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Wilcox TM, Kronenberger JA, Young MK, Mason DH, Franklin TW, Schwartz MK. The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa. Mol Ecol Resour 2024; 24:e13932. [PMID: 38263813 DOI: 10.1111/1755-0998.13932] [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: 02/23/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Taxon-specific quantitative PCR (qPCR) assays are commonly used for environmental DNA sampling-based inference of animal presence. These assays require thorough validation to ensure that amplification truly indicates detection of the target taxon, but a thorough validation is difficult when there are potentially many non-target taxa, some of which may have incomplete taxonomies. Here, we use a previously published, quantitative model of cross-amplification risk to describe a framework for assessing qPCR assay specificity when there is missing information and it is not possible to assess assay specificity for each individual non-target confamilial. In this framework, we predict assay specificity against unsampled taxa (non-target taxa without sequence data available) using the sequence information that is available for other confamilials. We demonstrate this framework using four case study assays for: (1) An endemic, freshwater arthropod (meltwater stonefly; Lednia tumana), (2) a globally distributed, marine ascidian (Didemnum perlucidum), (3) a continentally distributed freshwater crustacean (virile crayfish; Faxonius virilis, deanae and nais species complex) and (4) a globally distributed freshwater teleost (common carp; Cyprinus carpio and its close relative C. rubrofuscus). We tested the robustness of our approach to missing information by simulating application of our framework for all possible subsamples of 20-all non-target taxa. Our results suggest that the modelling framework results in estimates which are largely concordant with observed levels of cross-amplification risk using all available sequence data, even when there are high levels of data missingness. We explore potential limitations and extensions of this approach for assessing assay specificity and provide users with an R Markdown template for generating reproducible reports to support their own assay validation efforts.
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Affiliation(s)
- Taylor M Wilcox
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - John A Kronenberger
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Young
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Daniel H Mason
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Thomas W Franklin
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Schwartz
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
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2
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Ellis MR, Clark ZSR, Treml EA, Brown MS, Matthews TG, Pocklington JB, Stafford-Bell RE, Bott NJ, Nai YH, Miller AD, Sherman CDH. Detecting marine pests using environmental DNA and biophysical models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151666. [PMID: 34793806 DOI: 10.1016/j.scitotenv.2021.151666] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
The spread of marine pests is occurring at record rates due to globalisation and increasing trade. Environmental DNA (eDNA) is an emerging tool for pest surveillance, allowing for the detection of genetic material shed by organisms into the environment. However, factors influencing the spatial and temporal detection limits of eDNA in marine environments are poorly understood. In this study we use eDNA assays to assess the invasive ranges of two marine pests in south-eastern Australia, the kelp Undaria pinnatifida and the seastar Asterias amurensis. We explored the temporal and spatial detection limits of eDNA under different oceanographic conditions by combining estimates of eDNA decay with biophysical modelling. Positive eDNA detections at several new locations indicate the invasive range of both pest species is likely to be wider than currently assumed. Environmental DNA decay rates were similar for both species, with a decay rate constant of 0.035 h-1 for U. pinnatifida, and a decay rate constant of 0.041 h-1 for A. amurensis, resulting in a 57-73% decrease in eDNA concentrations in the first 24 h and decaying beyond the limits of detection after 3-4 days. Biophysical models informed by eDNA decay profiles indicate passive transport of eDNA up to a maximum of 10 to 20 km from its source, with a ~90-95% reduction in eDNA concentration within 1-3 km from the source, depending on local oceanography. These models suggest eDNA signals are likely to be highly localised, even in complex marine environments. This was confirmed with spatially replicated eDNA sampling around an established U. pinnatifida population indicating detection limits of ~750 m from the source. This study highlights the value of eDNA methods for marine pest surveillance and provides a much-needed description of the spatio-temporal detection limits of eDNA under different oceanographic conditions.
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Affiliation(s)
- Morgan R Ellis
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Zach S R Clark
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Eric A Treml
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Morgan S Brown
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Ty G Matthews
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Jacqueline B Pocklington
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Environment and Science Division, Parks Victoria, Melbourne, Victoria 3000, Australia
| | - Richard E Stafford-Bell
- Department of Jobs, Precincts and Regions, 475 Mickleham Road, Attwood, Vic. 3049, Australia
| | - Nathan J Bott
- School of Science, RMIT University, PO Box 71, Bundoora, VIC 3083, Australia
| | - Yi Heng Nai
- Centre for Regional and Rural Futures, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Victoria, 3220, Australia
| | - Adam D Miller
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia.
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3
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Couton M, Lévêque L, Daguin-Thiébaut C, Comtet T, Viard F. Water eDNA metabarcoding is effective in detecting non-native species in marinas, but detection errors still hinder its use for passive monitoring. BIOFOULING 2022; 38:367-383. [PMID: 35575060 DOI: 10.1080/08927014.2022.2075739] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Marinas are high-priority targets for marine non-indigenous species (NIS), where they compose a large portion of the biofouling communities. The practicality of water samples collection makes environmental DNA (eDNA) metabarcoding an interesting tool for routine NIS surveys. Here the effectiveness of water-eDNA-metabarcoding to identify biofouling NIS, in 10 marinas from western France, was examined. Morphological identification of specimens collected in quadrats brought out 18 sessile benthic NIS beneath floating pontoons. Water-eDNA-metabarcoding detected two thirds of them, failing to detect important NIS. However, sampling and bioinformatics filtering steps can be optimized to identify more species. In addition, this method allowed the detection of additional NIS from neighboring micro-habitats. Caution should, however, be taken when reporting putative novel NIS, because of errors in species assignment. This work highlights that water-eDNA-metabarcoding is effective for active (targeted) NIS surveys and could be significantly improved for its further use in marine NIS passive surveys.
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Affiliation(s)
- Marjorie Couton
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Laurent Lévêque
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Thierry Comtet
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Frédérique Viard
- Sorbonne Université, CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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4
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Cowart DA, Murphy KR, Cheng CHC. Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction. Methods Mol Biol 2022; 2498:225-251. [PMID: 35727547 DOI: 10.1007/978-1-0716-2313-8_11] [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] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.
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Affiliation(s)
- Dominique A Cowart
- Company for Open Ocean Observations and Logging (COOOL), Saint Leu, La Réunion, France
| | - Katherine R Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C-H Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana - Champaign, Urbana, IL, USA.
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5
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Gargan LM, Brooks PR, Vye SR, Ironside JE, Jenkins SR, Crowe TP, Carlsson J. The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02672-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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6
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Use of environmental DNA in early detection of Mnemiopsis leidyi in UK coastal waters. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02650-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Zhang Z, Capinha C, Karger DN, Turon X, MacIsaac HJ, Zhan A. Impacts of climate change on geographical distributions of invasive ascidians. MARINE ENVIRONMENTAL RESEARCH 2020; 159:104993. [PMID: 32662432 DOI: 10.1016/j.marenvres.2020.104993] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
Ocean warming associated with global climate change renders marine ecosystems susceptible to biological invasions. Here, we used species distribution models to project habitat suitability for eight invasive ascidians under present-day and future climate scenarios. Distance to shore and maximum sea surface temperature were identified as the most important variables affecting species distributions. Results showed that eight ascidians might respond differently to future climate change. Alarmingly, currently colonized areas are much smaller than predicted, suggesting ascidians may expand their invasive ranges. Areas such as Americas, Europe and Western Pacific have high risks of receiving new invasions. In contrast, African coasts, excluding the Mediterranean side, are not prone to new invasions, likely due to the high sea surface temperature there. Our results highlight the importance of climate change impacts on future invasions and the need for accurate modelling of invasion risks, which can be used as guides to develop management strategies.
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Affiliation(s)
- Zhixin Zhang
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo, 108-8477, Japan
| | - César Capinha
- Centro de Estudos Geográficos, Instituto de Geografia e Ordenamento do Território - IGOT, Universidade de Lisboa, Rua Branca Edmée Marques, 1600-276, Lisboa, Portugal
| | - Dirk N Karger
- Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Xavier Turon
- Centre for Advanced Studies of Blanes (CEAB, CSIC), Blanes, Catalonia, Spain
| | - Hugh J MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Kunming, China; Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
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8
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Trujillo-González A, Becker JA, Huerlimann R, Saunders RJ, Hutson KS. Can environmental DNA be used for aquatic biosecurity in the aquarium fish trade? Biol Invasions 2019. [DOI: 10.1007/s10530-019-02152-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water. Sci Rep 2019; 9:11559. [PMID: 31399606 PMCID: PMC6689084 DOI: 10.1038/s41598-019-47899-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022] Open
Abstract
Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.
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10
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Deiner K, Lopez J, Bourne S, Holman L, Seymour M, Grey EK, Lacoursière A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM. Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.28963] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol in these environments, seawater samples were collected in a commercial port and methodologies for concentrating and purifying eDNA were tested for their effect on eukaryotic DNA yield and subsequent richness of Operational Taxonomic Units (OTUs). Different filter materials [Cellulose Nitrate (CN) and Glass Fibre (GF)], with different pore sizes (0.5 µm, 0.7 µm and 1.2 µm) and three previously published liquid phase extraction methods were tested. The number of eukaryotic OTUs detected differed by a factor of three amongst the method combinations. The combination of CN filters with phenol-chloroform-isoamyl alcohol extractions recovered a higher amount of eukaryotic DNA and OTUs compared to GF filters and the chloroform-isoamyl alcohol extraction method. Pore size was not independent of filter material but did affect the yield of eukaryotic DNA. For the OTUs assigned to a highly successful non-indigenous species, Styelaclava, the two extraction methods with phenol significantly outperformed the extraction method without phenol; other experimental treatments did not contribute significantly to detection. These results highlight that careful consideration of methods is warranted because choice of filter material and extraction method create false negative detections of marine eukaryotic OTUs and underestimate taxonomic richness from environmental samples.
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11
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Wood SA, Pochon X, Ming W, von Ammon U, Woods C, Carter M, Smith M, Inglis G, Zaiko A. Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm ( Sabella spallanzanii) and club tunicate ( Styela clava) 1. Genome 2018; 62:137-146. [PMID: 30278148 DOI: 10.1139/gen-2018-0021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular techniques may provide effective tools to enhance marine biosecurity surveillance. Prior to routine implementation, evidence-based consideration of their benefits and limitations is needed. In this study, we assessed the efficiency and practicality of visual diver surveys and real-time PCR assays (targeting DNA and RNA) for detecting two marine invasive species whose infestation levels varied between species and location: Sabella spallanzanii and Styela clava. Filtered water samples (n = 171) were collected in parallel with dive surveys at two locations as part of the New Zealand Marine High Risk Site Surveillance programme: Nelson Harbour (27 sites) and Waitemata Harbour (30 sites). Diver surveys resulted in a greater number of detections compared to real-time PCR: S. clava - 21 versus 5 sites in Nelson, 6 versus 1 in Auckland; S. spallanzanii - 18 versus 10 in Auckland, no detections in Nelson. Occupancy modelling derived detection probabilities for the real-time PCR for S. clava were low (14%), compared to S. spallanzanii (66%). This could be related to abundances, or species-specific differences in DNA shedding. Only one RNA sample was positive, suggesting that most detections were from extracellular DNA or non-viable fragments. While molecular methods cannot yet replace visual observations, this study shows they provide useful complementary information.
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Affiliation(s)
- Susanna A Wood
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,c Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Witold Ming
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Ulla von Ammon
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,b School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chris Woods
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Megan Carter
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Matt Smith
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Graeme Inglis
- d National Institute of Water & Atmospheric Research Ltd., New Zealand
| | - Anastasija Zaiko
- a Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,b School of Biological Sciences, University of Auckland, Auckland, New Zealand
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12
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Bourne SD, Hudson J, Holman LE, Rius M. Marine Invasion Genomics: Revealing Ecological and Evolutionary Consequences of Biological Invasions. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Wangensteen OS, Cebrian E, Palacín C, Turon X. Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding. MARINE POLLUTION BULLETIN 2018; 127:54-66. [PMID: 29475694 DOI: 10.1016/j.marpolbul.2017.11.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 11/12/2017] [Accepted: 11/15/2017] [Indexed: 06/08/2023]
Abstract
We analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.
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Affiliation(s)
- Owen S Wangensteen
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Emma Cebrian
- Aquatic Ecology Institute, University of Girona, Campus Montilivi, Girona, Spain
| | - Creu Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute (IRBio), University of Barcelona, Barcelona, Spain
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Blanes (Girona), Spain.
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14
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Wood SA, Zaiko A, Richter I, Inglis GJ, Pochon X. Development of a real-time polymerase chain reaction assay for the detection of the invasive Mediterranean fanworm, Sabella spallanzanii, in environmental samples. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:17373-17382. [PMID: 28589279 DOI: 10.1007/s11356-017-9357-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
The Mediterranean fanworm, Sabella spallanzanii Gmelin 1791, was first detected in the Southern Hemisphere in the 1990s and is now abundant in many parts of southern Australia and in several locations around northern New Zealand. Once established, it can proliferate rapidly, reaching high densities with potential ecological and economic impacts. Early detection of new S. spallanzanii incursions is important to prevent its spread, guide eradication or control efforts and to increase knowledge on the species' dispersal pathways. In this study, we developed a TaqMan probe real-time polymerase chain reaction assay targeting a region of the mitochondrial cytochrome oxidase I gene. The assay was validated in silico and in vitro using DNA from New Zealand and Australian Sabellidae with no cross-reactivity detected. The assay has a linear range of detection over seven orders of magnitude with a limit of detection reached at 12.4 × 10-4 ng/μL of DNA. We analysed 145 environmental (water, sediment and biofouling) samples and obtained positive detections only from spiked samples and those collected at a port where S. spallanzanii is known to be established. This assay has the potential to enhance current morphological and molecular-based methods, through its ability to rapidly and accurately identify S. spallanzanii in environmental samples.
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Affiliation(s)
- Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.
- Environmental Research Institute, University of Waikato, Hamilton, New Zealand.
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Marine Science and Technology Centre, Klaipeda University, Klaipeda, Lithuania
| | - Ingrid Richter
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Graeme J Inglis
- National Institute of Water and Atmospheric Research Ltd, Christchurch, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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15
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Darling JA, Galil BS, Carvalho GR, Rius M, Viard F, Piraino S. Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems. MARINE POLICY 2017; 85:56-64. [PMID: 29681680 PMCID: PMC5909192 DOI: 10.1016/j.marpol.2017.08.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The European Union's Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain "Good Environmental Status" for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, United States Environmental
Protection Agency, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711,
USA
- Corresponding author.
(J.A. Darling)
| | - Bella S. Galil
- The Steinhardt Museum of Natural History, Israel National Center for
Biodiversity Studies, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Marc Rius
- Ocean and Earth Science, National Oceanography Centre, University of
Southampton, UK
- Centre for Ecological Genomics and Wildlife Conservation, University
of Johannesburg, South Africa
| | - Frédérique Viard
- Sorbonne Université, Université Paris 06, CNRS, UMR
7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff,
France
| | - Stefano Piraino
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali,
Università del Salento, Lecce, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare
(CoNISMa), Roma, Italy
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