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Sansom BJ, Ruiz-Ramos DV, Thompson NL, Roberts MO, Taylor ZA, Ortiz K, Jones JW, Richter CA, Klymus KE. Detection and transport of environmental DNA from two federally endangered mussels. PLoS One 2024; 19:e0304323. [PMID: 39418270 DOI: 10.1371/journal.pone.0304323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/09/2024] [Indexed: 10/19/2024] Open
Abstract
Environmental DNA (eDNA) offers a novel approach to supplement traditional surveys and provide increased spatial and temporal information on species detection, and it can be especially beneficial for detecting at risk or threatened species with minimal impact on the target species. The transport of eDNA in lotic environments is an important component in providing more informed descriptions of where and when a species is present, but eDNA transport phenomena are not well understood. In this study, we used species-specific assays to detect eDNA from two federally endangered mussels in two geographically distinct rivers. Using the eDNA concentrations measured from field samples, we developed a one-dimensional (1D) hydrodynamic transport model to predict the downstream fate and transport of eDNA. We detected eDNA from both federally endangered mussels across several seasons and flow rates and up to 3.5 km downstream from the source populations, but the detection rates and eDNA concentrations were highly variable across and within rivers and study reaches. Our 1D transport models successfully integrated the variability of the eDNA field samples into the model predictions and overall model results were generally within ±1 standard error of the eDNA field concentration values. Overall, the results of this study demonstrate the importance of optimizing the spatial locations from where eDNA is collected downstream from a source population, and it highlights the need to improve understanding on the shedding mechanisms and magnitude of eDNA from source populations and biogeomorphic processes that influence eDNA transport.
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Affiliation(s)
- Brandon J Sansom
- U.S. Geological Survey-Columbia Environmental Research Center, Columbia, MO, United States of America
| | - Dannise V Ruiz-Ramos
- U.S. Geological Survey-Columbia Environmental Research Center, Columbia, MO, United States of America
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, MD, United States of America
| | - Nathan L Thompson
- U.S. Geological Survey-Columbia Environmental Research Center, Columbia, MO, United States of America
| | - Maura O Roberts
- U.S. Geological Survey-Columbia Environmental Research Center, Columbia, MO, United States of America
| | - Zachary A Taylor
- Maryland Department of Natural Resources, Annapolis, MD, United States of America
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Katie Ortiz
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Jess W Jones
- Department of Fish and Wildlife Conservation, U.S. Fish and Wildlife Service, Blacksburg, VA, United States of America
| | - Catherine A Richter
- U.S. Geological Survey-Columbia Environmental Research Center, Columbia, MO, United States of America
| | - Katy E Klymus
- U.S. Geological Survey-Columbia Environmental Research Center, Columbia, MO, United States of America
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2
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Dass MA, Sherman CDH, van Oorschot RAH, Tuohey K, Hartman D, Carter G, Durdle A. Assessing eDNA capture method from aquatic environment to optimise recovery of human mt-eDNA. Forensic Sci Int 2024; 361:112085. [PMID: 38850619 DOI: 10.1016/j.forsciint.2024.112085] [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: 02/20/2024] [Revised: 05/05/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Previous studies have shown that environmental DNA (eDNA) from human sources can be recovered from natural bodies of water, and the generation of DNA profiles from such environmental samples may assist in forensic investigations. However, fundamental knowledge gaps exist around the factors influencing the probability of detecting human eDNA and the design of optimal sampling protocols. One of these is understanding the particle sizes eDNA signals are most strongly associated with and the most appropriate filter size needed for efficiently capturing eDNA particles. This study assessed the amount of mitochondrial eDNA associated with different particle sizes from human blood and skin cells recovered from freshwater samples. Samples (300 mL) were taken from experimental 10 L tanks of freshwater spiked with 50 µL of human blood or skin cells deposited by vigorously rubbing hands together for two minutes in freshwater. Subsamples were collected by passing 250 mL of experimental water sample through six different filter pore sizes (from 0.1 to 8 µm). This process was repeated at four time intervals after spiking over 72 hours to assess if the particle size of the amount of eDNA recovered changes as the eDNA degrades. Using a human-specific quantitative polymerase chain reaction (qPCR) assay targeting the HV1 mitochondrial gene region, the total amount of mitochondrial eDNA associated with different particle size fractions was determined. In the case of human blood, at 0 h, the 0.45 µm filter pore size captured the greatest amount of mitochondrial eDNA, capturing 42 % of the eDNA detected. The pattern then changed after 48 h, with the 5 µm filter pore size capturing the greatest amount of eDNA (67 %), and 81 % of eDNA at 72 h. Notably, a ten-fold dilution proved to be a valuable strategy for enhancing eDNA recovery from the 8 µm filter at all time points, primarily due to the PCR inhibition observed in hemoglobin. For human skin cells, the greatest amounts of eDNA were recovered from the 8 µm filter pore size and were consistent through time (capturing 37 %, 56 %, and 88 % of eDNA at 0 hours, 48 hours, and 72 hours respectively). There is a clear variation in the amount of eDNA recovered between different cell types, and in some forensic scenarios, there is likely to be a mix of cell types present. These results suggest it would be best to use a 5 µm filter pore size to capture human blood and an 8 µm filter pore size to capture human skin cells to maximize DNA recovery from freshwater samples. Depending on the cell type contributing to the eDNA, a combination of different filter pore sizes may be employed to optimize the recovery of human DNA from water samples. This study provides the groundwork for optimizing a strategy for the efficient recovery of human eDNA from aquatic environments, paving the way for its broader application in forensic and environmental sciences.
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Affiliation(s)
- Marie Antony Dass
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia.
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia; School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Kate Tuohey
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia
| | - Dadna Hartman
- Victorian Institute of Forensic Medicine, Southbank, VIC 3006, Australia; Department of Forensic Medicine, Monash University, Southbank, VIC 3006, Australia
| | - Gemma Carter
- Victorian Institute of Forensic Medicine, Southbank, VIC 3006, Australia
| | - Annalisa Durdle
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia
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3
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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1368-1384. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [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: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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4
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Pont D. Predicting downstream transport distance of fish eDNA in lotic environments. Mol Ecol Resour 2024; 24:e13934. [PMID: 38318749 DOI: 10.1111/1755-0998.13934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at the local scale. In addition to biophysical degradation and exchanges at the water-sediment interface, hydrological conditions control the transport distance. A new eDNA transport model described in this paper considers downstream retention and degradation processes in combination with hydraulic conditions and assumes that the sedimentation rate of very fine particles is a correct estimate of the eDNA deposition rate. Based on meta-analyses of available studies, the particle size distribution of fish eDNA (PSD), the relationship between the sedimentation rate and the size of very fine particles in suspension, and the influence of temperature on the degradation rate of fish eDNA were successively modelled. After combining the results in a mechanistic-based model, the eDNA uptake distances (distance required to retain 63.21% of the eDNA particles in the riverbed) observed in a compilation of previous experimental studies were correctly simulated. eDNA degradation is negligible at low flow and temperature but has a comparable influence to background transfer when hydraulic conditions allow a long uptake distance. The wide prediction intervals associated with the simulations reflect the complexity of the processes acting on eDNA after shedding. This model can be useful for estimating eDNA detection distance downstream from a source point and discussing the possibility of false positive detection in eDNA samples, as shown in an example.
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Affiliation(s)
- Didier Pont
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), University of Natural Resources and Life Sciences, Vienna, Austria
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5
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Fray D, McGovern CA, Casamatta DA, Biddanda BA, Hamsher SE. Metabarcoding reveals unique microbial mat communities and evidence of biogeographic influence in low-oxygen, high-sulfur sinkholes and springs. Ecol Evol 2024; 14:e11162. [PMID: 38529029 PMCID: PMC10961586 DOI: 10.1002/ece3.11162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/16/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
High-sulfur, low-oxygen environments formed by underwater sinkholes and springs create unique habitats populated by microbial mat communities. To explore the diversity and biogeography of these mats, samples were collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Our study investigated previously undescribed eukaryotic diversity in these habitats and further explored their bacterial communities. Mat samples and water parameters were collected from sulfur spring sites during the spring, summer, and fall of 2022. Cyanobacteria and diatoms were cultured from mat subsamples to create a culture-based DNA reference library. Remaining mat samples were used for metabarcoding of the 16S and rbcL regions to explore bacterial and diatom diversity, respectively. Analyses of water chemistry, alpha diversity, and beta diversity articulated a range of high-sulfur, low-oxygen habitats, each with distinct microbial communities. Conductivity, pH, dissolved oxygen, temperature, sulfate, and chloride had significant influences on community composition but did not describe the differences between communities well. Chloride concentration had the strongest correlation with microbial community structure. Mantel tests revealed that biogeography contributed to differences between communities as well. Our results provide novel information on microbial mat composition and present evidence that both local conditions and biogeography influence these unique communities.
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Affiliation(s)
- Davis Fray
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
| | | | - Dale A. Casamatta
- Department of BiologyUniversity of North FloridaJacksonvilleFloridaUSA
| | - Bopaiah A. Biddanda
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
| | - Sarah E. Hamsher
- Annis Water Resources InstituteGrand Valley State UniversityMuskegonMichiganUSA
- Department of BiologyGrand Valley State UniversityAllendaleMichiganUSA
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6
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Marques V, Loot G, Blanchet S, Miaud C, Planes S, Peyran C, Arnal V, Calvet C, Pioch S, Manel S. Optimizing detectability of the endangered fan mussel using eDNA and ddPCR. Ecol Evol 2024; 14:e10807. [PMID: 38288365 PMCID: PMC10822771 DOI: 10.1002/ece3.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 01/31/2024] Open
Abstract
Spatial and temporal monitoring of species threatened with extinction is of critical importance for conservation and ecosystem management. In the Mediterranean coast, the fan mussel (Pinna nobilis) is listed as critically endangered after suffering from a mass mortality event since 2016, leading to 100% mortality in most marine populations. Conventional monitoring for this macroinvertebrate is done using scuba, which is challenging in dense meadows or with low visibility. Here we developed an environmental DNA assay targeting the fan mussel and assessed the influence of several environmental parameters on the species detectability in situ. We developed and tested an eDNA molecular marker and collected 48 water samples in two sites at the Thau lagoon (France) with distinct fan mussel density, depths and during two seasons (summer and autumn). Our marker can amplify fan mussel DNA but lacks specificity since it also amplifies a conspecific species (Pinna rudis). We successfully amplified fan mussel DNA from in situ samples with 46 positive samples (out of 48) using ddPCR, although the DNA concentrations measured were low over almost all samples. Deeper sampling depth slightly increased DNA concentrations, but no seasonal effect was found. We highlight a putative spawning event on a single summer day with much higher DNA concentration compared to all other samples. We present an eDNA molecular assay able to detect the endangered fan mussel and provide guidelines to optimize the sampling protocol to maximize detectability. Effective and non-invasive monitoring tools for endangered species are promising to monitor remaining populations and have the potential of ecological restoration or habitat recolonization following a mass mortality event.
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Affiliation(s)
- Virginie Marques
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental System ScienceETH ZürichZürichSwitzerland
- Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Géraldine Loot
- EDB, Laboratoire Ecologie et Evolution (UMR 5174)Université de Toulouse, UPS, CNRS, IRDToulouseFrance
| | - Simon Blanchet
- SETE, Station d'Écologie Théorique et Expérimentale (UAR2029), Centre National pour la Recherche ScientifiqueMoulisFrance
| | - Claude Miaud
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Serge Planes
- PSL Research University: EPHE – UPVD – CNRS, UAR 3278 CRIOBEPerpignanFrance
| | - Claire Peyran
- PSL Research University: EPHE – UPVD – CNRS, UAR 3278 CRIOBEPerpignanFrance
| | - Véronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Coralie Calvet
- AgroParisTechParisFrance
- Montpellier Research in Management (MRM)Univ Montpellier, Univ Paul Valéry Montpellier 3, Univ Perpignan Via DomitiaMontpellierFrance
| | - Sylvain Pioch
- AgroParisTechParisFrance
- Montpellier Research in Management (MRM)Univ Montpellier, Univ Paul Valéry Montpellier 3, Univ Perpignan Via DomitiaMontpellierFrance
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRDMontpellierFrance
- Institut Universitaire de FranceParisFrance
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7
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Jo TS. Pooling of intra-site measurements inflates variability of the correlation between environmental DNA concentration and organism abundance. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:936. [PMID: 37436641 DOI: 10.1007/s10661-023-11539-5] [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: 11/15/2022] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Abstract
Environmental DNA (eDNA) analysis can promote efficient ecosystem monitoring and resource management. However, limited knowledge of the factors affecting the relationship between eDNA concentration and organism abundance causes uncertainty in relative abundance estimates based on eDNA concentration. Pooling of data points obtained from multiple locations within a site has been used to mitigate intra-site variation in eDNA and abundance estimates, but decreases the sample size used for estimating the relationship. I here assessed how the pooling of intra-site measurements of eDNA concentration and organism abundance impacted the reliability of the correlative relationship between eDNA concentration and organism abundance. Mathematical models were developed to simulate measurements of eDNA concentrations and organism abundances from multiple locations in a given survey site, and the CVs (coefficient of variability) of the correlations were compared depending on whether data points from different locations were individually treated or pooled. Although the mean and median values of the correlation coefficients were similar between the scenarios, the CVs of the simulated correlations were substantially higher under the pooled scenario than the individual scenario. Additionally, I re-analyzed two empirical studies conducted in lakes, both showing higher CVs of the correlations by pooling intra-site measurements. This study suggests that it would make eDNA-based abundance estimation more reliable and reproducible to individually analyze target eDNA concentrations and organism abundance estimates.
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Affiliation(s)
- Toshiaki S Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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8
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Van Driessche C, Everts T, Neyrinck S, Halfmaerten D, Haegeman A, Ruttink T, Bonte D, Brys R. Using environmental DNA metabarcoding to monitor fish communities in small rivers and large brooks: Insights on the spatial scale of information. ENVIRONMENTAL RESEARCH 2023; 228:115857. [PMID: 37059322 DOI: 10.1016/j.envres.2023.115857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Monitoring fish communities is central to the evaluation of ecological health of rivers. Both presence/absence of fish species and their relative quantity in local fish assemblages are crucial parameters to measure. Fish communities in lotic systems are traditionally monitored via electrofishing, characterized by a known limited efficiency and high survey costs. Analysis of environmental DNA could serve as a non-destructive alternative for detection and quantification of lotic fish communities, but this approach still requires further insights in practical sampling schemes incorporating transport and dilution of the eDNA particles; optimization of predictive power and quality assurance of the molecular detection method. Via a controlled cage experiment, we aim to extend the knowledge on streamreach of eDNA in small rivers and large brooks, as laid out in the European Water Framework Directive's water typology. Using a high and low source biomass in two river transects of a species-poor river characterized by contrasting river discharge rates, we found strong and significant correlations between the eDNA relative species abundances and the relative biomass per species in the cage community. Despite a decreasing correlation over distance, the underlying community composition remained stable from 25 to 300 m, or up to 1 km downstream of the eDNA source, depending on the river discharge rate. Such decrease in similarity between relative source biomass and the corresponding eDNA-based community profile with increasing distance downstream from the source, might be attributed to variation in species-specific eDNA persistence. Our findings offer crucial insights on eDNA behaviour and characterization of riverine fish communities. We conclude that water sampled from a relatively small river offers an adequate eDNA snapshot of the total fish community in the 300-1000 m upstream transect. The potential application for other river systems is further discussed.
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Affiliation(s)
- Charlotte Van Driessche
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium; Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium.
| | - Teun Everts
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium; KU Leuven, Department of Biology, Plant Conservation and Population Biology, Leuven, Belgium
| | - Sabrina Neyrinck
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
| | - David Halfmaerten
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
| | - Annelies Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Dries Bonte
- Ghent University, Department of Biology, Terrestrial Ecology Unit, Ghent, Belgium
| | - Rein Brys
- Research Institute for Nature and Forest (INBO), Genetic Diversity, Geraardsbergen, Belgium
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9
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Carraro L, Blackman RC, Altermatt F. Modelling environmental DNA transport in rivers reveals highly resolved spatio-temporal biodiversity patterns. Sci Rep 2023; 13:8854. [PMID: 37258598 DOI: 10.1038/s41598-023-35614-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity.
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Affiliation(s)
- Luca Carraro
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland.
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland.
| | - Rosetta C Blackman
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057, Zürich, Switzerland
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, 8600, Dübendorf, Switzerland
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10
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Bass D, Christison KW, Stentiford GD, Cook LSJ, Hartikainen H. Environmental DNA/RNA for pathogen and parasite detection, surveillance, and ecology. Trends Parasitol 2023; 39:285-304. [PMID: 36759269 DOI: 10.1016/j.pt.2022.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 02/11/2023]
Abstract
Detection of pathogens, parasites, and other symbionts in environmental samples via eDNA/eRNA (collectively eNA) is an increasingly important source of information about their occurrence and activity. There is great potential for using such detections as a proxy for infection of host organisms in connected habitats, for pathogen monitoring and surveillance, and for early warning systems for disease. However, many factors require consideration, and appropriate methods developed and verified, in order that eNA detections can be reliably interpreted and adopted for surveillance and assessment of disease risk, and potentially inclusion in international standards, such as the World Organisation for Animal Health guidelines. Disease manifestation results from host-symbiont-environment interactions between hosts, demanding a multifactorial approach to interpretation of eNA signals.
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Affiliation(s)
- David Bass
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
| | - Kevin W Christison
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa; Department of Forestry, Fisheries and the Environment, Private Bag X2, Vlaeberg, 8012, South Africa
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
| | - Lauren S J Cook
- International Centre of Excellence for Aquatic Animal Health, The Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK; Royal Holloway, University of London, Egham Hill, Egham TW20 0EX, UK
| | - Hanna Hartikainen
- University of Nottingham, School of Life Sciences, University Park, NG7 2RD, Nottingham, UK
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11
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Feng W, Lougheed SC. Integrating eDNA and citizen science observations to model distribution of a temperate freshwater turtle near its northern range limit. PeerJ 2023; 11:e15120. [PMID: 36987453 PMCID: PMC10040185 DOI: 10.7717/peerj.15120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
Background To determine species distributions and the factors underlying them, reliable occurrence data are crucial. Assembling such data can be challenging for species with cryptic life histories or that occur at low densities. Methods We developed species-specific eDNA protocols, from sampling through data interpretation, to detect the common musk turtle (Sternotherus odoratus) and tested whether eDNA occurrences change our understanding of the species distribution and the factors that shape its northern range limit. We used Species Distribution Models (SDMs) with full parameter optimization on citizen science observations of S. odoratus in Southern Ontario alone and together with eDNA occurrences. Results Our eDNA protocol was robust and sensitive. SDMs built from traditional observations and those supplemented with eDNA detections were comparable in prediction accuracy. However, models with eDNA detections suggested that the distribution of S. odoratus in Southern Ontario is underestimated, especially near its northern range limit, and that it is shaped by thermal conditions, hydrology, and elevation. Our study underscores the promise of eDNA for surveying cryptic aquatic organisms in undocumented areas, and how such insights can help us to improve our understanding of species distributions.
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Affiliation(s)
- Wenxi Feng
- Biology, Queen’s University, Kingston, Ontario, Canada
- College of Environment Science and Engineering, Tongji University, Shanghai, China
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12
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Zhao B, van Bodegom PM, Trimbos KB. Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA. Mol Ecol Resour 2023; 23:81-91. [PMID: 35899418 PMCID: PMC10087510 DOI: 10.1111/1755-0998.13691] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments.
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Affiliation(s)
- Beilun Zhao
- Department of Environmental BiologyInstitute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
| | - Peter M. van Bodegom
- Department of Environmental BiologyInstitute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
| | - Krijn B. Trimbos
- Department of Environmental BiologyInstitute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
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13
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Yao M, Zhang S, Lu Q, Chen X, Zhang SY, Kong Y, Zhao J. Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward. Mol Ecol 2022; 31:5132-5164. [PMID: 35972241 DOI: 10.1111/mec.16659] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022]
Abstract
Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods. Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and cost-effective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.
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Affiliation(s)
- Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shan Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Qi Lu
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Si-Yu Zhang
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yueqiao Kong
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Jindong Zhao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
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14
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Dalongeville A, Boulanger E, Marques V, Charbonnel E, Hartmann V, Santoni MC, Deter J, Valentini A, Lenfant P, Boissery P, Dejean T, Velez L, Pichot F, Sanchez L, Arnal V, Bockel T, Delaruelle G, Holon F, Milhau T, Romant L, Manel S, Mouillot D. Benchmarking eleven biodiversity indicators based on environmental
DNA
surveys: more diverse functional traits and evolutionary lineages inside marine reserves. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Emilie Boulanger
- Aix‐Marseille Université Université de Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110 Marseille France
| | - Virginie Marques
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - Eric Charbonnel
- Parc Marin de la Côte Bleue, Observatoire, plage du Rouet. 31 Av. J. Bart. BP 42. 13820 Carry‐le‐Rouet France
| | - Virginie Hartmann
- Reserve Naturelle Marine de Cerbère‐Banyuls, Département des Pyrénées‐Orientales, 5 rue Roger David 66650 Banyuls‐sur‐mer France
| | | | - Julie Deter
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
- Andromède Océanologie, 7 place Cassan – Carnon plage, 34130 Mauguio France
| | - Alice Valentini
- SPYGEN, 17 rue du Lac Saint‐André, 73370 Le Bourget‐du‐Lac France
| | - Philippe Lenfant
- Université Perpignan Via Domitia Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110, 58 Avenue Paul Alduy Perpignan France
| | - Pierre Boissery
- Agence de l’Eau Rhône‐Méditerranée‐Corse, Délégation de Marseille, 2 rue Barbusse, CS 90464, 13207 Marseille Cedex France
| | - Tony Dejean
- SPYGEN, 17 rue du Lac Saint‐André, 73370 Le Bourget‐du‐Lac France
| | - Laure Velez
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Franck Pichot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Loic Sanchez
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - Veronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - Thomas Bockel
- Andromède Océanologie, 7 place Cassan – Carnon plage, 34130 Mauguio France
| | | | - Florian Holon
- Andromède Océanologie, 7 place Cassan – Carnon plage, 34130 Mauguio France
| | - Tristan Milhau
- SPYGEN, 17 rue du Lac Saint‐André, 73370 Le Bourget‐du‐Lac France
| | - Lola Romant
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD, Univ Paul Valéry Montpellier 3 Montpellier France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD Montpellier France
- Institut Universitaire de France Paris France
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15
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Jo T, Yamanaka H. Fine‐tuning the performance of abundance estimation based on environmental
DNA
(
eDNA
) focusing on
eDNA
particle size and marker length. Ecol Evol 2022. [DOI: 10.1002/ece3.9234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Toshiaki Jo
- Faculty of Advanced Science and Technology Ryukoku University Otsu City Japan
- Ryukoku Center for Biodiversity Science Otsu City Japan
- Research Fellow of Japan Society for the Promotion of Science Chiyoda‐ku Japan
| | - Hiroki Yamanaka
- Faculty of Advanced Science and Technology Ryukoku University Otsu City Japan
- Ryukoku Center for Biodiversity Science Otsu City Japan
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16
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Dobson B, Barry S, Maes-Prior R, Mijic A, Woodward G, Pearse WD. Predicting catchment suitability for biodiversity at national scales. WATER RESEARCH 2022; 221:118764. [PMID: 35752096 DOI: 10.1016/j.watres.2022.118764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Biomonitoring of water quality and catchment management are often disconnected, due to mismatching scales. Considerable effort and money are spent each year on routine reach-scale surveying across many sites, particularly in countries like the UK, where nationwide sampling has been conducted using standardised techniques for many decades. Most of these traditional freshwater biomonitoring schemes focus on pre-defined indicators of organic pollution to compare observed vs expected subsets of common macroinvertebrate indicator species. Other taxa, including many threatened species, are often ignored due to their rarity, as are many invasive species, which are seen as undesirable despite becoming increasingly common and widespread in freshwaters, especially in urban ecosystems. Both these types of taxa are often monitored separately for reasons related to biodiversity concerns rather than for gauging water quality. Repurposing such data could therefore provide important new biomonitoring tools that can help catchment managers to directly link the water quality they aim to control with the biodiversity they are trying to protect. Here we used extensive data held in the England Non-Native and Rare/Protected species records that track these two groups of species as a proof-of-concept for linking catchment scale management of freshwater ecosystems and biodiversity to a range of potential drivers across England. We used national land use (Centre for Ecology and Hydrology land cover map) and water quality indicator (Environment Agency water quality data archive) datasets to predict, at the catchment scale, the presence or absence of 48 focal threatened or invasive species of concern routinely sampled by the English Environment Agency, with a median accuracy of 0.81 area under the receiver operating characteristic curve. A variety of water quality indicators and land-use types were useful in predictions, highlighting that future biomonitoring schemes could use such complementary measures to capture a wider spectrum of drivers and responses. In particular, the percentage of a catchment covered by freshwater was the single most important metric, reinforcing the need for space/habitat to support biodiversity, but we were also able to resolve a range of key environmental drivers for particular focal species. We show how our method could inform new catchment management approaches, by highlighting how key relationships can be identified and how to understand, visualise and prioritise catchments that are most suitable for restoration or water quality interventions. The scale of this work, in terms of number of species, drivers and locations, represents a significant step towards forging a new approach to catchment management that enables managers to link drivers they can control (water quality and land use) to the biota they are trying to protect (biodiversity).
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Affiliation(s)
- Barnaby Dobson
- Department of Civil and Environmental Engineering, Faculty of Engineering, Imperial College London.
| | - Saoirse Barry
- Department of Civil and Environmental Engineering, Faculty of Engineering, Imperial College London
| | - Robin Maes-Prior
- Department of Civil and Environmental Engineering, Faculty of Engineering, Imperial College London
| | - Ana Mijic
- Department of Civil and Environmental Engineering, Faculty of Engineering, Imperial College London
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire SL5 7PY, U.K
| | - William D Pearse
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire SL5 7PY, U.K
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17
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Jeliazkov A, Gavish Y, Marsh CJ, Geschke J, Brummitt N, Rocchini D, Haase P, Kunin WE, Henle K. Sampling and modelling rare species: Conceptual guidelines for the neglected majority. GLOBAL CHANGE BIOLOGY 2022; 28:3754-3777. [PMID: 35098624 DOI: 10.1111/gcb.16114] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 11/18/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Biodiversity conservation faces a methodological conundrum: Biodiversity measurement often relies on species, most of which are rare at various scales, especially prone to extinction under global change, but also the most challenging to sample and model. Predicting the distribution change of rare species using conventional species distribution models is challenging because rare species are hardly captured by most survey systems. When enough data are available, predictions are usually spatially biased towards locations where the species is most likely to occur, violating the assumptions of many modelling frameworks. Workflows to predict and eventually map rare species distributions imply important trade-offs between data quantity, quality, representativeness and model complexity that need to be considered prior to survey and analysis. Our opinion is that study designs need to carefully integrate the different steps, from species sampling to modelling, in accordance with the different types of rarity and available data in order to improve our capacity for sound assessment and prediction of rare species distribution. In this article, we summarize and comment on how different categories of species rarity lead to different types of occurrence and distribution data depending on choices made during the survey process, namely the spatial distribution of samples (where to sample) and the sampling protocol in each selected location (how to sample). We then clarify which species distribution models are suitable depending on the different types of distribution data (how to model). Among others, for most rarity forms, we highlight the insights from systematic species-targeted sampling coupled with hierarchical models that allow correcting for overdispersion and spatial and sampling sources of bias. Our article provides scientists and practitioners with a much-needed guide through the ever-increasing diversity of methodological developments to improve the prediction of rare species distribution depending on rarity type and available data.
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Affiliation(s)
| | - Yoni Gavish
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Charles J Marsh
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Ecology and Evolution & Yale Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
| | - Jonas Geschke
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Neil Brummitt
- Department of Life Sciences, Natural History Museum, London, UK
| | - Duccio Rocchini
- BIOME Lab, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
- Department of Spatial Sciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha - Suchdol, Czech Republic
| | - Peter Haase
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
- Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | | | - Klaus Henle
- Department of Conservation Biology & Social-Ecological Systems, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany
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18
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Rinaldo A, Rodriguez-Iturbe I. Ecohydrology 2.0. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2022; 33:245-270. [PMID: 35673327 PMCID: PMC9165276 DOI: 10.1007/s12210-022-01071-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/27/2022] [Indexed: 11/23/2022]
Abstract
This paper aims at a definition of the domain of ecohydrology, a relatively new discipline borne out of an intrusion-as advertised by this Topical Collection of the Rendiconti Lincei-of hydrology and geomorphology into ecology (or vice-versa, depending on the reader's background). The study of hydrologic controls on the biota proves, in our view, significantly broader than envisioned by its original focus that was centered on the critical zone where much of the action of soil, climate and vegetation interactions takes place. In this review of related topics and contributions, we propose a reasoned broadening of perspective, in particular by firmly centering ecohydrology on the fluvial catchment as its fundamental control volume. A substantial unity of materials and methods suggests that our advocacy may be considered legitimate.
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Affiliation(s)
- Andrea Rinaldo
- Accademia Nazionale dei Lincei, Rome, Italy
- Laboratory of Ecohydrology ENAC/IIE/ECHO, École Polytechinque Fédérale de Lausanne, Lausanne, Switzerland
- Dipartimento ICEA, Università degli studi di Padova, Padua, Italy
| | - Ignacio Rodriguez-Iturbe
- Department of Ocean Engineering, Texas A&M University, College Station, TX USA
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX USA
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19
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Ros A, Schmidt-Posthaus H, Brinker A. Mitigating human impacts including climate change on proliferative kidney disease in salmonids of running waters. JOURNAL OF FISH DISEASES 2022; 45:497-521. [PMID: 35100455 DOI: 10.1111/jfd.13585] [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: 08/30/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Over the last two decades, an increasing number of reports have identified a decline in salmonid populations, possibly linked to infection with the parasite Tetracapsuloides bryosalmonae and the corresponding disease, that is, proliferative kidney disease (PKD). The life cycle of this myxozoan parasite includes sessile bryozoan species as invertebrate host, which facilitates the distribution of the parasite in running waters. As the disease outcome is temperature dependent, the impact of the disease on salmonid populations is increasing with global warming due to climate change. The goal of this review is to provide a detailed overview of measures to mitigate the effects of PKD on salmonid populations. It first summarizes the parasite life cycle, temperature-driven disease dynamics and new immunological and molecular research into disease resistance and, based on this, discusses management possibilities. Sophisticated management actions focusing on local adaptation of salmonid populations, restoration of the riverine ecosystem and keeping water temperatures cool are necessary to reduce the negative effects of PKD. Such actions include temporary stocking with PKD-resistant salmonids, as this may assist in conserving current populations that fail to reproduce.
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Affiliation(s)
- Albert Ros
- Fisheries Research Station of Baden-Württemberg, LAZBW, Langenargen, Germany
| | - Heike Schmidt-Posthaus
- Institute for Fish and Wildlife Health, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Alexander Brinker
- Fisheries Research Station of Baden-Württemberg, LAZBW, Langenargen, Germany
- University of Konstanz, Konstanz, Germany
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20
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Shelton AO, Ramón-Laca A, Wells A, Clemons J, Chu D, Feist BE, Kelly RP, Parker-Stetter SL, Thomas R, Nichols KM, Park L. Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean. Proc Biol Sci 2022; 289:20212613. [PMID: 35317670 PMCID: PMC8941408 DOI: 10.1098/rspb.2021.2613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km2 to depths of 500 m) to understand the abundance and distribution of Pacific hake (Merluccius productus), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.
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Affiliation(s)
- Andrew Olaf Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Ana Ramón-Laca
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington at Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, WA 98112, USA
| | - Abigail Wells
- Lynker Technologies, Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Julia Clemons
- Fisheries Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Dezhang Chu
- Fisheries Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Blake E Feist
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Ryan P Kelly
- School of Marine and Environmental Affairs, University of Washington, 3707 Brooklyn Ave NE, Seattle, WA 98105, USA
| | - Sandra L Parker-Stetter
- Fisheries Resource Analysis and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA.,Resource Assessment and Conservation Engineering Division, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - Rebecca Thomas
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Krista M Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
| | - Linda Park
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA
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21
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Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Sci Rep 2021; 11:24241. [PMID: 34930992 PMCID: PMC8688430 DOI: 10.1038/s41598-021-03733-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022] Open
Abstract
Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the effectiveness of using riverine water eDNA to simultaneously monitor the riverine and terrestrial biodiversity information remains unidentified. Here, we proposed that the monitoring effectiveness could be approximated by the transportation effectiveness of land-to-river and upstream-to-downstream biodiversity information flows and described by three new indicators. Subsequently, we conducted a case study in a watershed on the Qinghai-Tibet Plateau. The results demonstrated that there was higher monitoring effectiveness on summer or autumn rainy days than in other seasons and weather conditions. The monitoring of the bacterial biodiversity information was more efficient than the monitoring of the eukaryotic biodiversity information. On summer rainy days, 43-76% of species information in riparian sites could be detected in adjacent riverine water eDNA samples, 92-99% of species information in riverine sites could be detected in a 1-km downstream eDNA sample, and half of dead bioinformation (the bioinformation labeling the biological material that lacked life activity and fertility) could be monitored 4-6 km downstream for eukaryotes and 13-19 km downstream for bacteria. The current study provided reference method and data for future monitoring projects design and for future monitoring results evaluation.
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22
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Yu D, Shen Z, Chang T, Li S, Liu H. Using environmental DNA methods to improve detectability in an endangered sturgeon (Acipenser sinensis) monitoring program. BMC Ecol Evol 2021; 21:216. [PMID: 34852759 PMCID: PMC8638369 DOI: 10.1186/s12862-021-01948-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/24/2021] [Indexed: 11/19/2022] Open
Abstract
Background To determine the presence and abundance of an aquatic species in large waterbodies, especially when populations are at low densities, is highly challenging for conservation biologists. Environmental DNA (eDNA) has the potential to offer a noninvasive and cost-effective method to complement traditional population monitoring, however, eDNA has not been extensively applied to study large migratory species. Chinese sturgeon (Acipenser sinensis), is the largest anadromous migratory fish in the Yangtze River, China, and in recent years its population has dramatically declined and spawning has failed, bringing this species to the brink of extinction. In this study, we aim to test the detectability of eDNA methods to determine the presence and relative abundance of reproductive stock of the species and whether eDNA can be used as a tool to reflect behavioral patterns. Chinese sturgeon eDNA was collected from four sites along the spawning ground across an eight month period, to investigate the temporal and spatial distribution using droplet digital PCR (ddPCR). Results We designed a pair of specific primers for Chinese sturgeon and demonstrated the high sensitivity of ddPCR to detect and quantify the Chinese sturgeon eDNA concentration with the limit of detection 0.17 copies/μl, with Chinese sturgeon eDNA been intermittently detected at all sampling sites. There was a consistent temporal pattern among four of the sampling sites that could reflect the movement characteristics of the Chinese sturgeon in the spawning ground, but without a spatial pattern. The eDNA concentration declined by approximately 2–3 × between December 2018 and December 2019. Conclusions The results prove the efficacy of eDNA for monitoring reproductive stock of the Chinese sturgeon and the e decreased eDNA concentration reflect that Chinese sturgeon may survive with an extremely small number of reproductive stock in the Yangtze River. Accordingly, we suggest future conservation measures should focus on both habitat restoration and matured fish restocking to ensure successful spawning. Overall, this study provides encouraging support for the application of eDNA methods to monitor endangered aquatic species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01948-w.
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Affiliation(s)
- Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Zhongyuan Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Chang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Sha Li
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, 443100, Hubei, China
| | - Huanzhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.
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23
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Yates MC, Cristescu ME, Derry AM. Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro-organism abundance. Mol Ecol 2021; 30:6531-6550. [PMID: 34592014 DOI: 10.1111/mec.16202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/03/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022]
Abstract
Research has demonstrated consistent positive correlations between organism abundance and absolute environmental DNA (eDNA) concentrations. Robust correlations in laboratory experiments indicate strong functional links, suggesting the potential for eDNA to monitor organism abundance in nature. However, correlations between absolute eDNA concentrations and organism abundance in nature tend to be weaker because myriad biotic and abiotic factors influence steady-state eDNA concentrations, decoupling its direct functional link with abundance. Additional technical challenges can also weaken correlations between relative organism abundance and relative eDNA data derived from metabarcoding. Future research must account for these factors to improve the inference of organism abundance from eDNA, including integrating the effects of organism physiology on eDNA production, eDNA dynamics in lentic/lotic systems, and key environmental parameters that impact estimated steady-state concentrations. Additionally, it is critical to manage expectations surrounding the accuracy and precision that eDNA can provide - eDNA, for example, cannot provide abundance estimates comparable to intensively managed freshwater fisheries that enumerate every individual fish. Recent developments, however, are encouraging. Current methods could provide meaningful information regarding qualitative conservation thresholds and emergent research has demonstrated that eDNA concentrations in natural ecosystems can provide rough quantitative estimates of abundance, particularly when models integrate physiology and/or eDNA dynamics. Operationalizing eDNA to infer abundance will probably require more than simple correlations with organism biomass/density. Nevertheless, the future is promising - models that integrate eDNA dynamics in nature could represent an effective means to infer abundance, particularly when traditional methods are considered too "costly" or difficult to obtain.
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Affiliation(s)
| | | | - Alison M Derry
- Université du Québec à Montréal, Montréal, Québec, Canada
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24
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Feng X, Li D, Liang W, Ruan T, Jiang G. Recognition and Prioritization of Chemical Mixtures and Transformation Products in Chinese Estuarine Waters by Suspect Screening Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9508-9517. [PMID: 33764750 DOI: 10.1021/acs.est.0c06773] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chemical mixtures in surface waters could have significant impacts on exposure risks to human beings and pollution stress to aquatic system. By suspect screening analysis of high-resolution mass spectrometry data, occurrence, and compositions of ToxCast chemicals were investigated in grab estuarine water samples from a combination of 20 rivers that represents approximately 70% of the total river flow discharge along the east coast of China. In total, 59 ToxCast chemicals in seven use categories were identified, in which pesticides, intermediates, and pharmaceuticals were the abundant analogues. Significant differences in pollutant composition profiles were noticed, which possibly reflected singular release pattern and geographical-relevant usage preference (especially for herbicides and fungicides in the pesticide category). With the aid of tentative quantitative/semiquantitative measurement, essential contributors to the cumulative pollutant mass discharges and aquatic acute toxicity potentials were focused onto few particular chemicals. Existence of transformation products was further explored, which indicated that the fates of the selected parent ToxCast chemicals could be influenced by dominating transformation reactions (e.g., N-dealkylation and hydroxylation) and possible environmental factors (i.e., microbial activity). The results emphasize the necessity of suspect screening analysis for assessing the influence of terrestrial emissions of pollutants to the surrounding environment.
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Affiliation(s)
- Xiaoxia Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqing Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Ruan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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25
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Macher TH, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F. Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.66557] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.
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26
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Feist SM, Lance RF. Advanced molecular-based surveillance of quagga and zebra mussels: A review of environmental DNA/RNA (eDNA/eRNA) studies and considerations for future directions. NEOBIOTA 2021. [DOI: 10.3897/neobiota.66.60751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sensitive methods, capable of rapidly and accurately detecting aquatic invasive species, are in demand. Molecular-based approaches, such as environmental DNA (eDNA) surveys, satisfy these requirements and have grown in popularity. As such, eDNA surveys could aid the effort to combat the colonisation and spread of two notoriously invasive freshwater mussel species, the quagga mussel (Dreissena rostriformis bugensis) and zebra mussel (D. polymorpha), through improved surveillance ability. Here, we provide a review of dreissenid eDNA literature (both grey and published), summarising efforts involved in the development of various assays for use in multiple different technologies (e.g. quantitative PCR, high-throughput sequencing and loop-mediated isothermal amplification) and sampling scenarios. We discuss important discoveries made along the way, including novel revelations involving environmental RNA (eRNA), as well as the advantages and limitations of available methods and instrumentation. In closing, we highlight critical remaining gaps, where further investigation could lead to advancements in dreissenid monitoring capacity.
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27
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Waldner K, Borkovec M, Borgwardt F, Unfer G, El‐Matbouli M. Effect of water temperature on the morbidity of Tetracapsuloides bryosalmonae (Myxozoa) to brown trout (Salmo trutta) under laboratory conditions. JOURNAL OF FISH DISEASES 2021; 44:1005-1013. [PMID: 33656753 PMCID: PMC8248319 DOI: 10.1111/jfd.13361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 05/08/2023]
Abstract
Proliferative kidney disease (PKD) is a disease found in salmonid fish that is widespread in Europe and North America. The dependency of the clinical signs on the water temperature is extensively reported in rainbow trout, but detailed information on brown trout is lacking. In this study, juvenile brown trout were exposed to the spores of Tetracapsuloides bryosalmonae and then kept at different ambient water temperatures (16°C, 19°C and 22°C) for 10 weeks along with recording of morbidity throughout the experiment. At 6, 8 and 10 weeks post-exposure, fish from each temperature group were sampled and underwent pathoanatomical examination to survey disease progression. At 16°C, brown trout showed a significantly higher survival probability compared to those kept in 19°C and 22°C water. Additionally, the parasitic burden (MSQ) was higher and the clinical signs were more pronounced in the brown trout kept at 19°C and 22°C compared with the ones kept at 16°C. This study highlights the correlation of PKD outbreaks and water temperature increases related to global climate change, which will impact the future distribution of brown trout in natural waters.
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Affiliation(s)
- Karoline Waldner
- Clinical Division for Fish MedicineUniversity of Veterinary MedicineViennaAustria
| | | | - Florian Borgwardt
- University of Natural Resources and Life SciencesVienna, Institute of Hydrobiology and Aquatic Ecosystem ManagementViennaAustria
| | - Günther Unfer
- University of Natural Resources and Life SciencesVienna, Institute of Hydrobiology and Aquatic Ecosystem ManagementViennaAustria
| | - Mansour El‐Matbouli
- Clinical Division for Fish MedicineUniversity of Veterinary MedicineViennaAustria
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28
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Jo T, Ikeda S, Fukuoka A, Inagawa T, Okitsu J, Katano I, Doi H, Nakai K, Ichiyanagi H, Minamoto T. Utility of environmental DNA analysis for effective monitoring of invasive fish species in reservoirs. Ecosphere 2021. [DOI: 10.1002/ecs2.3643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Toshiaki Jo
- Graduate School of Human Development and Environment Kobe University 3‐11, Tsurukabuto, Nada‐ku Kobe Hyogo657‐8501Japan
- Research Fellow of Japan Society for the Promotion of Science 5‐3‐1 Kojimachi Chiyoda‐ku Tokyo102‐0083Japan
| | - Saki Ikeda
- Faculty of Human Development Kobe University 3‐11, Tsurukabuto, Nada‐ku Kobe Hyogo657‐8501Japan
| | - Arisa Fukuoka
- Graduate School of Human Development and Environment Kobe University 3‐11, Tsurukabuto, Nada‐ku Kobe Hyogo657‐8501Japan
| | - Takashi Inagawa
- OYO Corporation 275, Aza‐Ishibata, Oaza‐Nishikata, Miharu‐machi Tamura‐gun Fukushima963‐7722Japan
| | - Jiro Okitsu
- OYO Corporation 275, Aza‐Ishibata, Oaza‐Nishikata, Miharu‐machi Tamura‐gun Fukushima963‐7722Japan
| | - Izumi Katano
- Faculty of Science Nara Women’s University Kitauoyahigashi‐machi Nara630‐8506Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies University of Hyogo Minatojima‐minamimachi Kobe Hyogo650‐0047Japan
| | - Katsuki Nakai
- Lake Biwa Museum 1091 Oroshimo Kusatsu Shiga525‐0001Japan
| | - Hidetaka Ichiyanagi
- Water Resources Environment Center 2‐14‐2, Kojimachi Chiyoda‐ku Tokyo102‐0083Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment Kobe University 3‐11, Tsurukabuto, Nada‐ku Kobe Hyogo657‐8501Japan
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29
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Blackman RC, Osathanunkul M, Brantschen J, Di Muri C, Harper LR, Mächler E, Hänfling B, Altermatt F. Mapping biodiversity hotspots of fish communities in subtropical streams through environmental DNA. Sci Rep 2021; 11:10375. [PMID: 33990677 PMCID: PMC8121892 DOI: 10.1038/s41598-021-89942-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/05/2021] [Indexed: 11/15/2022] Open
Abstract
Large tropical and subtropical rivers are among the most biodiverse ecosystems worldwide, but also suffer from high anthropogenic pressures. These rivers are hitherto subject to little or no routine biomonitoring, which would be essential for identification of conservation areas of high importance. Here, we use a single environmental DNA multi-site sampling campaign across the 200,000 km2 Chao Phraya river basin, Thailand, to provide key information on fish diversity. We found a total of 108 fish taxa and identified key biodiversity patterns within the river network. By using hierarchical clustering, we grouped the fish communities of all sites across the catchment into distinct clusters. The clusters not only accurately matched the topology of the river network, but also revealed distinct groups of sites enabling informed conservation measures. Our study reveals novel opportunities of large-scale monitoring via eDNA to identify relevant areas within whole river catchments for conservation and habitat protection.
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Affiliation(s)
- Rosetta C Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland. .,Research Priority Programme Global Change and Biodiversity (URPP GCB), University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
| | - Maslin Osathanunkul
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Research Centre in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland
| | - Cristina Di Muri
- Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Lynsey R Harper
- Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Elvira Mächler
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland.,Department for Infectious Diseases and Pathobiology, Vetsuisse Faculty, Centre for Fish and Wildlife Health, University of Bern, Länggassstrasse 122, 3012, Bern, Switzerland
| | - Bernd Hänfling
- Evolutionary and Environmental Genomics Group (EvoHull), School of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland. .,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, 8057, Zürich, Switzerland. .,Research Priority Programme Global Change and Biodiversity (URPP GCB), University of Zurich, Winterthurerstr. 190, 8057, Zurich, Switzerland.
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30
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Wang Y, Chen K, Gao J, Wang M, Dong J, Xie Y, Giesy JP, Jin X, Wang B. Environmental DNA of preservative ethanol performed better than water samples in detecting macroinvertebrate diversity using metabarcoding. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Yu Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Kai Chen
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Jin Gao
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Meng Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Jie Dong
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Yuwei Xie
- Toxicology Centre University of Saskatchewan Saskatoon Saskatchewan Canada
| | - John P. Giesy
- Toxicology Centre University of Saskatchewan Saskatoon Saskatchewan Canada
- Department of Veterinary Biomedical Sciences University of Saskatchewan Saskatoon Saskatchewan Canada
- Department of Environmental Sciences Baylor University Waco Texas USA
| | - Xiaowei Jin
- China National Environmental Monitoring Centre Beijing China
| | - Beixin Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
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31
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Environmental DNA provides higher resolution assessment of riverine biodiversity and ecosystem function via spatio-temporal nestedness and turnover partitioning. Commun Biol 2021; 4:512. [PMID: 33941836 PMCID: PMC8093236 DOI: 10.1038/s42003-021-02031-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Rapidly assessing biodiversity is essential for environmental monitoring; however, traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers enhanced scope for assessing biodiversity, while also increasing sampling efficiency and reducing processing time, compared to traditional methods. Here we investigated the effects of landuse and seasonality on headwater community richness and functional diversity, via spatio-temporal dynamics, using both eDNA and traditional sampling. We found that eDNA provided greater resolution in assessing biodiversity dynamics in time and space, compared to traditional sampling. Community richness was seasonally linked, peaking in spring and summer, with temporal turnover having a greater effect on community composition compared to localized nestedness. Overall, our assessment of ecosystem function shows that community formation is driven by regional resource availability, implying regional management requirements should be considered. Our findings show that eDNA based ecological assessment is a powerful, rapid and effective assessment strategy that enables complex spatio-temporal studies of community diversity and ecosystem function, previously infeasible using traditional methods. Mathew Seymour et al. compare eDNA with traditional biodiversity metrics to assess the functional diversity of a river basin in Wales over space and time and variable land use. Their results show that eDNA can generate greater biodiversity resolution and reliably detect spatio-temporal changes in community and functional diversity.
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32
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Farrell JA, Whitmore L, Duffy DJ. The Promise and Pitfalls of Environmental DNA and RNA Approaches for the Monitoring of Human and Animal Pathogens from Aquatic Sources. Bioscience 2021. [PMCID: PMC8083301 DOI: 10.1093/biosci/biab027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Novel forensics-inspired molecular approaches have revolutionized species detection in the wild and are particularly useful for tracing endangered or invasive species. These new environmental DNA or RNA (eDNA or eRNA)–based techniques are now being applied to human and animal pathogen surveillance, particularly in aquatic environments. They allow better disease monitoring (presence or absence and geographical spread) and understanding of pathogen occurrence and transmission, benefitting species conservation and, more recently, our understanding of the COVID-19 global human pandemic. In the present article, we summarize the benefits of eDNA-based monitoring, highlighted by two case studies: The first is a fibropapillomatosis tumor-associated herpesvirus (chelonid herpesvirus 5) driving a sea turtle panzootic, and the second relates to eRNA-based detection of the SARS-CoV-2 coronavirus driving the COVID-19 human pandemic. The limitations of eDNA- or eRNA-based approaches are also summarized, and future directions and recommendations of the field are discussed. Continuous eDNA- or eRNA-based monitoring programs can potentially improve human and animal health by predicting disease outbreaks in advance, facilitating proactive rather than reactive responses.
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Affiliation(s)
- Jessica A Farrell
- University of Florida's Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital (St. Augustine), and The University of Florida's Department of Biology in the College of Liberal Arts and Sciences (Gainesville), United States
| | - Liam Whitmore
- University of Limerick's Department of Biological Sciences in the School of Natural Sciences and Faculty of Science and Engineering, Limerick, Ireland
| | - David J Duffy
- University of Florida's Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital (St. Augustine), and The University of Florida's Department of Biology in the College of Liberal Arts and Sciences (Gainesville), United States
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33
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Clare EL, Economou CK, Faulkes CG, Gilbert JD, Bennett F, Drinkwater R, Littlefair JE. eDNAir: proof of concept that animal DNA can be collected from air sampling. PeerJ 2021; 9:e11030. [PMID: 33850648 PMCID: PMC8019316 DOI: 10.7717/peerj.11030] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Environmental DNA (eDNA) is one of the fastest developing tools for species biomonitoring and ecological research. However, despite substantial interest from research, commercial and regulatory sectors, it has remained primarily a tool for aquatic systems with a small amount of work in substances such as soil, snow and rain. Here we demonstrate that eDNA can be collected from air and used to identify mammals. Our proof of concept successfully demonstrated that eDNA sampled from air contained mixed templates which reflect the species known to be present within a confined space and that this material can be accessed using existing sampling methods. We anticipate this demonstration will initiate a much larger research programme in terrestrial airDNA sampling and that this may rapidly advance biomonitoring approaches. Lastly, we outline these and potential related applications we expect to benefit from this development.
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Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Chloe K Economou
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - James D Gilbert
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Frances Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Rosie Drinkwater
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Joanne E Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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34
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Hutchins PR, Sepulveda AJ, Hartikainen H, Staigmiller KD, Opitz ST, Yamamoto RM, Huttinger A, Cordes RJ, Weiss T, Hopper LR, Purcell MK, Okamura B. Exploration of the 2016 Yellowstone River fish kill and proliferative kidney disease in wild fish populations. Ecosphere 2021. [DOI: 10.1002/ecs2.3436] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Patrick R. Hutchins
- Northern Rocky Mountain Science Center U.S. Geological Survey 2327 University Way Suite 2 Bozeman Montana59715USA
| | - Adam J. Sepulveda
- Northern Rocky Mountain Science Center U.S. Geological Survey 2327 University Way Suite 2 Bozeman Montana59715USA
| | - Hanna Hartikainen
- School of Life Sciences University of Nottingham University Park NottinghamNG7 2RDUK
| | - Ken D. Staigmiller
- Fish Health Lab Montana Fish Wildlife and Parks 4801 Giant Springs Road Great Falls Montana59405USA
| | - Scott T. Opitz
- Montana Fish Wildlife and Parks 1400 South 19th Avenue Bozeman Montana59718USA
| | - Renee M. Yamamoto
- Bozeman Fish Health Center U.S. Fish and Wildlife Service 1805 South 22nd Avenue Suite 1 Bozeman Montana59718USA
| | - Amberly Huttinger
- Bozeman Fish Health Center U.S. Fish and Wildlife Service 1805 South 22nd Avenue Suite 1 Bozeman Montana59718USA
| | - Rick J. Cordes
- Bozeman Fish Health Center U.S. Fish and Wildlife Service 1805 South 22nd Avenue Suite 1 Bozeman Montana59718USA
| | - Tammy Weiss
- Bozeman Fish Health Center U.S. Fish and Wildlife Service 1805 South 22nd Avenue Suite 1 Bozeman Montana59718USA
| | - Lacey R. Hopper
- Bozeman Fish Health Center U.S. Fish and Wildlife Service 1805 South 22nd Avenue Suite 1 Bozeman Montana59718USA
| | - Maureen K. Purcell
- Western Fisheries Research Center U.S. Geological Survey 6505 NE 65th Street Seattle Washington98115USA
| | - Beth Okamura
- Department of Life Sciences Natural History Museum Cromwell Road LondonSW7 5BDUK
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35
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Marques V, Milhau T, Albouy C, Dejean T, Manel S, Mouillot D, Juhel J. GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13142] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Virginie Marques
- MARBEC Univ Montpellier CNRS Ifremer IRD Montpellier France
- CEFE EPHE CNRS UM UPV IRD PSL Research University Montpellier France
| | | | - Camille Albouy
- IFREMER Unité Ecologie et Modèles pour l’Halieutique Nantes cedex 3 Nantes France
| | | | - Stéphanie Manel
- CEFE EPHE CNRS UM UPV IRD PSL Research University Montpellier France
| | - David Mouillot
- MARBEC Univ Montpellier CNRS Ifremer IRD Montpellier France
- Australian Research Council Centre of Excellence for Coral Reef Studies James Cook University Townsville Qld Australia
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36
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Jo T, Minamoto T. Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses. Mol Ecol Resour 2021; 21:1490-1503. [PMID: 33580561 DOI: 10.1111/1755-0998.13354] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 11/28/2022]
Abstract
Understanding the processes of environmental DNA (eDNA) persistence and degradation is essential to determine the spatiotemporal scale of eDNA signals and accurately estimate species distribution. The effects of environmental factors on eDNA persistence have previously been examined; however, the influence of the physiochemical and molecular states of eDNA on its persistence is not completely understood. Here, we performed meta-analyses including 26 previously published papers on the estimation of first-order eDNA decay rate constants, and assessed the effects of filter pore size, DNA fragment size, target gene, and environmental conditions on eDNA decay rates. Almost all supported models included the interactions between the filter pore size and water temperature, between the target gene and water temperature, and between the target gene and water source, implying the influence of complex interactions between the eDNA state and environmental conditions on eDNA persistence. These findings were generally consistent with the results of a reanalysis of a previous tank experiment which measured the time-series changes in marine fish eDNA concentrations in multiple size fractions after fish removal. Our results suggest that the mechanism of eDNA persistence and degradation cannot be fully understood without knowing not only environmental factors but also cellular and molecular states of eDNA in water. Further verification of the relationship between eDNA state and persistence is required by obtaining more information on eDNA persistence in various experimental and environmental conditions, which will enhance our knowledge on eDNA persistence and support our findings.
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Affiliation(s)
- Toshiaki Jo
- Graduate School of Human Development and Environment, Kobe University Kobe City, Hyogo, Japan.,Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University Kobe City, Hyogo, Japan
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Lacoursière-Roussel A, Deiner K. Environmental DNA is not the tool by itself. JOURNAL OF FISH BIOLOGY 2021; 98:383-386. [PMID: 31644816 DOI: 10.1111/jfb.14177] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 10/22/2019] [Indexed: 05/19/2023]
Affiliation(s)
- Anaïs Lacoursière-Roussel
- St. Andrews Biological Station (SABS), Fisheries and Oceans Canada (DFO), St. Andrews, New Brunswick, Canada
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Know your enemy - transcriptome of myxozoan Tetracapsuloides bryosalmonae reveals potential drug targets against proliferative kidney disease in salmonids. Parasitology 2021; 148:726-739. [PMID: 33478602 PMCID: PMC8056827 DOI: 10.1017/s003118202100010x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The myxozoan Tetracapsuloides bryosalmonae is a widely spread endoparasite that causes proliferative kidney disease (PKD) in salmonid fish. We developed an in silico pipeline to separate transcripts of T. bryosalmonae from the kidney tissue of its natural vertebrate host, brown trout (Salmo trutta). After stringent filtering, we constructed a partial transcriptome assembly T. bryosalmonae, comprising 3427 transcripts. Based on homology-restricted searches of the assembled parasite transcriptome and Atlantic salmon (Salmo salar) proteome, we identified four protein targets (Endoglycoceramidase, Legumain-like protease, Carbonic anhydrase 2, Pancreatic lipase-related protein 2) for the development of anti-parasitic drugs against T. bryosalmonae. Earlier work of these proteins on parasitic protists and helminths suggests that the identified anti-parasitic drug targets represent promising chemotherapeutic candidates also against T. bryosalmonae, and strengthen the view that the known inhibitors can be effective in evolutionarily distant organisms. In addition, we identified differentially expressed T. bryosalmonae genes between moderately and severely infected fish, indicating an increased abundance of T. bryosalmonae sporogonic stages in fish with low parasite load. In conclusion, this study paves the way for future genomic research in T. bryosalmonae and represents an important step towards the development of effective drugs against PKD.
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Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller E, Schulman L, Tilley L, Robertson T. White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e62361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure (RI) is presently in its preparatory phase. DiSSCo is developing a new distributed RI to operate as a one-stop-shop for the envisaged European Natural Science Collection (NSC) and all its derived information. Through mass digitisation, DiSSCo will transform the fragmented landscape of NSCs, including an estimated 1.5 billion specimens, into an integrated knowledge base that will provide interconnected evidence of the natural world. Data derived from European NSCs underpin countless discoveries and innovations, including tens of thousands of scholarly publications and official reports annually (supporting legislative and regulatory processes on sustainability, environmental change, land use, societal infrastructure, health, food, security, etc.); base-line biodiversity data; inventions and products essential to bio-economy; databases, maps and descriptions of scientific observations; educational material for students; and instructive and informative resources for the public. To expand the user community, DiSSCo will strengthen capacity building across Europe for maximum engagement of stakeholders in the biodiversity-related field and beyond, including industry and the private sector, but also policy-driving entities. Hence, it is opportune to reach out to relevant stakeholders in the European environmental policy domain represented by the European Environment Agency (EEA). The EEA aims to support sustainable development by helping to achieve significant and measurable improvement in Europe's environment, through the provision of timely, targeted, relevant and reliable information to policy-making agents and the public. The EEA provides information through the European Environment Information and Observation System (Eionet). The aim of this white paper is to open the discussion between DiSSCo and the EEA and identify the common service interests that are relevant for the European environmental policy domain. The first section describes the significance of (digital) Natural Science Collections (NHCs). Section two describes the DiSSCo programme with all DiSSCo aligned projects. Section three provides background information on the EEA and the biodiversity infrastructures that are developed and maintained by the EEA. The fourth section illustrates a number of use cases where the DiSSCo consortium sees opportunities for interaction between the DiSSCo RI and the Eionet portal of the EEA. Opening the discussion with the EEA in this phase of maturity of DiSSCo will ensure that the infrastructural design of DiSSCo and the development of e-Services accommodate the present and future needs of the EEA and assure data interoperability between the two infrastructures.
The aim of this white paper is to present benefits from identifying the common service interests of DiSSCo and the EEA. A brief introduction to natural science collections as well as the two actors is given to facilitate the understanding of the needs and possibilities in the alignment of DiSSCo with the EEA.
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40
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Blackman RC, Ling KKS, Harper LR, Shum P, Hänfling B, Lawson‐Handley L. Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water. Ecol Evol 2020; 10:13248-13259. [PMID: 33304534 PMCID: PMC7713958 DOI: 10.1002/ece3.6921] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022] Open
Abstract
The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS-particularly during the early stages of an invasion.Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK.All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor. Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.
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Affiliation(s)
- Rosetta C. Blackman
- Department of Aquatic EcologyEawagSwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Kar Keun Sean Ling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lynsey R. Harper
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Peter Shum
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Bernd Hänfling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lori Lawson‐Handley
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
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41
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Darling JA, Jerde CL, Sepulveda AJ. What do you mean by false positive. ENVIRONMENTAL DNA (HOBOKEN, N.J.) 2020; 3:879-883. [PMID: 35330629 PMCID: PMC8941663 DOI: 10.1002/edn3.194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Misunderstandings regarding the term "false positive" present a significant hurdle to broad adoption of eDNA monitoring methods. Here, we identify three challenges to clear communication of false-positive error between scientists, managers, and the public. The first arises from a failure to distinguish between false-positive eDNA detection at the sample level and false-positive inference of taxa presence at the site level. The second is based on the large proportion of false positives that may occur when true-positive detections are likely to be rare, even when rates of contamination or other error are low. And the third misunderstanding occurs when conventional species detection approaches, often based on direct capture, are used to confirm eDNA approaches without acknowledging or quantifying the conventional approach's detection probability. The solutions to these issues include careful and consistent communication of error definitions, managing expectations of error rates, and providing a balanced discussion not only of alternative sources of species DNA, but also of the detection limitations of conventional methods. We argue that the benefit of addressing these misunderstandings will be increased confidence in the utility of eDNA methods and, ultimately, improved resource management using eDNA approaches. The term false positive is often misused in eDNA research and natural resource management. There are issues of scale of inference, the base rate fallacy, and confirmation errors using conventional methods of detection. We offer a perspective to guide discussions of errors in species detection.
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Affiliation(s)
- John A. Darling
- Center for Environmental Measurement & Modeling, United States Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | - Adam J. Sepulveda
- Northern Rocky Mountain Science Center, U.S. Geological Survey, Bozeman, MT, USA
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42
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Sieber N, Hartikainen H, Vorburger C. Validation of an eDNA-based method for the detection of wildlife pathogens in water. DISEASES OF AQUATIC ORGANISMS 2020; 141:171-184. [PMID: 33089822 DOI: 10.3354/dao03524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Monitoring the occurrence and density of parasites and pathogens can identify high infection-risk areas and facilitates disease control and eradication measures. Environmental DNA (eDNA) techniques are increasingly used for pathogen detection due to their relative ease of application. Since many factors affect the reliability and efficacy of eDNA-based detection, rigorous validation and assessment of method limitations is a crucial first step. We evaluated an eDNA detection method using in situ filtration of large-volume water samples, developed to detect and quantify aquatic wildlife parasites by quantitative PCR (qPCR). We assessed method reliability using Batrachochytrium dendrobatidis, a pathogenic fungus of amphibians and the myxozoan Tetracapsuloides bryosalmonae, causative agent of salmonid proliferative kidney disease, in a controlled experimental setup. Different amounts of parasite spores were added to tanks containing either clean tap water or water from a semi-natural mesocosm community. Overall detection rates were higher than 80%, but detection was not consistent among replicate samples. Within-tank variation in detection emphasises the need for increased site-level replication when dealing with parasites and pathogens. Estimated parasite DNA concentrations in water samples were highly variable, and a significant increase with higher spore concentrations was observed only for B. dendrobatidis. Despite evidence for PCR inhibition in DNA extractions from mesocosm water samples, the type of water did not affect detection rates significantly. Direct spiking controls revealed that the filtration step reduced detection sensitivity. Our study identifies sensitive quantification and sufficient replication as major remaining challenges for the eDNA-based methods for detection of parasites in water.
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Affiliation(s)
- Natalie Sieber
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
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43
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Jo T, Murakami H, Masuda R, Minamoto T. Selective collection of long fragments of environmental DNA using larger pore size filter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 735:139462. [PMID: 32474249 DOI: 10.1016/j.scitotenv.2020.139462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Environmental DNA (eDNA) can exist in water with various sizes and states. Among them, relative to extra-cellular DNA, intra-cellular DNA such as cell and tissue fragments can mainly be detected at larger size fractions, and may be protected from enzymatic DNA degradation processes. Here, we verified the hypothesis that the selective collection of such large-sized eDNA enhances the efficiency of capturing less-degraded eDNA, based on a tank experiment using Japanese Jack Mackerel (Trachurus japonicus) as a model species. We concentrated different volumes of rearing water using the filters with different pore sizes (0.7 μm and 2.7 μm), and quantified the copy number of short and long mitochondrial and short nuclear DNA fragments of target species in water samples. As a result, the ratio of long to short eDNA concentrations was higher in the larger pore size filter, which would support our stated hypothesis. In addition, the ratio of nuclear to mitochondrial eDNA was lower in the larger pore size filter. These results imply a difference in the persistence of nuclear and mitochondrial DNA between intra- and extra-cellular environments. Moreover, larger filter pore size did not necessarily decrease the yields of eDNA, and there was little difference in yields in smaller filtration volumes. The findings of this study indicate the potential to select information from eDNA signals by focusing on eDNA of specific size and state, which may contribute to efficient utilization of the information on species taxonomy and physiology in water samples.
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Affiliation(s)
- Toshiaki Jo
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe City, Hyogo 657-8501, Japan; Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan.
| | - Hiroaki Murakami
- Maizuru Fisheries Research Station, Field Science Education, and Research Center, Kyoto University, Maizuru, Kyoto 625-0086, Japan
| | - Reiji Masuda
- Maizuru Fisheries Research Station, Field Science Education, and Research Center, Kyoto University, Maizuru, Kyoto 625-0086, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11, Tsurukabuto, Nada-ku, Kobe City, Hyogo 657-8501, Japan
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44
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Fukaya K, Murakami H, Yoon S, Minami K, Osada Y, Yamamoto S, Masuda R, Kasai A, Miyashita K, Minamoto T, Kondoh M. Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling. Mol Ecol 2020; 30:3057-3067. [PMID: 32608023 DOI: 10.1111/mec.15530] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/03/2020] [Accepted: 06/23/2020] [Indexed: 01/03/2023]
Abstract
Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.
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Affiliation(s)
- Keiichi Fukaya
- National Institute for Environmental Studies, Tsukuba, Japan.,The Institute of Statistical Mathematics, Tachikawa, Japan
| | - Hiroaki Murakami
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Maizuru, Japan
| | - Seokjin Yoon
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Kenji Minami
- Estuary Research Center, Shimane University, Matsue, Japan
| | - Yutaka Osada
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan.,National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Kanazawa, Yokohama, Japan
| | - Satoshi Yamamoto
- Laboratory of Animal Ecology, Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Reiji Masuda
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University, Maizuru, Japan
| | - Akihide Kasai
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Kazushi Miyashita
- Field Science Center for Northern Biosphere, Hokkaido University, Hakodate, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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45
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Carraro L, Mächler E, Wüthrich R, Altermatt F. Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems. Nat Commun 2020; 11:3585. [PMID: 32680984 PMCID: PMC7367889 DOI: 10.1038/s41467-020-17337-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/25/2020] [Indexed: 11/17/2022] Open
Abstract
The alarming declines of freshwater biodiversity call for efficient biomonitoring at fine spatiotemporal scales, such that conservation measures be grounded upon accurate biodiversity data. Here, we show that combining environmental DNA (eDNA) extracted from stream water samples with models based on hydrological first principles allows upscaling biodiversity estimates for aquatic insects at very high spatial resolution. Our model decouples the diverse upstream contributions to the eDNA data, enabling the reconstruction of taxa distribution patterns. Across a 740-km2 basin, we obtain a space-filling biodiversity prediction at a grain size resolution of 1-km long stream sections. The model's accuracy in matching direct observations of aquatic insects' local occurrence ranges between 57-100%. Our results demonstrate how eDNA can be used for high-resolution biodiversity assessments in rivers with minimal prior knowledge of the system. Our approach allows identification of biodiversity hotspots that could be otherwise overlooked, enabling implementation of focused conservation strategies.
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Affiliation(s)
- Luca Carraro
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.
| | - Elvira Mächler
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - Remo Wüthrich
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
- gutwasser GmbH, Geerenweg 2, CH-8048, Zürich, Switzerland
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.
- University Research Priority Programme (URPP) on Global Change and Biodiversity, University of Zurich, Winterthurerstr. 190, CH-8057, Zürich, Switzerland.
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46
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Crookes S, Heer T, Castañeda RA, Mandrak NE, Heath DD, Weyl OLF, MacIsaac HJ, Foxcroft LC. Monitoring the silver carp invasion in Africa: a case study using environmental DNA (eDNA) in dangerous watersheds. NEOBIOTA 2020. [DOI: 10.3897/neobiota.56.47475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Biodiverse habitats are increasingly subject to an intensification of anthropogenic stressors that may severely diminish species richness. Invasive species pose a dominant threat to biodiversity and biosecurity, particularly in biodiversity hotspots like Kruger National Park, South Africa. The invasive silver carp, Hypophthalmichthys molitrix, was introduced into the Olifants River and may experience range spread owing to favorable environmental conditions. Intensive monitoring protocols are necessary to effectively manage invasions of species like silver carp. Unfortunately, tropical and sub-tropical aquatic systems are difficult to monitor using conventional methods (e.g., netting, electrofishing and snorkeling) owing to a range of factors including the presence of dangerous megafauna. Conservation of such systems may be advanced by the adoption of novel methods, including environmental DNA (eDNA) detection. Here, we explore the utility of environmental DNA (eDNA) to conduct safe, reliable and repeatable surveys in dangerous watersheds using silver carp as a case study. We conducted eDNA surveys at 12 sites in two neighbouring watersheds, and determined that the species has expanded its range within the Olifants River and to the south in the Sabie River. Expansion in the former is consistent with the presence of suitable spawning conditions. We discuss the implications of this survey for biodiversity monitoring in similar aquatic systems in the tropics and advocate an integrative approach to biomonitoring in these ecosystems.
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47
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Wood SA, Biessy L, Latchford JL, Zaiko A, von Ammon U, Audrezet F, Cristescu ME, Pochon X. Release and degradation of environmental DNA and RNA in a marine system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135314. [PMID: 31780169 DOI: 10.1016/j.scitotenv.2019.135314] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 05/21/2023]
Abstract
Over the last decade, there has been growing interest in the analysis of environmental DNA (eDNA) to infer the presence of organisms in aquatic environments. The efficacy of eDNA/eRNA based tools are highly depend on the turnover rate of the molecule (their release and degradation). Environmental DNA has been shown to persist for days, weeks or years in environmental samples. Environmental RNA (eRNA) is thought to degrade faster than eDNA, however to our knowledge, no experimental studies have explored this. Here we present an aquarium study to investigate eDNA and eRNA shedding rates and degradation for two sessile marine invertebrates. The copy numbers for eDNA and eRNA were assessed using droplet digital PCR targeting the mitochondrial Cytochrome c Oxidase subunit 1 (COI) gene. Environmental RNA persisted after organism removal for much longer than expected with detections for up to 13 h. In contrast, eDNA was detected is samples collected up to 94 h after organism removal. There was no evidence that the decay rates constants for eDNA and eRNA were different (p = 0.6, Kruskal-Wallis tests). Both eDNA and eRNA was detected in biofilms collected at the end of the experiment (day 21). This suggests binding with organic or inorganic compounds or stabilization of these molecules in the biofilm matrix. The finding of the prolonged persistence of eRNA may provide new opportunities for improved biodiversity surveys through reducing false positives caused by legacy DNA and could also facilitate new research on environmental transcriptomics.
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Affiliation(s)
- Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Janie L Latchford
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Ulla von Ammon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - François Audrezet
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
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48
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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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Xiong W, Huang X, Chen Y, Fu R, Du X, Chen X, Zhan A. Zooplankton biodiversity monitoring in polluted freshwater ecosystems: A technical review. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2019; 1:100008. [PMCID: PMC9488063 DOI: 10.1016/j.ese.2019.100008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 05/26/2023]
Abstract
Freshwater ecosystems harbor a vast diversity of micro-eukaryotes (rotifers, crustaceans and protists), and such diverse taxonomic groups play important roles in ecosystem functioning and services. Unfortunately, freshwater ecosystems and biodiversity therein are threatened by many environmental stressors, particularly those derived from intensive human activities such as chemical pollution. In the past several decades, significant efforts have been devoted to halting biodiversity loss to recover services and functioning of freshwater ecosystems. Biodiversity monitoring is the first and a crucial step towards diagnosing pollution impacts on ecosystems and making conservation plans. Yet, bio-monitoring of ubiquitous micro-eukaryotes is extremely challenging, owing to many technical issues associated with micro-zooplankton such as microscopic size, fuzzy morphological features, and extremely high biodiversity. Here, we review current methods used for monitoring zooplankton biodiversity to advance management of impaired freshwater ecosystems. We discuss the development of traditional morphology-based identification methods such as scanning electron microscope (SEM) and ZOOSCAN and FlowCAM automatic systems, and DNA-based strategies such as metabarcoding and real-time quantitative PCR. In addition, we summarize advantages and disadvantages of these methods when applied for monitoring impacted ecosystems, and we propose practical DNA-based monitoring workflows for studying biological consequences of environmental pollution in freshwater ecosystems. Finally, we propose possible solutions for existing technical issues to improve accuracy and efficiency of DNA-based biodiversity monitoring. Freshwater ecosystems and associated biodiversity have been highly degraded. Biodiversity monitoring is crucial for diagnosing degradation degrees. Here we review available methods for monitoring zooplankton biodiversity. We propose possible solutions for existing technical issues.
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Affiliation(s)
- Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xun Du
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xingyu Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- College of Resources, Environment and Tourism, Capital Normal University, 105 West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
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50
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Harvey MG, Singhal S, Rabosky DL. Beyond Reproductive Isolation: Demographic Controls on the Speciation Process. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024701] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of speciation typically investigate the evolution of reproductive isolation between populations, but several other processes can serve as key steps limiting the formation of species. In particular, the probability of successful speciation can be influenced by factors that affect the frequency with which population isolates form as well as their persistence through time. We suggest that population isolation and persistence have an inherently spatial dimension that can be profitably studied using a conceptual framework drawn from metapopulation ecology. We discuss models of speciation that incorporate demographic processes and highlight the need for a broader application of phylogenetic comparative approaches to evaluate the general importance of population isolation, persistence, and reproductive isolation in speciation. We review diverse and nontraditional data sources that can be leveraged to study isolation and persistence in a comparative framework. This incorporation of spatial demographic information facilitates the integration of perspectives on speciation across disciplines and timescales.
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Affiliation(s)
- Michael G. Harvey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, California 90747, USA
| | - Daniel L. Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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