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Rishan ST, Kline RJ, Rahman MS. Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution. CHEMOSPHERE 2024; 351:141238. [PMID: 38242519 DOI: 10.1016/j.chemosphere.2024.141238] [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: 07/04/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
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2
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Simpson TJS, Wellington CM, Lukehurst SS, Huerlimann R, Veilleux H, Snow M, Dias J, McDonald JI. Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica ( Crustacea, Portunidae). PeerJ 2023; 11:e15522. [PMID: 37334135 PMCID: PMC10269569 DOI: 10.7717/peerj.15522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica. In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross amplify with other closely related species. Field samples and environmental samples spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments.
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Affiliation(s)
- Tiffany JS Simpson
- Conservation and Fisheries Directorate, Ascension Island Government, Georgetown, Ascension Island, South Atlantic, United Kingdom
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University of Technology, Perth, Western Australia, Australia
| | - Claire M. Wellington
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD), Perth, Western Australia, Australia
| | - Sherralee S. Lukehurst
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University of Technology, Perth, Western Australia, Australia
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Roger Huerlimann
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Heather Veilleux
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Ecometrix Incorporated, Mississauga, Ontario, Canada
| | - Michael Snow
- Genotyping Australia, Perth, Western Australia, Australia
| | - Joana Dias
- School of Biological, Environmental and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Justin I. McDonald
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD), Perth, Western Australia, Australia
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Baroja U, Garin I, Vallejo N, Caro A, Ibáñez C, Basso A, Goiti U. Molecular assays to reliably detect and quantify predation on a forest pest in bats faeces. Sci Rep 2022; 12:2243. [PMID: 35145165 PMCID: PMC8831491 DOI: 10.1038/s41598-022-06195-7] [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: 08/07/2021] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Targeted molecular methods such as conventional PCR (cPCR) and quantitative PCR (qPCR), combined with species-specific primers and probes, are widely applied for pest species detection. Besides, the potential of qPCR to quantify DNA in samples makes it an invaluable molecular tool to infer the predation levels on specific prey by analysing predators’ stools. Nevertheless, studies on the diet of bats failed to find any empirical relationship, and it remains to be evaluated. Thus, we developed and evaluated two species-specific PCR assays to detect and quantify DNA of a major forest pest, the pine processionary, Thaumetopoea pityocampa, in bats’ faeces. Further, we empirically compared a range of different known DNA concentrations (input) of the target species mixed with mocks and bat faecal samples against DNA abundances yielded by qPCR (output) for a quantitative assessment. Overall, cPCR showed a lower detection rate than qPCR, but augmenting the replicate effort from one to three replicates led to a greater increase in the detection rate of the cPCR (from 57 to 80%) than the qPCR (from 90 to 99%). The quantitative experiment results showed a highly significant correlation between the input and output DNA concentrations (t = 10.84, p < 0.001) with a mean slope value of 1.05, indicating the accuracy of our qPCR assay to estimate DNA abundance of T. pityocampa in bat faeces. The framework of this study can be taken as a model to design similar assays applicable to other species of interest, such as agricultural pests or insects of public health concern.
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Affiliation(s)
- Unai Baroja
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain.
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
| | - Nerea Vallejo
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
| | - Amaia Caro
- Department of Zoology and Animal Cell Biology, Faculty of Pharmacy, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Basque Country, Spain
| | - Carlos Ibáñez
- Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avenida Américo Vespucio 26, 41092, Seville, Spain
| | - Andrea Basso
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, 10, 35020, Legnaro, Padova, Italy
| | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology, Faculty of Science, University of the Basque Country, UPV/EHU, Leioa, Basque Country, Spain
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Malashenkov DV, Dashkova V, Zhakupova K, Vorobjev IA, Barteneva NS. Comparative analysis of freshwater phytoplankton communities in two lakes of Burabay National Park using morphological and molecular approaches. Sci Rep 2021; 11:16130. [PMID: 34373491 PMCID: PMC8352915 DOI: 10.1038/s41598-021-95223-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
We analyzed phytoplankton assemblages' variations in oligo-mesotrophic Shchuchie and Burabay lakes using traditional morphological and next-generation sequencing (NGS) approaches. The total phytoplankton biodiversity and abundance estimated by both microscopy and NGS were significantly higher in Lake Burabay than in Lake Shchuchie. NGS of 16S and 18S rRNA amplicons adequately identify phytoplankton taxa only on the genera level, while species composition obtained by microscopic examination was significantly larger. The limitations of NGS analysis could be related to insufficient coverage of freshwater lakes phytoplankton by existing databases, short algal sequences available from current instrumentation, and high homology of chloroplast genes in eukaryotic cells. However, utilization of NGS, together with microscopy allowed us to perform a complete taxonomic characterization of phytoplankton lake communities including picocyanobacteria, often overlooked by traditional microscopy. We demonstrate the high potential of an integrated morphological and molecular approach in understanding the processes of organization in aquatic ecosystem assemblages.
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Affiliation(s)
- Dmitry V. Malashenkov
- grid.428191.70000 0004 0495 7803National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan ,grid.14476.300000 0001 2342 9668Present Address: Department of General Ecology and Hydrobiology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Veronika Dashkova
- grid.428191.70000 0004 0495 7803National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan ,grid.428191.70000 0004 0495 7803School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Kymbat Zhakupova
- grid.428191.70000 0004 0495 7803Core Facilities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ivan A. Vorobjev
- grid.428191.70000 0004 0495 7803National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan ,grid.428191.70000 0004 0495 7803Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Natasha S. Barteneva
- grid.428191.70000 0004 0495 7803National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan ,grid.428191.70000 0004 0495 7803Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan ,grid.428191.70000 0004 0495 7803EREC, Nazarbayev University, Nur-Sultan, Kazakhstan
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Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance. WATER 2021. [DOI: 10.3390/w13081113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.
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Audrézet F, Zaiko A, Lear G, Wood SA, Tremblay LA, Pochon X. Biosecurity implications of drifting marine plastic debris: Current knowledge and future research. MARINE POLLUTION BULLETIN 2021; 162:111835. [PMID: 33220912 DOI: 10.1016/j.marpolbul.2020.111835] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
The introduction and spread of marine non-indigenous species (NIS) and pathogens into new habitats are a major threat to biodiversity, ecosystem services, human health, and can have substantial economic consequences. Shipping is considered the main vector for marine biological invasions; less well understood is the increased spread of marine NIS and pathogens rafting on marine plastic debris (MPD). Despite an increasing research interest and recent progress in characterizing the plastisphere, this manuscript highlights critical knowledge gaps and research priorities towards a better understanding of the biosecurity implications of MPD. We advocate for future research to (i) investigate plastisphere community succession and the factors influencing NIS propagules and pathogens recruitment through robust experimental investigations; (ii) combine microscopy and molecular approaches to effectively assess the presence of specific taxa; (iii) include additional genetic markers to thoroughly characterize the biodiversity associated with MPD and explore the presence of specific marine pests.
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Affiliation(s)
- François Audrézet
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand.
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Louis A Tremblay
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand; School of Biological Sciences, University of Auckland, 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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Zaiko A, Wood SA, Pochon X, Biessy L, Laroche O, Croot P, Garcia-Vazquez E. Elucidating Biodiversity Shifts in Ballast Water Tanks during a Cross-Latitudinal Transfer: Complementary Insights from Molecular Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8443-8454. [PMID: 32436694 DOI: 10.1021/acs.est.0c01931] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, the evolution of ballast water (BW) assemblages across different trophic levels was characterized over a 21 day cross-latitudinal vessel transit using a combination of molecular methods. Triplicate BW samples were collected every second day and size-fractionated (<2.7, 10, >50 μm). Measurements of adenosine triphosphate (ATP) and metabarcoding of environmental nucleic acid (DNA and RNA) analyses, complemented by microscopy and flow cytometry, were performed on each sample. Measured ATP concentrations exhibited high variance between replicates and a strong negative trend in the large (≥50 μm) fraction over the voyage. In concert with microscopy, the metabarcoding data indicated a die-off of larger metazoans during the first week of study and gradual reductions in dinoflagellates and ochrophytes. The ATP and metabarcoding data signaled persistent or increased cellular activity of heterotrophic bacteria and protists in the BW, which was supported by flow cytometry. The metabarcoding showed the presence of active bacteria in all size fractions, suggesting that the sequential filtration approach does not ensure taxonomical differentiation, which has implications for BW quality assessment. Although our data show that ATP and metabarcoding have potential for indicative BW screening for BW compliance monitoring, further research and technological development is needed to improve representativeness of sampling and deliver the unequivocal response criteria required by the international Ballast Water Management Convention.
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Affiliation(s)
- Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
- Marine Research Institute, Klaipeda University, H.Manto 84, 92294 Klaipeda, Lithuania
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- Institute of Marine Science, University of Auckland, Private Bag 349, Warkworth 0941, New Zealand
| | - Laura Biessy
- Coastal and Freshwater Group, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Olivier Laroche
- Benthic Resources, The Norwegian Institute of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Peter Croot
- Irish Centre for Research in Applied Geoscience (iCRAG), Earth and Ocean Sciences, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain
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Hatfield RG, Batista FM, Bean TP, Fonseca VG, Santos A, Turner AD, Lewis A, Dean KJ, Martinez-Urtaza J. The Application of Nanopore Sequencing Technology to the Study of Dinoflagellates: A Proof of Concept Study for Rapid Sequence-Based Discrimination of Potentially Harmful Algae. Front Microbiol 2020; 11:844. [PMID: 32457722 PMCID: PMC7227484 DOI: 10.3389/fmicb.2020.00844] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/08/2020] [Indexed: 01/05/2023] Open
Abstract
Harmful algal blooms (HABs) are a naturally occurring global phenomena that have the potential to impact fisheries, leisure and ecosystems, as well as posing a significant hazard to animal and human health. There is significant interest in the development and application of methodologies to study all aspects of the causative organisms and toxins associated with these events. This paper reports the first application of nanopore sequencing technology for the detection of eukaryotic harmful algal bloom organisms. The MinION sequencing platform from Oxford Nanopore technologies provides long read sequencing capabilities in a compact, low cost, and portable format. In this study we used the MinION to sequence long-range PCR amplicons from multiple dinoflagellate species with a focus on the genus Alexandrium. Primers applicable to a wide range of dinoflagellates were selected, meaning that although the study was primarily focused on Alexandrium the applicability to three additional genera of toxic algae, namely; Gonyaulax, Prorocentrum, and Lingulodinium was also demonstrated. The amplicon generated here spanned approximately 3 kb of the rDNA cassette, including most of the 18S, the complete ITS1, 5.8S, ITS2 and regions D1 and D2 of the 28S. The inclusion of barcode genes as well as highly conserved regions resulted in identification of organisms to the species level. The analysis of reference cultures resulted in over 99% of all sequences being attributed to the correct species with an average identity above 95% from a reference list of over 200 species (see Supplementary Material 1). The use of mock community analysis within environmental samples highlighted that complex matrices did not prevent the ability to distinguish between phylogenetically similar species. Successful identification of causative organisms in environmental samples during natural toxic events further highlighted the potential of the assay. This study proves the suitability of nanopore sequencing technology for taxonomic identification of harmful algal bloom organisms and acquisition of data relevant to the World Health Organisations "one health" approach to marine monitoring.
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Affiliation(s)
- Robert G. Hatfield
- Centre for Environment, Fisheries and Aquaculture Science, Dorset, United Kingdom
| | - Frederico M. Batista
- Centre for Environment, Fisheries and Aquaculture Science, Dorset, United Kingdom
| | | | - Vera G. Fonseca
- Centre for Environment, Fisheries and Aquaculture Science, Dorset, United Kingdom
| | - Andres Santos
- Centre for Environment, Fisheries and Aquaculture Science, Dorset, United Kingdom
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Andrew D. Turner
- Centre for Environment, Fisheries and Aquaculture Science, Dorset, United Kingdom
| | - Adam Lewis
- Centre for Environment, Fisheries and Aquaculture Science, Dorset, United Kingdom
| | - Karl J. Dean
- Centre for Environment, Fisheries and Aquaculture Science, Dorset, United Kingdom
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Huhn M, Madduppa HH, Khair M, Sabrian A, Irawati Y, Anggraini NP, Wilkinson SP, Simpson T, Iwasaki K, Setiamarga DHE, Dias PJ. Keeping up with introduced marine species at a remote biodiversity hotspot: awareness, training and collaboration across different sectors is key. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02126-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Hatfield RG, Bean T, Turner AD, Lees DN, Lowther J, Lewis A, Baker-Austin C. Development of a TaqMan qPCR assay for detection of Alexandrium spp and application to harmful algal bloom monitoring. Toxicon X 2019; 2:100011. [PMID: 32550568 PMCID: PMC7285902 DOI: 10.1016/j.toxcx.2019.100011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/21/2019] [Accepted: 02/24/2019] [Indexed: 11/19/2022] Open
Abstract
The Genus Alexandrium is a widespread dinoflagellate marine phytoplankton that is the primary causative organism causing Paralytic Shellfish Poisoning (PSP) intoxications in European waters. EU food safety directives specify that EU Member States must implement a routine monitoring programme to mitigate risks associated with bio-accumulation of biotoxins by bivalve shellfish, such as those produced by Alexandrium. This strategic drive comprises of both direct testing of bivalve flesh for the presence of regulated toxins and an early warning phytoplankton monitoring programme. In the UK the flesh testing moved away from animal bio-assays to analytical chemistry techniques, whereas phytoplankton monitoring methods have seen little technological advancement since implementation. Methods currently utilize light microscopy and manual enumeration of different algal species. These methods although proven are time consuming, reliant on highly trained staff, have high limits of detection (LOD) with low specificity, unable to reliably identify Alexandrium to species level. The implications of these limitations of the techniques mean that in the case of Alexandrium the LOD is also the action limit and as such it is easy to miss positive samples affecting the efficacy of any early warning strategy. This study outlines the development, preliminary method characterisation, validation and trial implementation of an alternative early warning technique, utilizing quantitative PCR to identify water samples containing Alexandrium cells. The approach outlined in this document, showed an improved correlation with flesh toxicity, improved sensitivity, improved throughput compared to traditional light microscopy methods and there was also good correlation with higher cell abundance samples when compared to the light microscopy results. The application of this approach to routine water samples was explored and was found to demonstrate potential as a corroborative method for use during flesh intoxication episodes. This study offers potential for future improvements in the accuracy and sensitivity of phytoplankton monitoring whilst ensuring continuity of public safety, providing cost savings and offering new research opportunities.
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Affiliation(s)
- Robert G. Hatfield
- Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Timothy Bean
- Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Andrew D. Turner
- Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - David N. Lees
- Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - James Lowther
- Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Adam Lewis
- Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | - Craig Baker-Austin
- Centre for Environment Fisheries and Aquaculture Science, Weymouth, Dorset, UK
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Sow A, Brévault T, Benoit L, Chapuis MP, Galan M, Coeur d'acier A, Delvare G, Sembène M, Haran J. Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding. Sci Rep 2019; 9:3646. [PMID: 30842584 PMCID: PMC6403368 DOI: 10.1038/s41598-019-40243-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/12/2019] [Indexed: 12/26/2022] Open
Abstract
An accurate estimation of parasitism rates and diversity of parasitoids of crop insect pests is a prerequisite for exploring processes leading to efficient natural biocontrol. Traditional methods such as rearing have been often limited by taxonomic identification, insect mortality and intensive work, but the advent of high-throughput sequencing (HTS) techniques, such as DNA metabarcoding, is increasingly seen as a reliable and powerful alternative approach. Little has been done to explore the benefits of such an approach for estimating parasitism rates and parasitoid diversity in an agricultural context. In this study, we compared the composition of parasitoid species and parasitism rates between rearing and DNA metabarcoding of host eggs and larvae of the millet head miner, Heliocheilus albipunctella De Joannis (Lepidoptera, Noctuidae), collected from millet fields in Senegal. We first assessed the detection threshold for the main ten endoparasitoids, by sequencing PCR products obtained from artificial dilution gradients of the parasitoid DNAs in the host moth. We then assessed the potential of DNA metabarcoding for diagnosing parasitism rates in samples collected from the field. Under controlled conditions, our results showed that relatively small quantities of parasitoid DNA (0.07 ng) were successfully detected within an eight-fold larger quantity of host DNA. Parasitoid diversity and parasitism rate estimates were always higher for DNA metabarcoding than for host rearing. Furthermore, metabarcoding detected multi-parasitism, cryptic parasitoid species and differences in parasitism rates between two different sampling sites. Metabarcoding shows promise for gaining a clearer understanding of the importance and complexity of host-parasitoid interactions in agro-ecosystems, with a view to improving pest biocontrol strategies.
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Affiliation(s)
- Ahmadou Sow
- Département de Biologie Animale, FST-UCAD, Dakar, Senegal. .,BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal.
| | - Thierry Brévault
- BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal.,CIRAD, UPR AIDA, F-34398, Montpellier, France.,AIDA, University Montpellier, CIRAD, Montpellier, France
| | - Laure Benoit
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Marie-Pierre Chapuis
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Armelle Coeur d'acier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Gérard Delvare
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
| | - Mbacké Sembène
- Département de Biologie Animale, FST-UCAD, Dakar, Senegal.,BIOPASS, CIRAD-IRD-ISRA-UCAD, Dakar, Senegal
| | - Julien Haran
- CIRAD, CBGP, Montpellier, France.,CBGP, CIRAD, INRA, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France
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Ojaveer H, Galil BS, Carlton JT, Alleway H, Goulletquer P, Lehtiniemi M, Marchini A, Miller W, Occhipinti-Ambrogi A, Peharda M, Ruiz GM, Williams SL, Zaiko A. Historical baselines in marine bioinvasions: Implications for policy and management. PLoS One 2018; 13:e0202383. [PMID: 30114232 PMCID: PMC6095587 DOI: 10.1371/journal.pone.0202383] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The human-mediated introduction of marine non-indigenous species is a centuries- if not millennia-old phenomenon, but was only recently acknowledged as a potent driver of change in the sea. We provide a synopsis of key historical milestones for marine bioinvasions, including timelines of (a) discovery and understanding of the invasion process, focusing on transfer mechanisms and outcomes, (b) methodologies used for detection and monitoring, (c) approaches to ecological impacts research, and (d) management and policy responses. Early (until the mid-1900s) marine bioinvasions were given little attention, and in a number of cases actively and routinely facilitated. Beginning in the second half of the 20th century, several conspicuous non-indigenous species outbreaks with strong environmental, economic, and public health impacts raised widespread concerns and initiated shifts in public and scientific perceptions. These high-profile invasions led to policy documents and strategies to reduce the introduction and spread of non-indigenous species, although with significant time lags and limited success and focused on only a subset of transfer mechanisms. Integrated, multi-vector management within an ecosystem-based marine management context is urgently needed to address the complex interactions of natural and human pressures that drive invasions in marine ecosystems.
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Affiliation(s)
- Henn Ojaveer
- Estonian Marine Institute, University of Tartu, Pärnu, Estonia
| | - Bella S. Galil
- The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - James T. Carlton
- Maritime Studies Program of Williams College and Mystic Seaport, Mystic, Connecticut, United States of America
| | - Heidi Alleway
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| | | | - Maiju Lehtiniemi
- Marine Research Centre, Finnish Environment Institute, Helsinki, Finland
| | - Agnese Marchini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Whitman Miller
- Marine Invasion Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | | | | | - Gregory M. Ruiz
- Marine Invasion Research Laboratory, Smithsonian Environmental Research Center, Edgewater, Maryland, United States of America
| | - Susan L. Williams
- Bodega Marine Laboratory and Department of Evolution and Ecology, University of California at Davis, Bodega Bay, California, United States of America
| | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Marine Research Institute, Klaipeda University, Klaipeda, Lithuania
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13
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PCR-based assay for Mya arenaria detection from marine environmental samples and tracking its invasion in coastal ecosystems. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2018.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Engesmo A, Strand D, Gran-Stadniczeñko S, Edvardsen B, Medlin LK, Eikrem W. Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae). HARMFUL ALGAE 2018; 75:105-117. [PMID: 29778220 DOI: 10.1016/j.hal.2018.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
Blooms of ichthyotoxic microalgae pose a great challenge to the aquaculture industry world-wide, and there is a need for fast and specific methods for their detection and quantification in monitoring programs. In this study, quantitative real-time PCR (qPCR) assays for the detection and enumeration of three ichthyotoxic flagellates: the dinoflagellate Karenia mikimotoi (Miyake & Kominami ex Oda) Hansen & Moestrup and the two raphidophytes Heterosigma akashiwo (Hada) Hada ex Hara & Chihara and Fibrocapsa japonica Toriumi & Takano were developed. Further, a previously published qPCR assay for the dinoflagellate Karlodinium veneficum (Ballantine) Larsen was used. Monthly samples collected for three years (Aug 2009-Jun 2012) in outer Oslofjorden, Norway were analysed, and the results compared with light microscopy cell counts. The results indicate a higher sensitivity and a lower detection limit (down to 1 cell L-1) for both qPCR assays. Qualitative and semi-quantitative results were further compared with those obtained by environmental 454 high throughput sequencing (HTS, metabarcoding) and scanning electron microscopy (SEM) examination from the same samplings. All four species were detected by qPCR and HTS and/or SEM in outer Oslofjorden (Aug 2009-Jun 2012); Karlodinium veneficum was present year-round, whereas Karenia mikimotoi, Heterosigma akashiwo and Fibrocapsa japonica appeared mainly during the autumn in all three years. This is the first observation of Fibrocapsa japonica in Norwegian coastal waters. This species has previously been recorded off the Swedish west coast and German Bight, which may suggest a northward dispersal.
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Affiliation(s)
- Anette Engesmo
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway.
| | - David Strand
- Norwegian Veterinary Institute, P.O. box 750 Sentrum, 0106, Oslo, Norway.
| | | | - Bente Edvardsen
- University of Oslo, Department of Biosciences, P. O. box 1066 Blindern, 0316, Oslo, Norway.
| | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, Pl1 2PB, United Kingdom.
| | - Wenche Eikrem
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway; University of Oslo, Department of Biosciences, P. O. box 1066 Blindern, 0316, Oslo, Norway.
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15
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Borrell YJ, Miralles L, Mártinez-Marqués A, Semeraro A, Arias A, Carleos CE, García-Vázquez E. Metabarcoding and post-sampling strategies to discover non-indigenous species: A case study in the estuaries of the central south Bay of Biscay. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2017.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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Darling JA, Frederick RM. Nucleic acids-based tools for ballast water surveillance, monitoring, and research. JOURNAL OF SEA RESEARCH 2018; 133:43-52. [PMID: 30147432 PMCID: PMC6104837 DOI: 10.1016/j.seares.2017.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Understanding the risks of biological invasion posed by ballast water-whether in the context of compliance testing, routine monitoring, or basic research-is fundamentally an exercise in biodiversity assessment, and as such should take advantage of the best tools available for tackling that problem. The past several decades have seen growing application of genetic methods for the study of biodiversity, driven in large part by dramatic technological advances in nucleic acids analysis. Monitoring approaches based on such methods have the potential to increase dramatically sampling throughput for biodiversity assessments, and to improve on the sensitivity, specificity, and taxonomic accuracy of traditional approaches. The application of targeted detection tools (largely focused on PCR but increasingly incorporating novel probe-based methodologies) has led to a paradigm shift in rare species monitoring, and such tools have already been applied for early detection in the context of ballast water surveillance. Rapid improvements in community profiling approaches based on high throughput sequencing (HTS) could similarly impact broader efforts to catalogue biodiversity present in ballast tanks, and could provide novel opportunities to better understand the risks of biotic exchange posed by ballast water transport-and the effectiveness of attempts to mitigate those risks. These various approaches still face considerable challenges to effective implementation, depending on particular management or research needs. Compliance testing, for instance, remains dependent on accurate quantification of viable target organisms; while tools based on RNA detection show promise in this context, the demands of such testing require considerable additional investment in methods development. In general surveillance and research contexts, both targeted and community-based approaches are still limited by various factors: quantification remains a challenge (especially for taxa in larger size classes), gaps in nucleic acids reference databases are still considerable, uncertainties in taxonomic assignment methods persist, and many applications have not yet matured sufficiently to offer standardized methods capable of meeting rigorous quality assurance standards. Nevertheless, the potential value of these tools, their growing utilization in biodiversity monitoring, and the rapid methodological advances over the past decade all suggest that they should be seriously considered for inclusion in the ballast water surveillance toolkit.
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Affiliation(s)
- John A. Darling
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Raymond M. Frederick
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, Edison, NJ, USA
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17
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Simpson TJS, Dias PJ, Snow M, Muñoz J, Berry T. Real-time PCR detection of Didemnum perlucidum (Monniot, 1983) and Didemnum vexillum (Kott, 2002) in an applied routine marine biosecurity context. Mol Ecol Resour 2016; 17:443-453. [PMID: 27483456 DOI: 10.1111/1755-0998.12581] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/30/2016] [Accepted: 07/11/2016] [Indexed: 11/28/2022]
Abstract
Prevention and early detection are well recognized as the best strategies for minimizing the risks posed by nonindigenous species (NIS) that have the potential to become marine pests. Central to this is the ability to rapidly and accurately identify the presence of NIS, often from complex environmental samples like biofouling and ballast water. Molecular tools have been increasingly applied to assist with the identification of NIS and can prove particularly useful for taxonomically difficult groups like ascidians. In this study, we have developed real-time PCR assays suited to the specific identification of the ascidians Didemnum perlucidum and Didemnum vexillum. Despite being recognized as important global pests, this is the first time specific molecular detection methods have been developed that can support the early identification and detection of these species from a broad range of environmental sample types. These fast, robust and high-throughput assays represent powerful tools for routine marine biosecurity surveillance, as detection and confirmation of the early presence of species could assist in the timely establishment of emergency responses and control strategies. This study applied the developed assays to confirm the ability to detect Didemnid eDNA in water samples. While previous work has focused on detection of marine larvae from water samples, the development of real-time PCR assays specifically aimed at detecting eDNA of sessile invertebrate species in the marine environment represents a world first and a significant step forwards in applied marine biosecurity surveillance. Demonstrated success in the detection of D. perlucidum eDNA from water samples at sites where it could not be visually identified suggests value in incorporating such assays into biosecurity survey designs targeting Didemnid species.
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Affiliation(s)
- Tiffany J S Simpson
- Department of Fisheries, Government of Western Australia, Western Australia Fisheries and Marine Research Laboratories, PO Box 20, North Beach, WA, 6920, Australia.,School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - P Joana Dias
- Department of Fisheries, Government of Western Australia, Western Australia Fisheries and Marine Research Laboratories, PO Box 20, North Beach, WA, 6920, Australia.,School of Animal Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Michael Snow
- Department of Fisheries, Government of Western Australia, Western Australia Fisheries and Marine Research Laboratories, PO Box 20, North Beach, WA, 6920, Australia
| | - Julieta Muñoz
- Department of Fisheries, Government of Western Australia, Western Australia Fisheries and Marine Research Laboratories, PO Box 20, North Beach, WA, 6920, Australia
| | - Tina Berry
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Kent Street, Bentley, WA, 6102, Australia
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18
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A sensitive environmental DNA (eDNA) assay leads to new insights on Ruffe (Gymnocephalus cernua) spread in North America. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1209-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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Zaiko A, Martinez JL, Ardura A, Clusa L, Borrell YJ, Samuiloviene A, Roca A, Garcia-Vazquez E. Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring. MARINE ENVIRONMENTAL RESEARCH 2015; 112:64-72. [PMID: 26174116 DOI: 10.1016/j.marenvres.2015.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 06/20/2015] [Accepted: 07/01/2015] [Indexed: 06/04/2023]
Abstract
Detecting the presence of potential invasive species in ballast water is a priority for preventing their spread into new environments. Next generation sequencing technologies are being increasingly used for exploring and assessing biodiversity from environmental samples. Here we apply high throughput sequencing from DNA extracted from ballast water (BW) samples employing two different platforms, Ion Torrent and 454, and compare the putative species catalogues from the resulting Operational Taxonomic Units (OTU). Water samples were taken from the RV Polastern ballast tank in five different days between the second and the twentieth navigation day. Pronounced decrease of oxygen concentration and increase of temperature occurred in the BW during this time, coincident with a progressively higher proportion of unassigned OTU and short reads indicating DNA degradation. Discrepancy between platforms for species catalogues was consistent with previously published bias in AT-rich sequences for Ion Torrent platform. Some putative species detected from the two platforms increased in frequency during the Polarstern travel, which suggests they were alive and therefore tolerant to adverse conditions. OTU assigned to the highly invasive red alga Polysiphonia have been detected at low but increasing frequency from the two platforms. Although in this moment NGST could not replace current methods of sampling, sorting and individual taxonomic identification of BW biota, it has potential as an exploratory methodology especially for detecting scarce species.
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Affiliation(s)
- Anastasija Zaiko
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand
| | - Jose L Martinez
- Sequencing Unit, Edificio Severo Ochoa, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Alba Ardura
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Laura Clusa
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Yaisel J Borrell
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Aurelija Samuiloviene
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Department of Ecology and Biology, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania
| | - Agustín Roca
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Eva Garcia-Vazquez
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain.
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20
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Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, Turon X. Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons. PLoS One 2015; 10:e0139633. [PMID: 26436773 PMCID: PMC4593591 DOI: 10.1371/journal.pone.0139633] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/14/2015] [Indexed: 12/22/2022] Open
Abstract
Marine sediments are home to one of the richest species pools on Earth, but logistics and a dearth of taxonomic work-force hinders the knowledge of their biodiversity. We characterized α- and β-diversity of deep-sea assemblages from submarine canyons in the western Mediterranean using an environmental DNA metabarcoding. We used a new primer set targeting a short eukaryotic 18S sequence (ca. 110 bp). We applied a protocol designed to obtain extractions enriched in extracellular DNA from replicated sediment corers. With this strategy we captured information from DNA (local or deposited from the water column) that persists adsorbed to inorganic particles and buffered short-term spatial and temporal heterogeneity. We analysed replicated samples from 20 localities including 2 deep-sea canyons, 1 shallower canal, and two open slopes (depth range 100–2,250 m). We identified 1,629 MOTUs, among which the dominant groups were Metazoa (with representatives of 19 phyla), Alveolata, Stramenopiles, and Rhizaria. There was a marked small-scale heterogeneity as shown by differences in replicates within corers and within localities. The spatial variability between canyons was significant, as was the depth component in one of the canyons where it was tested. Likewise, the composition of the first layer (1 cm) of sediment was significantly different from deeper layers. We found that qualitative (presence-absence) and quantitative (relative number of reads) data showed consistent trends of differentiation between samples and geographic areas. The subset of exclusively benthic MOTUs showed similar patterns of β-diversity and community structure as the whole dataset. Separate analyses of the main metazoan phyla (in number of MOTUs) showed some differences in distribution attributable to different lifestyles. Our results highlight the differentiation that can be found even between geographically close assemblages, and sets the ground for future monitoring and conservation efforts on these bottoms of ecological and economic importance.
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Affiliation(s)
- Magdalena Guardiola
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - María Jesús Uriz
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Pierre Taberlet
- Université Grenoble Alpes, Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Eric Coissac
- Université Grenoble Alpes, Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
- Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Ecologie Alpine (LECA), F-38000, Grenoble, France
| | - Owen Simon Wangensteen
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- Department of Animal Biology, University of Barcelona, Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
- * E-mail:
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21
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Egan SP, Grey E, Olds B, Feder JL, Ruggiero ST, Tanner CE, Lodge DM. Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4113-4121. [PMID: 25686279 DOI: 10.1021/es5058659] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.
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Affiliation(s)
- Scott P Egan
- †Department of BioSciences, Rice University, Houston, Texas 77005, United States
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Erin Grey
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ∥College of Science, Governors State University, University Park, Illinois 60484, United States
| | - Brett Olds
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jeffery L Feder
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven T Ruggiero
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Carol E Tanner
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - David M Lodge
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
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22
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Zaiko A, Martinez JL, Schmidt-Petersen J, Ribicic D, Samuiloviene A, Garcia-Vazquez E. Metabarcoding approach for the ballast water surveillance--an advantageous solution or an awkward challenge? MARINE POLLUTION BULLETIN 2015; 92:25-34. [PMID: 25627196 DOI: 10.1016/j.marpolbul.2015.01.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Revised: 01/09/2015] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Abstract
Transfer of organisms with ships' ballast water is recognized as a major pathway of non-indigenous species introduction and addressed in a few recent legislative initiatives. Among other they imply scientific and technical research and monitoring to be conducted in a efficient and reliable way. The recent development of DNA barcoding and metabarcoding technologies opens new opportunities for biodiversity and biosecurity surveillance. In the current study, the performance of metabarcoding approach was assessed in comparison to the conventional (visual) observations, during the en route experimental ballast water survey. Opportunities and limitations of the molecular method were identified from taxonomical datasets rendered by two molecular markers of different degree of universality - the universal cytochrome oxydase sub-unit I gene and a fragment of RuBisCO gene. The cost-efficacy and possible improvements of these methods are discussed for the further successful development and implementation of the approach in ballast water control and NIS surveillance.
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Affiliation(s)
- Anastasija Zaiko
- Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand.
| | - Jose L Martinez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain.
| | - Julia Schmidt-Petersen
- Biology Department, Marine Biology Section, Ghent University, Krijgslaan, 281/S8, B-9000 Gent, Belgium.
| | - Deni Ribicic
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgsons gt. 1, N-7006 Trondheim, Norway.
| | | | - Eva Garcia-Vazquez
- Department of Functional Biology, University of Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain.
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23
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DNA (meta)barcoding of biological invasions: a powerful tool to elucidate invasion processes and help managing aliens. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0854-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Rius M, Turon X, Bernardi G, Volckaert FAM, Viard F. Marine invasion genetics: from spatio-temporal patterns to evolutionary outcomes. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0792-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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25
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Darling JA. Genetic studies of aquatic biological invasions: closing the gap between research and management. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0726-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Pochon X, Bott NJ, Smith KF, Wood SA. Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS One 2013; 8:e73935. [PMID: 24023913 PMCID: PMC3762713 DOI: 10.1371/journal.pone.0073935] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 07/30/2013] [Indexed: 11/19/2022] Open
Abstract
Most surveillance programmes for marine invasive species (MIS) require considerable taxonomic expertise, are laborious, and are unable to identify species at larval or juvenile stages. Therefore, marine pests may go undetected at the initial stages of incursions when population densities are low. In this study, we evaluated the ability of the benchtop GS Junior™ 454 pyrosequencing system to detect the presence of MIS in complex sample matrices. An initial in-silico evaluation of the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear small subunit ribosomal DNA (SSU) genes, found that multiple primer sets (targeting a ca. 400 base pair region) would be required to obtain species level identification within the COI gene. In contrast a single universal primer set was designed to target the V1-V3 region of SSU, allowing simultaneous PCR amplification of a wide taxonomic range of MIS. To evaluate the limits of detection of this method, artificial contrived communities (10 species from 5 taxonomic groups) were created using varying concentrations of known DNA samples and PCR products. Environmental samples (water and sediment) spiked with one or five 160 hr old Asterias amurensis larvae were also examined. Pyrosequencing was able to recover DNA/PCR products of individual species present at greater than 0.64% abundance from all tested contrived communities. Additionally, single A. amurensis larvae were detected from both water and sediment samples despite the co-occurrence of a large array of environmental eukaryotes, indicating an equivalent sensitivity to quantitative PCR. NGS technology has tremendous potential for the early detection of marine invasive species worldwide.
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Affiliation(s)
- Xavier Pochon
- Environmental Technologies, Cawthron Institute, Nelson, New Zealand
- * E-mail:
| | - Nathan J. Bott
- Aquatic Sciences, South Australian Research and Development Institute, Adelaide, Australia
| | - Kirsty F. Smith
- Environmental Technologies, Cawthron Institute, Nelson, New Zealand
| | - Susanna A. Wood
- Environmental Technologies, Cawthron Institute, Nelson, New Zealand
- School of Biological Sciences, University of Waikato, Hamilton, New Zealand
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Greeff MR, Christison KW, Macey BM. Development and preliminary evaluation of a real-time PCR assay for Halioticida noduliformans in abalone tissues. DISEASES OF AQUATIC ORGANISMS 2012; 99:103-117. [PMID: 22691979 DOI: 10.3354/dao02468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Abalone Haliotis midae exhibiting typical clinical signs of tubercle mycosis were discovered in South African culture facilities in 2006, posing a significant threat to the industry. The fungus responsible for the outbreak was identified as a Peronosporomycete, Halioticida noduliformans. Currently, histopathology and gross observation are used to diagnose this disease, but these 2 methods are neither rapid nor sensitive enough to provide accurate and reliable diagnosis. Real-time quantitative PCR (qPCR) is a rapid and reliable method for the detection and quantification of a variety of pathogens, so therefore we aimed to develop a qPCR assay for species-specific detection and quantification of H. noduliformans. Effective extraction of H. noduliformans genomic DNA from laboratory grown cultures, as well as from spiked abalone tissues, was accomplished by grinding samples using a pellet pestle followed by heat lysis in the presence of Chelax-100 beads. A set of oligonucleotide primers was designed to specifically amplify H. noduliformans DNA in the large subunit (LSU) rRNA gene, and tested for cross-reactivity to DNA extracted from related and non-related fungi isolated from seaweeds, crustaceans and healthy abalone; no cross-amplification was detected. When performing PCR assays in an abalone tissue matrix, an environment designed to be a non-sterile simulation of environmental conditions, no amplification occurred in the negative controls. The qPCR assay sensitivity was determined to be approximately 0.28 pg of fungal DNA (~2.3 spores) in a 25 µl reaction volume. Our qPCR technique will be useful for monitoring and quantifying H. noduliformans for the surveillance and management of abalone tubercle mycosis in South Africa.
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Affiliation(s)
- Mariska R Greeff
- Biodiversity and Conservation Biology, University of Western Cape, Bellville, South Africa
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Ebenezer V, Medlin LK, Ki JS. Molecular detection, quantification, and diversity evaluation of microalgae. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:129-142. [PMID: 22200918 DOI: 10.1007/s10126-011-9427-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 12/02/2011] [Indexed: 05/31/2023]
Abstract
This study reviews the available molecular methods and new high-throughput technologies for their practical use in the molecular detection, quantification, and diversity assessment of microalgae. Molecular methods applied to other groups of organisms can be adopted for microalgal studies because they generally detect universal biomolecules, such as nucleic acids or proteins. These methods are primarily related to species detection and discrimination among various microalgae. Among current molecular methods, some molecular tools are highly valuable for small-scale detection [e.g., single-cell polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), and biosensors], whereas others are more useful for large-scale, high-throughput detection [e.g., terminal restriction length polymorphism, isothermal nucleic acid sequence-based amplification, loop-mediated isothermal amplification, microarray, and next generation sequencing (NGS) techniques]. Each molecular technique has its own strengths in detecting microalgae, but they may sometimes have limitations in terms of detection of other organisms. Among current technologies, qPCR may be considered the best method for molecular quantification of microalgae. Metagenomic microalgal diversity can easily be achieved by 454 pyrosequencing rather than by the clone library method. Current NGS, third and fourth generation technologies pave the way for the high-throughput detection and quantification of microalgal diversity, and have significant potential for future use in field monitoring.
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Affiliation(s)
- Vinitha Ebenezer
- Department of Green Life Science, College of Convergence, Sangmyung University, Seoul 110-743, South Korea
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Darling JA, Mahon AR. From molecules to management: adopting DNA-based methods for monitoring biological invasions in aquatic environments. ENVIRONMENTAL RESEARCH 2011; 111:978-988. [PMID: 21353670 DOI: 10.1016/j.envres.2011.02.001] [Citation(s) in RCA: 219] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 05/30/2023]
Abstract
Recent technological advances have driven rapid development of DNA-based methods designed to facilitate detection and monitoring of invasive species in aquatic environments. These tools promise to improve on traditional monitoring approaches by enhancing detection sensitivity, reducing analytical turnaround times and monitoring costs, and increasing specificity of target identifications. However, despite the promise of DNA-based monitoring methods, the adoption of these tools in decision-making frameworks remains challenging. Here, rather than explore technical aspects of method development, we examine impediments to effective translation of those methods into management contexts. In addition to surveying current use of DNA-based tools for aquatic invasive species monitoring, we explore potential sources of uncertainty associated with molecular technologies and possibilities for limiting that uncertainty and effectively communicating its implications for decision-making. We pay particular attention to the recent adoption of DNA-based methods for detection of invasive Asian carp species in the United States Great Lakes region, as this example illustrates many of the challenges associated with applying molecular tools to achieve desired management outcomes. Our goal is to provide a useful assessment of the obstacles associated with integrating DNA-based methods into aquatic invasive species management, and to offer recommendations for future efforts aimed at overcoming those obstacles.
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Affiliation(s)
- John A Darling
- United States Environmental Protection Agency, National Exposure Research Laboratory, Molecular Ecology Research Branch, Cincinnati, OH 45268, USA.
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Molecular detection of invasive species in heterogeneous mixtures using a microfluidic carbon nanotube platform. PLoS One 2011; 6:e17280. [PMID: 21364993 PMCID: PMC3041796 DOI: 10.1371/journal.pone.0017280] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 01/27/2011] [Indexed: 11/20/2022] Open
Abstract
Screening methods to prevent introductions of invasive species are critical for the protection of environmental and economic benefits provided by native species and uninvaded ecosystems. Coastal ecosystems worldwide remain vulnerable to damage from aquatic species introductions, particularly via ballast water discharge from ships. Because current ballast management practices are not completely effective, rapid and sensitive screening methods are needed for on-site testing of ships in transit. Here, we describe a detection technology based on a microfluidic chip containing DNA oligonucleotide functionalized carbon nanotubes. We demonstrate the efficacy of the chip using three ballast-transported species either established (Dreissena bugensis) or of potential threat (Eriocheir sinensis and Limnoperna fortuneii) to the Laurentian Great Lakes. With further refinement for on-board application, the technology could lead to real-time ballast water screening to improve ship-specific management and control decisions.
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