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Poyntz-Wright IP, Harrison XA, Pedersen S, Tyler CR. Effectiveness of eDNA for monitoring riverine macroinvertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173621. [PMID: 38815833 DOI: 10.1016/j.scitotenv.2024.173621] [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: 04/12/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Environmental DNA (eDNA) is a technique increasingly used for monitoring organisms in the natural environment including riverine macroinvertebrates. However, the effectiveness of eDNA for monitoring riverine macroinvertebrates compared with the more traditional method of sampling the organisms directly and identifying them via morphological analysis, has not been well established. Furthermore, the ability of the various gene markers and PCR primer sets to detect the full range of riverine invertebrate taxa has not been quantified. Here we conducted a meta-analysis of the available literature, to assess the effectiveness of eDNA sampling for detecting riverine macroinvertebrates compared with sampling for the organisms directly and applying morphological analysis. We found, on average, eDNA sampling, irrespective of the gene marker used, detected fewer riverine invertebrates than morphological sampling. The most effective PCR primer set for identifying taxa was mlCOIintF/jgHCO2198, (mlCOIintF- forward primer, jgHCO2198, - reverse primer). Regardless of the gene marker or primer sets used, however, many taxa were not detected by eDNA metabarcoding that were detected by sampling directly for these invertebrates, including over 100 members of Arthropoda. eDNA sampling failed to detect any species belonging to Nematoda, Platyhelminthes, Cnidaria or Nematomorpha and these markers applied for eDNA sampling in terrestrial systems also do not detect members of Nematoda. In addition to these issues, uncertainties relating to false positives from upstream DNA sources, the stability of DNA from different species, differences in the propensity for DNA release into the environment for different organisms, and lack of available sequence information for numerous taxa illustrates the use of eDNA is not yet applicable as a robust stand-alone method for the monitoring of riverine invertebrates. As a primary consideration, further methodological developments are needed to ensure eDNA captures some of the key freshwater taxa, notably taxa belonging to the phyla Arthropoda, Nematoda, Platyhelminthes, Cnidaria and Nematomorpha.
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Affiliation(s)
- Imogen P Poyntz-Wright
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
| | - Xavier A Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
| | - Siffreya Pedersen
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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2
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Korbel KL, Hose GC, Karwautz C, Greenfield P, Wang H, Chariton AA, Griebler C. Detection, movement and persistence of invertebrate eDNA in groundwater. Sci Rep 2024; 14:17151. [PMID: 39060364 PMCID: PMC11282260 DOI: 10.1038/s41598-024-67349-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Sampling groundwater biodiversity is difficult because of limited access and issues with species identification. Environmental DNA (eDNA) provides a viable alternative to traditional sampling approaches, however limited knowledge of the abundance and fate of DNA in groundwater hinders the interpretation of data from these environments. Groundwater environments are dark and have lower oxygen concentrations and microbial activity than surface waters. Consequently, assumptions about DNA fate in surface ecosystems may not apply to groundwaters. Here, we test the longevity and transport of eDNA in groundwater within a static microcosm and a flow-through mesocosm. A variety of invertebrates were placed within a mesocosm and microcosm to enable DNA shedding, and then removed. DNA persisted for up to 5 weeks after their removal in the static experiment and was detected between 9 and 33 days in the flow-through experiment. Sediments and water both proved important for eDNA detection. Crustacean DNA was detected sporadically and unpredictably, whereas non-crustacean DNA was detected more frequently despite their lower densities. We suggest that detecting crustaceans poses a challenge to utilising eDNA approaches for stygofauna monitoring. This is confounded by the scarcity of sequences for stygofauna in reference databases. Further research is needed before eDNA alone can be routinely employed for stygofauna detection.
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Affiliation(s)
- K L Korbel
- School of Natural Sciences, Macquarie University, Sydney, Australia.
| | - G C Hose
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - C Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - P Greenfield
- Energy Business Unit, Common wealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, New South Wales, Australia
| | - H Wang
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Workgroup of Limnology and Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | - A A Chariton
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - C Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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Bhendarkar M, Rodriguez-Ezpeleta N. Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:617. [PMID: 38874640 DOI: 10.1007/s10661-024-12788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.
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Affiliation(s)
- Mukesh Bhendarkar
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain.
- ICAR-National Institute of Abiotic Stress Management, Baramati, 413 115, Maharashtra, India.
| | - Naiara Rodriguez-Ezpeleta
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain
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4
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Nakai M, Masumoto T, Asaeda T, Rahman M. Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA. PLoS One 2024; 19:e0301197. [PMID: 38557776 PMCID: PMC10984549 DOI: 10.1371/journal.pone.0301197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.
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Affiliation(s)
- Masahiko Nakai
- Japan International Consultants for Transportation Co., Ltd, Tokyo, Japan
| | - Taku Masumoto
- Energy Planning Department, East Japan Railway Company, Tokyo, Japan
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Wu L, Osugi T, Inagawa T, Okitsu J, Sakamoto S, Minamoto T. Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons. Mol Ecol Resour 2024; 24:e13875. [PMID: 37830396 DOI: 10.1111/1755-0998.13875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.
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Affiliation(s)
- Luhan Wu
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Hyogo, Japan
| | | | | | | | | | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe City, Hyogo, Japan
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Duarte S, Simões L, Costa FO. Current status and topical issues on the use of eDNA-based targeted detection of rare animal species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166675. [PMID: 37647964 DOI: 10.1016/j.scitotenv.2023.166675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Animal detection through DNA present in environmental samples (eDNA) is a valuable tool for detecting rare species, that are difficult to observe and monitor. eDNA-based tools are underpinned by molecular evolutionary principles, key to devising tools to efficiently single out a targeted species from an environmental sample. Here, we present a comprehensive review of the use of eDNA-based methods for the detection of targeted animal species, such as rare, endangered, or invasive species, through the analysis of 549 publications (2008-2022). Aquatic ecosystems have been the most surveyed, in particular, freshwaters (74 %), and to a less extent marine (14 %) and terrestrial systems (10 %). Vertebrates, in particular, fish (38 %), and endangered species, have been the focus of most of these studies, and Cytb and COI are the most employed markers. Among invertebrates, assays have been mainly designed for Mollusca and Crustacea species (21 %), in particular, to target invasive species, and COI the most employed marker. Targeted molecular approaches, in particular qPCR, have been the most adopted (75 %), while eDNA metabarcoding has been rarely used to target single or few species (approx. 6 %). However, less attention has been given in these studies to the effects of environmental factors on the amount of shed DNA, the differential amount of shed DNA among species, or the sensitivity of the markers developed, which may impact the design of the assays, particularly to warrant the required detection level and avoid false negatives and positives. The accuracy of the assays will also depend on the availability of genetic data and vouchered tissue or DNA samples from closely related species to assess both marker and primers' specificity. In addition, eDNA-based assays developed for a particular species may have to be refined for use in a new geographic area taking into account site-specific populations, as well as any intraspecific variation.
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Affiliation(s)
- Sofia Duarte
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Luara Simões
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Filipe O Costa
- Centre of Molecular and Environmental Biology (CBMA) and ARNET-Aquatic Research Network, Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Casabella-Herrero G, Martín-Torrijos L, Diéguez-Uribeondo J. eDNA monitoring as a tool for evaluating the reintroduction of Austropotamobius pallipes after a crayfish plague outbreak. J Invertebr Pathol 2023; 201:108026. [PMID: 38007177 DOI: 10.1016/j.jip.2023.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 11/27/2023]
Abstract
The crayfish plague, a severe disease caused by the oomycete Aphanomyces astaci, is responsible for most population declines of susceptible crayfish in Europe. This pathogen has been devastating native populations of Austropotamobius pallipes since the 1970s in the Iberian Peninsula. In this study, we report a massive mortality event in one of the most important Spanish populations of A. pallipes. We aimed to: (i) identify the cause of the mortality, and (ii) evaluate the reintroduction viability of the species. Over the course of six months, we used environmental DNA (eDNA) and traditional trap-based methods to detect the presence of A. astaci or of native or invasive crayfish in order to evaluate the reintroduction viability of A. pallipes to the affected population. We did not capture any live crayfish or detect the presence of A. astaci in the reservoir water during the six months following the mass mortality event. Our analyses indicated that it was feasible to initiate a reintroduction program at the site, which will continue to be monitored for three to five years and will help improve the conservation status of A. pallipes.
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Affiliation(s)
| | - Laura Martín-Torrijos
- Mycology Department, Real Jardín Botánico-CSIC, Plaza Murillo 2, 28014 Madrid, Spain.
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8
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Rees HC, Measures GH, Kane SD, Maddison BC. Quantitative PCR (qPCR) assay for the specific detection of the Chinese mystery snail (Cipangopaludina chinensis) in the UK. PLoS One 2023; 18:e0292163. [PMID: 37796948 PMCID: PMC10553251 DOI: 10.1371/journal.pone.0292163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Cipangopaludina chinensis Gray 1833 is an East Asian freshwater snail and invasive species in many parts of the world (Global Invasive Species Database, 2022). Within the UK, it was first found at the Pevensey Levels, Sussex, and has since been reported at a second site at Southampton Common, Hampshire. Both sites are designated as Sites of Special Scientific Interest (SSSI) for their wildlife importance. Although the impacts of this species within the UK have not yet been investigated several exotic parasites of the snail have been reported and research suggests that its presence can negatively impact native snail species. This is especially important at the Pevensey Levels due to the presence of the rare freshwater mollusc Anisus vorticulus (Little Whirlpool Rams's-horn snail). Here, we have developed a qPCR-based eDNA assay for the detection of C. chinensis and compared water samples tested for eDNA with results from manual survey of the ditches at the Pevensey Levels. Our eDNA analysis exhibited an overall observed percentage agreement of 80% with a kappa coefficient of agreement between manual and eDNA surveys of 0.59 (95% CI 0.31 to 0.88). Some samples which were qPCR negative for C. chinensis were positive by manual survey, and vice versa revealing the potential for improved overall detection rates when using a combination of manual and eDNA methodologies. eDNA analysis can therefore augment manual survey techniques for C. chinensis as a relatively quick and inexpensive tool for collecting presence and distribution data that could be used to inform further manual surveys and control measures within the ditches.
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Affiliation(s)
- Helen C. Rees
- Biotechnology, RSK ADAS Ltd, Nottingham, United Kingdom
| | - Gavin H. Measures
- Species Recovery and Reintroductions Team, Natural England, Peterborough, United Kingdom
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9
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Hebert PDN, Bock DG, Prosser SWJ. Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness. PLoS One 2023; 18:e0286620. [PMID: 37289794 PMCID: PMC10249859 DOI: 10.1371/journal.pone.0286620] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 06/10/2023] Open
Abstract
The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.
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Affiliation(s)
- Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dan G. Bock
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Sean W. J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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Wang Z, Yang L, Zhou F, Li J, Wu X, Zhong X, Lv H, Yi S, Gao Q, Yang Z, Zhao P, Wu Y, Wu C, Zhang L, Wang H, Zhang L. Integrated comparative transcriptome and weighted gene co-expression network analysis provide valuable insights into the response mechanisms of crayfish (Procambarus clarkii) to copper stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130820. [PMID: 36860031 DOI: 10.1016/j.jhazmat.2023.130820] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
One of the significant limitations of aquaculture worldwide is the prevalence of divalent copper (Cu). Crayfish (Procambarus clarkii) are economically important freshwater species adapted to a variety of environmental stimuli, including heavy metal stresses; however, large-scale transcriptomic data of the hepatopancreas of crayfish in response to Cu stress are still scarce. Here, integrated comparative transcriptome and weighted gene co-expression network analyses were initially applied to investigate gene expression profiles of the hepatopancreas of crayfish subjected to Cu stress for different periods. As a result, 4662 significant differentially expressed genes (DEGs) were identified following Cu stress. Bioinformatics analyses revealed that the "focal adhesion" pathway was one of the most significantly upregulated response pathways following Cu stress, and seven DEGs mapped to this pathway were identified as hub genes. Furthermore, the seven hub genes were examined by quantitative PCR, and each was found to have a substantial increase in transcript abundance, suggesting a critical role of the "focal adhesion" pathway in the response of crayfish to Cu stress. Our transcriptomic data can be a good resource for the functional transcriptomics of crayfish, and these results may provide valuable insights into the molecular response mechanisms underlying crayfish to Cu stress.
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Affiliation(s)
- Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Lianlian Yang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Fan Zhou
- Zhejiang Fisheries Technical Extension Center, Hangzhou 310023, China
| | - Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - He Lv
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Quanxin Gao
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Zi Yang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Pengfei Zhao
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yi Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Choufei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Hua Wang
- Huzhou Key Laboratory of Medical and Environmental Application Technologies, College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Lixia Zhang
- Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
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11
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Soto I, Ahmed DA, Beidas A, Oficialdegui FJ, Tricarico E, Angeler DG, Amatulli G, Briski E, Datry T, Dohet A, Domisch S, England J, Feio MJ, Forcellini M, Johnson RK, Jones JI, Larrañaga A, L'Hoste L, Murphy JF, Schäfer RB, Shen LQ, Kouba A, Haubrock PJ. Long-term trends in crayfish invasions across European rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161537. [PMID: 36640879 DOI: 10.1016/j.scitotenv.2023.161537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Europe has experienced a substantial increase in non-indigenous crayfish species (NICS) since the mid-20th century due to their extensive use in fisheries, aquaculture and, more recently, pet trade. Despite relatively long invasion histories of some NICS and negative impacts on biodiversity and ecosystem functioning, large spatio-temporal analyses of their occurrences are lacking. Here, we used a large freshwater macroinvertebrate database to evaluate what information on NICS can be obtained from widely applied biomonitoring approaches and how usable such data is for descriptions of trends in identified NICS species. We found 160 time-series containing NICS between 1983 and 2019, to infer temporal patterns and environmental drivers of species and region-specific trends. Using a combination of meta-regression and generalized linear models, we found no significant temporal trend for the abundance of any species (Procambarus clarkii, Pacifastacus leniusculus or Faxonius limosus) at the European scale, but identified species-specific predictors of abundances. While analysis of the spatial range expansion of NICS was positive (i.e. increasing spread) in England and negative (significant retreat) in northern Spain, no trend was detected in Hungary and the Dutch-German-Luxembourg region. The average invasion velocity varied among countries, ranging from 30 km/year in England to 90 km/year in Hungary. The average invasion velocity gradually decreased over time in the long term, with declines being fastest in the Dutch-German-Luxembourg region, and much slower in England. Considering that NICS pose a substantial threat to aquatic biodiversity across Europe, our study highlights the utility and importance of collecting high resolution (i.e. annual) biomonitoring data using a sampling protocol that is able to estimate crayfish abundance, enabling a more profound understanding of NICS impacts on biodiversity.
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Affiliation(s)
- Ismael Soto
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic.
| | - Danish A Ahmed
- Center for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
| | - Ayah Beidas
- Center for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
| | | | - Elena Tricarico
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
| | - David G Angeler
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Uppsala, Sweden; Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, Victoria, Australia; University of Nebraska - Lincoln, School of Natural Resources, Lincoln, NE, USA; The PRODEO Institute, San Francisco, CA, USA
| | - Giuseppe Amatulli
- Yale University, School of the Environment, 195 Prospect St, New Haven, CT 06511, USA
| | | | - Thibault Datry
- INRAE, UR RiverLy, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626 Villeurbanne, Cedex, France
| | - Alain Dohet
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Sami Domisch
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Community and Ecosystem Ecology, Müggelseedamm 310, 12587 Berlin, Germany
| | - Judy England
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Maria J Feio
- MARE - Marine and Environmental Sciences Centre, Associate Laboratory ARNET, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Maxence Forcellini
- INRAE, UR RiverLy, Centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626 Villeurbanne, Cedex, France
| | - Richard K Johnson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J Iwan Jones
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Aitor Larrañaga
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Lionel L'Hoste
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - John F Murphy
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ralf B Schäfer
- RPTU Kaiserslautern-Landau, Institute for Environmental Sciences, Landau, Germany
| | - Longzhu Q Shen
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Community and Ecosystem Ecology, Müggelseedamm 310, 12587 Berlin, Germany; Carnegie Mellon University, Institute for Green Science, 4400 Forbes Ave., Pittsburgh, PA 15213, USA
| | - Antonín Kouba
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Phillip J Haubrock
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25 Vodňany, Czech Republic; Center for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait; Senckenberg Research Institute and Natural History Museum Frankfurt, Department of River Ecology and Conservation, Gelnhausen, Germany
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12
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Dominant barriers and the solutions to the social application of environmental DNA. LANDSCAPE AND ECOLOGICAL ENGINEERING 2023. [DOI: 10.1007/s11355-023-00549-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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13
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Sanders M, Tardani R, Locher A, Geller K, Partridge CG. Development of Novel Early Detection Technology for Hemlock Woolly Adelgid, Adelges tsugae (Hemiptera: Adelgidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:168-180. [PMID: 36421054 PMCID: PMC9912136 DOI: 10.1093/jee/toac175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Indexed: 06/16/2023]
Abstract
Hemlock woolly adelgid (HWA), Adelges tsugae Annand, threatens hemlock forests throughout eastern North America. Management efforts focus on early detection of HWA to ensure rapid management responses to control and stop the spread of this pest. This study's goal was to identify an affordable, efficient trap to aid with airborne environmental DNA (eDNA) sampling approaches as an early monitoring tool for HWA. We initially compared HWA detection success between a standard sticky trap, commonly used for HWA monitoring, and trap designs potentially compatible with eDNA protocols (i.e., passive trap, funnel trap, and motorized trap). Passive, funnel, and motorized traps' estimated capture success probabilities compared to sticky traps were 0.87, 0.8, and 0.4, respectively. A secondary evaluation of a modified version of the motorized trap further assessed trap performance and determined the number of traps needed in a set area to efficiently detect HWA. By modifying the original motorized trap design, its estimated capture success probability increased to 0.67 compared to a sticky trap. Overall, the cumulative capture success over the 16-week sampling period for the motorized trap was 94% and 99% for the sticky trap. The number of traps did impact capture success, and trap elevation and distance to infested hemlocks influenced the number of adelgids captured per trap. As eDNA-based monitoring approaches continue to become incorporated into invasive species surveying, further refinement with these types of traps can be useful as an additional tool in the manager's toolbox.
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Affiliation(s)
| | - Renee Tardani
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
| | - Alexandra Locher
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Kathryn Geller
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
| | - Charlyn G Partridge
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Drive, Muskegon, MI 49441, USA
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14
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Environmental DNA (eDNA): Powerful Technique for Biodiversity Conservation. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Porco D, Hermant S, Purnomo CA, Horn M, Marson G, Colling G. Getting rid of ‘rain’ and ‘stars’: Mitigating inhibition effects on ddPCR data analysis, the case study of the invasive crayfish Pacifastacus leniusculus in the streams of Luxembourg. PLoS One 2022; 17:e0275363. [PMCID: PMC9668142 DOI: 10.1371/journal.pone.0275363] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
ddPCR is becoming one of the most widely used tool in the field of eDNA-based aquatic monitoring. Although emulsion PCR used in ddPCR confers a partial mitigation to inhibition due to the high number of reactions for a single sample (between 10K and 20K), it is not impervious to it. Our results showed that inhibition impacts the amplitude of fluorescence in positive droplets with a different intensity among rivers. This signal fluctuation could jeopardize the use of a shared threshold among samples from different origin, and thus the accurate assignment of the positive droplets which is particularly important for low concentration samples such as eDNA ones: amplification events are scarce, thus their objective discrimination as positive is crucial. Another issue, related to target low concentration, is the artifactual generation of high fluorescence droplets (‘stars’). Indeed, these could be counted as positive with a single threshold solution, which in turn could produce false positive and incorrect target concentration assessments. Approximating the positive and negative droplets distribution as normal, we proposed here a double threshold method accounting for both high fluorescence droplets (‘stars’) and PCR inhibition impact in delineating positive droplets clouds. In the context of low concentration template recovered from environmental samples, the application of this method of double threshold establishment could allow for a consistent sorting of the positive and negative droplets throughout ddPCR data generated from samples with varying levels of inhibitor contents. Due to low concentrations template and inhibition effects, Quantasoft software produced an important number of false negatives and positive comparatively to the double threshold method developed here. This case study allowed the detection of the invasive crayfish P. leniusculus in 32 out of 34 sampled sites from two main rivers (Alzette and Sûre) and five of their tributaries (Eisch, Attert, Mamer, Wiltz and Clerve).
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Affiliation(s)
- David Porco
- Musée National d’histoire Naturelle, Life Science Department—Invertebrate Zoology, Population Biology and Evolution, Luxembourg, Luxembourg
- Fondation Faune Flore, Luxembourg, Luxembourg
- * E-mail:
| | - Sylvie Hermant
- Musée National d’histoire Naturelle, Life Science Department—Invertebrate Zoology, Population Biology and Evolution, Luxembourg, Luxembourg
| | - Chanistya Ayu Purnomo
- Musée National d’histoire Naturelle, Life Science Department—Invertebrate Zoology, Population Biology and Evolution, Luxembourg, Luxembourg
- Fondation Faune Flore, Luxembourg, Luxembourg
| | - Mario Horn
- Musée National d’histoire Naturelle, Life Science Department—Invertebrate Zoology, Population Biology and Evolution, Luxembourg, Luxembourg
| | - Guy Marson
- Musée National d’histoire Naturelle, Life Science Department—Invertebrate Zoology, Population Biology and Evolution, Luxembourg, Luxembourg
| | - Guy Colling
- Musée National d’histoire Naturelle, Life Science Department—Invertebrate Zoology, Population Biology and Evolution, Luxembourg, Luxembourg
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16
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Sard NM, Smith KR, Roth BM, Nathan LR, Herbst SJ, Scribner KT. Multiple sources implicated in the red swamp crayfish invasion in Michigan, USA. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02938-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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17
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MacAulay S, Ellison AR, Kille P, Cable J. Moving towards improved surveillance and earlier diagnosis of aquatic pathogens: From traditional methods to emerging technologies. REVIEWS IN AQUACULTURE 2022; 14:1813-1829. [PMID: 36250037 PMCID: PMC9544729 DOI: 10.1111/raq.12674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 06/16/2023]
Abstract
Early and accurate diagnosis is key to mitigating the impact of infectious diseases, along with efficient surveillance. This however is particularly challenging in aquatic environments due to hidden biodiversity and physical constraints. Traditional diagnostics, such as visual diagnosis and histopathology, are still widely used, but increasingly technological advances such as portable next generation sequencing (NGS) and artificial intelligence (AI) are being tested for early diagnosis. The most straightforward methodologies, based on visual diagnosis, rely on specialist knowledge and experience but provide a foundation for surveillance. Future computational remote sensing methods, such as AI image diagnosis and drone surveillance, will ultimately reduce labour costs whilst not compromising on sensitivity, but they require capital and infrastructural investment. Molecular techniques have advanced rapidly in the last 30 years, from standard PCR through loop-mediated isothermal amplification (LAMP) to NGS approaches, providing a range of technologies that support the currently popular eDNA diagnosis. There is now vast potential for transformative change driven by developments in human diagnostics. Here we compare current surveillance and diagnostic technologies with those that could be used or developed for use in the aquatic environment, against three gold standard ideals of high sensitivity, specificity, rapid diagnosis, and cost-effectiveness.
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Affiliation(s)
| | | | - Peter Kille
- School of Biosciences, Cardiff UniversityCardiffUK
| | - Joanne Cable
- School of Biosciences, Cardiff UniversityCardiffUK
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18
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Ogata S, Doi H, Igawa T, Komaki S, Takahara T. Environmental
DNA
methods for detecting two invasive alien species (American bullfrog and red swamp crayfish) in Japanese ponds. Ecol Res 2022. [DOI: 10.1111/1440-1703.12341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shigeki Ogata
- Graduate School of Life and Environmental Sciences Shimane University Matsue Shimane Japan
| | - Hideyuki Doi
- Graduate School of Information Science University of Hyogo Kobe Hyogo Japan
| | - Takeshi Igawa
- Amphibian Research Center Hiroshima University Higashi‐Hiroshima, Hiroshima Japan
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima, Hiroshima Japan
| | - Shohei Komaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center Iwate Medical University Iwate Japan
| | - Teruhiko Takahara
- Faculty of Life and Environmental Sciences Shimane University Matsue Japan
- Estuary Research Center Shimane University Matsue Japan
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19
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eDNA-based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity. Sci Rep 2022; 12:6553. [PMID: 35449180 PMCID: PMC9023534 DOI: 10.1038/s41598-022-10545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
LAMP assays are becoming increasingly popular in the field of invasive species detection but are still underused in eDNA-based monitoring. Here, we propose a LAMP assay designed to detect the North American crayfish species Pacifastacus leniusculus in water samples from streams. The presence of P. leniusculus was detected through this new LAMP assay in all but one of the nine sites sampled. No correlation was found between ddPCR absolute concentration measurements and the number of LAMP-positive technical replicates. However, we showed that using dependent technical replicates could significantly enhance the detection sensitivity of the LAMP assay. Applied to other assays, it could improve sensitivity and thus allow for a more efficient use of eDNA-based LAMP assays for invasive species detection in aquatic ecosystems.
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20
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Challenges in eDNA detection of the invasive European green crab, Carcinus maenas. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02757-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AbstractThe early detection of invasive species is essential to cease the spread of the species before it can cause irreversible damage to the environment. The analysis of environmental DNA (eDNA) has emerged as a non-harmful method to detect the presence of a species before visual detection and is a promising approach to monitor invasive species. Few studies have investigated the use of eDNA for arthropods, as their exoskeleton is expected to limit the release of eDNA into the environment. We tested published primers for the invasive European green crab, Carcinus maenas, in the Gulf of Maine and found them not species-specific enough for reliable use outside of the area for which they were designed for. We then designed new primers, tested them against a broad range of local faunal species, and validated these primers in a field study. We demonstrate that eDNA analyses can be used for crustaceans with an exoskeleton and suggest that primers and probe sequences must be tested on local fauna at each location of use to ensure no positive amplification of these other species.
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21
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Danziger AM, Olson ZH, Frederich M. Limitations of eDNA analysis for Carcinus maenas abundance estimations. BMC Ecol Evol 2022; 22:14. [PMID: 35130838 PMCID: PMC8822865 DOI: 10.1186/s12862-022-01969-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background Environmental DNA (eDNA) is an effective tool for the detection and monitoring of presence or absence of rare and invasive species. These techniques have been extended to quantify biomass in vertebrates, particularly in fish species. However, the efficacy of eDNA techniques to quantify biomass in invertebrate species has rarely been examined. This study tested whether eDNA could be used to determine the biomass of the world-wide invasive green crab, Carcinus maenas. In a controlled laboratory study, the relationship between biomass and C. maenas eDNA concentration was examined in the context of different biotic (activity) and abiotic (temperature) parameters. Results When incubating different numbers of crabs in sterile saltwater for up to 7 days, a relationship between eDNA concentration and biomass was observed at temperatures of 6.7 ℃ and 18.7 ℃, but not at 12.8 ℃. Additionally, motor activity, aggression level, time of sampling, and features of organismal decay had significant impact on the concentration of C. maenas eDNA collected. Conclusions We show that eDNA concentration did not correlate with biomass, and that biomass, temperature, organismal characteristics, and potentially many more parameters affect shedding and degradation rates for eDNA in this species, thus, impacting the recoverable eDNA concentration. Therefore, eDNA techniques are not likely to provide a reliable signal of biomass in the invasive invertebrate species C. maenas. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01969-z.
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22
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King AC, Krieg R, Weston A, Zenker AK. Using eDNA to simultaneously detect the distribution of native and invasive crayfish within an entire country. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:113929. [PMID: 34688048 DOI: 10.1016/j.jenvman.2021.113929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/03/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
The introduction of invasive crayfish has led to a decline of many European native species of crayfish across their range. In this study, novel duplex assays for all crayfish occurring in Switzerland were developed. We aimed to identify the distribution of the seven species using a traditional trap surveillance method as well by collecting water samples to detect eDNA by species-specific quantitative real-time PCR. We reveal our overall experience in finding optimal field and laboratory techniques to discover the distribution and abundance of native and invasive species in order to enhance knowledge of early invasive species invasion and highlight important pockets of populations where native species remain, for implementation of conservation strategies. Using eDNA, important populations of native noble and white-clawed crayfish were revealed in multiple waters across various cantons. The successful identification of native and invasive crayfish species in Switzerland using eDNA can be applied to future nationwide projects. This method which has the ability to detect all species simultaneously across an entire country, will allow an improvement in freshwater crayfish conservation management.
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Affiliation(s)
- Alex C King
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
| | - Raphael Krieg
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
| | - Anna Weston
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland
| | - Armin K Zenker
- University of Applied Sciences and Arts North-western Switzerland, Hofackerstrasse 30, CH-4132, Muttenz, Switzerland.
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23
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Coster SS, Dillon MN, Moore W, Merovich GT. The update and optimization of an eDNA assay to detect the invasive rusty crayfish (Faxonius rusticus). PLoS One 2021; 16:e0259084. [PMID: 34714850 PMCID: PMC8555798 DOI: 10.1371/journal.pone.0259084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022] Open
Abstract
Environmental DNA (eDNA) is nuclear or mitochondrial DNA shed into the environment, and amplifying this DNA can serve as a reliable, noninvasive way to monitor aquatic systems for the presence of an invasive species. Assays based on the collection of eDNA are becoming increasingly popular, and, when optimized, can aid in effectively and efficiently tracking invasion fronts. We set out to update an eDNA assay to detect the invasive rusty crayfish, Faxonius rusticus. We tested for species specificity compared to other stream crayfish and field tested the assay at sites with known presence (N = 3) and absence (N = 4) in the Juniata River watershed in central Pennsylvania, USA. To maximize sensitivity, we field tested different storage buffers (Longmire's buffer and ethanol), DNA extraction methods (Qiagen's DNEasy and PowerWater kits), and quantitative polymerase chain reaction (qPCR) chemistries (TaqMan and SYBR green). Our assay confirmed the presence data and performed optimally when filter samples were stored in Longmire's buffer, DNA was extracted with DNeasy Blood and Tissue Kit, and TaqMan qPCR chemistry was utilized. With proper sample processing, our assay allows for accurate, noninvasive detection of F. rusticus in streams.
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Affiliation(s)
- Stephanie S. Coster
- Department of Biology, Randolph-Macon College, Ashland, Virginia, United States of America
| | - Megan N. Dillon
- Department of Biology, Randolph-Macon College, Ashland, Virginia, United States of America
| | - William Moore
- Department of Biology, Randolph-Macon College, Ashland, Virginia, United States of America
| | - George T. Merovich
- Department of Environmental Science, Fisheries and Aquatic Sciences Program, Juniata College, Huntingdon, Pennsylvania, United States of America
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24
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Thomson-Laing G, Parai R, Kelly LT, Pochon X, Newnham R, Vandergoes MJ, Howarth JD, Wood SA. Development of droplet digital Polymerase Chain Reaction assays for the detection of long-finned ( Anguilla dieffenbachii) and short-finned ( Anguilla australis) eels in environmental samples. PeerJ 2021; 9:e12157. [PMID: 34692247 PMCID: PMC8483004 DOI: 10.7717/peerj.12157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Freshwater eels are ecologically, and culturally important worldwide. The New Zealand long-finned eel (Anguilla dieffenbachii) and short-finned eel (Anguilla australis) are apex predators, playing an important role in ecosystem functioning of rivers and lakes. Recently, there has been a national decline in their populations due to habitat destruction and commercial harvest. The emergence of targeted environmental DNA detection methodologies provides an opportunity to enhance information about their past and present distributions. In this study we successfully developed species-specific droplet digital Polymerase Chain Reaction (ddPCR) assays to detect A. dieffenbachii and A. australis DNA in water and sediment samples. Assays utilized primers and probes designed for regions of the mitochondrial cytochrome b and 16S ribosomal RNA genes in A. dieffenbachii and A. australis, respectively. River water samples (n = 27) were analyzed using metabarcoding of fish taxa and were compared with the ddPCR assays. The presence of A. dieffenbachii and A. australis DNA was detected in a greater number of water samples using ddPCR in comparison to metabarcoding. There was a strong and positive correlation between gene copies (ddPCR analyses) and relative eel sequence reads (metabarcoding analyses) when compared to eel biomass. These ddPCR assays provide a new method for assessing spatial distributions of A. dieffenbachii and A. australis in a range of environments and sample types.
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Affiliation(s)
| | | | | | - Xavier Pochon
- Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | - Rewi Newnham
- Victoria University of Wellington, Wellington, New Zealand
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25
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Persistence and accumulation of environmental DNA from an endangered dragonfly. Sci Rep 2021; 11:18987. [PMID: 34556696 PMCID: PMC8460674 DOI: 10.1038/s41598-021-98099-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 07/28/2021] [Indexed: 11/10/2022] Open
Abstract
Detection of environmental DNA (eDNA) has become a commonly used surveillance method for threatened or invasive vertebrates in both aquatic and terrestrial environments. However, most studies in this field favor vertebrate target species. Environmental DNA protocols can be especially useful for endangered invertebrates such as the Hine’s emerald dragonfly (Somatochlora hineana) where conservation efforts have been greatly hindered by training, time, overall costs, and environmental impacts associated with conducting surveys in the calcareous fens occupied by this species. An essential step in developing such a protocol is to evaluate the dynamics of eDNA concentration under controlled conditions. We used the quantitative polymerase chain reaction (qPCR) to examine seasonal shifts in the persistence and net-accumulation of eDNA from captive S. hineana larvae in experimental mesocosms at temperatures corresponding with their overwintering (5.0 °C) and active (16.0 °C) seasons. Environmental DNA persisted longer at 5.0 °C but accumulated more readily at 16.0 °C. Differences in the accumulation and persistence of eDNA reflect differences in the longevity of eDNA at different temperatures and seasonal differences in larval S. hineana behavior. This study highlights the importance of considering how seasonal changes in temperature influence not only the speed of eDNA degradation but also the target species’ eDNA shedding rates.
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26
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Ponce JJ, Arismendi I, Thomas A. Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail ( Potamopyrgus antipodarum) in freshwaters. PeerJ 2021; 9:e11835. [PMID: 34434646 PMCID: PMC8359795 DOI: 10.7717/peerj.11835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/01/2021] [Indexed: 12/03/2022] Open
Abstract
Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.
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Affiliation(s)
- Jake J Ponce
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, United States of America
| | - Ivan Arismendi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, OR, United States of America
| | - Austen Thomas
- Molecular Division, Smith-Root, Inc., Vancouver, WA, United States of America
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27
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Mouser JB, Brewer SK, Niemiller ML, Mollenhauer R, Van Den Bussche RA. Refining sampling protocols for cavefishes and cave crayfishes to account for environmental variation. SUBTERRANEAN BIOLOGY 2021. [DOI: 10.3897/subtbiol.39.64279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting detection probability using traditional visual surveys and eDNA surveys for both cavefishes and cave crayfishes and demonstrated how detection affects survey efforts for these taxa. We sampled 40 sites (179 visual and 183 eDNA surveys) across the Ozark Highlands ecoregion. We estimated the detection probability of cave crayfishes and cavefishes using both survey methods under varying environmental conditions. The effectiveness of eDNA or visual surveys varied by environmental conditions (i.e., water volume, prevailing substrate, and water velocity) and the target taxa. When sampling in areas with average water velocity, no flow, and coarse substrate, eDNA surveys had a higher detection probability (0.49) than visual surveys (0.35) for cavefishes and visual surveys (0.67) had a higher detection probability than eDNA surveys (0.40) for cave crayfishes. Under the same sampling conditions, 5 visual surveys compared to 10 eDNA surveys would be needed to confidently detect cave crayfishes and 9 visual surveys compared to 4 eDNA surveys for cavefishes. Environmental DNA is a complementary tool to traditional visual surveys; however, the limitations we identified indicate eDNA currently cannot replace visual surveys in subterranean environments. Although sampling designs that account for imperfect sampling are particularly useful, they may not be practical; thus, increasing sampling efforts to offset known detection bias would benefit conservation strategies.
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Troth CR, Sweet MJ, Nightingale J, Burian A. Seasonality, DNA degradation and spatial heterogeneity as drivers of eDNA detection dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144466. [PMID: 33736342 DOI: 10.1016/j.scitotenv.2020.144466] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
In recent years, eDNA-based assessments have evolved as valuable tools for research and conservation. Most eDNA-based applications rely on comparisons across time or space. However, temporal, and spatial dynamics of eDNA concentrations are shaped by various drivers that can affect the reliability of such comparative approaches. Here, we assessed (i) seasonal variability, (ii) degradation rates and (iii) micro-habitat heterogeneity of eDNA concentrations as key factors likely to inflict uncertainty in across site and time comparisons. In a controlled mesocosm experiment, using the white-clawed crayfish as a model organism, we found detection probabilities of technical replicates to vary substantially and range from as little as 20 to upwards of 80% between seasons. Further, degradation rates of crayfish eDNA were low and target eDNA was still detectable 14-21 days after the removal of crayfish. Finally, we recorded substantial small-scale in-situ heterogeneity and large variability among sampling sites in a single pond of merely 1000m2 in size. Consequently, all three tested drivers of spatial and temporal variation have the potential to severely impact the reliability of eDNA-based site comparisons and need to be accounted for in sampling design and data analysis of field-based applications.
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Affiliation(s)
- Christopher R Troth
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK; SureScreen Scientifics Ltd, Morley Retreat, Church Lane, Morley DE7 6DE, UK.
| | - Michael J Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK.
| | - Jen Nightingale
- Bristol Zoological Society, Clifton, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alfred Burian
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK; Marine Ecology Department, Lurio University, Nampula, Mozambique
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29
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Wang Y, Chen K, Gao J, Wang M, Dong J, Xie Y, Giesy JP, Jin X, Wang B. Environmental DNA of preservative ethanol performed better than water samples in detecting macroinvertebrate diversity using metabarcoding. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Yu Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Kai Chen
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Jin Gao
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Meng Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Jie Dong
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Yuwei Xie
- Toxicology Centre University of Saskatchewan Saskatoon Saskatchewan Canada
| | - John P. Giesy
- Toxicology Centre University of Saskatchewan Saskatoon Saskatchewan Canada
- Department of Veterinary Biomedical Sciences University of Saskatchewan Saskatoon Saskatchewan Canada
- Department of Environmental Sciences Baylor University Waco Texas USA
| | - Xiaowei Jin
- China National Environmental Monitoring Centre Beijing China
| | - Beixin Wang
- Department of Entomology Nanjing Agricultural University Nanjing China
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30
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Farrell JA, Whitmore L, Duffy DJ. The Promise and Pitfalls of Environmental DNA and RNA Approaches for the Monitoring of Human and Animal Pathogens from Aquatic Sources. Bioscience 2021. [PMCID: PMC8083301 DOI: 10.1093/biosci/biab027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Novel forensics-inspired molecular approaches have revolutionized species detection in the wild and are particularly useful for tracing endangered or invasive species. These new environmental DNA or RNA (eDNA or eRNA)–based techniques are now being applied to human and animal pathogen surveillance, particularly in aquatic environments. They allow better disease monitoring (presence or absence and geographical spread) and understanding of pathogen occurrence and transmission, benefitting species conservation and, more recently, our understanding of the COVID-19 global human pandemic. In the present article, we summarize the benefits of eDNA-based monitoring, highlighted by two case studies: The first is a fibropapillomatosis tumor-associated herpesvirus (chelonid herpesvirus 5) driving a sea turtle panzootic, and the second relates to eRNA-based detection of the SARS-CoV-2 coronavirus driving the COVID-19 human pandemic. The limitations of eDNA- or eRNA-based approaches are also summarized, and future directions and recommendations of the field are discussed. Continuous eDNA- or eRNA-based monitoring programs can potentially improve human and animal health by predicting disease outbreaks in advance, facilitating proactive rather than reactive responses.
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Affiliation(s)
- Jessica A Farrell
- University of Florida's Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital (St. Augustine), and The University of Florida's Department of Biology in the College of Liberal Arts and Sciences (Gainesville), United States
| | - Liam Whitmore
- University of Limerick's Department of Biological Sciences in the School of Natural Sciences and Faculty of Science and Engineering, Limerick, Ireland
| | - David J Duffy
- University of Florida's Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital (St. Augustine), and The University of Florida's Department of Biology in the College of Liberal Arts and Sciences (Gainesville), United States
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31
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Coutant O, Richard-Hansen C, de Thoisy B, Decotte JB, Valentini A, Dejean T, Vigouroux R, Murienne J, Brosse S. Amazonian mammal monitoring using aquatic environmental DNA. Mol Ecol Resour 2021; 21:1875-1888. [PMID: 33787010 DOI: 10.1111/1755-0998.13393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/14/2021] [Accepted: 03/22/2021] [Indexed: 11/26/2022]
Abstract
Environmental DNA (eDNA) metabarcoding has emerged as one of the most efficient methods to assess aquatic species presence. While the method can in theory be used to investigate nonaquatic fauna, its development for inventorying semi-aquatic and terrestrial fauna is still at an early stage. Here we investigated the potential of aquatic eDNA metabarcoding for inventorying mammals in Neotropical environments, be they aquatic, semi-aquatic or terrestrial. We collected aquatic eDNA in 96 sites distributed along three Guianese watersheds and compared our inventories to expected species distributions and field observations derived from line transects located throughout French Guiana. Species occurrences and emblematic mammalian fauna richness patterns were consistent with the expected distribution of fauna and our results revealed that aquatic eDNA metabarcoding brings additional data to line transect samples for diurnal nonaquatic (terrestrial and arboreal) species. Aquatic eDNA also provided data on species not detectable in line transect surveys such as semi-aquatic, aquatic and nocturnal terrestrial and arboreal species. Although the application of eDNA to inventory mammals still needs some developments to optimize sampling efficiency, it can now be used as a complement to traditional surveys.
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Affiliation(s)
- Opale Coutant
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | | | | | | | | | - Tony Dejean
- VIGILIFE, Le Bourget-du-Lac, France.,SPYGEN, Le Bourget-du-Lac, France
| | - Régis Vigouroux
- Laboratoire Environnement de Petit Saut, HYDRECO, Kourou Cedex, French Guiana
| | - Jérôme Murienne
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
| | - Sébastien Brosse
- Laboratoire Evolution et Diversité Biologique, CNRS, IRD, UPS, (UMR5174) - Université de Toulouse, Toulouse, France
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32
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Doi H, Minamoto T, Takahara T, Tsuji S, Uchii K, Yamamoto S, Katano I, Yamanaka H. Compilation of real‐time
PCR
conditions toward the standardization of
environmental DNA
methods. Ecol Res 2021. [DOI: 10.1111/1440-1703.12217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Hideyuki Doi
- Graduate School of Simulation Studies University of Hyogo Kobe Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment Kobe University Kobe Japan
| | - Teruhiko Takahara
- Faculty of Life and Environmental Sciences Shimane University Matsue Japan
| | - Satsuki Tsuji
- Graduate School of Science and Technology for Innovation Yamaguchi University Ube Japan
| | - Kimiko Uchii
- Faculty of Pharmacy Osaka Ohtani University Tondabayashi Japan
| | - Satoshi Yamamoto
- Department of Zoology, Graduate School of Science Kyoto University Kyoto Japan
| | - Izumi Katano
- Graduate School of Humanities and Sciences Nara Women's University Nara Japan
| | - Hiroki Yamanaka
- Faculty of Advanced Science and Technology Ryukoku University Otsu Japan
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33
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Russo T, Maiello G, Talarico L, Baillie C, Colosimo G, D'Andrea L, Di Maio F, Fiorentino F, Franceschini S, Garofalo G, Scannella D, Cataudella S, Mariani S. All is fish that comes to the net: metabarcoding for rapid fisheries catch assessment. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02273. [PMID: 33290575 DOI: 10.1002/eap.2273] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/04/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
Monitoring marine resource exploitation is a key activity in fisheries science and biodiversity conservation. Since research surveys are time consuming and costly, fishery-dependent data (i.e., derived directly from fishing vessels) are increasingly credited with a key role in expanding the reach of ocean monitoring. Fishing vessels may be seen as widely ranging data-collecting platforms, which could act as a fleet of sentinels for monitoring marine life, in particular exploited stocks. Here, we investigate the possibility of assessing catch composition of single hauls carried out by trawlers by applying DNA metabarcoding to the dense water draining from fishing nets just after the end of hauling operations (hereafter "slush"). We assess the performance of this approach in portraying β-diversity and examining the quantitative relationship between species abundances in the catch and DNA amount in the slush (read counts generated by amplicon sequencing). We demonstrate that the assemblages identified using DNA in the slush satisfactorily mirror those returned by visual inspection of net content (about 71% of species and 86% of families of fish) and detect a strong relationship between read counts and species abundances in the catch. We therefore argue that this approach could be upscaled to serve as a powerful source of information on the structure of demersal assemblages and the impact of fisheries.
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Affiliation(s)
- Tommaso Russo
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Giulia Maiello
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- PhD program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Talarico
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Giuliano Colosimo
- San Diego Zoo, Institute for Conservation Research, San Diego, California, 92027, USA
| | - Lorenzo D'Andrea
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Federico Di Maio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- National Research Council, Institute for Marine Biological Resources and Biotechnology, Mazara del Vallo, Italy
| | - Fabio Fiorentino
- National Research Council, Institute for Marine Biological Resources and Biotechnology, Mazara del Vallo, Italy
| | | | - Germana Garofalo
- National Research Council, Institute for Marine Biological Resources and Biotechnology, Mazara del Vallo, Italy
| | - Danilo Scannella
- National Research Council, Institute for Marine Biological Resources and Biotechnology, Mazara del Vallo, Italy
| | | | - Stefano Mariani
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
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34
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Brys R, Halfmaerten D, Neyrinck S, Mauvisseau Q, Auwerx J, Sweet M, Mergeay J. Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis). JOURNAL OF FISH BIOLOGY 2021; 98:399-414. [PMID: 32154579 DOI: 10.1111/jfb.14315] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/24/2019] [Accepted: 03/07/2020] [Indexed: 06/10/2023]
Abstract
The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)-based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA-based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl-1 , respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017-2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample-specific estimates of effective DNA quantity (Qe ) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false-negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.
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Affiliation(s)
- Rein Brys
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | | | - Sabrina Neyrinck
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Quentin Mauvisseau
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
- SureScreen Scientifics Ltd, Morley, UK
| | - Johan Auwerx
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, UK
- SureScreen Scientifics Ltd, Morley, UK
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
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35
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Troth CR, Burian A, Mauvisseau Q, Bulling M, Nightingale J, Mauvisseau C, Sweet MJ. Development and application of eDNA-based tools for the conservation of white-clawed crayfish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:141394. [PMID: 32814295 DOI: 10.1016/j.scitotenv.2020.141394] [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: 02/24/2020] [Revised: 06/20/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
eDNA-based methods represent non-invasive and cost-effective approaches for species monitoring and their application as a conservation tool has rapidly increased within the last decade. Currently, they are primarily used to determine the presence/absence of invasive, endangered or commercially important species, but they also hold potential to contribute to an improved understanding of the ecological interactions that drive species distributions. However, this next step of eDNA-based applications requires a thorough method development. We developed an eDNA assay for the white-clawed crayfish (Austropotamobius pallipes), a flagship species of conservation in the UK and Western Europe. Multiple subsequent in-situ and ex-situ validation tests aimed at improving method performance allowed us to apply eDNA-based surveys to evaluate interactions between white-clawed crayfish, crayfish plague and invasive signal crayfish. The assay performed well in terms of specificity (no detection of non-target DNA) and sensitivity, which was higher compared to traditional methods (in this case torching). The eDNA-based quantification of species biomass was, however, less reliable. Comparison of eDNA sampling methods (precipitation vs. various filtration approaches) revealed that optimal sampling method differed across environments and might depend on inhibitor concentrations. Finally, we applied our methodology together with established assays for crayfish plague and the invasive signal crayfish, demonstrating their significant interactions in a UK river system. Our analysis highlights the importance of thorough methodological development of eDNA-based assays. Only a critical evaluation of methodological strengths and weaknesses will allow us to capitalise on the full potential of eDNA-based methods and use them as decision support tools in environmental monitoring and conservation practice.
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Affiliation(s)
- Christopher R Troth
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK; SureScreen Scientifics Ltd, Morley Retreat, Church Lane, Morley DE7 6DE, UK.
| | - Alfred Burian
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Quentin Mauvisseau
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK; SureScreen Scientifics Ltd, Morley Retreat, Church Lane, Morley DE7 6DE, UK
| | - Mark Bulling
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Jen Nightingale
- Bristol Zoological Society, Clifton, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK
| | - Christophe Mauvisseau
- Fédération de Pêche et de Protection du Milieu Aquatique du Loir-et-Cher, 11 Rue Robert Nau, 41000 Blois, France
| | - Michael J Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK.
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36
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Blackman RC, Ling KKS, Harper LR, Shum P, Hänfling B, Lawson‐Handley L. Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water. Ecol Evol 2020; 10:13248-13259. [PMID: 33304534 PMCID: PMC7713958 DOI: 10.1002/ece3.6921] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022] Open
Abstract
The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densities are likely to be low. Environmental DNA (eDNA) analysis is a highly promising technique for the detection of INNS-particularly during the early stages of an invasion.Here, we compared the use of traditional kick-net sampling with two eDNA approaches (targeted detection using both conventional and quantitative PCR and passive detection via metabarcoding with conserved primers) for detection of quagga mussel, Dreissena rostriformis bugensis, a high priority INNS, along a density gradient on the River Wraysbury, UK.All three molecular tools outperformed traditional sampling in terms of detection. Conventional PCR and qPCR both had 100% detection rate in all samples and outperformed metabarcoding when the target species was at low densities. Additionally, quagga mussel DNA copy number (qPCR) and relative read count (metabarcoding) were significantly influenced by both mussel density and distance from source population, with distance being the most significant predictor. Synthesis and application. All three molecular approaches were more sensitive than traditional kick-net sampling for the detection of the quagga mussel in flowing water, and both qPCR and metabarcoding enabled estimates of relative abundance. Targeted approaches were more sensitive than metabarcoding, but metabarcoding has the advantage of providing information on the wider community and consequently the impacts of INNS.
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Affiliation(s)
- Rosetta C. Blackman
- Department of Aquatic EcologyEawagSwiss Federal Institute of Aquatic Science and TechnologyDübendorfSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Kar Keun Sean Ling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lynsey R. Harper
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Peter Shum
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Bernd Hänfling
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
| | - Lori Lawson‐Handley
- Evolutionary and Environmental Genomics Group (EvoHull)Department of Biological and Marine SciencesUniversity of HullHullUK
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37
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Harper LR, Lawson Handley L, Sayer CD, Read DS, Benucci M, Blackman RC, Hill MJ, Hänfling B. Assessing the impact of the threatened crucian carp (Carassius carassius) on pond invertebrate diversity: A comparison of conventional and molecular tools. Mol Ecol 2020; 30:3252-3269. [PMID: 33002225 DOI: 10.1111/mec.15670] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Fishes stocked for recreation and angling can damage freshwater habitats and negatively impact biodiversity. The pond-associated crucian carp (Carassius carassius) is rare across Europe and is stocked for conservation management in England, but its impacts on pond biota are understudied. Freshwater invertebrates contribute substantially to aquatic biodiversity, encompassing many rare and endemic species, but their small size and high abundance complicate their assessment. Practitioners have employed sweep-netting and kick-sampling with microscopy (morphotaxonomy), but specimen size/quality and experience can bias identification. DNA and environmental DNA (eDNA) metabarcoding offer alternative means of invertebrate assessment. We compared invertebrate diversity in ponds (N = 18) with and without crucian carp using morphotaxonomic identification, DNA metabarcoding and eDNA metabarcoding. Five 2 L water samples and 3 min sweep-net samples were collected at each pond. Inventories produced by morphotaxonomic identification of netted samples, DNA metabarcoding of bulk tissue samples and eDNA metabarcoding of water samples were compared. Alpha diversity was greatest with DNA or eDNA metabarcoding, depending on whether standard or unbiased methods were considered. DNA metabarcoding reflected morphotaxonomic identification, whereas eDNA metabarcoding produced markedly different communities. These complementary tools should be combined for comprehensive invertebrate assessment. Crucian carp presence minimally reduced alpha diversity in ponds, but positively influenced beta diversity through taxon turnover (i.e., ponds with crucian carp contained different invertebrates to fishless ponds). Crucian carp presence contributes to landscape-scale invertebrate diversity, supporting continued conservation management in England. Our results show that molecular tools can enhance freshwater invertebrate assessment and facilitate development of more accurate and ecologically effective pond management strategies.
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Affiliation(s)
- Lynsey R Harper
- Department of Biological and Marine Sciences, University of Hull, Hull, UK.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | | | - Carl D Sayer
- Pond Restoration Research Group, Environmental Change Research Centre, Department of Geography, University College London, London, UK
| | - Daniel S Read
- Centre for Ecology & Hydrology (CEH), Wallingford, Oxfordshire, UK
| | - Marco Benucci
- Department of Biological and Marine Sciences, University of Hull, Hull, UK
| | - Rosetta C Blackman
- Department of Biological and Marine Sciences, University of Hull, Hull, UK.,Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Matthew J Hill
- School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | - Bernd Hänfling
- Department of Biological and Marine Sciences, University of Hull, Hull, UK
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38
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Rusch JC, Mojžišová M, Strand DA, Svobodová J, Vrålstad T, Petrusek A. Simultaneous detection of native and invasive crayfish and Aphanomyces astaci from environmental DNA samples in a wide range of habitats in Central Europe. NEOBIOTA 2020. [DOI: 10.3897/neobiota.58.49358] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Crayfish of North American origin are amongst the most prominent high-impact invasive invertebrates in European freshwaters. They contribute to the decline of European native crayfish species by spreading the pathogen causing crayfish plague, the oomyceteAphanomyces astaci. In this study we validated the specificity of four quantitative PCR (qPCR) assays, either published or newly developed, usable for environmental DNA (eDNA) screening for widely distributed native and non-native crayfish present in Central Europe:Astacus astacus,Pacifastacus leniusculus,Faxonius limosusandProcambarus virginalis. We then conducted an eDNA monitoring survey of these crayfish as well as the crayfish plague pathogen in a wide variety of habitat types representative for Central and Western Europe. The specificity of qPCR assays was validated against an extensive collection of crayfish DNA isolates, containing most crayfish species documented from European waters. The three assays developed in this study were sufficiently species-specific, but the published assay forF. limosusdisplayed a weak cross-reaction with multiple other crayfish species of the family Cambaridae. In the field study, we infrequently detected eDNA ofA. astacitogether with the three non-native crayfish species under examination. We never detected eDNA fromA. astacitogether with native crayfish, but in a few locations eDNA from both native and non-native crayfish was captured, due either to passive transport of eDNA from upstream populations or co-existence in the absence of infected crayfish carriers ofA. astaci. In the study, we evaluated a robust, easy-to-use and low-cost version of the eDNA sampling equipment, based mostly on items readily available in garden stores and hobby markets, for filtering relatively large (~5 l) water samples. It performed just as well as the far more expensive equipment industrially designed for eDNA water sampling, thus opening the possibility of collecting suitable eDNA samples to a wide range of stakeholders. Overall, our study confirms that eDNA-based screening for crayfish and their associated pathogen is a feasible alternative to traditional monitoring.
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39
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Curtis AN, Larson ER. No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment. PeerJ 2020; 8:e9333. [PMID: 32566410 PMCID: PMC7293857 DOI: 10.7717/peerj.9333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/19/2020] [Indexed: 01/23/2023] Open
Abstract
Environmental DNA (eDNA) is an emerging tool for monitoring invasive and imperiled species, particularly at low densities. However, the factors that control eDNA production, transport, and persistence in aquatic systems remain poorly understood. For example, the extent to which carcasses produce detectable eDNA is unknown. If positive detections are associated with dead organisms, this could confound monitoring for imperiled or invasive species. Here, we present results from one of the first studies to examine carcass eDNA in situ by deploying carcasses of the invasive red swamp crayfish (Procambarus clarkii) in a stream enclosure experiment for 28 days. We predicted that carcasses would initially produce eDNA that would decline over time as carcasses decayed. Unsurprisingly, crayfish carcasses lost biomass over time, but at the conclusion of our experiment much of the carapace and chelae remained. However, no eDNA of P. clarkii was detected in any of our samples at the crayfish density (15 P. clarkii carcasses at ∼615 g of biomass initially), stream flow (520-20,319 L/s), or temperature (∼14-25 °C) at our site. Subsequent analyses demonstrated that these results were not the consequence of PCR inhibition in our field samples, poor performance of the eDNA assay for intraspecific genetic diversity within P. clarkii, or due to the preservation and extraction procedure used. Therefore, our results suggest that when crayfish are relatively rare, such as in cases of new invasive populations or endangered species, carcasses may not produce detectable eDNA. In such scenarios, positive detections from field studies may be more confidently attributed to the presence of live organisms. We recommend that future studies should explore how biomass, flow, and differences in system (lentic vs. lotic) influence the ability to detect eDNA from carcasses.
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Affiliation(s)
- Amanda N Curtis
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Eric R Larson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.,Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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40
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Qualitative and quantitative detection using eDNA technology: A case study of Fenneropenaeus chinensis in the Bohai Sea. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Liu Q, Zhang Y, Wu H, Liu F, Peng W, Zhang X, Chang F, Xie P, Zhang H. A Review and Perspective of eDNA Application to Eutrophication and HAB Control in Freshwater and Marine Ecosystems. Microorganisms 2020; 8:E417. [PMID: 32188048 PMCID: PMC7143994 DOI: 10.3390/microorganisms8030417] [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: 02/12/2020] [Revised: 03/03/2020] [Accepted: 03/14/2020] [Indexed: 11/16/2022] Open
Abstract
Changing ecological communities in response to anthropogenic activities and climate change has become a worldwide problem. The eutrophication of waterbodies in freshwater and seawater caused by the effects of human activities and nutrient inputs could result in harmful algae blooms (HABs), decreases water quality, reductions in biodiversity and threats to human health. Rapid and accurate monitoring and assessment of aquatic ecosystems are imperative. Environmental DNA (eDNA) analysis using high-throughput sequencing has been demonstrated to be an effective and sensitive assay for detecting and monitoring single or multiple species in different samples. In this study, we review the potential applications of eDNA approaches in controlling and mitigating eutrophication and HABs in freshwater and marine ecosystems. We use recent studies to highlight how eDNA methods have been shown to be a useful tool for providing comprehensive data in studies of eutrophic freshwater and marine environments. We also provide perspectives on using eDNA techniques to reveal molecular mechanisms in biological processes and mitigate eutrophication and HABs in aquatic ecosystems. Finally, we discuss the feasible applications of eDNA for monitoring biodiversity, surveying species communities and providing instructions for the conservation and management of the environment by integration with traditional methods and other advanced techniques.
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Affiliation(s)
- Qi Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
| | - Yun Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
| | - Han Wu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
| | - Fengwen Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
| | - Wei Peng
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
| | - Ping Xie
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, CAS, Wuhan 430072, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China; (Q.L.); (Y.Z.); (H.W.); (F.L.); (W.P.); (X.Z.); (F.C.); (P.X.)
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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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West KM, Stat M, Harvey ES, Skepper CL, DiBattista JD, Richards ZT, Travers MJ, Newman SJ, Bunce M. eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem. Mol Ecol 2020; 29:1069-1086. [PMID: 32045076 DOI: 10.1111/mec.15382] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 01/30/2020] [Accepted: 02/06/2020] [Indexed: 01/10/2023]
Abstract
Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)-a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.
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Affiliation(s)
- Katrina M West
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Euan S Harvey
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Craig L Skepper
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Joseph D DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Zoe T Richards
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michael J Travers
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Environmental Protection Authority, Wellington, New Zealand
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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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45
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Xiong W, Huang X, Chen Y, Fu R, Du X, Chen X, Zhan A. Zooplankton biodiversity monitoring in polluted freshwater ecosystems: A technical review. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2019; 1:100008. [PMCID: PMC9488063 DOI: 10.1016/j.ese.2019.100008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 05/26/2023]
Abstract
Freshwater ecosystems harbor a vast diversity of micro-eukaryotes (rotifers, crustaceans and protists), and such diverse taxonomic groups play important roles in ecosystem functioning and services. Unfortunately, freshwater ecosystems and biodiversity therein are threatened by many environmental stressors, particularly those derived from intensive human activities such as chemical pollution. In the past several decades, significant efforts have been devoted to halting biodiversity loss to recover services and functioning of freshwater ecosystems. Biodiversity monitoring is the first and a crucial step towards diagnosing pollution impacts on ecosystems and making conservation plans. Yet, bio-monitoring of ubiquitous micro-eukaryotes is extremely challenging, owing to many technical issues associated with micro-zooplankton such as microscopic size, fuzzy morphological features, and extremely high biodiversity. Here, we review current methods used for monitoring zooplankton biodiversity to advance management of impaired freshwater ecosystems. We discuss the development of traditional morphology-based identification methods such as scanning electron microscope (SEM) and ZOOSCAN and FlowCAM automatic systems, and DNA-based strategies such as metabarcoding and real-time quantitative PCR. In addition, we summarize advantages and disadvantages of these methods when applied for monitoring impacted ecosystems, and we propose practical DNA-based monitoring workflows for studying biological consequences of environmental pollution in freshwater ecosystems. Finally, we propose possible solutions for existing technical issues to improve accuracy and efficiency of DNA-based biodiversity monitoring. Freshwater ecosystems and associated biodiversity have been highly degraded. Biodiversity monitoring is crucial for diagnosing degradation degrees. Here we review available methods for monitoring zooplankton biodiversity. We propose possible solutions for existing technical issues.
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Affiliation(s)
- Wei Xiong
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xun Du
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
| | - Xingyu Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- College of Resources, Environment and Tourism, Capital Normal University, 105 West Third Ring Road, Haidian District, Beijing, 100048, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
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46
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Hajibabaei M, Porter TM, Robinson CV, Baird DJ, Shokralla S, Wright MTG. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS One 2019; 14:e0225409. [PMID: 31830042 PMCID: PMC6907778 DOI: 10.1371/journal.pone.0225409] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022] Open
Abstract
Biomonitoring programs have evolved beyond the sole use of morphological identification to determine the composition of invertebrate species assemblages in an array of ecosystems. The application of DNA metabarcoding in freshwater systems for assessing benthic invertebrate communities is now being employed to generate biological information for environmental monitoring and assessment. A possible shift from the extraction of DNA from net-collected bulk benthic samples to its extraction directly from water samples for metabarcoding has generated considerable interest based on the assumption that taxon detectability is comparable when using either method. To test this, we studied paired water and benthos samples from a taxon-rich wetland complex, to investigate differences in the detection of arthropod taxa from each sample type. We demonstrate that metabarcoding of DNA extracted directly from water samples is a poor surrogate for DNA extracted from bulk benthic samples, focusing on key bioindicator groups. Our results continue to support the use of bulk benthic samples as a basis for metabarcoding-based biomonitoring, with nearly three times greater total richness in benthic samples compared to water samples. We also demonstrated that few arthropod taxa are shared between collection methods, with a notable lack of key bioindicator EPTO taxa in the water samples. Although species coverage in water could likely be improved through increased sample replication and/or increased sequencing depth, benthic samples remain the most representative, cost-effective method of generating aquatic compositional information via metabarcoding.
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Affiliation(s)
- Mehrdad Hajibabaei
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Teresita M. Porter
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada
| | - Chloe V. Robinson
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Donald J. Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Shadi Shokralla
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Michael T. G. Wright
- Centre for Biodiversity Genomics and Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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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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48
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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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49
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Muha TP, Skukan R, Borrell YJ, Rico JM, Garcia de Leaniz C, Garcia‐Vazquez E, Consuegra S. Contrasting seasonal and spatial distribution of native and invasive Codium seaweed revealed by targeting species-specific eDNA. Ecol Evol 2019; 9:8567-8579. [PMID: 31410262 PMCID: PMC6686311 DOI: 10.1002/ece3.5379] [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: 02/21/2019] [Revised: 05/20/2019] [Accepted: 05/28/2019] [Indexed: 11/25/2022] Open
Abstract
AIM Codium fragile, an invasive seaweed, has spread widely during the last century, impacting on local seaweed communities through competition and disturbance. Early detection of C. fragile can help on its control and management. Environmental DNA (eDNA) has proved successful for early detection of aquatic invasive species but its potential use for seaweed remains understudied. We used a species-specific eDNA qPCR approach to investigate the spatial distribution, abundance, and coexistence of the invasive C. fragile and three native Codium species (Codium vermilara, Codium tomentosum, and Codium decorticatum) in the Cantabrian Sea. LOCATION Bay of Biscay, Northern Atlantic Coast of the Iberian Peninsula; two ports, a beach and a rocky cliff. METHODS We designed species-specific primers in barcoding regions targeting short fragments of the rbcL gene for the invasive Codium species, and the elongation factor Tu (tufA) gene for the native species, to assess their spatial and seasonal distributions using quantitative real-time PCR in samples collected during summer, autumn, and winter. RESULTS We found seasonal differences in the presence of the invasive Codium fragile and two of the native Codium species, but did not detect C. decorticatum at any point. Species distribution patterns produced with qPCR targeting species-specific eDNA coincided with the known distribution based on previous conventional sampling, with a seasonal alternance of C. fragile and C. vermilara, and a marked dominance of invasive C. fragile in ports, which are known hotspots for invasive species. MAIN CONCLUSIONS Our results demonstrate the utility of using eDNA for early detection and monitoring of invasive seaweed. Native and invasive Codium spp. displayed significant seasonal and spatial differentiation that needs to be taken into account in risk management. Regular monitoring of ports and adjacent areas using eDNA should help to assess the potential expansion of invasive Codium and the need for management interventions to avoid the displacement of native seaweed.
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Affiliation(s)
| | | | | | - José M. Rico
- Department of Biology of Organisms and Systems (BOS)University of OviedoOviedoSpain
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50
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Dufresnes C, Déjean T, Zumbach S, Schmidt BR, Fumagalli L, Ramseier P, Dubey S. Early detection and spatial monitoring of an emerging biological invasion by population genetics and environmental DNA metabarcoding. CONSERVATION SCIENCE AND PRACTICE 2019. [DOI: 10.1111/csp2.86] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Christophe Dufresnes
- Hintermann & Weber SA Montreux Switzerland
- Laboratory for Conservation Biology, Department of Ecology and EvolutionUniversity of Lausanne Lausanne Switzerland
| | | | | | - Benedikt R. Schmidt
- Info fauna—karch, UNiMail Neuchâtel Switzerland
- Institut für Evolutionsbiologie und UmweltwissenschaftenUniversität Zürich Zürich Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology, Department of Ecology and EvolutionUniversity of Lausanne Lausanne Switzerland
| | | | - Sylvain Dubey
- Hintermann & Weber SA Montreux Switzerland
- Laboratory for Conservation Biology, Department of Ecology and EvolutionUniversity of Lausanne Lausanne Switzerland
- Agrosustain SA Nyon Switzerland
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