151
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Di Muri C, Lawson Handley L, Bean CW, Li J, Peirson G, Sellers GS, Walsh K, Watson HV, Winfield IJ, Hänfling B. Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.56959] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems is still not fully understood. Previous studies have shown positive but sometimes weak correlations between abundance estimates from eDNA metabarcoding data and from conventional capture methods. As both methods have independent biases a lack of concordance is difficult to interpret. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of the absolute abundance of fish in holding ponds with known fish biomass and number of individuals. Environmental DNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used. This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.
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152
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Shea D, Bateman A, Li S, Tabata A, Schulze A, Mordecai G, Ogston L, Volpe JP, Neil Frazer L, Connors B, Miller KM, Short S, Krkošek M. Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms. Proc Biol Sci 2020; 287:20202010. [PMID: 33081614 PMCID: PMC7661312 DOI: 10.1098/rspb.2020.2010] [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] [Indexed: 01/15/2023] Open
Abstract
The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.
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Affiliation(s)
- Dylan Shea
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Andrew Bateman
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada.,Pacific Salmon Foundation, Vancouver, British Columbia, Canada
| | - Shaorong Li
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Angela Schulze
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Gideon Mordecai
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lindsey Ogston
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - John P Volpe
- School of Environmental Studies, University of Victoria, Victoria, British Columbia, Canada
| | - L Neil Frazer
- Department of Earth Sciences, University of Hawaii at Mānoa, Honolulu, Hawaii, Canada
| | - Brendan Connors
- Institute of Ocean Sciences, Fisheries and Oceans Canada, Sidney, British Columbia, Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Steven Short
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Department of Biology, University of Toronto Mississauga, Mississauga, British Columbia, Canada
| | - Martin Krkošek
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada.,Salmon Coast Field Station, Simoom Sound, British Columbia, Canada
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153
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Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding. PLoS One 2020; 15:e0231127. [PMID: 33022692 PMCID: PMC7538199 DOI: 10.1371/journal.pone.0231127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022] Open
Abstract
Biodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river.
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154
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Kirtane A, Atkinson JD, Sassoubre L. Design and Validation of Passive Environmental DNA Samplers Using Granular Activated Carbon and Montmorillonite Clay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11961-11970. [PMID: 32659082 DOI: 10.1021/acs.est.0c01863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Environmental DNA (eDNA) analysis is gaining prominence as a tool for species and biodiversity monitoring in aquatic environments. eDNA shed by organisms is captured in grab samples, concentrated by filtration, extracted, and analyzed using molecular methods. Conventional capture and filtration methods are limited because (1) filtration does not capture all extracellular DNA, (2) eDNA can degrade during sample transport and storage, (3) filters often clog in turbid waters, reducing the eDNA captured, and (4) grab samples are time sensitive due to pulse eDNA inputs. To address these limitations, this work designs and validates Passive Environmental DNA Samplers (PEDS). PEDS consist of an adsorbent-filled sachet that is suspended in water to collect eDNA over time. Both extracellular and cellular DNA are captured, and the extracellular DNA is protected from degradation. The eDNA captured over time may be more representative than a grab sample. Two adsorbents, Montmorillonite Clay (MC) and Granular Activated Carbon (GAC), are tested. In laboratory experiments, MC-PEDS adsorbed five times more extracellular DNA and desorbed up to four times more than GAC-PEDS (despite high levels of eDNA loss during desorption). In microcosm and field experiments, GAC-PEDS captured over an order of magnitude more eDNA than MC-PEDS. Field results further validated PEDS as an effective eDNA capture method compared to conventional methods.
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Affiliation(s)
- Anish Kirtane
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
| | - John D Atkinson
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
| | - Lauren Sassoubre
- Department of Civil, Structural, and Environmental Engineering, The State University of New York at Buffalo, Buffalo, New York 14228, United States
- Department of Engineering, University of San Francisco, San Francisco, California 94117, United States
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155
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Yatsuyanagi T, Araki H. Understanding seasonal migration of Shishamo smelt in coastal regions using environmental DNA. PLoS One 2020; 15:e0239912. [PMID: 33002065 PMCID: PMC7529200 DOI: 10.1371/journal.pone.0239912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022] Open
Abstract
Migratory organisms have their own life histories that efficiently link multiple ecosystems. Therefore, comprehensive understanding of migration ecologies of these organisms is essential for both species conservation and ecosystem management. However, monitoring migration at fine spatiotemporal scales, especially in open marine systems, often requires huge costs and effort. Recently, environmental DNA (eDNA) techniques that utilize DNA released from living organisms into their environment became available for monitoring wild animals without direct handling. In this study, we conducted an eDNA survey for understanding marine migration of an endemic fish species, Shishamo smelt (Spirinchus lanceolatus). We examined 1) seasonal habitat changes in coastal regions and 2) environmental factors potentially driving the migration of this species. The eDNA concentrations along a 100 km-long coastline exhibited spatiotemporal variation, suggesting that this species shifts their habitat away from nearshore areas between spring and summer. We also found a significantly negative association between the eDNA concentration and sea surface temperature. That finding suggests that the offshore migration of this species is associated with increased sea surface temperature. This study reveals new aspects of S. lanceolatus life history in coastal regions. Together with our previous eDNA study on the freshwater migration of S. lanceolatus, this study illustrates the potential of eDNA techniques for understanding the whole life history of this migratory species.
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Affiliation(s)
- Tetsu Yatsuyanagi
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hitoshi Araki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail:
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156
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Ahn H. Variation of Japanese eel eDNA in sequentially changing conditions and in different sample volumes. JOURNAL OF FISH BIOLOGY 2020; 97:1238-1241. [PMID: 32654144 DOI: 10.1111/jfb.14460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/28/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Environmental DNA (eDNA) surveys have been conducted to evaluate the distribution and abundance of Japanese eels. However, various environmental and biological factors may influence eDNA concentrations. An experiment was conducted using three water sample replicates (50, 100 and 200 ml) of the same group of eels in a tank that were exposed to sequential nonfeeding/feeding and low/high temperature conditions. Slightly higher concentrations occurred at higher temperature (22-23°C) with nonfeeding, and the highest concentrations occurred when feeding started even though it was in the lower temperature (16-17°C) condition, but sample volume had no effect.
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Affiliation(s)
- Hyojin Ahn
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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157
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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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158
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Abstract
The timing and location of spawning events are important data for managers seeking to control invasive grass carp populations. Ichthyoplankton tows for grass carp eggs and larvae can be used to detect spawning events; however, these samples can be highly debris-laden, and are expensive and laborious to process. An alternative method, environmental DNA (eDNA) technology, has proven effective in determining the presence of aquatic species. The objectives of this project were to assess the use of eDNA collections and quantitative eDNA analysis to assess the potential spawning of grass carp in five reservoir tributaries, and to compare those results to the more traditional method of ichthyoplankton tows. Grass carp eDNA was detected in 56% of sampling occasions and was detected in all five rivers. Concentrations of grass carp eDNA were orders of magnitude higher in June, corresponding to elevated discharge and egg presence. Grass carp environmental DNA flux (copies/h) was lower when no eggs were present and was higher when velocities and discharge increased and eggs were present. There was a positive relationship between grass carp eDNA flux and egg flux. Our results support the further development of eDNA analysis as a method to detect the spawning events of grass carp or other rheophilic spawners.
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159
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Snyder MR, Stepien CA. Increasing confidence for discerning species and population compositions from metabarcoding assays of environmental samples: case studies of fishes in the Laurentian Great Lakes and Wabash River. METABARCODING AND METAGENOMICS 2020. [DOI: 10.3897/mbmg.4.53455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Community composition data are essential for conservation management, facilitating identification of rare native and invasive species, along with abundant ones. However, traditional capture-based morphological surveys require considerable taxonomic expertise, are time consuming and expensive, can kill rare taxa and damage habitats, and often are prone to false negatives. Alternatively, metabarcoding assays can be used to assess the genetic identity and compositions of entire communities from environmental samples, comprising a more sensitive, less damaging, and relatively time- and cost-efficient approach. However, there is a trade-off between the stringency of bioinformatic filtering needed to remove false positives and the potential for false negatives. The present investigation thus evaluated use of four mitochondrial (mt) DNA metabarcoding assays and a customized bioinformatic Bioinformatic pipeline to increase confidence in species identifications by removing false positives, while achieving high detection probability. Positive controls were used to calculate sequencing error, and results that fell below those cutoff values were removed, unless found with multiple assays. The performance of this approach was tested to discern and identify North American freshwater fishes using lab experiments (mock communities and aquarium experiments) and processing of a bulk ichthyoplankton sample. The method then was applied to field environmental (e) DNA water samples taken concomitant with electrofishing surveys and morphological identifications. This protocol detected 100% of species present in concomitant electrofishing surveys in the Wabash River and an additional 21 that were absent from traditional sampling. Using single 1 L water samples collected from just four locations, the metabarcoding assays discerned 73% of the total fish species that were discerned during four months of an extensive electrofishing river survey in the Maumee River, along with an additional nine species. In both rivers, total fish species diversity was best resolved when all four metabarcoding assays were used together, which identified 35 additional species missed by electrofishing. Ecological distinction and diversity levels among the fish communities also were better resolved with the metabarcoding assays than with morphological sampling and identifications, especially using all four assays together. At the population-level, metabarcoding analyses targeting the invasive round goby Neogobius melanostomus and the silver carp Hypophthalmichthys molitrix identified all population haplotype variants found using Sanger sequencing of morphologically sampled fish, along with additional intra-specific diversity, meriting further investigation. Overall findings demonstrated that the use of multiple metabarcoding assays and custom bioinformatics that filter potential error from true positive detections improves confidence in evaluating biodiversity.
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160
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Remote, autonomous real-time monitoring of environmental DNA from commercial fish. Sci Rep 2020; 10:13272. [PMID: 32764624 PMCID: PMC7413362 DOI: 10.1038/s41598-020-70206-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/21/2020] [Indexed: 12/04/2022] Open
Abstract
Environmental DNA (eDNA) is increasingly used for monitoring marine organisms; however, offshore sampling and time lag from sampling to results remain problematic. In order to overcome these challenges a robotic sampler, a 2nd generation Environmental Sample Processor (ESP), was tested for autonomous analysis of eDNA from four commercial fish species in a 4.5 million liter mesocosm. The ESP enabled in situ analysis, consisting of water collection, filtration, DNA extraction and qPCR analysis, which allowed for real-time remote reporting and archival sample collection, consisting of water collection, filtration and chemical preservation followed by post-deployment laboratory analysis. The results demonstrate that the 2G ESP was able to consistently detect and quantify target molecules from the most abundant species (Atlantic mackerel) both in real-time and from the archived samples. In contrast, detection of low abundant species was challenged by both biological and technical aspects coupled to the ecology of eDNA and the 2G ESP instrumentation. Comparison of the in situ analysis and archival samples demonstrated variance, which potentially was linked to diel migration patterns of the Atlantic mackerel. The study demonstrates strong potential for remote autonomous in situ monitoring which open new possibilities for the field of eDNA and marine monitoring.
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161
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Yates MC, Glaser DM, Post JR, Cristescu ME, Fraser DJ, Derry AM. The relationship between eDNA particle concentration and organism abundance in nature is strengthened by allometric scaling. Mol Ecol 2020; 30:3068-3082. [PMID: 32638451 DOI: 10.1111/mec.15543] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 06/15/2020] [Accepted: 06/26/2020] [Indexed: 01/02/2023]
Abstract
Organism abundance is a critical parameter in ecology, but its estimation is often challenging. Approaches utilizing eDNA to indirectly estimate abundance have recently generated substantial interest. However, preliminary correlations observed between eDNA concentration and abundance in nature are typically moderate in strength with significant unexplained variation. Here, we apply a novel approach to integrate allometric scaling coefficients into models of eDNA concentration and organism abundance. We hypothesize that eDNA particle production scales nonlinearly with mass, with scaling coefficients < 1. Wild populations often exhibit substantial variation in individual body size distributions; we therefore predict that the distribution of mass across individuals within a population will influence population-level eDNA production rates. To test our hypothesis, we collected standardized body size distribution and mark-recapture abundance data using whole-lake experiments involving nine populations of brook trout. We correlated eDNA concentration with three metrics of abundance: density (individuals/ha), biomass (kg/ha) and allometrically scaled mass (ASM) (∑(individual mass0.73 )/ha). Density and biomass were both significantly positively correlated with eDNA concentration (adj. r2 = 0.59 and 0.63, respectively), but ASM exhibited improved model fit (adj. r2 = 0.78). We also demonstrate how estimates of ASM derived from eDNA samples in "unknown" systems can be converted to biomass or density estimates with additional size-structure data. Future experiments should empirically validate allometric scaling coefficients for eDNA production, particularly where substantial intraspecific size distribution variation exists. Incorporating allometric scaling may improve predictive models to the extent that eDNA concentration may become a reliable indicator of abundance in nature.
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Affiliation(s)
- M C Yates
- Université du Québec à Montréal, Montréal, Québec, Canada
| | - D M Glaser
- University of Calgary Calgary, Alberta, Canada
| | - J R Post
- University of Calgary Calgary, Alberta, Canada
| | | | - D J Fraser
- Concordia University Montreal, Quebec, Canada
| | - A M Derry
- Université du Québec à Montréal, Montréal, Québec, Canada
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162
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Goutte A, Molbert N, Guérin S, Richoux R, Rocher V. Monitoring freshwater fish communities in large rivers using environmental DNA metabarcoding and a long-term electrofishing survey. JOURNAL OF FISH BIOLOGY 2020; 97:444-452. [PMID: 32412670 DOI: 10.1111/jfb.14383] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Monitoring freshwater fish communities in a large human-impacted river is a challenging task. The structure of fish assemblages has been monitored yearly in the Marne and the Seine Rivers, across the Paris conurbation, France, using traditional electrofishing (EF) surveys since 1990, in accordance with the European Water Framework Directive. In addition, metabarcoding of DNA extracted from environmental samples (eDNA) was concomitantly conducted in nine sampling sites in 2017 and in 2018 to compare the estimates of species richness and relative abundance among three methods: annual, long-term EF monitoring and eDNA. The present study confirms better detection of fish species using eDNA compared to annual EF. eDNA metabarcoding was also more efficient for species detection than a 3-6-year EF survey but was similar or less efficient than a long-term EF survey of 14 years of monitoring. In addition, the numbers of reads per species relative to the total number of reads significantly increased with (a) increasing relative abundance (relative percentage of individuals caught per species) and (b) increasing number of years that a fish species was detected during the 2000-2018 period. These results suggest that eDNA could reflect local population persistence.
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Affiliation(s)
- Aurélie Goutte
- Sorbonne Université, CNRS, EPHE, UMR METIS, Paris, France
- EPHE, PSL Research University, Paris, France
| | - Noëlie Molbert
- Sorbonne Université, CNRS, EPHE, UMR METIS, Paris, France
| | - Sabrina Guérin
- Syndicat Interdépartemental pour l'Assainissement de l'Agglomération Parisienne (SIAAP), Colombes, France
| | - Robin Richoux
- Syndicat Interdépartemental pour l'Assainissement de l'Agglomération Parisienne (SIAAP), Colombes, France
| | - Vincent Rocher
- Syndicat Interdépartemental pour l'Assainissement de l'Agglomération Parisienne (SIAAP), Colombes, France
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163
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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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164
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Ortega A, Geraldi NR, Díaz-Rúa R, Ørberg SB, Wesselmann M, Krause-Jensen D, Duarte CM. A DNA mini-barcode for marine macrophytes. Mol Ecol Resour 2020; 20:920-935. [PMID: 32279439 DOI: 10.1111/1755-0998.13164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/13/2020] [Accepted: 03/27/2020] [Indexed: 11/26/2022]
Abstract
Studies focusing on marine macrophyte metabarcoding from environmental samples are scarce, due to the lack of a universal barcode for these taxa, and to their poor representation in DNA databases. Here, we searched for a short barcode able to identify marine macrophytes from tissue samples; then, we created a DNA reference library which was used to identify macrophytes in eDNA from coastal sediments. Barcoding of seagrasses, mangroves and marine macroalgae (Chlorophyta, Rhodophyta and Phaeophyceae) was tested using 18 primer pairs from six barcoding genes: the plant barcodes rbcL, matK and trnL, plus the genes ITS2, COI and 18S. The 18S gene showed the highest universality among marine macrophytes, amplifying 95%-100% of samples; amplification performance of the other barcodes was limited. Taxonomy was assigned using a phylogeny-based approach to create an 18S DNA reference library. Macrophyte tissue sequences were accurately identified within their phyla (88%), order (76%), genus (71%) and species (23%). Nevertheless, out of 86 macrophytes tested, only 48% and 15% had a reference sequence at genus and at species level, respectively. Identification at these levels can be improved by more inclusive reference libraries. Using the 18S mini-barcode and the reference library, we recovered eDNA from 21 marine macrophytes in sediments, demonstrating the barcode's ability to trace primary producers that contribute to blue carbon. We expect this barcode to also be useful for other ecological questions, such as tracing macro primary producers in marine food webs.
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Affiliation(s)
- Alejandra Ortega
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nathan R Geraldi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rubén Díaz-Rúa
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sarah B Ørberg
- Department of Bioscience, and Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Marlene Wesselmann
- Global Change Research Group, Institut Mediterrani d'Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Spain
| | - Dorte Krause-Jensen
- Department of Bioscience, and Arctic Research Centre, Aarhus University, Aarhus, Denmark
| | - Carlos M Duarte
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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165
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Exploration of Environmental DNA (eDNA) to Detect Kirtland's Snake ( Clonophis kirtlandii). Animals (Basel) 2020; 10:ani10061057. [PMID: 32575432 PMCID: PMC7341209 DOI: 10.3390/ani10061057] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 01/16/2023] Open
Abstract
Simple Summary Small and difficult to find species of conservation concern such as the Kirtland’s Snake require significant survey effort using traditional methods. Surveying for DNA shed into the environment, or environmental DNA, we set out to improve detection probability and efficiency to aid in future conservation efforts for this species. Field surveys revealed temporal and spatial variation in Kirtland’s Snake activity. More snakes were found in the spring, during the first field season, and in areas with abundant grass, herbaceous vegetation, and shrubs. We collected environmental samples and developed a molecular assay to detect eDNA across this spatial and temporal gradient of snake activity. We also tested the persistence of DNA in the microenvironment snakes are expected to use by introducing feces into artificial burrows. We were able to detect snake eDNA in only a single environmental sample and found that eDNA in artificial burrows appears to decline within a week. We explored the potential methodological and biological causes of this low detection success to aid future research employing eDNA detection as a survey method in snakes. Abstract Environmental DNA (eDNA) surveys utilize DNA shed by organisms into their environment in order to detect their presence. This technique has proven effective in many systems for detecting rare or cryptic species that require high survey effort. One potential candidate for eDNA surveying is Kirtland’s Snake (Clonophis kirtlandii), a small natricine endemic to the midwestern USA and threatened throughout its range. Due to its cryptic and fossorial lifestyle, it is also a notoriously difficult snake to survey, which has limited efforts to understand its ecology. Our goal was to utilize eDNA surveys for this species to increase detection probability and improve survey efficiency to assist future conservation efforts. We conducted coverboard surveys and habitat analyses to determine the spatial and temporal activity of snakes, and used this information to collect environmental samples in areas of high and low snake activity. In addition, we spiked artificial crayfish burrows with Kirtland’s Snake feces to assess the persistence of eDNA under semi-natural conditions. A quantitative PCR (qPCR) assay using a hydrolysis probe was developed to screen the environmental samples for Kirtland’s Snake eDNA that excluded closely related and co-occurring species. Our field surveys showed that snakes were found in the spring during the first of two seasons, and in areas with abundant grass, herbaceous vegetation, and shrubs. We found that eDNA declines within a week under field conditions in artificial crayfish burrows. In environmental samples of crayfish burrow water and sediment, soil, and open water, a single detection was found out of 380 samples. While there may be physicochemical and biological explanations for the low detection observed, characteristics of assay performance and sampling methodology may have also increased the potential for false negatives. We explored these outcomes in an effort to refine and advance the successful application of eDNA surveying in snakes and groundwater microhabitats.
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166
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Hempel CA, Peinert B, Beermann AJ, Elbrecht V, Macher JN, Macher TH, Jacobs G, Leese F. Using Environmental DNA to Monitor the Reintroduction Success of the Rhine Sculpin (Cottus rhenanus) in a Restored Stream. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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167
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Detection of the Amphibian Pathogens Chytrid Fungus ( Batrachochytrium dendrobatidis) and Ranavirus in West Texas, USA, Using Environmental DNA. J Wildl Dis 2020; 56:702-706. [PMID: 32243244 DOI: 10.7589/2019-08-212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Environmental DNA (eDNA) methods provide novel options for the detection of pathogens. The amphibian pathogens Batrachochytrium dendrobatidis (Bd) and Ranavirus have been relatively understudied in Texas, US, so we applied eDNA assays for the surveillance of these pathogens in the upper Brazos River basin near the Texas panhandle. We collected water samples from five urban playa lakes and one reservoir in and around Lubbock, Texas. Quantitative PCR detected both Bd and Ranavirus at one playa lake, representing novel detection of both pathogens in the region. Based on these results, we recommend increased monitoring for the pathogens and symptoms of amphibian disease throughout the region.
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168
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Nebbak A, Almeras L. Identification of Aedes mosquitoes by MALDI-TOF MS biotyping using protein signatures from larval and pupal exuviae. Parasit Vectors 2020; 13:161. [PMID: 32238178 PMCID: PMC7110738 DOI: 10.1186/s13071-020-04029-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/24/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) biotyping is an innovative strategy, applied successfully for the identification of numerous arthropod families including mosquitoes. The effective mosquito identification using this emerging tool was demonstrated possible at different steps of their life-cycle, including eggs, immature and adult stages. Unfortunately, for species identification by MS, the euthanasia of the mosquito specimen is required. METHODS To avoid mosquito euthanasia, the present study assessed whether aedine mosquitoes could be identified by MALDI-TOF MS biotyping, using their respective exuviae. In this way, exuviae from the fourth-instar and pupal stages of Aedes albopictus and Aedes aegypti were submitted to MALDI-TOF MS analysis. RESULTS Reproducible and specific MS spectra according to aedine species and stage of exuviae were observed which were objectified by cluster analyses, composite correlation index (CCI) tool and principal components analysis (PCA). The query of our reference MS spectra database (DB) upgraded with MS spectra of exuviae from fourth-instar larvae and pupae of both Aedes species revealed that 100% of the samples were correctly classified at the species and stage levels. Among them, 93.8% (135/144) of the MS profiles reached the threshold log score value (LSV > 1.8) for reliable identification. CONCLUSIONS The extension of reference MS spectra DB to exuviae from fourth-instar and pupal stages made now possible the identification of mosquitoes throughout their life-cycle at aquatic and aerial stages. The exuviae presenting the advantage to avoid specimen euthanasia, allowing to perform complementary analysis on alive mosquitoes.
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Affiliation(s)
- Amira Nebbak
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, Marseille, France.,Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques (CRAPC), Zone Industrielle, BP 384 Bou-Ismail, Tipaza, Algérie
| | - Lionel Almeras
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, Marseille, France. .,Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,IHU-Méditerranée Infection, Marseille, France.
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169
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Schistosoma species detection by environmental DNA assays in African freshwaters. PLoS Negl Trop Dis 2020; 14:e0008129. [PMID: 32203507 PMCID: PMC7117781 DOI: 10.1371/journal.pntd.0008129] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 04/02/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Background Schistosomiasis is a neglected tropical parasitic disease associated with severe pathology, mortality and economic loss worldwide. Programs for disease control may benefit from specific and sensitive diagnostic methods to detect Schistosoma trematodes in aquatic environments. Here we report the development of novel environmental DNA (eDNA) qPCR assays for the presence of the human-infecting species Schistosoma mansoni, S. haematobium and S. japonicum. Methodology/Principal findings We first tested the specificity of the assays across the three species using genomic DNA preparations which showed successful amplification of target sequences with no cross amplification between the three focal species. In addition, we evaluated the specificity of the assays using synthetic DNA of multiple Schistosoma species, and demonstrated a high overall specificity; however, S. japonicum and S. haematobium assays showed cross-species amplification with very closely-related species. We next tested the effectiveness of the S. mansoni assay using eDNA samples from aquaria containing infected host gastropods, with the target species revealed as present in all infected aquaria. Finally, we evaluated the effectiveness of the S. mansoni and S. haematobium assays using eDNA samples from eight discrete natural freshwater sites in Tanzania, and demonstrated strong correspondence between infection status established using eDNA and conventional assays of parasite prevalence in host snails. Conclusions/Significance Collectively, our results suggest that eDNA monitoring is able to detect schistosomes in freshwater bodies, but refinement of the field sampling, storage and assay methods are likely to optimise its performance. We anticipate that environmental DNA-based approaches will help to inform epidemiological studies and contribute to efforts to control and eliminate schistosomiasis in endemic areas. Schistosomiasis, otherwise known as bilharzia or snail fever, is a prevalent human disease found across tropical regions of the world and is a major cause of disability. The disease is acquired from exposure to the schistosome infectious larvae released by infected host snails in freshwaters. Programs to restrict the transmission of schistosomiasis would benefit from rapid and reliable diagnostic methods to detect schistosomes. Here we report a study that has developed new diagnostic tools to identify the DNA from three human-infecting Schistosoma species within water samples. This “environmental DNA” (eDNA) approach requires the filtering and laboratory analyses of water samples, and avoids the requirements to locate, identify and individually test the infectious status of host snails. Our results showed that eDNA methods detect the presence of the parasite in freshwater bodies. However, there is need for further refinement for sampling and laboratory techniques to improve the performance of the assays. We anticipate that eDNA approaches will provide information on the distribution and abundance the water-borne parasites, and potentially contribute to the control and elimination of schistosomiasis.
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170
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Nukazawa K, Akahoshi K, Suzuki Y. Are bacteria potential sources of fish environmental DNA? PLoS One 2020; 15:e0230174. [PMID: 32163471 PMCID: PMC7067479 DOI: 10.1371/journal.pone.0230174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 02/24/2020] [Indexed: 12/02/2022] Open
Abstract
The environmental DNA (eDNA) method is being increasingly applied in various environments. Although eDNA undergoes rapid degradation in aqueous environments, it has been detected in streams up to 10 km downstream from its source. As environmental bacteria can uptake free DNA, transfer their genetic traits, and amplify, there is a potential risk that they, rather than a target aquatic species, could become a source of measured eDNA. This study examined whether bacteria with incorporated fish DNA could be such a source by investigating the detectability of fish DNA generated by bacteria inhabiting river water and riverbed sediment. We attempted to detect common carp (Cyprinus carpio) eDNA in stream water and sediment samples and the DNA of common carp produced by bacterial colonies (Escherichia coli, total coliform, and heterotrophic bacteria) cultured from the samples. The eDNA was detected in the environmental samples but the carp DNA from the targeted bacteria was rarely detected in both water and riverbed sediment samples. Our results suggest that the risk of bacterium-induced false positive detection for fish eDNA is negligible.
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Affiliation(s)
- Kei Nukazawa
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
- * E-mail:
| | - Kentaro Akahoshi
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Yoshihiro Suzuki
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
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171
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Shu L, Ludwig A, Peng Z. Standards for Methods Utilizing Environmental DNA for Detection of Fish Species. Genes (Basel) 2020; 11:E296. [PMID: 32168762 PMCID: PMC7140814 DOI: 10.3390/genes11030296] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/13/2020] [Accepted: 03/07/2020] [Indexed: 11/30/2022] Open
Abstract
Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.
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Affiliation(s)
- Lu Shu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China;
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, 10315 Berlin, Germany
- Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, 10115 Berlin, Germany
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China;
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172
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van der Heyde M, Bunce M, Wardell-Johnson G, Fernandes K, White NE, Nevill P. Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding. Mol Ecol Resour 2020; 20. [PMID: 32065512 DOI: 10.1111/1755-0998.13148] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/30/2019] [Accepted: 02/10/2020] [Indexed: 11/26/2022]
Abstract
Biological surveys based on visual identification of the biota are challenging, expensive and time consuming, yet crucial for effective biomonitoring. DNA metabarcoding is a rapidly developing technology that can also facilitate biological surveys. This method involves the use of next generation sequencing technology to determine the community composition of a sample. However, it is uncertain as to what biological substrate should be the primary focus of metabarcoding surveys. This study aims to test multiple sample substrates (soil, scat, plant material and bulk arthropods) to determine what organisms can be detected from each and where they overlap. Samples (n = 200) were collected in the Pilbara (hot desert climate) and Swan Coastal Plain (hot Mediterranean climate) regions of Western Australia. Soil samples yielded little plant or animal DNA, especially in the Pilbara, probably due to conditions not conducive to long-term preservation. In contrast, scat samples contained the highest overall diversity with 131 plant, vertebrate and invertebrate families detected. Invertebrate and plant sequences were detected in the plant (86 families), pitfall (127 families) and vane trap (126 families) samples. In total, 278 families were recovered from the survey, 217 in the Swan Coastal Plain and 156 in the Pilbara. Aside from soil, 22%-43% of the families detected were unique to the particular substrate, and community composition varied significantly between substrates. These results demonstrate the importance of selecting appropriate metabarcoding substrates when undertaking terrestrial surveys. If the aim is to broadly capture all biota then multiple substrates will be required.
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Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Grant Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kristen Fernandes
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia.,Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, Perth, WA, Australia
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173
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Riaz M, Kuemmerlen M, Wittwer C, Cocchiararo B, Khaliq I, Pfenninger M, Nowak C. Combining environmental DNA and species distribution modeling to evaluate reintroduction success of a freshwater fish. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02034. [PMID: 31680362 DOI: 10.1002/eap.2034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 07/18/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Active species reintroduction is an important conservation tool when aiming for the restoration of biological communities and ecosystems. The effective monitoring of reintroduction success is a crucial factor in this process. Here, we used a combination of environmental DNA (eDNA) techniques and species distribution models (SDMs) to evaluate the success of recent reintroductions of the freshwater fish Alburnoides bipunctatus in central Germany. We built SDMs without and with eDNA presence data to locate further suitable reintroduction sites and potentially overlooked populations of the species. We successfully detected eDNA of A. bipunctatus at all reintroduction sites, as well as several adjacent sites mostly in downstream direction, which supports the success of reintroduction efforts. eDNA-based species detection considerably improved SDMs for A. bipunctatus, which allowed to identify species presence in previously unknown localities. Our results confirm the usefulness of eDNA techniques as standard tool to monitor reintroduced fish populations. We propose that combining eDNA with SDMs is a highly effective approach for long-term monitoring of reintroduction success in aquatic species.
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Affiliation(s)
- Maria Riaz
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Mathias Kuemmerlen
- Department of Systems Analysis, Integrated Assessment and Modelling, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, 8600, Duebendorf, Switzerland
| | - Claudia Wittwer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Imran Khaliq
- Department of Zoology, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Markus Pfenninger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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174
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Suarez-Menendez M, Planes S, Garcia-Vazquez E, Ardura A. Early Alert of Biological Risk in a Coastal Lagoon Through eDNA Metabarcoding. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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175
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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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176
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Zhang X, Li J, Yao MC, Fan WY, Yang CW, Yuan L, Sheng GP. Unrecognized Contributions of Dissolved Organic Matter Inducing Photodamages to the Decay of Extracellular DNA in Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1614-1622. [PMID: 31976657 DOI: 10.1021/acs.est.9b06029] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Extracellular DNA (eDNA), which is derived from lysis or secretion of cells, is ubiquitous in various environments and crucial for gene dissemination, bacterial metabolism, biofilm integrity, and aquatic monitoring. However, these processes are largely influenced by damage to eDNA. Photodamage to eDNA, one of the most important types of DNA damage in natural waters, thus far remains unclear. In particular, the roles of the ubiquitous dissolved organic matter (DOM) in this process have yet to be determined. In this study, eDNA photodamage, including both deoxynucleoside damage and strand breaks, proved to be significantly influenced by DOM. DOM competed with eDNA for photons to inhibit the direct photodamage of eDNA. Nevertheless, DOM was photosensitized to produce reactive oxygen species (ROS) (i.e., hydroxyl radicals (·OH) and singlet oxygen (1O2)) to enhance the indirect photodamage of eDNA. The ·OH induced damage to four deoxynucleosides and strand breaks, and the 1O2 substantially enhanced deoxyguanosine damage. The presence of DOM changed the main photodamage products of deoxynucleosides, additional oxidation products induced by ROS formed besides pyrimidine dimers caused by UV. Results indicate that DOM-mediated indirect photodamage contributed significantly to eDNA photodamage in most water bodies. This study revealed the previously unrecognized crucial role of DOM in the decay of eDNA in waters.
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Affiliation(s)
- Xin Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Jing Li
- School of Life Sciences , University of Science and Technology of China , Hefei 230026 , China
| | - Mu-Cen Yao
- School of Life Sciences , University of Science and Technology of China , Hefei 230026 , China
| | - Wen-Yuan Fan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Chuan-Wang Yang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Li Yuan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
| | - Guo-Ping Sheng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry , University of Science and Technology of China , Hefei 230026 , China
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177
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Zhang Y, Pavlovska M, Stoica E, Prekrasna I, Yang J, Slobodnik J, Zhang X, Dykyi E. Holistic pelagic biodiversity monitoring of the Black Sea via eDNA metabarcoding approach: From bacteria to marine mammals. ENVIRONMENT INTERNATIONAL 2020; 135:105307. [PMID: 31881429 DOI: 10.1016/j.envint.2019.105307] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/31/2019] [Accepted: 11/03/2019] [Indexed: 06/10/2023]
Abstract
As the largest semi-closed marine ecosystem in the world, the Black Sea has been heavily affected by human activities for a long time. Describing the biodiversity of multi-trophic biota in pelagic zone of the Black Sea and identifying the dominant environmental factors are prerequisites for protecting the sustainability of ecosystems. However, up to now, the taxonomic and distributional information about the Black Sea biota is not clear. Here, we employed a Tree-of-Life metabarcoding to analyze the biodiversity of eight communities in the Black Sea, investigated their biogeographical distribution, and further analyzed the influence of biological and abiotic factors on biota on large scales. We found that, (1) Over 8900 OTUs were detected in the Black Sea, of which 630 species were identified, covering the holistic biota from single-celled (bacteria 5620 OTUs 141 species; algae 1096 OTUs 185 species; protozoa 546 OTUs 146 species) to multicellular organisms (invertebrate metazoans 150 OTUs 34 species; fishes 1369 OTUs 76 species; large marine mammals 39 OTUs 5 species). (2) Higher trophic organisms (fishes and large mammals) distributed more evenly in space than the lower (microorganisms, protozoa and invertebrates). For lower trophic organisms, the vertical stratification was more obvious than the horizontal stratification (vertical p < 0.02, horizontal p < 0.05). (3) The bottom trophic organisms (bacteria and algae) of the food web significantly affected the distribution and composition of the others through biological interactions (Mantel p < 0.05). (4) At the level of abiotic factors, the effect of local species sorting on the composition of communities was 15% higher than that of mass dispersal effect. For the first time, this study monitored and profiled the holistic biodiversity in the pelagic zone of the Black Sea, and provided technological advances and preliminary knowledge for the ongoing Black Sea ecosystem protection efforts.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Mariia Pavlovska
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odesa, Ukraine; State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Blvd. Mamaia no. 300, RO-900581 Constanţa 3, Romania
| | - Ievgeniia Prekrasna
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odesa, Ukraine; State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | | | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China.
| | - Evgen Dykyi
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odesa, Ukraine; State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
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178
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Bedwell ME, Goldberg CS. Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems. Ecol Evol 2020; 10:1602-1612. [PMID: 32076537 PMCID: PMC7029092 DOI: 10.1002/ece3.6014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/31/2022] Open
Abstract
The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow-legged frog (Rana sierrae) and the foothill yellow-legged frog (Rana boylii). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2-9.19X) in our protocol, from a probability of 0.51-0.85 per technical replicate. Lake sample volumes were limited by filter clogging, and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3-2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow-legged frog eDNA captured in streams ceased between 100 and 200 m, indicating that sampling at close intervals is important.
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179
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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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180
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Hauger AN, Hollis-Etter KM, Etter DR, Roloff GJ, Mahon AR. Use of environmental DNA (eDNA) in streams to detect feral swine ( Sus scrofa). PeerJ 2020; 8:e8287. [PMID: 31915583 PMCID: PMC6942673 DOI: 10.7717/peerj.8287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/24/2019] [Indexed: 11/20/2022] Open
Abstract
Invasive feral swine can damage ecosystems, disrupt plant and animal populations, and transmit diseases. Monitoring of feral swine populations requires expensive and labor-intensive techniques such as aerial surveys, field surveys for sign, trail cameras, and verifying landowner reports. Environmental DNA (eDNA) provides an alternative method for locating feral swine. To aid in detection of this harmful invasive species, a novel assay was developed incorporating molecular methods. From August 2017 to April 2018, water samples and stream data were collected along 400 m transects in two different stream types where swine DNA was artificially introduced to investigate potential factors affecting detection. A generalized linear model (family binomial) was used to characterize environmental conditions affecting swine DNA detection; detection was the dependent variable and stream measurements included stream type, distance downstream, water temperature, velocity, turbidity, discharge, and pH as independent variables. Parameters from the generalized linear model were deemed significant if 95% confidence intervals did not overlap 0. Detection probability for swine DNA negatively related to water temperature (β = − 0.21, 95% CI [−0.35 to −0.09]), with the highest detection probability (0.80) at 0 °C and lowest detection probability (0.05) at 17.9 °C water temperature. Results indicate that sampling for swine eDNA in free-flowing stream systems should occur at lower water temperatures to maximize detection probability. This study provides a foundation for further development of field and sampling techniques for utilizing eDNA as a viable alternative to monitoring a terrestrial invasive species in northern regions of the United States.
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Affiliation(s)
- Amberly N Hauger
- Biology Department, University of Michigan-Flint, Flint, MI, United States of America
| | - Karmen M Hollis-Etter
- Biology Department, University of Michigan-Flint, Flint, MI, United States of America
| | - Dwayne R Etter
- Wildlife Division, Michigan Department of Natural Resources, East Lansing, MI, United States of America
| | - Gary J Roloff
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States of America
| | - Andrew R Mahon
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America
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181
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Eble JA, Daly-Engel TS, DiBattista JD, Koziol A, Gaither MR. Marine environmental DNA: Approaches, applications, and opportunities. ADVANCES IN MARINE BIOLOGY 2020; 86:141-169. [PMID: 32600544 DOI: 10.1016/bs.amb.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Environmental DNA (eDNA) is increasingly being used to document species distributions and habitat use in marine systems, with much of the recent effort focused on leveraging advances in next-generation DNA sequencing to assess and track biodiversity across taxonomic groups. Environmental DNA offers a number of important advantages over traditional survey techniques, including non-invasive sampling, sampling where traditional approaches are impractical or inefficient (e.g. deep oceans), reduced cost, and increased detection sensitivity. However, eDNA applications are currently limited because of an insufficient understanding of the influence of sample source, analytical approach, and marker type on eDNA detections. Because approaches vary considerably among eDNA studies, we present a summary of the current state of the field and emerging best practices. The impact of observed variation in rates of eDNA production, persistence, and transport are also discussed and future research needs are highlighted with the goal of expanding eDNA applications, including the development of statistical models to improve the predictability of eDNA detection and quantification.
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Affiliation(s)
- Jeff A Eble
- Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, United States.
| | - Toby S Daly-Engel
- Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia; School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Adam Koziol
- Evolutionary Genomics, GLOBE institute, University of Copenhagen, Copenhagen, Denmark
| | - Michelle R Gaither
- Genomics and Bioinformatics Cluster, Department of Biology, University of Central Florida, Orlando, FL, United States
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182
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Santos HM, Tsai CY, Maquiling KRA, Tayo LL, Mariatulqabtiah AR, Lee CW, Chuang KP. Diagnosis and potential treatments for acute hepatopancreatic necrosis disease (AHPND): a review. AQUACULTURE INTERNATIONAL : JOURNAL OF THE EUROPEAN AQUACULTURE SOCIETY 2020; 28:169-185. [PMID: 32834683 PMCID: PMC7223513 DOI: 10.1007/s10499-019-00451-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/04/2019] [Indexed: 05/05/2023]
Abstract
Acute hepatopancreatic necrosis disease (AHPND) or formerly known as early mortality syndrome (EMS) is an emerging disease that has caused significant economic losses to the aquaculture industry. The primary causative agent of AHPND is Vibrio parahaemolyticus, a Gram-negative rod-shaped bacterium that has gained plasmids encoding the fatal binary toxins Pir A/Pir B that cause rapid death of the infected shrimp. In this review, the current research studies and information about AHPND in shrimps have been presented. Molecular diagnostic tools and potential treatments regarding AHPND were also included. This review also includes relevant findings which may serve as guidelines that can help for further investigation and studies on AHPND or other shrimp diseases.
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Affiliation(s)
- Harvey M. Santos
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
| | - Ching-Yi Tsai
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
| | - Kenth Roger A. Maquiling
- School of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, 1002 Intramuros, Manila Philippines
| | - Lemmuel L. Tayo
- School of Chemical, Biological and Materials Engineering and Sciences, Mapúa University, 1002 Intramuros, Manila Philippines
| | - Abdul R. Mariatulqabtiah
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Chi-Wen Lee
- Department of Post-Baccalaureate Veterinary Medicine, Asia University, Taichung, 41354 Taiwan
| | - Kuo Pin Chuang
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, 912 Pingtung Taiwan
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183
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184
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Griffin JE, Matechou E, Buxton AS, Bormpoudakis D, Griffiths RA. Modelling environmental DNA data; Bayesian variable selection accounting for false positive and false negative errors. J R Stat Soc Ser C Appl Stat 2019. [DOI: 10.1111/rssc.12390] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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185
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Kakuda A, Doi H, Souma R, Nagano M, Minamoto T, Katano I. Environmental DNA detection and quantification of invasive red-eared sliders, Trachemy scripta elegans, in ponds and the influence of water quality. PeerJ 2019; 7:e8155. [PMID: 31824768 PMCID: PMC6901006 DOI: 10.7717/peerj.8155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 11/04/2019] [Indexed: 11/20/2022] Open
Abstract
Environmental DNA (eDNA) is a powerful tool for monitoring the distribution of aquatic macro-organisms. However, environmental factors, including the water temperature and water quality, can affect the inhibition and/or degradation of eDNA, which complicates accurate estimations of eDNA concentrations and the detection of the presence/absence of species in natural habitats. Further very few eDNA studies have been conducted for reptiles, especially with respect to estimating their biomass and/or abundances. Here we examined the relationship between the visually-observed number of red-eared sliders (Trachemys scripta elegans) and eDNA concentrations across 100 ponds. Additionally, we evaluated the effect of water quality on red-eared slider eDNA concentration in these ponds. We found that there was a significant positive correlation between the observed number of red-eared sliders and the eDNA concentration in the ponds. On comparing various water quality indicators, including dissolved nitrogen, dissolved phosphorous, organic matter, and chlorophyll a (Chl. a), we found that only Chl. a had a negative correlation with the red-eared slider eDNA concentration, while we did not find any inhibition in the quantitative PCR. We conclude that concentrations of eDNA can potentially be used for estimating the abundance of the red-eared slider. Additionally, Chl. a might indirectly influence the degradation of eDNA through the microorganisms bonded to the phytoplankton in the ponds, as microbial activity is thought to decrease eDNA persistence.
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Affiliation(s)
- Aozora Kakuda
- Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | | | - Mariko Nagano
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Izumi Katano
- Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
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186
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Fornillos RJC, Sato MO, Tabios IKB, Sato M, Leonardo LR, Chigusa Y, Minamoto T, Kikuchi M, Legaspi ER, Fontanilla IKC. Detection of Schistosoma japonicum and Oncomelania hupensis quadrasi environmental DNA and its potential utility to schistosomiasis japonica surveillance in the Philippines. PLoS One 2019; 14:e0224617. [PMID: 31747401 PMCID: PMC6867693 DOI: 10.1371/journal.pone.0224617] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/17/2019] [Indexed: 11/25/2022] Open
Abstract
In recent years, the prevalence and infection intensity of Schistosoma japonicum in endemic areas of the Philippines have significantly decreased due to yearly population-based treatment strategies, yet transmission rates remain high and uninterrupted. An important indicator of active disease transmission is the presence of Schistosoma japonicum and its snail intermediate host Oncomelania hupensis quadrasi in freshwater habitats. In this study, we sought to apply a species-specific real-time PCR (qPCR) assay for the detection of S. japonicum and O. hupensis quadrasi in freshwater samples using environmental DNA approach that can complement the commonly utilized malacological survey in determining potential transmission foci in order to have a more effective snail surveillance strategy for schistosomiasis japonica in endemic areas. The newly developed assay was specific to S. japonicum and O. hupensis quadrasi with no amplification detected against non-target trematode Fasciola spp. and snails such as Lymnaea spp., Pomacea canaliculata, and Melanoides spp. that typically co-exist in the same environment. The assay effectiveness was determined using 19 environmental water samples collected from Northern Samar (N = 5 sites), Leyte (N = 11 sites) and Compostela Valley (N = 3 sites) and compared to malacological survey for determining O. hupensis quadrasi snail colonies and snail crushing to visualize S. japonicum cercariae. TaqMan qPCR targeting a short fragment of the cytochrome c oxidase subunit 1 (cox1) gene was positive for S. japonicum in 9 sites, for O. hupensis quadrasi in 9 sites, and for both S. japonicum and O. hupensis quadrasi in 5 sampling sites. Moreover, it was able to detect O. hupensis quadrasi in 3 out of 12 sites found negative and 6 out of 7 sites found positive through malacological survey, and in 4 of the 5 snail sites positive for snails with cercariae. Overall, this method can complement malacological surveys for monitoring of schistosomes in endemic areas of the Philippines, especially those with high risk of human infection.
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Affiliation(s)
- Raffy Jay C. Fornillos
- DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
- Natural Sciences Research Institute, University of the Philippines Diliman, P. Velasquez St. Diliman, Quezon City, Philippines
| | - Marcello Otake Sato
- Department of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Ian Kim B. Tabios
- College of Medicine, University of the Philippines Manila, Ermita Manilla, Philippines
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata, Japan
| | - Lydia R. Leonardo
- DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
- Graduate School, University of the East Ramon Magsaysay Memorial Medical Center, Quezon City, Philippines
| | - Yuichi Chigusa
- Department of Tropical Medicine and Parasitology, Dokkyo Medical University, Tochigi, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto, Nada-ku, Kobe, Japan
| | - Mihoko Kikuchi
- Department of Immunogenetics, Institute of Tropical Medicine, Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Emelda R. Legaspi
- Medical Zoology Laboratory, Schistosomiasis Research and Training Center, Palo Leyte, Philippines
| | - Ian Kendrich C. Fontanilla
- DNA Barcoding Laboratory, Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
- Natural Sciences Research Institute, University of the Philippines Diliman, P. Velasquez St. Diliman, Quezon City, Philippines
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187
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Harrison JB, Sunday JM, Rogers SM. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc Biol Sci 2019; 286:20191409. [PMID: 31744434 DOI: 10.1098/rspb.2019.1409] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
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Affiliation(s)
- Jori B Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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188
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Lin Y, Zhan A, Hernandez MR, Paolucci E, MacIsaac HJ, Briski E. Can chlorination of ballast water reduce biological invasions? J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yaping Lin
- GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel Kiel Germany
- Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Aibin Zhan
- Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Marco R. Hernandez
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada
| | - Esteban Paolucci
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” and Consejo Nacional de Investigaciones Cientı́ficas y Técnicas Buenos Aires Argentina
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research University of Windsor Windsor ON Canada
- School of Ecology and Environmental Sciences Yunnan University Kunming China
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189
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The effect of bivalve filtration on eDNA-based detection of aquatic organisms. PLoS One 2019; 14:e0222830. [PMID: 31721779 PMCID: PMC6853284 DOI: 10.1371/journal.pone.0222830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/09/2019] [Indexed: 11/19/2022] Open
Abstract
As the use of environmental-DNA (eDNA) expands as a method to detect the presence and quantity of aquatic taxa, factors potentially impacting the efficacy of this technique must be investigated. Many studies have examined the effects of abiotic parameters on the degradation of environmental-DNA (e.g. UV radiation, pH, temperature, etc.), however, few have focused on biotic effectors. Through high-filtering rates coupled with dense colonization, Asian clams (Corbicula fluminea) are able to drastically alter the quantity of particulate matter through translocation into the sediment, potentially including sources of eDNA in lotic and lentic systems. Using a longitudinal, laboratory experiment, we tested the effect of varying densities of Asian clams on the translocation rate of common goldfish (Carassius auratus) DNA. Target DNA in testing tanks was quantified through quantitative PCR (qPCR) at regular intervals and compared. Tanks housing the highest density of Asian clams produced significantly lower DNA concentrations over time compared to tanks of lower densities. These results show, for the first time, a density-dependent reduction of local eDNA sources by bivalve filtration that may lead to the obstructed detection of target species through the sampling of eDNA. Based on these findings, we recommend highly concentrated bivalve populations be taken into consideration when choosing the time and locality of eDNA sampling efforts.
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190
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Wang P, Yan Z, Yang S, Wang S, Zheng X, Fan J, Zhang T. Environmental DNA: An Emerging Tool in Ecological Assessment. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 103:651-656. [PMID: 31583422 DOI: 10.1007/s00128-019-02720-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
Environmental DNA (eDNA), as a recent research hotspot in environmental science, the use of eDNA in biological monitoring has the advantages of sensitivity and time/labor saving. The eDNA technology combined with scientific advancement has been applied in investigations of target species (such as invasive species, endangered species and other rare species), biomass, and biodiversity. In addition, ecotoxicology studies and environmental pollution impact assessments based on the development of eDNA technology have gradually emerged in recent years. In this article, we summarizes the application of eDNA in ecological assessment, include species diversity assessment and chemical contamination impacts assessment, provide guiding questions for study design. We additionally discuss current challenges associated with eDNA. Finally, looking to the future, we discuss the opportunities of eDNA technology in environmental protein, environmental sample processor and ecogenomic sensors.
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Affiliation(s)
- Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, People's Republic of China
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, People's Republic of China.
| | - Suwen Yang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing, 100012, People's Republic of China
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, People's Republic of China
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, People's Republic of China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, People's Republic of China
| | - Tianxu Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, People's Republic of China
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191
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Yang B, Qin C, Hu X, Xia K, Lu C, Gudda FO, Ma Z, Gao Y. Enzymatic degradation of extracellular DNA exposed to chlorpyrifos and chlorpyrifos-methyl in an aqueous system. ENVIRONMENT INTERNATIONAL 2019; 132:105087. [PMID: 31430607 DOI: 10.1016/j.envint.2019.105087] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 05/25/2023]
Abstract
The persistence of extracellular DNA (eDNA) is crucial for ensuring species diversity and ecological function in aquatic systems. However, scarce information exists about the impact of pesticides on eDNA, although they often co-exist in the aquatic environment. Using a variety of spectroscopic analyses, eDNA degradation and the associated alterations in DNA secondary structure was investigated by exposing DNase I to tested DNA in the presence of chlorpyrifos, a commonly used organophosphate pesticide. Molecular dynamics simulation was used to explore the weak interactions between the tested DNA and chlorpyrifos. The results indicated that chlorpyrifos significantly enhanced DNA degradation without affecting the enzyme activity of DNase I in an aqueous system. Spectroscopic experiments confirmed that chlorpyrifos and the analog chlorpyrifos-methyl could bind with DNA to cause the bases noncovalent stacking interaction. Molecular simulations further demonstrated that pesticide binding with DNA molecules caused widening of the DNA grooves and destruction of the hydrated layer, which enhanced DNA degradation. The findings presented herein provide novel insight into the genotoxicity and ecotoxicity of chlorpyrifos and chlorpyrifos-methyl, as well as their impacts on DNA persistence in aquatic environments.
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Affiliation(s)
- Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Kang Xia
- School of Plant and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China.
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192
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Shum P, Barney BT, O'Leary JK, Palumbi SR. Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems. Mol Ecol Resour 2019; 19:1470-1485. [PMID: 31436907 DOI: 10.1111/1755-0998.13067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/05/2019] [Accepted: 07/17/2019] [Indexed: 01/04/2023]
Abstract
Kelp forest ecosystems dominate 150,000 km of global temperate coastline, rivalling the coastal occurrence of coral reefs. Despite the astounding biological diversity and productive ecological communities associated with kelp forests, patterns of species richness and composition are difficult to monitor and compare. Crustose coralline algae are a critically important substrate for propagule settlement for a range of kelp forest species. Coralline-covered cobbles are home to hundreds of species of benthic animals and algae and form a replicable unit for ecological assays. Here, we use DNA metabarcoding of bulk DNA extracts sampled from cobbles to explore patterns of species diversity in kelp forests of the central California coast. The data from 97 cobbles within kelp forest ecosystems at three sites in Central California show the presence of 752 molecular operational taxonomic units (MOTUs) and 53 MOTUs assigned up to the species level with >95% similarity to current databases. We are able to detect spatial patterns of important management targets such as abalone recruits, and localized abundance of sea stars in 2012. Comparison of classic ecological surveys of these sites reveals large differences in species targets for these two approaches. In order to make such comparisons more quantitative, we use Presence/Absence Metabarcoding, using the fraction of replicate cobbles showing a species as a measure of its local abundance. This approach provides a fast and repeatable survey method that can be applied for biodiversity assessments across systems to shed light on the impact of different ecological disturbances and the role played by marine protected areas.
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Affiliation(s)
- Peter Shum
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - Bryan T Barney
- Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Jennifer K O'Leary
- The Nature Conservancy, Tanzania Marine Parks Unit, Kenya Wildlife Service, & Seychelles National Parks Authority, Mombasa, Kenya
- California Sea Grant, 1 Grand Ave, San Luis Obispo, USA
- California Polytechnic State University, 1 Frand Ave, San Luis Obispo, USA
| | - Stephen R Palumbi
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
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193
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Pourmoghadam MN, Poorbagher H, de Oliveira Fernandes JM, Jafari O. Diazinon negatively affects the integrity of environmental DNA stability: a case study with common carp (Cyprinus carpio). ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:672. [PMID: 31650301 DOI: 10.1007/s10661-019-7816-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Environmental DNA (eDNA) has been used to detect the presence of various species in aquatic ecosystems, but its degradation by several environmental factors can influence the correct identification of aquatic organisms. The present study examined the effects of a pesticide, diazinon, on breakage of Cyprinus carpio eDNA. The specimens were exposed to 0 (control), 0.06, 0.1, and 1 ppm of diazinon for 9 days. Water samples were collected at three time points (3, 6, and 9 days postexposure, dpe), and eDNA was extracted. The cytochrome oxidase I (COI) gene was successfully amplified by PCR, and a fuzzy inference system was used to convert DNA smears and breakage to numerical values. eDNA breakage percentage increased with diazinon concentration at all sampling times. At 3 dpe, the maximum eDNA breakage percentage occurred at 0.06 and 0.1 ppm of diazinon; whereas at 6 and 9 dpe, the maximum breakage was found at 1 ppm of diazinon, while exposure time had no significant effect. To the best of our knowledge, this is the first study to demonstrate that eDNA integrity can be compromised by a diazinon in surface waters. Hence, it is recommended that future eDNA studies take into account pesticide pollution when detecting aquatic species.
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Affiliation(s)
- Maryam Nasrolah Pourmoghadam
- Department of Fisheries, Faculty of Natural Resources, University of Tehran, Box 4314, Karaj, PO, Iran
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Hadi Poorbagher
- Department of Fisheries, Faculty of Natural Resources, University of Tehran, Box 4314, Karaj, PO, Iran.
| | | | - Omid Jafari
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
- Department of Fisheries, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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194
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Collins MK, Spear SF, Groves JD, Williams LA, Kuchta SR. Searching for a Salamander: Distribution and Habitat of the Mudpuppy (Necturus maculosus) in Southeast Ohio Using eDNA as a Rapid Assessment Technique. AMERICAN MIDLAND NATURALIST 2019. [DOI: 10.1674/0003-0031-182.2.191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Merri K. Collins
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens 45701
| | | | | | | | - Shawn R. Kuchta
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, 45701
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195
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Zhai H, Wang L, Putnis CV. Molecular-Scale Investigations Reveal Noncovalent Bonding Underlying the Adsorption of Environmental DNA on Mica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11251-11259. [PMID: 31478650 DOI: 10.1021/acs.est.9b04064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mineral-soil organic matter (SOM including DNA, proteins, and polysaccharides) associations formed through various interactions, play a key role in regulating long-term SOM preservation. The mechanisms underlying DNA-mineral and DNA-protein/polysaccharide interactions at nanometer and molecular scales in environmentally relevant solutions remain uncertain. Here, we present a model mineral-SOM system consisting of mineral (mica)-nucleic acid (environmental DNA, eDNA)/protein (bovine serum albumin)/polysaccharide (alginate), and combine atomic force microscopy (AFM)-based dynamic force spectroscopy and PeakForce quantitative nanomechanical mapping using DNA-decorated tips. Single-molecule binding and adhesion force of eDNA to mineral and to mineral adsorbed by protein/polysaccharide reveal the noncovalent bonds and that systematically changing ion compositions, ionic strength, and pH result in significant differences in organic-organic and organic-mineral binding energies. Consistent with the bond-strength measurements, protein, rather than polysaccharide, promotes mineral-bound DNA molecules by ex situ AFM deposition observations in relatively high concentrations of divalent cation-containing acidic solutions. These molecular-scale determinations and nanoscale observations should substantially improve our understanding of how environmental factors influence the organic-mineral interfacial interactions through the synergy of collective noncovalent and/or covalent bonds in mineral-organic associations.
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Affiliation(s)
- Hang Zhai
- College of Resources and Environment , Huazhong Agricultural University , Wuhan 430070 , China
| | - Lijun Wang
- College of Resources and Environment , Huazhong Agricultural University , Wuhan 430070 , China
| | - Christine V Putnis
- Institut für Mineralogie , University of Münster , 48149 Münster , Germany
- Department of Chemistry , Curtin University , Perth 6845 , Australia
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196
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Yuan QB, Huang YM, Wu WB, Zuo P, Hu N, Zhou YZ, Alvarez PJJ. Redistribution of intracellular and extracellular free & adsorbed antibiotic resistance genes through a wastewater treatment plant by an enhanced extracellular DNA extraction method with magnetic beads. ENVIRONMENT INTERNATIONAL 2019; 131:104986. [PMID: 31299601 DOI: 10.1016/j.envint.2019.104986] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/31/2019] [Accepted: 06/30/2019] [Indexed: 05/13/2023]
Abstract
Due to the limitations of current extraction methods, extracellular DNA (eDNA) is rarely discerned from intracellular DNA (iDNA) despite having unique contributions to antibiotic resistance genes (ARGs) propagation. Furthermore, eDNA may be free (f-eDNA) or adsorbed to or suspended solids, including cells (a-eDNA), which affects ARG persistence and transmissivity. We developed a novel method using magnetic beads to separate iDNA, a-eDNA, and f-eDNA to assess how these physical states of ARGs change across a wastewater treatment plant. This method efficiently extracted eDNA (>85.3%) with higher recovery than current methods such as alcohol precipitation, CTAB-based extraction, and DNA extraction kits (<10%). Biological treatment and UV disinfection decreased the concentration of intracellular ARGs (iARGs) and adsorbed extracellular ARGs (a-eARGs), causing an increase of released free extracellular ARGs (f-eARGs). More ARGs were discharged through the wasted biosolids than in the effluent; iARGs and a-eARGs are prevalent in wasted biosolids ((73.9 ± 22.5) % and (23.4 ± 15.3) % of total ARGs respectively), while f-eARGs were prevalent in the effluent ((90.3 ± 16.5) %). Bacterial community analysis showed significant correlations between specific genera and ARGs (e.g., Aeromonas, Pseudomonas and Acinetobacter were strongly correlated with multidrug-resistance gene blaTEM). This treatment system decreased the discharge of iARGs to receiving environments, however, increased eARG concentrations were present in the effluent, which may contribute to the environmental resistome.
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Affiliation(s)
- Qing-Bin Yuan
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China; Department of Civil and Environmental Engineering, Rice University, Houston, TX 77251, USA.
| | - Ya-Meng Huang
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Wen-Bin Wu
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Pengxiao Zuo
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77251, USA
| | - Nan Hu
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yong-Zhang Zhou
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77251, USA.
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197
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Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02102-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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198
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Zulkefli NS, Kim KH, Hwang SJ. Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16183339. [PMID: 31510040 PMCID: PMC6765872 DOI: 10.3390/ijerph16183339] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022]
Abstract
Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day−1. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.
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Affiliation(s)
| | - Keon-Hee Kim
- Human & Eco-Care Center, Department of Environmental Health Science, Konkuk University, Seoul 05029, Korea.
| | - Soon-Jin Hwang
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Korea.
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199
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Spatiotemporal distribution of juvenile chum salmon in Otsuchi Bay, Iwate, Japan, inferred from environmental DNA. PLoS One 2019; 14:e0222052. [PMID: 31483846 PMCID: PMC6726237 DOI: 10.1371/journal.pone.0222052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/20/2019] [Indexed: 11/21/2022] Open
Abstract
To understand the ecology of juvenile chum salmon during early marine life after their downstream migration, we developed a quantitative PCR-based environmental DNA (eDNA) method specific for chum salmon and investigated the spatiotemporal distribution of eDNA in Otsuchi Bay, Iwate, Japan. Indoor aquarium experiments demonstrated the following characteristics of chum salmon eDNA: (1) the eDNA shedding and degradation were time- and water temperature-dependent and the bacterial abundance could contribute to the eDNA decay, (2) fecal discharge may not be the main source of eDNA, and (3) a strong positive Pearson correlation was found between the number of juveniles and the eDNA amounts. As we discovered strong PCR inhibition from the seawater samples of the bay, we optimized the eDNA assay protocol for natural seawater samples by adding a further purification step and modification of PCR mixture. The intensive eDNA analysis in the spring of 2017 and 2018 indicated that juvenile chum salmon initially inhabited in shallow waters in the shorefront area and then spread over the bay from January to June. The eDNA data also pointed out that outmigration of juvenile chum salmon to open ocean temporarily suspended in April, possibly being associated with the dynamics of the Oyashio Current as suggested by a previous observation. The eDNA method thus enables us large-scale and comprehensive surveys without affecting populations to understand the spatiotemporal dynamics of juvenile chum salmon.
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200
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Mize EL, Erickson RA, Merkes CM, Berndt N, Bockrath K, Credico J, Grueneis N, Merry J, Mosel K, Tuttle-Lau M, Von Ruden K, Woiak Z, Amberg JJ, Baerwaldt K, Finney S, Monroe E. Refinement of eDNA as an early monitoring tool at the landscape-level: study design considerations. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01951. [PMID: 31188494 DOI: 10.1002/eap.1951] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/19/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Natural resource managers use data on the spatial range of species to guide management decisions. These data come from survey or monitoring efforts that use a wide variety of tools. Environmental DNA (eDNA) is a surveillance tool that uses genetic markers for detecting species and holds potential as a tool for large-scale monitoring programs. Two challenges of eDNA-based studies are uncertainties created by imperfect capture of eDNA in collection samples (e.g., water field samples) and imperfect detection of eDNA using molecular methods (e.g., quantitative PCR). Occurrence models can be used to address these challenges, thus we use an occurrence model to address two objectives: first, to determine how many samples were required to detect species using eDNA; second, to examine when and where to take samples. We collected water samples from three different habitat types in the Upper Mississippi River when both Bighead Carp and Silver Carp were known to be present based on telemetry detections. Each habitat type (backwater, tributary, and impoundment) was sampled during April, May, and November. Detections of eDNA for both species varied across sites and months, but were generally low, 0-19.3% of samples were positive for eDNA. Overall, we found that eDNA-based sampling holds promise to be a powerful monitoring tool for resource managers; however, limitations of eDNA-based sampling include different biological and ecological characteristics of target species such as seasonal habitat usage patterns as well as aspects of different physical environments that impact the implementation of these methods such as water temperature.
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Affiliation(s)
- E L Mize
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - R A Erickson
- Upper Midwest Environmental Sciences Center, U.S. Geological Service, 2630 Fanta Reed Road, La Crosse, Wisconsin, 54603, USA
| | - C M Merkes
- Upper Midwest Environmental Sciences Center, U.S. Geological Service, 2630 Fanta Reed Road, La Crosse, Wisconsin, 54603, USA
| | - N Berndt
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - K Bockrath
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - J Credico
- Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - N Grueneis
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - J Merry
- La Crosse Fish and Wildlife Conservation Office, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - K Mosel
- La Crosse Fish and Wildlife Conservation Office, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - M Tuttle-Lau
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - K Von Ruden
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - Z Woiak
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - J J Amberg
- Upper Midwest Environmental Sciences Center, U.S. Geological Service, 2630 Fanta Reed Road, La Crosse, Wisconsin, 54603, USA
| | - K Baerwaldt
- Midwest Region, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - S Finney
- La Crosse Fish and Wildlife Conservation Office, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
| | - E Monroe
- Whitney Genetics Laboratory, Midwest Fisheries Center, U.S. Fish and Wildlife Service, 555 Lester Avenue, Onalaska, Wisconsin, 54650, USA
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