine whether a "snapshot" eDNA sampling approach (i.e., samples taken at fixed points in chronological time) could reveal areas of critical habitat including spawning sites for our target species Petromyzon marinus. We utilized a species-specific qPCR assay to monitor spatial and temporal patterns in eDNA concentration within two river catchments in Ireland over three consecutive years. We found that eDNA concentration increased at the onset of observed spawning activity and patterns of concentration increased from downstream to upstream over time, suggesting dispersal into the higher reaches as the spawning season progressed. We found P. marinus to be present upstream of several potential barriers to migration, sometimes in significant numbers. Our results also show that the addition of a lamprey-specific fish pass at an "impassable" weir, although assisting in ascent, did not have any significant impact on eDNA concentration upstream after the pass had been installed. eDNA concentration was also found to be significantly correlated with both the number of fish and the number of nests encountered. The application of snapshot sampling techniques for species monitoring therefore has substantial potential for the management of low-density species in fast-moving aquatic systems.
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Affiliation(s)
- Fiona S. A. Bracken
- Area 52 Research Group, School of Biology and Environmental Science/Earth InstituteUniversity College DublinDublinIreland
| | | | - Mary Kelly‐Quinn
- School of Biology and Environmental ScienceUniversity College Dublin, Science Centre WestBelfieldDublin 4Ireland
| | | | - Jens Carlsson
- Area 52 Research Group, School of Biology and Environmental Science/Earth InstituteUniversity College DublinDublinIreland
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Feist SM, Jones RL, Copley JL, Pearson LS, Berry GA, Qualls CP. Development and Validation of an Environmental DNA Method for Detection of the Alligator Snapping Turtle (Macrochelys temminckii). CHELONIAN CONSERVATION AND BIOLOGY 2018. [DOI: 10.2744/ccb-1315.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sheena M. Feist
- Mississippi Department of Wildlife, Fisheries, and Parks, Museum of Natural Science, 2148 Riverside
| | - Robert L. Jones
- Mississippi Department of Wildlife, Fisheries, and Parks, Museum of Natural Science, 2148 Riverside
| | - Jeremy L. Copley
- Mississippi Department of Wildlife, Fisheries, and Parks, Museum of Natural Science, 2148 Riverside
| | - Luke S. Pearson
- University of Southern Mississippi, Department of Biological Sciences, 118 College Drive #5018, Hatt
| | - Gabrielle A. Berry
- University of Southern Mississippi, Department of Biological Sciences, 118 College Drive #5018, Hatt
| | - Carl P. Qualls
- University of Southern Mississippi, Department of Biological Sciences, 118 College Drive #5018, Hatt
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Stoeckle MY, Das Mishu M, Charlop-Powers Z. GoFish: A versatile nested PCR strategy for environmental DNA assays for marine vertebrates. PLoS One 2018; 13:e0198717. [PMID: 30533051 PMCID: PMC6289459 DOI: 10.1371/journal.pone.0198717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/21/2018] [Indexed: 12/30/2022] Open
Abstract
Here we describe GoFish, a strategy for single-species environmental DNA (eDNA) presence/absence assays using nested PCR. The assays amplify a mitochondrial 12S rDNA segment with vertebrate metabarcoding primers, followed by nested PCR with M13-tailed, species-specific primers. Sanger sequencing confirms positives detected by gel electrophoresis. We first obtained 12S sequences from 77 fish specimens for 36 northwestern Atlantic taxa not well documented in GenBank. Using these and existing 12S records, we designed GoFish assays for 11 bony fish species common in the lower Hudson River estuary and tested seasonal abundance and habitat preference at two sites. Additional assays detected nine cartilaginous fish species and a marine mammal, bottlenose dolphin, in southern New York Bight. GoFish sensitivity was equivalent to Illumina MiSeq metabarcoding. Unlike quantitative PCR (qPCR), GoFish does not require tissues of target and related species for assay development and a basic thermal cycler is sufficient. Unlike Illumina metabarcoding, indexing and batching samples are unnecessary and advanced bioinformatics expertise is not needed. From water collection to Sanger sequencing results, the assay can be carried out in three days. The main limitations to this approach, which employs metabarcoding primers, are the same as for metabarcoding, namely, inability to distinguish species with shared target sequences and inconsistent amplification of rarer eDNA. In addition, the performance of the 20 assays reported here as compared to other single-species eDNA assays is not known. This approach will be a useful addition to current eDNA methods when analyzing presence/absence of known species, when turnaround time is important, and in educational settings.
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Affiliation(s)
- Mark Y. Stoeckle
- Program for the Human Environment, The Rockefeller University, New York, New York, United States of America
| | | | - Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY, United States of America
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Maruyama A, Sugatani K, Watanabe K, Yamanaka H, Imamura A. Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers. Ecol Evol 2018; 8:11964-11974. [PMID: 30598791 PMCID: PMC6303803 DOI: 10.1002/ece3.4653] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022] Open
Abstract
Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three-lips (Opsariichthys uncirostris uncirostris), was non-invasively monitored by quantitative PCR of species-specific environmental DNA (eDNA), the usefulness of which has been not sufficiently explored. Water sampling and from-shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species-specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log-transformed individual counts from visual inspection were positively correlated with log-transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. Both eDNA concentration and individual counts gradually increased from May-July, and decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.
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Affiliation(s)
- Atsushi Maruyama
- Faculty of Science and TechnologyRyukoku UniversityOtsuShigaJapan
| | - Kousuke Sugatani
- Faculty of Science and TechnologyRyukoku UniversityOtsuShigaJapan
| | - Kazuki Watanabe
- Faculty of Science and TechnologyRyukoku UniversityOtsuShigaJapan
| | - Hiroki Yamanaka
- Faculty of Science and TechnologyRyukoku UniversityOtsuShigaJapan
| | - Akio Imamura
- Hokkaido University of EducationAsahikawaHokkaidoJapan
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Farrell MJ, Govender D, Hajibabaei M, van der Bank M, Davies TJ. Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach 1. Genome 2018; 62:229-242. [PMID: 30495980 DOI: 10.1139/gen-2018-0064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteria are essential components of natural environments. They contribute to ecosystem functioning through roles as mutualists and pathogens for larger species, and as key components of food webs and nutrient cycles. Bacterial communities respond to environmental disturbances, and the tracking of these communities across space and time may serve as indicators of ecosystem health in areas of conservation concern. Recent advances in DNA sequencing of environmental samples allow for rapid and culture-free characterization of bacterial communities. Here we conduct the first metabarcoding survey of bacterial diversity in the waterholes of the Kruger National Park, South Africa. We show that eDNA can be amplified from waterholes and find strongly structured microbial communities, likely reflecting local abiotic conditions, animal ecology, and anthropogenic disturbance. Over timescales from days to weeks we find increased turnover in community composition, indicating bacteria may represent host-associated taxa of large vertebrates visiting the waterholes. Through taxonomic annotation we also identify pathogenic taxa, demonstrating the utility of eDNA metabarcoding for surveillance of infectious diseases. These samples serve as a baseline survey of bacterial diversity in the Kruger National Park, and in the future, spatially distinct microbial communities may be used as markers of ecosystem disturbance, or biotic homogenization across the park.
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Affiliation(s)
- Maxwell J Farrell
- a Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal, QC H3A 0G4, Québec, Canada
| | - Danny Govender
- b Scientific Services, Kruger National Park, SANParks, Private Bag X402, Skukuza, 1350, South Africa.,c Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | - Mehrdad Hajibabaei
- d Integrative Biology & Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Michelle van der Bank
- e African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, Johannesburg, South Africa
| | - T Jonathan Davies
- e African Centre for DNA Barcoding, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, Johannesburg, South Africa.,f Botany, Forest & Conservation Sciences, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada
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eDNA-based crayfish plague detection as practical tool for biomonitoring and risk assessment of A. astaci-positive crayfish populations. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1886-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Cristescu ME, Hebert PD. Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062306] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The study of environmental DNA (eDNA) has the potential to revolutionize biodiversity science and conservation action by enabling the census of species on a global scale in near real time. To achieve this promise, technical challenges must be resolved. In this review, we explore the main uses of eDNA as well as the complexities introduced by its misuse. Current eDNA methods require refinement and improved calibration and validation along the entire workflow to lessen false positives/negatives. Moreover, there is great need for a better understanding of the “natural history” of eDNA—its origins, state, lifetime, and transportation—and for more detailed insights concerning the physical and ecological limitations of eDNA use. Although eDNA analysis can provide powerful information, particularly in freshwater and marine environments, its impact is likely to be less significant in terrestrial settings. The broad adoption of eDNA tools in conservation will largely depend on addressing current uncertainties in data interpretation.
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Affiliation(s)
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Ontario N1G 2W1, Canada
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Plough LV, Ogburn MB, Fitzgerald CL, Geranio R, Marafino GA, Richie KD. Environmental DNA analysis of river herring in Chesapeake Bay: A powerful tool for monitoring threatened keystone species. PLoS One 2018; 13:e0205578. [PMID: 30383750 PMCID: PMC6211659 DOI: 10.1371/journal.pone.0205578] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/27/2018] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) sampling has emerged as a powerful tool to detect and quantify species abundance in aquatic environments. However, relatively few studies have compared the performance of eDNA-based abundance estimates to traditional catch or survey approaches in the field. Here, we have developed and field-tested a qPCR assay to detect eDNA from alewife and blueback herring (collectively known as ‘river herring’), comparing eDNA-based presence and abundance data to traditional methods of quantification (ichthyoplankton sampling and adult observations). Overall, the qPCR assay showed very high target specificity in lab trials, and was successful in detecting river herring for 11/12 Chesapeake Bay tributaries in spring 2015 and 2016, with 106 out of 445 samples exhibiting positive eDNA hits. We found a strong correlation between eDNA abundance and ichthyoplankton count data (Spearman’s Rho = 0.52), and Phi-tests (correlation of presence/absence data) showed higher correlation between eDNA and ichthyoplankton data (Phi = 0.45) than adult data (Phi = 0.35). Detection probability was significantly lower on western vs. eastern shore tributaries of Chesapeake Bay, and blueback herring and alewife were more likely detected on the western and eastern shores, respectively. Temporal patterns of eDNA abundance over the spring spawning season revealed that alewife were present in high abundances weeks ahead of blueback herring, which aligns with known differences in spawning behavior of the species. In summary, the eDNA abundance data corresponded well to other field methods and has great potential to assist future monitoring efforts of river herring abundance and habitat use.
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Affiliation(s)
- Louis V. Plough
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
- * E-mail:
| | - Matthew B. Ogburn
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Catherine L. Fitzgerald
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Rose Geranio
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, United States of America
| | - Gabriella A. Marafino
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Kimberly D. Richie
- Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
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Aguilera J, Aguilera‐Gomez M, Barrucci F, Cocconcelli PS, Davies H, Denslow N, Lou Dorne J, Grohmann L, Herman L, Hogstrand C, Kass GEN, Kille P, Kleter G, Nogué F, Plant NJ, Ramon M, Schoonjans R, Waigmann E, Wright MC. EFSA Scientific Colloquium 24 – 'omics in risk assessment: state of the art and next steps. ACTA ACUST UNITED AC 2018. [DOI: 10.2903/sp.efsa.2018.en-1512] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Lutz Grohmann
- Federal Office of Consumer Protection and Food Safety
| | | | | | | | | | | | - Fabien Nogué
- French National Institute for Agricultural Research INRA
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Environmental DNA (eDNA): A Promising Biological Survey Tool for Aquatic Species Detection. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s12595-018-0268-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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