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Kim HS, Kim T, Park J, Park TG, Ki JS. Development of saxitoxin biosynthesis gene sxtB-targeted qPCR assay for the quantification of toxic dinoflagellates Alexandrium catenella (group I) and A. pacificum (group IV) occurring in the Korean coast. HARMFUL ALGAE 2024; 134:102603. [PMID: 38705609 DOI: 10.1016/j.hal.2024.102603] [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: 10/04/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 05/07/2024]
Abstract
Toxic dinoflagellate Alexandrium can produce saxitoxins (STXs) and cause paralytic shellfish poisoning (PSP), and thus they are monitored for environmental safety management. Microscopic discrimination of dinoflagellates is difficult to distinguish between toxic and non-toxic species due to their similar morphology. Meanwhile, an alternative quantitative PCR (qPCR) assay is sensitive, rapid, and cost-effective for harmful species monitoring. Herein, we developed a novel qPCR assay to detect the STXs biosynthesis gene sxtB of Alexandrium catenella and A. pacificum, the leading cause of PSP outbreaks in Asian coasts and worldwide. The newly designed sxtB TaqMan probes target the species without any positive signal in other relative dinoflagellates. Deming regression analysis revealed that the sxtB copy number of A. catenella and A. pacificum was 3.6 and 4.1 copies per cell, respectively. During the blooming periods (April 13th-14th, 2020), only A. catenella cells were detected through the qPCR assay, ranging from 5.0 × 10 to 2.5 × 104 eq cells L-1. In addition, sxtB qPCR quantified more accurately compared to large subunit (LSU) rRNA targeting qPCR assay that overestimate cell density. Besides, the sensitivity of sxtB was higher compared to the microscope when the species were rarely present (5.0 × 102 cells L-1). These suggest that the sxtB qPCR assay can be applied to toxic Alexandrium monitoring in the Korean coast, even in the early stage of bloomings.
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Affiliation(s)
- Han-Sol Kim
- Department of Life Science, Sangmyung University, Seoul 03016, Korea
| | - Taehee Kim
- Department of Life Science, Sangmyung University, Seoul 03016, Korea
| | - Jaeyeon Park
- Environment & Resource Convergence Center, Advanced Institute of Convergence Technologies, Suwon 16229, Korea
| | - Tae Gyu Park
- National Institute of Fisheries Science (NIFS), Busan 46083, Korea
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul 03016, Korea.
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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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Ahn S, Kulis DM, Erdner DL, Anderson DM, Walt DR. Fiber-optic microarray for simultaneous detection of multiple harmful algal bloom species. Appl Environ Microbiol 2006; 72:5742-9. [PMID: 16957189 PMCID: PMC1563625 DOI: 10.1128/aem.00332-06] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 mum) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.
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Affiliation(s)
- Soohyoun Ahn
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA 02155, USA
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Ki JS, Han MS. A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain. Biosens Bioelectron 2006; 21:1812-21. [PMID: 16246543 DOI: 10.1016/j.bios.2005.09.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 09/15/2005] [Accepted: 09/19/2005] [Indexed: 11/15/2022]
Abstract
A low-density oligonucleotide array approach based on the hybridization of consensus PCR products of LSU rDNA was developed in order to simultaneously detect various harmful algae. A set of oligonucleotide probes for the hybridization of specific LSU rDNA D2 regions was developed for the identification of 10 representative harmful microalgae. Each probe was spotted onto a streptoavidin-coated glass slide by pipetting. Universal primers were designed within the conserved regions adjacent to the D2 regions of all harmful algae and used to PCR amplify the complete D2 regions. The PCR products were hybridized to the oligonucleotides arrayed on the slide. The array produced unique hybridization patterns for each species of harmful algae and allowed us to differentiate the closely related species. Furthermore, we were able to simultaneously detect several predominant HAB species from a mixture of culture strains and from a natural sample. These results show that DNA microarray can be a new technical platform for parallel discrimination of harmful algae and has great potential to alter the manner in which researchers monitor these microorganisms.
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Affiliation(s)
- Jang-Seu Ki
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea.
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Hosoi-Tanabe S, Sako Y. Species-specific detection and quantification of toxic marine dinoflagellates Alexandrium tamarense and A. catenella by Real-time PCR assay. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2005; 7:506-14. [PMID: 16007374 DOI: 10.1007/s10126-004-4128-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Accepted: 12/23/2004] [Indexed: 05/03/2023]
Abstract
A Real-time polymerase chain reaction (PCR) assay was designed and evaluated for rapid detection and quantification of the toxic dinoflagellates Alexandrium catenella and A. tamarense, which cause paralytic shellfish poisoning. Two sets of PCR primers and fluorogenic probes targeting these two species were derived from the sequence of 28S ribosomal DNA. PCR specificity was examined in closely related Alexandrium spp. and many other microalgae. A. catenella-specific primers and probe detected the PCR amplification only from A. catenella strains, and nonspecific signals were not detected from any microalgae. Also, A. tamarense-specific primers and probe also detected the targeted species, suggesting the strict species specificity of each PCR. This assay could detect one cell of each species, showing its high sensitivity. Moreover, using the developed standard curves, A. tamarense and A. catenella could be quantified in agreement with the quantification by optical microscopy. The performance characteristics of species specificity, sensitivity, and rapidity suggest that this method is applicable to the monitoring of the toxic A. tamarense and A. catenella.
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Affiliation(s)
- Shoko Hosoi-Tanabe
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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Kröger S, Law RJ. Biosensors for marine applications. We all need the sea, but does the sea need biosensors? Biosens Bioelectron 2005; 20:1903-13. [PMID: 15741057 DOI: 10.1016/j.bios.2004.08.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 08/12/2004] [Accepted: 08/12/2004] [Indexed: 11/19/2022]
Abstract
The aim of the paper is to explain the rationale behind marine biosensor applications, give an overview of measurement strategies currently employed, summarise some of the relevant available biosensor technology as well as instrumentation requirements for marine sensors and attempt a forward look at what the future might hold in terms of needs and developments. Application areas considered are eutrophication, organism detection, food safety, pollutants, trace metals and ecotoxicology. The drivers for many of these studies are discussed and the policy environment for current and future measurements is outlined.
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Affiliation(s)
- Silke Kröger
- Centre for Environment, Fisheries and Aquaculture Science, CEFAS Lowestoft Laboratory, Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK.
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Saito K, Drgon T, Robledo JAF, Krupatkina DN, Vasta GR. Characterization of the rRNA locus of Pfiesteria piscicida and development of standard and quantitative PCR-based detection assays targeted to the nontranscribed spacer. Appl Environ Microbiol 2002; 68:5394-407. [PMID: 12406730 PMCID: PMC129931 DOI: 10.1128/aem.68.11.5394-5407.2002] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pfiesteria piscicida is a heterotrophic dinoflagellate widely distributed along the middle Atlantic shore of the United States and associated with fish kills in the Neuse River (North Carolina) and the Chesapeake Bay (Maryland and Virginia). We constructed a genomic DNA library from clonally cultured P. piscicida and characterized the nontranscribed spacer (NTS), small subunit, internal transcribed spacer 1 (ITS1), 5.8S region, ITS2, and large subunit of the rRNA gene cluster. Based on the P. piscicida ribosomal DNA sequence, we developed a PCR-based detection assay that targets the NTS. The assay specificity was assessed by testing clonal P. piscicida and Pfiesteria shumwayae, 35 additional dinoflagellate species, and algal prey (Rhodomonas sp.). Only P. piscicida and nine presumptive P. piscicida isolates tested positive. All PCR-positive products yielded identical sequences for P. piscicida, suggesting that the PCR-based assay is species specific. The assay can detect a single P. piscicida zoospore in 1 ml of water, 10 resting cysts in 1 g of sediment, or 10 fg of P. piscicida DNA in 1 micro g of heterologous DNA. An internal standard for the PCR assay was constructed to identify potential false-negative results in testing of environmental sediment and water samples and as a competitor for the development of a quantitative competitive PCR assay format. The specificities of both qualitative and quantitative PCR assay formats were validated with >200 environmental samples, and the assays provide simple, rapid, and accurate methods for the assessment of P. piscicida in water and sediments.
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Affiliation(s)
- Keiko Saito
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA
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Kröger S, Piletsky S, Turner APF. Biosensors for marine pollution research, monitoring and control. MARINE POLLUTION BULLETIN 2002; 45:24-34. [PMID: 12398364 DOI: 10.1016/s0025-326x(01)00309-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Measurement of ecological, climatic and anthropogenic changes underpins the formulation of effective management strategies for sustainable use and protection of the marine environment. Sensors are traditionally used in marine studies to determine physical parameters, but there is increasing demand for real-time information about chemical and biological parameters. These parameters are currently measured in samples collected at sea and subsequently analysed in the laboratory. Biosensors fuse the exquisite sensitivity and specificity of living systems with the processing power of microelectronics to deliver simple, inexpensive measurement systems for use in the field or deployment in situ. While their potential for use in the marine environment is enormous, much published work to date has focussed on applications in freshwater and wastewater. Marine applications pose a substantial challenge in the robustness required for remote application, but recent developments in portable medical devices and receptor design suggest that these demands can now be realistically tackled.
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Affiliation(s)
- Silke Kröger
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, Suffolk, UK.
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