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Ruvindy R, Ajani PA, Ashlin S, Hallegraeff G, Klemm K, Bolch CJ, Ugalde S, Van Asten M, Woodcock S, Tesoriero M, Murray SA. An On-Farm Workflow for Predictive Management of Paralytic Shellfish Toxin-Producing Harmful Algal Blooms for the Aquaculture Industry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6924-6933. [PMID: 38608723 PMCID: PMC11044886 DOI: 10.1021/acs.est.3c10502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 04/14/2024]
Abstract
Paralytic shellfish toxins (PSTs) produced by marine dinoflagellates significantly impact shellfish industries worldwide. Early detection on-farm and with minimal training would allow additional time for management decisions to minimize economic losses. Here, we describe and test a standardized workflow based on the detection of sxtA4, an initial gene in the biosynthesis of PSTs. The workflow is simple and inexpensive and does not require a specialized laboratory. It consists of (1) water collection and filtration using a custom gravity sampler, (2) buffer selection for sample preservation and cell lysis for DNA, and (3) an assay based on a region of sxtA, DinoDtec lyophilized quantitative polymerase chain reaction (qPCR) assay. Water samples spiked with Alexandrium catenella showed a cell recovery of >90% when compared to light microscopy counts. The performance of the lysis method (90.3% efficient), Longmire's buffer, and the DinoDtec qPCR assay (tested across a range of Alexandrium species (90.7-106.9% efficiency; r2 > 0.99)) was found to be specific, sensitive, and efficient. We tested the application of this workflow weekly from May 2016 to 30th October 2017 to compare the relationship between sxtA4 copies L-1 in seawater and PSTs in mussel tissue (Mytilus galloprovincialis) on-farm and spatially (across multiple sites), effectively demonstrating an ∼2 week early warning of two A. catenella HABs (r = 0.95). Our tool provides an early, accurate, and efficient method for the identification of PST risk in shellfish aquaculture.
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Affiliation(s)
- Rendy Ruvindy
- School
of Life Sciences, University of Technology
Sydney, Ultimo 2007, Australia
| | - Penelope A. Ajani
- School
of Life Sciences, University of Technology
Sydney, Ultimo 2007, Australia
| | | | - Gustaaf Hallegraeff
- Institute
for Marine and Antarctic Studies, University
of Tasmania, Hobart 7004, Australia
| | - Kerstin Klemm
- Alfred
Wegener Institute for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Christopher J. Bolch
- Institute
for Marine and Antarctic Studies, University
of Tasmania, Hobart 7004, Australia
| | - Sarah Ugalde
- Institute
for Marine and Antarctic Studies, University
of Tasmania, Hobart 7004, Australia
- Centre
for Marine Socioecology, University of Tasmania, Hobart 7004, Australia
| | - Mark Van Asten
- Diagnostic
Technology, Belrose 2085, Australia
- School
of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia
| | - Stephen Woodcock
- School
of Life Sciences, University of Technology
Sydney, Ultimo 2007, Australia
| | - Matthew Tesoriero
- School
of Life Sciences, University of Technology
Sydney, Ultimo 2007, Australia
| | - Shauna A. Murray
- School
of Life Sciences, University of Technology
Sydney, Ultimo 2007, Australia
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2
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Hyung JH, Moon SJ, Kim EJ, Kim DW, Park J. Quantification of Alexandrium catenella (Group I) using sxtA4-based digital PCR for screening of paralytic shellfish toxins in Jinhae-Masan Bay, Korea. MARINE POLLUTION BULLETIN 2024; 200:116048. [PMID: 38271916 DOI: 10.1016/j.marpolbul.2024.116048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024]
Abstract
We employed a detection method to quantify Alexandrium catenella (Group I), one of the causative species for paralytic shellfish poisoning (PSP) in Jinhae-Masan Bay, Korea, targets sxtA4, via chip-based digital PCR. Additionally, we explored the dynamics of Alexandrium during the spring of 2022 using an rDNA-based quantitative PCR (qPCR) assay to enhance the performance of the dPCR assay. In matching dPCR results with PSP monitoring reports, we optimized a cell regulatory threshold of 102 cells L-1, the maximum cell density when shellfish harvesting was permitted, for the dPCR assay. This threshold functioned similar to the PST threshold used in mouse bioassays (MBAs). Furthermore, we validated a total concordance rate of 83.8 % between the two assays for 2020-2022, reaching a maximum of 96.2 % in 2020. Thus, the result of dPCR could complement MBAs, facilitating the early detection of PSP outbreaks.
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Affiliation(s)
- Jun-Ho Hyung
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Republic of Korea.
| | - Seung Joo Moon
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Republic of Korea.
| | - Eun Joo Kim
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Republic of Korea.
| | - Dong Wook Kim
- Food Safety and Processing Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea.
| | - Jaeyeon Park
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Republic of Korea.
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3
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Ayala ZR, Judge S, Anglès S, Greenfield DI. A comparison between the FlowCam 8100, microscopy, and sandwich hybridization assay for quantifying abundances of the saxitoxin-producing dinoflagellate, Alexandrium catenella. HARMFUL ALGAE 2023; 125:102423. [PMID: 37220976 DOI: 10.1016/j.hal.2023.102423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 05/25/2023]
Abstract
Light microscopy, FlowCam, and sandwich hybridization assay (SHA) are three approaches that facilitate the monitoring of harmful algal bloom (HAB) forming phytoplankton. Yet, cross-comparisons among these techniques have not been conducted. This study addressed that gap using the saxitoxin-producing 'red tide' dinoflagellate Alexandrium catenella, a species responsible for blooms and paralytic shellfish poisoning worldwide. To achieve this goal, the dynamic ranges of each technique were compared using A. catenella cultures spanning low (pre-bloom), moderate (bloom), and high (dense bloom) levels. To assess field detection, water samples containing very low (<3 cells mL-1) A. catenella levels were collected from Long Island Sound, USA (Jun-Aug 2021) and evaluated using each method. Field samples were also spiked with A. catenella to high (160 cells mL-1) or low (40 cells mL-1) concentrations. In general, microscopy, FlowCam, and SHA returned comparable A. catenella cell concentrations for all tests. Mean cell concentrations from laboratory intercalibration experiments were not significantly different for any method or concentration (ANOVA, p > 0.05). However, relative to microscopy at times SHA produced non-detect signals <2 cells mL-1 in field samples and the FlowCam slightly underestimated cell concentrations when A. catenella abundances were high in laboratory and field samples. Mean cell concentrations of spike experiments were not significantly different for any test date, sampling location, or method, despite variability among methods within the high concentration treatment (ANOVA, p > 0.05 for all treatments). Findings are relevant to HAB researchers, managers, and public health officials because they help reconcile disparate cell abundance datasets that inform numerical models and enhance HAB monitoring and prediction. Results are also likely broadly applicable to several HAB species.
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Affiliation(s)
- Zabdiel Roldan Ayala
- School of Earth and Environmental Sciences, Queens College, 65-30 Kissena Blvd, 11367 Queens, NY, USA; Advanced Science Research Center at the Graduate Center, 85 St Nicholas Terrace, 10031 New York, NY, USA
| | - Savannah Judge
- Yokogawa Fluid Imaging Technologies, Inc., 200 Enterprise Dr, 04074 Scarborough, ME, USA
| | - Silvia Anglès
- Advanced Science Research Center at the Graduate Center, 85 St Nicholas Terrace, 10031 New York, NY, USA; Division of Integrated Science and Engineering, California Department of Water Resources, 3500 Industrial Blvd., West Sacramento, CA 95691, USA
| | - Dianne I Greenfield
- School of Earth and Environmental Sciences, Queens College, 65-30 Kissena Blvd, 11367 Queens, NY, USA; Advanced Science Research Center at the Graduate Center, 85 St Nicholas Terrace, 10031 New York, NY, USA.
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4
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Einarsson SV, Lowry KE, Lin P, Pickart RS, Ashjian CJ, Chappell PD. Alexandrium on the Alaskan Beaufort Sea shelf: Impact of upwelling in a warming Arctic. HARMFUL ALGAE 2022; 120:102346. [PMID: 36470603 DOI: 10.1016/j.hal.2022.102346] [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: 07/22/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
The harmful algal genus Alexandrium has characteristically been found in temperate and subtropical regions; however recent evidence suggests global warming may be expanding its range into high latitude waters. Alexandrium cysts have previously been documented in the Chukchi Sea and we hypothesize that Alexandrium may be expanding further into the Arctic due to distribution by the Beaufort shelfbreak jet. Here we document the presence of Alexandrium catenella along the Alaskan Beaufort Sea shelf, marking an expansion of its known range. The observations of A. catenella were made using three different methods: FlowCAM imaging, 18S eukaryotic sequencing, and real-time quantitative PCR. Four occupations of a shelf/slope transect spanned the evolution of a strong wind-driven upwelling event over a 5-day period. A nearby mooring provided the physical context for the event, revealing that enhanced easterly winds reversed the Beaufort shelfbreak jet to the west and induced upwelling of colder, denser water onto the outer shelf. A. catenella sequences dominated the surface phytoplankton community at the onset of the upwelling event. This signal vanished during and after the event, likely due to a combination of alongstream advection, cross-stream advection, and wind mixing. These results suggest contrasting physical processes that are both subject to global warming amplification, delivery of warm waters via the Beaufort shelfbreak jet and upwelling, may control the proliferation of this potential harmful alga into the Arctic.
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Affiliation(s)
- Sveinn V Einarsson
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, USA
| | - Kate E Lowry
- Science Philanthropy Alliance, Palo Alto, CA, USA; Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Peigen Lin
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | | | - P Dreux Chappell
- Department of Ocean and Earth Sciences, Old Dominion University, Norfolk, VA, USA.
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5
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Ajani PA, Henriquez-Nunez HF, Verma A, Nagai S, Uchida H, Tesoriero MJ, Farrell H, Zammit A, Brett S, Murray SA. Mapping the development of a Dinophysis bloom in a shellfish aquaculture area using a novel molecular qPCR assay. HARMFUL ALGAE 2022; 116:102253. [PMID: 35710205 DOI: 10.1016/j.hal.2022.102253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/03/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Diarrhetic shellfish toxins produced by certain species of the marine dinoflagellate Dinophysis can accumulate in shellfish in high concentrations, representing a significant food safety issue worldwide. This risk is routinely managed by monitoring programs in shellfish producing areas, however the methods used to detect these harmful marine microbes are not usually automated nor conducted onsite, and are often expensive and require specialized expertise. Here we designed a quantitative real-time polymerase chain reaction (qPCR) assay based on the ITS-5.8S ribosomal region of Dinophysis spp. and evaluated its specificity, efficiency, and sensitivity to detect species belonging to this genus. We designed and tested twenty sets of primers pairs using three species of Dinophysis - D. caudata, D. fortii and D. acuminata. We optimized a qPCR assay using the primer pair that sufficiently amplified each of the target species (Dacu_11F/Dacu_11R), and tested this assay for cross-reactivity with other dinoflagellates and diatoms in the laboratory (11 species) and in silico 8 species (15 strains) of Dinophysis, 3 species of Ornithocercus and 2 species of Phalacroma. The qPCR assay returned efficiencies of 92.4% for D. caudata, 91.3% for D fortii, and 91.5% for D. acuminata, while showing no cross-reactivity with other phytoplankton taxa. Finally, we applied this assay to a D. acuminata bloom which occurred in an oyster producing estuary in south eastern Australia, and compared cell numbers inferred by qPCR to those determined by microscopy counts (max abund. ∼6.3 × 103 and 5.3 × 103 cells L-1 respectively). Novel molecular tools such as qPCR have the potential to be used on-farm, be automated, and provide an early warning for the management of harmful algal blooms.
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Affiliation(s)
- Penelope A Ajani
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 175 Pitt St, Sydney, NSW 2000, Australia.
| | - Hernan F Henriquez-Nunez
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 175 Pitt St, Sydney, NSW 2000, Australia
| | - Arjun Verma
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 175 Pitt St, Sydney, NSW 2000, Australia
| | - Satoshi Nagai
- Coastal and Inland Fisheries Ecosystems Division, Fisheries Technology Institute, Japan Fisheries Research and Education Agency. 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Hajime Uchida
- Seafood Safety and Technology Division, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Matthew J Tesoriero
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 175 Pitt St, Sydney, NSW 2000, Australia
| | - Hazel Farrell
- NSW Food Authority, NSW Department of Primary Industries, PO Box 232, Taree 2430, Australia
| | - Anthony Zammit
- NSW Food Authority, NSW Department of Primary Industries, PO Box 232, Taree 2430, Australia
| | - Steve Brett
- Microalgal Services, 308 Tucker Rd, Ormond 3204, Australia
| | - Shauna A Murray
- University of Technology Sydney, School of Life Sciences, Sydney, PO Box 123, Broadway, NSW 2007, Australia; Food Agility CRC Ltd, 175 Pitt St, Sydney, NSW 2000, Australia
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6
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Liu F, Zhang C, Wang Y, Chen G. A review of the current and emerging detection methods of marine harmful microalgae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152913. [PMID: 34999066 DOI: 10.1016/j.scitotenv.2022.152913] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
In recent years, the scale and frequency of outbreaks of harmful algal blooms (HABs) have increased year by year due to the intensification of seawater eutrophication and global climate change. HABs have become a global marine ecological and environmental problem, which poses a serious threat to human health, marine ecological security, and economic development. The establishment of detection technology for harmful microalgae is fundamental to the early warning and prevention of HABs. To date, several detection methods have been developed for harmful microalgae, they however lack a unified classification standard. It is difficult to use a reasonable mix of all the developed methods to improve the accuracy of detection results. Here, all of the established detection methods for harmful microalgae were reviewed, including morphological structure-based detection methods, cytochrome-based detection techniques, immunoassays, and nucleic acid-based detection methods. The principles, advantages, and weaknesses of these methods were highlighted. Their application in the detection of harmful microalgae was summarized. Overall, different detection methods are suitable for different purposes. Further development of more accurate, cost-effective, efficient, and rapid detection technology is required in the future. This review is expected to provide a reference for research related to the monitoring of marine environment, early warning of HABs, and the molecular identification of harmful microalgae.
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Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
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7
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Hyung JH, Hwang J, Moon SJ, Kim EJ, Kim DW, Park J. Development of a Method for Detecting Alexandrium pacificum Based on the Quantification of sxtA4 by Chip-Based Digital PCR. Toxins (Basel) 2022; 14:111. [PMID: 35202138 PMCID: PMC8877084 DOI: 10.3390/toxins14020111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/28/2022] [Accepted: 01/29/2022] [Indexed: 11/18/2022] Open
Abstract
Alexandrium pacificum, which produces the paralytic shellfish toxin (PST) saxitoxin (STX), is one of the causative species of paralytic shellfish poisoning outbreaks in coastal areas of Korea. In this study, we developed a chip-based digital PCR (dPCR) method for A. pacificum detection and tested it for monitoring in Jinhae-Masan Bay. Using the sequence of an A. pacificum strain isolated in 2017, species-specific primers targeting sxtA4 (a STX biosynthesis-related gene) were designed and used in a dPCR, detecting 2.0 ± 0.24 gene copies per cell of A. pacificum. Cell abundance in field samples, estimated by a chip-based dPCR, was compared with the PST content, and measured using a mouse bioassay. A comparison with shellfish PST concentrations indicated that cell concentrations above 500 cells L-1, as measured using the dPCR assay, may cause shellfish PST concentrations to exceed the allowed limits for PSTs. Concordance rates between dPCR and PST results were 62.5% overall in 2018-2021, reaching a maximum of 91.7% in 2018-2019. The sensitivity of the dPCR assay was higher than that of microscopy and sxtA4-based qPCRs. Absolute quantification by chip-based dPCRs targeting sxtA4 in A. pacificum exhibits potential as a complementary approach to mouse bioassay PST monitoring for the prevention of toxic blooms.
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Affiliation(s)
- Jun-Ho Hyung
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (J.-H.H.); (S.-J.M.); (E.-J.K.)
| | - Jinik Hwang
- West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 22383, Korea;
| | - Seung-Joo Moon
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (J.-H.H.); (S.-J.M.); (E.-J.K.)
| | - Eun-Joo Kim
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (J.-H.H.); (S.-J.M.); (E.-J.K.)
| | - Dong-Wook Kim
- Food Safety and Processing Research Division, National Institute of Fisheries Science, Busan 46083, Korea;
| | - Jaeyeon Park
- Environment and Resource Convergence Center, Advanced Institute of Convergence Technology, Suwon 16229, Korea; (J.-H.H.); (S.-J.M.); (E.-J.K.)
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8
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Yarimizu K, Sildever S, Hamamoto Y, Tazawa S, Oikawa H, Yamaguchi H, Basti L, Mardones JI, Paredes-Mella J, Nagai S. Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR. HARMFUL ALGAE 2021; 103:102008. [PMID: 33980448 DOI: 10.1016/j.hal.2021.102008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Recent increase of Harmful Algal Blooms (HAB) causes world-wide ecological, economical, and health issues, and more attention is paid to frequent coastal monitoring for the early detection of HAB species to prevent or reduce such impacts. Use of molecular tools in addition to traditional microscopy-based observation has become one of the promising methodologies for coastal monitoring. However, as ribosomal RNA (rRNA) genes are commonly targeted in molecular studies, variability in the rRNA gene copy number within and between species must be considered to provide quantitative information in quantitative PCR (qPCR), digital PCR (dPCR), and metabarcoding analyses. Currently, this information is only available for a limited number of species. The present study utilized a dPCR technology to quantify copy numbers of rRNA genes per single cell in 16 phytoplankton species, the majority of which are toxin-producers, using a newly developed universal primer set accompanied by a labeled probe with a fluorophore and a double-quencher. In silico PCR using the newly developed primers allowed the detection of taxa from 8 supergroups, demonstrating universality and broad coverage of the primer set. Chelex buffer was found to be suitable for DNA extraction to obtain DNA fragments with suitable size to avoid underestimation of the copy numbers. The study successfully demonstrated the first comparison of absolute quantification of 18S rRNA copy numbers per cell from 16 phytoplankton species by the dPCR technology.
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Affiliation(s)
- Kyoko Yarimizu
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 22 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Sirje Sildever
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Department of Marine Systems, Tallinn University of Technology, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Yoko Hamamoto
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Satoshi Tazawa
- AXIOHELIX Co. Ltd, 12-17 Kandaizumicho, Chiyoda-ku, Tokyo 101-0024, Japan
| | - Hiroshi Oikawa
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Sciences, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Leila Basti
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | - Jorge I Mardones
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Javier Paredes-Mella
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan.
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9
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Lee HG, Kim HM, Min J, Park C, Jeong HJ, Lee K, Kim KY. Quantification of the paralytic shellfish poisoning dinoflagellate Alexandrium species using a digital PCR. HARMFUL ALGAE 2020; 92:101726. [PMID: 32113599 DOI: 10.1016/j.hal.2019.101726] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/01/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
A ubiquitous dinoflagellate, Alexandrium, produces paralytic shellfish toxin (PST), and its outbreaks have negative impacts on aquaculture, fisheries, human health, and the marine ecosystem. To minimize such damages, a routine monitoring program of toxic species must be implemented with a suitable analytical technique for their identification and quantification. However, the taxonomic identification and cell quantification of Alexandrium species based on their external morphology under a light microscope, or by using conventional molecular approaches have limited sensitivity and reproducibility. To address these challenges, we have developed an advanced protocol using droplet-digital PCR (ddPCR) for the discrimination and enumeration of three co-occurring Alexandrium species (A. affine, A. catenella, and A. pacificum) in environmental samples. Copies of species-specific internal transcribed spacer (ITS) per cell, which were calculated from environmental samples spiked with various numbers of culture cells, were used to estimate the abundance of species in the field samples. There were no significant differences in ITS copies estimated by the digital PCR assay between environmental samples from different localities, spiked artificially with a consistent number of cells from Alexandrium cultures. This sensitive assay was applied to determine the abundance and vertical distribution of those populations in the southern coastal waters of Korea. In spring, A. catenella was the dominant species, followed by the non-toxic A. affine in summers. A novel digital PCR assay can also be used to monitor other harmful marine protists that require high sample throughput and low detection limit with high accuracy and precision.
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Affiliation(s)
- Hyun-Gwan Lee
- Department of Oceanography, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea; Marine Ecosystem Disturbing and Harmful Organisms (MEDHO) Research Center, Gwangju 61186, Republic of Korea
| | - Hye Mi Kim
- Department of Oceanography, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea; Marine Ecosystem Disturbing and Harmful Organisms (MEDHO) Research Center, Gwangju 61186, Republic of Korea
| | - Juhee Min
- Department of Oceanography, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea; Marine Ecosystem Disturbing and Harmful Organisms (MEDHO) Research Center, Gwangju 61186, Republic of Korea
| | - Chungoo Park
- Marine Ecosystem Disturbing and Harmful Organisms (MEDHO) Research Center, Gwangju 61186, Republic of Korea; School of Biological Sciences and Technology, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Kitack Lee
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Kwang Young Kim
- Department of Oceanography, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea; Marine Ecosystem Disturbing and Harmful Organisms (MEDHO) Research Center, Gwangju 61186, Republic of Korea.
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10
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Wang L, Chen G, Zhang C, Wang Y, Sun R. Application of loop-mediated isothermal amplification combined with lateral flow dipstick to rapid and sensitive detection of Alexandrium catenella. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:4246-4257. [PMID: 31828710 DOI: 10.1007/s11356-019-06889-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Alexandrium catenella is one of the globally distributed toxic marine microalgae to cause paralytic shellfish poisoning that poses a great threat to marine fisheries, economy, and public health. Development of efficient and sensitive methods for accurate identification of A. catenella to minimize its damage is therefore necessary. In this study, a novel method referred to as loop-mediated isothermal amplification (LAMP) combined with lateral flow dipstick (LFD) (LAMP-LFD) was established for rapid and sensitive detection of A. catenella. The internal transcribed spacer (ITS) gene of A. catenella was cloned for sequencing and used as target for LAMP-LFD. Three sets of LAMP primers (AcLF1, AcLF2, and AcLF3) targeting the ITS were successfully designed, among which AcLF2 displaying the best performance was used in the subsequent tests. A specific LFD probe targeting the amplification region of AcLF2 was further designed. The LAMP-LFD detection system was established and the amplification conditions were optimized. Cross-reactivity tests with common marine microalgae showed that the LAMP-LFD was exclusively specific for A. catenella. The detection limits of LAMP-LFD for A. catenella genomic DNA and the plasmid containing the ITS were 4.63 × 10-4 ng μL-1 and 1.26 × 104 copies μL-1, displaying a sensitivity that is 10 times higher than that of SYBR Green I assay and 100 times higher than that of conventional PCR, respectively. Finally, the practicability of LAMP-LFD was confirmed by test with spiked samples. LAMP-LFD revealed a detection limit of approximately 0.1 cell mL-1, which was 100 times more sensitive than conventional PCR. The optimized LAMP-LFD protocol can be completed within 75 min. Therefore, the established LAMP-LFD is a specific, sensitive, and rapid method that is possibly applicable to the field monitoring of A. catenella.
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Affiliation(s)
- Liang Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, People's Republic of China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China.
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Rui Sun
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
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11
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Murray SA, Ruvindy R, Kohli GS, Anderson DM, Brosnahan ML. Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1. Sci Rep 2019; 9:14532. [PMID: 31601884 PMCID: PMC6787220 DOI: 10.1038/s41598-019-51074-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022] Open
Abstract
Alexandrium catenella (formerly A. tamarense Group 1, or A. fundyense) is the leading cause of Paralytic Shellfish Poisoning in North and South America, Europe, Africa, Australia and Asia. The quantification of A.catenella via sxtA, a gene involved in Paralytic Shellfish Toxin synthesis, may be a promising approach, but has not been evaluated in situ on blooms of A. catenella, in which cell abundances may vary from not detectable to in the order of 106 cells L-1. In this study, we compared sxtA assay performance to a qPCR assay targeted to a species-specific region of ribosomal DNA (rDNA) and an established fluorescent in situ hybridization (FISH) microscopy method. Passing-Bablok regression analyses revealed the sxtA assay to overestimate abundances when <5 cell equivalents A. catenella DNA were analysed, but otherwise was closer to microscopy estimates than the rDNA assay, which overestimated abundance across the full range of concentrations analysed, indicative of a copy number difference between the bloom population and a culture used for assay calibration a priori. In contrast, the sxtA assay performed more consistently, indicating less copy number variation. The sxtA assay was generally reliable, fast and effective in quantifying A. catenella and was predictive of PST contamination of shellfish.
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Affiliation(s)
- Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Gurjeet S Kohli
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Ramaciotti Centre for Gene Function Analysis, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Donald M Anderson
- Woods Hole Oceanographic Institution, MS # 32, 266 Woods Hole Road, Woods Hole, Massachusetts, 02543, United States
| | - Michael L Brosnahan
- Woods Hole Oceanographic Institution, MS # 32, 266 Woods Hole Road, Woods Hole, Massachusetts, 02543, United States
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Verma A, Barua A, Ruvindy R, Savela H, Ajani PA, Murray SA. The Genetic Basis of Toxin Biosynthesis in Dinoflagellates. Microorganisms 2019; 7:E222. [PMID: 31362398 PMCID: PMC6722697 DOI: 10.3390/microorganisms7080222] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 02/07/2023] Open
Abstract
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia.
| | - Abanti Barua
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
- Department of Microbiology, Noakhali Science and Technology University, Chittagong 3814, Bangladesh
| | - Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Henna Savela
- Finnish Environment Institute, Marine Research Centre, 00790 Helsinki, Finland
| | - Penelope A Ajani
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
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Ruvindy R, Bolch CJ, MacKenzie L, Smith KF, Murray SA. qPCR Assays for the Detection and Quantification of Multiple Paralytic Shellfish Toxin-Producing Species of Alexandrium. Front Microbiol 2018; 9:3153. [PMID: 30619217 PMCID: PMC6305576 DOI: 10.3389/fmicb.2018.03153] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/05/2018] [Indexed: 11/30/2022] Open
Abstract
Paralytic shellfish toxin producing dinoflagellates have negatively impacted the shellfish aquaculture industry worldwide, including in Australia and New Zealand. Morphologically identical cryptic species of dinoflagellates that may differ in toxicity, in particular, species of the former Alexandrium tamarense species complex, co-occur in Australia, as they do in multiple regions in Asia and Europe. To understand the dynamics and the ecological drivers of the growth of each species in the field, accurate quantification at the species level is crucial. We have developed the first quantitative polymerase chain reaction (qPCR) primers for A. australiense, and new primers targeting A. ostenfeldii, A. catenella, and A. pacificum. We showed that our new primers for A. pacificum are more specific than previously published primer pairs. These assays can be used to quantify planktonic cells and cysts in the water column and in sediment samples with limits of detection of 2 cells/L for the A. catenella and A. australiense assays, 2 cells/L and 1 cyst/mg sediment for the A. pacificum assay, and 1 cells/L for the A. ostenfeldii assay, and efficiencies of >90%. We utilized these assays to discriminate and quantify co-occurring A. catenella, A. pacificum, and A. australiense in samples from the east coast of Tasmania, Australia.
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Affiliation(s)
- Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Christopher J. Bolch
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS, Australia
| | | | | | - Shauna A. Murray
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
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Molecular Techniques for the Detection of Organisms in Aquatic Environments, with Emphasis on Harmful Algal Bloom Species. SENSORS 2017; 17:s17051184. [PMID: 28531156 PMCID: PMC5470929 DOI: 10.3390/s17051184] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/18/2017] [Accepted: 05/20/2017] [Indexed: 02/08/2023]
Abstract
Molecular techniques to detect organisms in aquatic ecosystems are being gradually considered as an attractive alternative to standard laboratory methods. They offer faster and more accurate means of detecting and monitoring species, with respect to their traditional homologues based on culture and microscopic counting. Molecular techniques are particularly attractive when multiple species need to be detected and/or are in very low abundance. This paper reviews molecular techniques based on whole cells, such as microscope-based enumeration and Fluorescence In-Situ Hybridization (FISH) and molecular cell-free formats, such as sandwich hybridization assay (SHA), biosensors, microarrays, quantitative polymerase chain reaction (qPCR) and real time PCR (RT-PCR). Those that combine one or several laboratory functions into a single integrated system (lab-on-a-chip) and techniques that generate a much higher throughput data, such as next-generation systems (NGS), were also reviewed. We also included some other approaches that enhance the performance of molecular techniques. For instance, nano-bioengineered probes and platforms, pre-concentration and magnetic separation systems, and solid-phase hybridization offer highly pre-concentration capabilities. Isothermal amplification and hybridization chain reaction (HCR) improve hybridization and amplification techniques. Finally, we presented a study case of field remote sensing of harmful algal blooms (HABs), the only example of real time monitoring, and close the discussion with future directions and concluding remarks.
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15
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Vandersea MW, Kibler SR, Van Sant SB, Tester PA, Sullivan K, Eckert G, Cammarata C, Reece K, Scott G, Place A, Holderied K, Hondolero D, Litaker RW. qPCR assays for Alexandrium fundyense and A. ostenfeldii (Dinophyceae) identified from Alaskan waters and a review of species-specific Alexandrium molecular assays. PHYCOLOGIA 2017; 56:303-320. [PMID: 32831405 PMCID: PMC7441911 DOI: 10.2216/16-41.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 11/23/2016] [Indexed: 05/09/2023]
Abstract
Paralytic shellfish poisoning (PSP) poses a serious health threat in Alaska and prevents effective utilization of shellfish resources by subsistence and recreational harvesters. Substantial economic losses also affect shellfish growers during PSP events. The toxins responsible for PSP are produced by dinoflagellates in the genus Alexandrium. Despite the persistent threat posed by PSP and the long history of shellfish toxicity research, there is still confusion concerning the Alexandrium species that cause PSP in Alaska. The primary objective of this study was to identify the toxic Alexandrium species present in Alaska and to develop polymerase chain reaction (PCR) assays for use in screening phytoplankton and sediment samples. Before developing the PCR assays for this study, we evaluated published assays and many were not adequate because of primer dimer formation or because of cross-reactivity. Rather than continue to grapple with the uncertainty and inadequacy of published assays, we developed new assays for the Alexandrium species most likely to be present in Alaska. Only Alexandrium fundyense Group I and A. ostenfeldii were identified from four sampling regions from southeast Alaska to Kodiak Island, indicating that these two species are widely distributed. PCR assays for these two species were converted to quantitative (q)PCR format for use in monitoring programs. During the course of this study, we realized that a systematic evaluation of all published (~150) Alexandrium species-specific assays would be of benefit. Toward this objective, we collated published Alexandrium PCR, qPCR, and in situ hybridization assay primers and probes that targeted the small-subunit (SSU), internal transcribed spacer (ITS/5.8S), or D1-D3 large-subunit (LSU) (SSU/ITS/LSU) ribosomal DNA genes. Each individual primer or probe was screened against the GenBank database and Alexandrium gene sequence alignments constructed as part of this study. These data were used to identify a suite of species-specific Alexandrium assays that can be recommended for evaluation by the global harmful algal bloom community.
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Affiliation(s)
- Mark W. Vandersea
- NCCOS/NOAA, Center for Coastal Fisheries and Habitat
Research, 101 Pivers Island Road, Beaufort, North Carolina 28516, USA
| | - Steven R. Kibler
- NCCOS/NOAA, Center for Coastal Fisheries and Habitat
Research, 101 Pivers Island Road, Beaufort, North Carolina 28516, USA
| | - Scott B. Van Sant
- NMFS/NOAA, Southeast Fishery Science Center, 127 Cardinal
Drive Ext, Wilmington, North Carolina 28405, USA
| | - Patricia A. Tester
- NCCOS/NOAA, Center for Coastal Fisheries and Habitat
Research, 101 Pivers Island Road, Beaufort, North Carolina 28516, USA
- Ocean Tester, LLC, 381 Gillikin Road, Beaufort, North
Carolina 28516, USA
| | - Kate Sullivan
- Southeast Alaska Regional Dive Fisheries Association, PO
Box 5417, Ketchikan, Alaska 99901, USA
| | - Ginny Eckert
- Fisheries Department, University of Alaska, 17101 Point
Lena Loop Road, Juneau, Alaska 99801, USA
| | - Charlayna Cammarata
- Texas A&M University, Department of Wildlife &
Fisheries Sciences, College of Agriculture, 2258 TAMU, College Station, Texas 77843,
USA
| | - Kim Reece
- Virginia Institute of Marine Science, School of Marine
Science, College of William and Mary, Gloucester Point, Virginia 23062-1346,
USA
| | - Gail Scott
- Virginia Institute of Marine Science, School of Marine
Science, College of William and Mary, Gloucester Point, Virginia 23062-1346,
USA
| | - Allen Place
- University of Maryland Center for Environmental Science,
Institute of Marine and Environmental Technology, 701 East Pratt Street, Columbus
Center, Suite 236, Baltimore, Maryland 21202, USA
| | - Kris Holderied
- NCCOS/NOAA, Kasitsna Bay Laboratory, Center for Coastal
Fisheries and Habitat Research, Homer, Alaska 99603, USA
| | - Dominic Hondolero
- NCCOS/NOAA, Kasitsna Bay Laboratory, Center for Coastal
Fisheries and Habitat Research, Homer, Alaska 99603, USA
| | - R. Wayne Litaker
- NCCOS/NOAA, Center for Coastal Fisheries and Habitat
Research, 101 Pivers Island Road, Beaufort, North Carolina 28516, USA
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Park TG, Kim JJ, Kim WJ, Won KM. Development of real-time RT-PCR for detecting viable Cochlodinium polykrikoides (Dinophyceae) cysts in sediment. HARMFUL ALGAE 2016; 60:36-44. [PMID: 28073561 DOI: 10.1016/j.hal.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/09/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
Morphological observations have confirmed that cysts are produced by dinoflagellates. However, finding a seed bed or unknown cysts in field samples by microscopy is extremely time consuming. Real-time PCR has been used to facilitate the detection of dinoflagellate cysts in sediment. However, DNA from dead vegetative cells remaining on the surface sediment may persist for a long period of time, which can cause false positive DNA detection. In this study, a non-quantitative RNA targeted probe using real-time RT-PCR was developed for detection of viable cysts in sediment. Large-subunit rRNA was used to develop a species-specific RNA targeted probe for the ichthyotoxic dinoflagellate Cochlodinium polykrikoides. The sediment samples were sieved and incubated at 30°C for 3h prior to RNA extraction to remove RNA from dead cells remaining in the sediment. Nested-PCR was conducted to maximize assay sensitivity. A field survey to determine the distribution of cysts at 155 sampling stations in the western and southern part of the Korean peninsula showed that C. polykrikoides cysts were detected at five sampling stations.
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Affiliation(s)
- Tae Gyu Park
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea.
| | - Jin Joo Kim
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea
| | - Won Jin Kim
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea
| | - Kyoung Mi Won
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea
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Hallegraeff G, Bolch C. Unprecedented toxic algal blooms impact on Tasmanian seafood industry. MICROBIOLOGY AUSTRALIA 2016. [DOI: 10.1071/ma16049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
While most microscopic algae provide food for filter-feeding shellfish and larvae of crustaceans and finfish, other so-called Harmful Algal Blooms (HABs) can have negative effects, causing severe economic losses to aquaculture, fisheries and tourism. Of greatest concern to human society are blooms of toxic HAB species that cause illness and death of fish, seabirds and mammals via toxins transferred through the food web. Unprecedented Alexandrium (Dinophyceae) blooms along the East Coast of Tasmania in 2012 and 2015, a previously low biotoxin risk area, led to major impacts on the local oyster, mussel, scallop and rock lobster industries. Four human hospitalisations also occurred from eating wild shellfish.
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High Specificity of a Quantitative PCR Assay Targeting a Saxitoxin Gene for Monitoring Toxic Algae Associated with Paralytic Shellfish Toxins in the Yellow Sea. Appl Environ Microbiol 2015; 81:6973-81. [PMID: 26231652 DOI: 10.1128/aem.00417-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/19/2015] [Indexed: 01/15/2023] Open
Abstract
The identification of core genes involved in the biosynthesis of saxitoxin (STX) offers a great opportunity to detect toxic algae associated with paralytic shellfish toxins (PST). In the Yellow Sea (YS) in China, both toxic and nontoxic Alexandrium species are present, which makes it a difficult issue to specifically monitor PST-producing toxic algae. In this study, a quantitative PCR (qPCR) assay targeting sxtA4, a domain in the sxt gene cluster that encodes a unique enzyme involved in STX biosynthesis, was applied to analyze samples collected from the YS in spring of 2012. The abundance of two toxic species within the Alexandrium tamarense species complex, i.e., A. fundyense and A. pacificum, was also determined with TaqMan-based qPCR assays, and PSTs in net-concentrated phytoplankton samples were analyzed with high-performance liquid chromatography coupled with a fluorescence detector. It was found that the distribution of the sxtA4 gene in the YS was consistent with the toxic algae and PSTs, and the quantitation results of sxtA4 correlated well with the abundance of the two toxic species (r=0.857). These results suggested that the two toxic species were major PST producers during the sampling season and that sxtA-based qPCR is a promising method to detect toxic algae associated with PSTs in the YS. The correlation between PST levels and sxtA-based qPCR results, however, was less significant (r=0.552), implying that sxtA-based qPCR is not accurate enough to reflect the toxicity of PST-producing toxic algae. The combination of an sxtA-based qPCR assay and chemical means might be a promising method for monitoring toxic algal blooms.
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Gao Y, Yu RC, Chen JH, Zhang QC, Kong FZ, Zhou MJ. Distribution of Alexandrium fundyense and A. pacificum (Dinophyceae) in the Yellow Sea and Bohai Sea. MARINE POLLUTION BULLETIN 2015; 96:210-219. [PMID: 26026250 DOI: 10.1016/j.marpolbul.2015.05.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 05/04/2015] [Accepted: 05/12/2015] [Indexed: 06/04/2023]
Abstract
This study characterizes the distribution of two closely related, causative species of paralytic shellfish poisoning – Alexandrium fundyense and A. pacificum – within the Yellow Sea (YS) and Bohai Sea (BS). These two Alexandrium species are distinguished for the first time in a regional field study using species-specific, quantitative PCR (qPCR) based assays. Both qPCR assays target the large subunit ribosomal DNA gene and were used to analyze net-concentrated phytoplankton samples collected in May 2012. A. fundyense was mainly distributed in YS, while A. pacificum was confined to an area adjacent to the Changjiang River estuary. The different distribution of the two species is interpreted as evidence of their distinct bloom ecology. Expanded efforts implementing these assays offer the ability to discriminate the dynamics of A. fundyense and A. pacificum blooms and provide a more sound basis for monitoring toxic Alexandrium species in this region.
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Affiliation(s)
- Yan Gao
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ren-Cheng Yu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Jian-Hua Chen
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Chun Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fan-Zhou Kong
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ming-Jiang Zhou
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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Molecular detection of a potentially toxic diatom species. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:4921-41. [PMID: 25955528 PMCID: PMC4454946 DOI: 10.3390/ijerph120504921] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/24/2015] [Accepted: 04/16/2015] [Indexed: 12/27/2022]
Abstract
A few diatom species produce toxins that affect human and animal health. Among these, members of the Pseudo-nitzschia genus were the first diatoms unambiguously identified as producer of domoic acid, a neurotoxin affecting molluscan shell-fish, birds, marine mammals, and humans. Evidence exists indicating the involvement of another diatom genus, Amphora, as a potential producer of domoic acid. We present a strategy for the detection of the diatom species Amphora coffeaeformis based on the development of species-specific oligonucleotide probes and their application in microarray hybridization experiments. This approach is based on the use of two marker genes highly conserved in all diatoms, but endowed with sufficient genetic divergence to discriminate diatoms at the species level. A region of approximately 450 bp of these previously unexplored marker genes, coding for elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), was used to design oligonucleotide probes that were tested for specificity in combination with the corresponding fluorescently labeled DNA targets. The results presented in this work suggest a possible use of this DNA chip technology for the selective detection of A. coffeaeformis in environmental settings where the presence of this potential toxin producer may represent a threat to human and animal health. In addition, the same basic approach can be adapted to a wider range of diatoms for the simultaneous detection of microorganisms used as biomarkers of different water quality levels.
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Approaches for the detection of harmful algal blooms using oligonucleotide interactions. Anal Bioanal Chem 2014; 407:95-116. [PMID: 25381608 DOI: 10.1007/s00216-014-8193-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/02/2014] [Accepted: 09/15/2014] [Indexed: 01/14/2023]
Abstract
Blooms of microscopic algae in our waterways are becoming an increasingly important environmental concern. Many are sources of harmful biotoxins that can lead to death in humans, marine life and birds. Additionally, their biomass can cause damage to ecosystems such as oxygen depletion, displacement of species and habitat alteration. Globally, the number and frequency of harmful algal blooms has increased over the last few decades, and monitoring and detection strategies have become essential for managing these events. This review discusses developments in the use of oligonucleotide-based 'molecular probes' for the selective monitoring of algal cell numbers. Specifically, hybridisation techniques will be a focus.
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22
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Wiese M, Murray SA, Alvin A, Neilan BA. Gene expression and molecular evolution of sxtA4 in a saxitoxin producing dinoflagellate Alexandrium catenella. Toxicon 2014; 92:102-12. [PMID: 25301480 DOI: 10.1016/j.toxicon.2014.09.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 09/25/2014] [Indexed: 10/24/2022]
Abstract
Dinoflagellates of the genus Alexandrium produce the neurotoxin saxitoxin (STX), responsible for paralytic shellfish poisoning (PSP) and accumulates in marine invertebrates. The recent identification of STX biosynthesis genes allowed us to investigate the expression of sxtA4 at different growth stages in Alexandrium catenella Group IV. We found no significant differences in expression of sxtA4, despite significant differences in STX levels at different growth stages (P < 0.023). Three reference genes were tested for normalisation: actin, cytochrome b (cob), and the large subunit ribosomal RNA (LSU rDNA). cob was most stably expressed but the combination of two reference genes, actin and cob, resulted in the best stability factor. Most genomic sequences of sxtA4 from A. catenella were in a clade that included sequences from Alexandrium fundyense Group I, however, one paralogue was not related to the others, suggesting recombination or lateral transfer. A comparison of the sxtA4 cDNA sequences with genomic DNA sequences indicated the possibility of transcript editing and the preferential transcription of certain genomic DNA loci. The results show that, in dinoflagellates, post-transcriptional mechanisms play a major role in the regulation of saxitoxin biosynthesis.
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Affiliation(s)
- Maria Wiese
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW 2088, Australia.
| | - Shauna A Murray
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW 2088, Australia; Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, NSW 2007, Australia
| | - Alfonsus Alvin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW 2088, Australia.
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Wiese M, Murray SA, Alvin A, Neilan BA. WITHDRAWN: Gene expression and molecular evolution of sxtA4 in a saxitoxin producing dinoflagellate Alexandrium catenella. Toxicon 2014:S0041-0101(14)00193-7. [PMID: 25080311 DOI: 10.1016/j.toxicon.2014.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/08/2014] [Accepted: 07/15/2014] [Indexed: 10/25/2022]
Abstract
This article has been withdrawn at the request of the authors and editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Maria Wiese
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW 2088, Australia
| | - Shauna A Murray
- Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW 2088, Australia; Plant Functional Biology and Climate Change Cluster, University of Technology, Sydney, NSW 2007, Australia
| | - Alfonsus Alvin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW 2088, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW 2088, Australia
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Biology of the Marine Heterotrophic Dinoflagellate Oxyrrhis marina: Current Status and Future Directions. Microorganisms 2013; 1:33-57. [PMID: 27694763 PMCID: PMC5029500 DOI: 10.3390/microorganisms1010033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/02/2013] [Accepted: 10/08/2013] [Indexed: 11/17/2022] Open
Abstract
Heterotrophic dinoflagellates are prevalent protists in marine environments, which play an important role in the carbon cycling and energy flow in the marine planktonic community. Oxyrrhismarina (Dinophyceae), a widespread heterotrophic dinoflagellate, is a model species used for a broad range of ecological, biogeographic, and evolutionary studies. Despite the increasing research effort on this species, there lacks a synthesis of the existing data and a coherent picture of this organism. Here we reviewed the literature to provide an overview of what is known regarding the biology of O. marina, and identify areas where further studies are needed. As an early branch of the dinoflagellate lineage, O. marina shares similarity with typical dinoflagellates in permanent condensed chromosomes, less abundant nucleosome proteins compared to other eukaryotes, multiple gene copies, the occurrence of trans-splicing in nucleus-encoded mRNAs, highly fragmented mitochondrial genome, and disuse of ATG as a start codon for mitochondrial genes. On the other hand, O. marina also exhibits some distinct cytological features (e.g., different flagellar structure, absence of girdle and sulcus or pustules, use of intranuclear spindle in mitosis, presence of nuclear plaque, and absence of birefringent periodic banded chromosomal structure) and genetic features (e.g., a single histone-like DNA-associated protein, cob-cox3 gene fusion, 5' oligo-U cap in the mitochondrial transcripts of protein-coding genes, the absence of mRNA editing, the presence of stop codon in the fused cob-cox3 mRNA produced by post-transcriptional oligoadenylation, and vestigial plastid genes). The best-studied biology of this dinoflagellate is probably the prey and predators types, which include a wide range of organisms. On the other hand, the abundance of this species in the natural waters and its controlling factors, genome organization and gene expression regulation that underlie the unusual cytological and ecological characteristics are among the areas that urgently need study.
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Penna A, Galluzzi L. The quantitative real-time PCR applications in the monitoring of marine harmful algal bloom (HAB) species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6851-62. [PMID: 23247526 PMCID: PMC3782655 DOI: 10.1007/s11356-012-1377-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/29/2012] [Indexed: 05/15/2023]
Abstract
In the last decade, various molecular methods (e.g., fluorescent hybridization assay, sandwich hybridization assay, automatized biosensor detection, real-time PCR assay) have been developed and implemented for accurate and specific identification and estimation of marine toxic microalgal species. This review focuses on the recent quantitative real-time PCR (qrt-PCR) technology developed for the control and monitoring of the most important taxonomic phytoplankton groups producing biotoxins with relevant negative impact on human health, the marine environment, and related economic activities. The high specificity and sensitivity of the qrt-PCR methods determined by the adequate choice of the genomic target gene, nucleic acid purification protocol, quantification through the standard curve, and type of chemical detection method make them highly efficient and therefore applicable to harmful algal bloom phenomena. Recent development of qrt-PCR-based assays using the target gene of toxins, such as saxitoxin compounds, has allowed more precise quantification of toxigenic species (i.e., Alexandrium catenella) abundance. These studies focus only on toxin-producing species in the marine environment. Therefore, qrt-PCR technology seems to offer the advantages of understanding the ecology of harmful algal bloom species and facilitating the management of their outbreaks.
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Affiliation(s)
- Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, Pesaro, Italy,
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Caron DA. Towards a Molecular Taxonomy for Protists: Benefits, Risks, and Applications in Plankton Ecology. J Eukaryot Microbiol 2013; 60:407-13. [DOI: 10.1111/jeu.12044] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/11/2013] [Indexed: 11/26/2022]
Affiliation(s)
- David A. Caron
- Department of Biological Sciences; University of Southern California; Los Angeles California
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Hariganeya N, Tanimoto Y, Yamaguchi H, Nishimura T, Tawong W, Sakanari H, Yoshimatsu T, Sato S, Preston CM, Adachi M. Quantitative PCR method for enumeration of cells of cryptic species of the toxic marine dinoflagellate Ostreopsis spp. in coastal waters of Japan. PLoS One 2013; 8:e57627. [PMID: 23593102 PMCID: PMC3596365 DOI: 10.1371/journal.pone.0057627] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 01/23/2013] [Indexed: 11/18/2022] Open
Abstract
Monitoring of harmful algal bloom (HAB) species in coastal waters is important for assessment of environmental impacts associated with HABs. Co-occurrence of multiple cryptic species such as toxic dinoflagellate Ostreopsis species make reliable microscopic identification difficult, so the employment of molecular tools is often necessary. Here we developed new qPCR method by which cells of cryptic species can be enumerated based on actual gene number of target species. The qPCR assay targets the LSU rDNA of Ostreopsis spp. from Japan. First, we constructed standard curves with a linearized plasmid containing the target rDNA. We then determined the number of rDNA copies per cell of target species from a single cell isolated from environmental samples using the qPCR assay. Differences in the DNA recovery efficiency was calculated by adding exogenous plasmid to a portion of the sample lysate before and after DNA extraction followed by qPCR. Then, the number of cells of each species was calculated by division of the total number of rDNA copies of each species in the samples by the number of rDNA copies per cell. To test our procedure, we determined the total number of rDNA copies using environmental samples containing no target cells but spiked with cultured cells of several species of Ostreopsis. The numbers estimated by the qPCR method closely approximated total numbers of cells added. Finally, the numbers of cells of target species in environmental samples containing cryptic species were enumerated by the qPCR method and the total numbers also closely approximated the microscopy cell counts. We developed a qPCR method that provides accurate enumeration of each cryptic species in environments. This method is expected to be a powerful tool for monitoring the various HAB species that occur as cryptic species in coastal waters.
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Affiliation(s)
| | - Yuko Tanimoto
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, Japan
| | | | - Tomohiro Nishimura
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, Japan
| | - Wittaya Tawong
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, Japan
| | | | | | - Shinya Sato
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Christina M. Preston
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
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Jedlicki A, Fernández G, Astorga M, Oyarzún P, Toro JE, Navarro JM, Martínez V. Molecular detection and species identification of Alexandrium (Dinophyceae) causing harmful algal blooms along the Chilean coastline. AOB PLANTS 2012; 2012:pls033. [PMID: 23259043 PMCID: PMC3526335 DOI: 10.1093/aobpla/pls033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 09/25/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS On the basis of morphological evidence, the species involved in South American Pacific coast harmful algal blooms (HABs) has been traditionally recognized as Alexandrium catenella (Dinophyceae). However, these observations have not been confirmed using evidence based on genomic sequence variability. Our principal objective was to accurately determine the species of Alexandrium involved in local HABs in order to implement a real-time polymerase chain reaction (PCR) assay for its rapid and easy detection on filter-feeding shellfish, such as mussels. METHODOLOGY For species-specific determination, the intergenic spacer 1 (ITS1), 5.8S subunit, ITS2 and the hypervariable genomic regions D1-D5 of the large ribosomal subunit of local strains were sequenced and compared with two data sets of other Alexandrium sequences. Species-specific primers were used to amplify signature sequences within the genomic DNA of the studied species by conventional and real-time PCR. PRINCIPAL RESULTS Phylogenetic analysis determined that the Chilean strain falls into Group I of the tamarensis complex. Our results support the allocation of the Chilean Alexandrium species as a toxic Alexandrium tamarense rather than A. catenella, as currently defined. Once local species were determined to belong to Group I of the tamarensis complex, a highly sensitive and accurate real-time PCR procedure was developed to detect dinoflagellate presence in Mytilus spp. (Bivalvia) samples after being fed (challenged) in vitro with the Chilean Alexandrium strain. The results show that real-time PCR is useful to detect Alexandrium intake in filter-feeding molluscs. CONCLUSIONS It has been shown that the classification of local Alexandrium using morphological evidence is not very accurate. Molecular methods enabled the HAB dinoflagellate species of the Chilean coast to be assigned as A. tamarense rather than A. catenella. Real-time PCR analysis based on A. tamarense primers allowed the detection of dinoflagellate DNA in Mytilus spp. samples exposed to this alga. Through the specific assignment of dinoflagellate species involved in HABs, more reliable preventive policies can be implemented.
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Affiliation(s)
- Ana Jedlicki
- FAVET-INBIOGEN, Faculty of Veterinary
Sciences, University of Chile, Santa
Rosa No 11.735 (PO 8820808), Santiago, Chile
| | - Gonzalo Fernández
- FAVET-INBIOGEN, Faculty of Veterinary
Sciences, University of Chile, Santa
Rosa No 11.735 (PO 8820808), Santiago, Chile
| | - Marcela Astorga
- Aquaculture Institute,
Austral University of Chile, Los Pinos (PO. 1327),
Puerto Montt, Chile
| | - Pablo Oyarzún
- Limnological and Marine Science
Institute, Austral University of Chile (PO. 567),
Valdivia, Chile
| | - Jorge E. Toro
- Limnological and Marine Science
Institute, Austral University of Chile (PO. 567),
Valdivia, Chile
| | - Jorge M. Navarro
- Limnological and Marine Science
Institute, Austral University of Chile (PO. 567),
Valdivia, Chile
| | - Víctor Martínez
- FAVET-INBIOGEN, Faculty of Veterinary
Sciences, University of Chile, Santa
Rosa No 11.735 (PO 8820808), Santiago, Chile
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Caron DA, Countway PD, Jones AC, Kim DY, Schnetzer A. Marine protistan diversity. ANNUAL REVIEW OF MARINE SCIENCE 2012; 4:467-493. [PMID: 22457984 DOI: 10.1146/annurev-marine-120709-142802] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Protists have fascinated microbiologists since their discovery nearly 350 years ago. These single-celled, eukaryotic species span an incredible range of sizes, forms, and functions and, despite their generally diminutive size, constitute much of the genetic diversity within the domain Eukarya. Protists in marine ecosystems play fundamental ecological roles as primary producers, consumers, decomposers, and trophic links in aquatic food webs. Much of our knowledge regarding the diversity and ecological activities of these species has been obtained during the past half century, and only within the past few decades have hypotheses depicting the evolutionary relationships among the major clades of protists attained some degree of consensus. This recent progress is attributable to the development of genetic approaches, which have revealed an unexpectedly large diversity of protists, including cryptic species and previously undescribed clades of protists. New genetic tools now exist for identifying protistan species of interest and for reexamining long-standing debates regarding the biogeography of protists. Studies of protistan diversity provide insight regarding how species richness and community composition contribute to ecosystem function. These activities support the development of predictive models that describe how microbial communities will respond to natural or anthropogenically mediated changes in environmental conditions.
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Affiliation(s)
- David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371, USA.
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Garneau MÈ, Schnetzer A, Countway PD, Jones AC, Seubert EL, Caron DA. Examination of the seasonal dynamics of the toxic dinoflagellate Alexandrium catenella at Redondo Beach, California, by quantitative PCR. Appl Environ Microbiol 2011; 77:7669-80. [PMID: 21926210 PMCID: PMC3209152 DOI: 10.1128/aem.06174-11] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 08/29/2011] [Indexed: 11/20/2022] Open
Abstract
The presence of neurotoxic species within the genus Alexandrium along the U.S. coastline has raised concern of potential poisoning through the consumption of contaminated seafood. Paralytic shellfish toxins (PSTs) detected in shellfish provide evidence that these harmful events have increased in frequency and severity along the California coast during the past 25 years, but the timing and location of these occurrences have been highly variable. We conducted a 4-year survey in King Harbor, CA, to investigate the seasonal dynamics of Alexandrium catenella and the presence of a particulate saxitoxin (STX), the parent compound of the PSTs. A quantitative PCR (qPCR) assay was developed for quantifying A. catenella in environmental microbial assemblages. This approach allowed for the detection of abundances as low as 12 cells liter⁻¹, 2 orders of magnitude below threshold abundances that can impact food webs. A. catenella was found repeatedly during the study, particularly in spring, when cells were detected in 38% of the samples (27 to 5,680 cells liter⁻¹). This peak in cell abundances was observed in 2006 and corresponded to a particulate STX concentration of 12 ng liter⁻¹, whereas the maximum STX concentration of 26 ng liter⁻¹ occurred in April 2008. Total cell abundances and toxin levels varied strongly throughout each year, but A. catenella was less abundant during summer, fall, and winter, when only 2 to 11% of the samples yielded positive qPCR results. The qPCR method developed here provides a useful tool for investigating the ecology of A. catenella at subbloom and bloom abundances.
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Affiliation(s)
- Marie-Ève Garneau
- Limnological Station, Institute of Plant Biology, University of Zurich, Seestrasse 187, 8802 Kilchberg, Switzerland.
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Murray SA, Wiese M, Stüken A, Brett S, Kellmann R, Hallegraeff G, Neilan BA. sxtA-based quantitative molecular assay to identify saxitoxin-producing harmful algal blooms in marine waters. Appl Environ Microbiol 2011; 77:7050-7. [PMID: 21841034 PMCID: PMC3187097 DOI: 10.1128/aem.05308-11] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022] Open
Abstract
The recent identification of genes involved in the production of the potent neurotoxin and keystone metabolite saxitoxin (STX) in marine eukaryotic phytoplankton has allowed us for the first time to develop molecular genetic methods to investigate the chemical ecology of harmful algal blooms in situ. We present a novel method for detecting and quantifying the potential for STX production in marine environmental samples. Our assay detects a domain of the gene sxtA that encodes a unique enzyme putatively involved in the sxt pathway in marine dinoflagellates, sxtA4. A product of the correct size was recovered from nine strains of four species of STX-producing Alexandrium and Gymnodinium catenatum and was not detected in the non-STX-producing Alexandrium species, other dinoflagellate cultures, or an environmental sample that did not contain known STX-producing species. However, sxtA4 was also detected in the non-STX-producing strain of Alexandrium tamarense, Tasmanian ribotype. We investigated the copy number of sxtA4 in three strains of Alexandrium catenella and found it to be relatively constant among strains. Using our novel method, we detected and quantified sxtA4 in three environmental blooms of Alexandrium catenella that led to STX uptake in oysters. We conclude that this method shows promise as an accurate, fast, and cost-effective means of quantifying the potential for STX production in marine samples and will be useful for biological oceanographic research and harmful algal bloom monitoring.
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Affiliation(s)
- Shauna A Murray
- Sydney Institute of Marine Sciences, Chowder Bay Road, Mosman, NSW 2088, Australia.
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Kavanagh S, Brennan C, O'Connor L, Moran S, Salas R, Lyons J, Silke J, Maher M. Real-time PCR detection of Dinophysis species in Irish coastal waters. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:534-542. [PMID: 19946723 DOI: 10.1007/s10126-009-9238-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 10/16/2009] [Indexed: 05/28/2023]
Abstract
Diarrhetic shellfish toxin-producing Dinophysis species occur in Irish coastal waters throughout the year. Dinophysis acuta and Dinophysis acuminata are the most commonly occurring species and are responsible for the majority of closures of Irish mussel farms. This study describes the development of a qualitative real-time polymerase chain reaction (PCR) assay for identification of D. acuta and D. acuminata in Irish coastal waters. DNA sequence information for the D1-D2 region of the large ribosomal sub-unit (LSU) was obtained, following single-cell PCR of D. acuta and D. acuminata cells isolated from Irish coastal locations. PCR primers and hybridization probes, specific for the detection of D. acuta, were designed for real-time PCR on the LightCycler™. The LightCycler™ software melt curve analysis programme determined that D. acuta was identified by a melt-peak at 61°C, while D. acuminata cells produced a melt peak at 48°C. The limit of detection of the real-time PCR assay was determined to be one to ten plasmid copies of the LSU D1-D2 target region for both species and one to five D. acuminata cells. Lugol's preserved water samples were also tested with the assay. The real-time PCR assay identified Dinophysis species in 100% of samples found to contain Dinophysis species by light microscopy and had a greater than 90% correlation with light microscopy for identification of D. acuta and D. acuminata in the samples. The assay can identify and discriminate D. acuta and D. acuminata at low numbers in Irish waters and has the potential to add value to the Irish phytoplankton monitoring programme.
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Affiliation(s)
- Siobhán Kavanagh
- Molecular Diagnostics Research Group, National University of Ireland, Galway, Ireland
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Touzet N, Keady E, Raine R, Maher M. Evaluation of taxa-specific real-time PCR, whole-cell FISH and morphotaxonomy analyses for the detection and quantification of the toxic microalgae Alexandrium minutum (Dinophyceae), Global Clade ribotype. FEMS Microbiol Ecol 2009; 67:329-41. [DOI: 10.1111/j.1574-6941.2008.00627.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Scorzetti G, Brand L, Hitchcock G, Rein K, Sinigalliano C, Fell J. Multiple simultaneous detection of Harmful Algal Blooms (HABs) through a high throughput bead array technology, with potential use in phytoplankton community analysis. HARMFUL ALGAE 2009; 8:196-211. [PMID: 20046212 PMCID: PMC2615561 DOI: 10.1016/j.hal.2008.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As an alternative to traditional, morphology-based methods, molecular techniques can provide detection of multiple species within the HAB community and, more widely, the phytoplankton community in a rapid, accurate and simultaneous qualitative analysis. These methods require detailed knowledge of the molecular diversity within taxa in order to design efficient specific primers and specific probes able to avoid cross-reaction with non-target sequences. Isolates from Florida coastal communities were sequence-analyzed and compared with the GenBank database. Almost 44% of the genotypes obtained did not match any sequence in GenBank, showing the existence of a large and still unexplored biodiversity among taxa. Based on these results and on the GenBank database, we designed 14 species-specific probes and 4 sets of specific primers. Multiple simultaneous detection was achieved with a bead array method based on the use of a flow cytometer and color-coded microspheres, which are conjugated to the developed probes. Following a parallel double PCR amplification, which employed universal primers in a singleplex reaction and a set of species-specific primers in multiplex, detection was performed in a cost effective and highly specific analysis. This multi-format assay, which required less than 4 h to complete from sample collection, can be expanded according to need. Up to 100 different species can be identified simultaneously in a single sample, which allows for additional use of this method in community analyses extended to all phytoplankton species. Our initial field trials, which were based on the 14 species-specific probes, showed the co-existence and dominance of two or more species of Karenia during toxic blooms in Florida waters.
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Affiliation(s)
- G. Scorzetti
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
- Corresponding author. Tel.: +1 305 421 4938. E-mail address: (G. Scorzetti)
| | - L.E. Brand
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - G.L. Hitchcock
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - K.S. Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - C.D. Sinigalliano
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Miami, FL, United States
| | - J.W. Fell
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
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Miyaguchi H, Kurosawa N, Toda T. Real-time polymerase chain reaction assays for rapid detection and quantification of Noctiluca scintillans zoospore. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:133-140. [PMID: 17917779 DOI: 10.1007/s10126-007-9031-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 06/02/2007] [Indexed: 05/25/2023]
Abstract
Application and availability of real-time polymerase chain reaction (PCR) assay to detect and quantify the Noctiluca scintillans zoospore were investigated seasonally. Specific primer set for N. scintillans 18S rDNA was designed and applied to real-time PCR assay using the serial dilutions of N. scintillans zoospores. The real-time PCR assays with Ns63F and Ns260R primers were applied to sea water samples collected weekly in Manazuru Port of Sagami Bay, Japan from April 2005 to June 2006. We developed effective DNA preparation steps for collecting the template DNA of N. scintillans zoospore: size fraction and filter concentration of the water samples, fixation with Lugol solution, cell lysis, and purification. This method is useful for the monitoring of the zoospores of N. scintillans, and can also be used for other small and physiologically fragile planktonic cell. Variation in the density of zoospore was successfully detected in the field samples. The peak density of N. scintillans zoospore was observed to occur just before or at the same time as the peak of the vegetative cells. Moreover, zoospores were detected in seawater even when the vegetative cells were not observed. The presence of zoospore was found all year round in the present study. In this regards, this information is essential for the study of the life cycle and seasonal variation of N. scintillans in the coastal waters.
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Affiliation(s)
- Hideo Miyaguchi
- Department of Environmental Engineering for Symbiosis, Faculty of Engineering, Soka University, 1-236, Tangi-cho, Hachiouji, Tokyo 192-8577, Japan.
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PCR Techniques as Diagnostic Tools for the Identification and Enumeration of Toxic Marine Phytoplankton Species. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8480-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
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Camacho FG, Rodríguez JG, Mirón AS, García MCC, Belarbi EH, Chisti Y, Grima EM. Biotechnological significance of toxic marine dinoflagellates. Biotechnol Adv 2006; 25:176-94. [PMID: 17208406 DOI: 10.1016/j.biotechadv.2006.11.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Accepted: 11/28/2006] [Indexed: 10/23/2022]
Abstract
Dinoflagellates are microalgae that are associated with the production of many marine toxins. These toxins poison fish, other wildlife and humans. Dinoflagellate-associated human poisonings include paralytic shellfish poisoning, diarrhetic shellfish poisoning, neurotoxic shellfish poisoning, and ciguatera fish poisoning. Dinoflagellate toxins and bioactives are of increasing interest because of their commercial impact, influence on safety of seafood, and potential medical and other applications. This review discusses biotechnological methods of identifying toxic dinoflagellates and detecting their toxins. Potential applications of the toxins are discussed. A lack of sufficient quantities of toxins for investigational purposes remains a significant limitation. Producing quantities of dinoflagellate bioactives requires an ability to mass culture them. Considerations relating to bioreactor culture of generally fragile and slow-growing dinoflagellates are discussed. Production and processing of dinoflagellates to extract bioactives, require attention to biosafety considerations as outlined in this review.
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Affiliation(s)
- F Garcia Camacho
- Department of Chemical Engineering, University of Almería, 04120 Almería, Spain.
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Kamikawa R, Asai J, Miyahara T, Murata K, Oyama K, Yoshimatsu S, Yoshida T, Sako Y. Application of a Real-time PCR Assay to a Comprehensive Method of Monitoring Harmful Algae. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.163] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ryoma Kamikawa
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University
| | - Junko Asai
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University
| | - Takahiro Miyahara
- Shallow Sea Research Institute, Fisheries Experimental Station, Agriculture, Forestry, and Fisheries Research Centre of Oita Prefecture
| | - Keisuke Murata
- Division of Fishery Environment, Kagoshima Perfectual Fisheries Technology and Development Centre
| | | | | | - Takashi Yoshida
- Department of Marine Bioscience, Fukui Prefectural University
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University
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