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Wang KJ, Huang Y, Kartzinel T, Majaneva M, Richter N, Liao S, Andresen CS, Vermassen F. Group 2i Isochrysidales thrive in marine and lacustrine systems with ice cover. Sci Rep 2024; 14:11449. [PMID: 38769380 PMCID: PMC11106077 DOI: 10.1038/s41598-024-62162-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
Global warming is causing rapid changes to the cryosphere. Predicting the future trajectory of the cryosphere requires quantitative reconstruction of its past variations. A recently identified sea-ice-associated haptophyte, known as Group 2i Isochrysidales, has given rise to a new sea-ice proxy with its characteristic alkenone distributions. However, apart from the occurrence of Group 2i Isochrysidales in regions with sea ice, and the empirical relationship between C37:4 alkenone abundance and sea-ice concentration, little is known about the ecology of these haptophyte species. Here, we systematically mapped the spatial and temporal occurrence of known Group 2i Isochrysidales based on environmental DNA in both marine and lacustrine environments. Our results indicate Group 2i is widely distributed in icy marine and lacustrine environments in both Northern and Southern Hemisphere, but is absent in warm environments. Temporally, Group 2i is part of the sea-ice algae bloom during the cold seasons, in contrast to other Isochrysidales that bloom in open waters during warm seasons. Our results indicate that ice is a prerequisite for the occurrence of the psychrophilic Group 2i haptophytes in marine and lacustrine ecosystems and further affirms its value for past ice reconstructions.
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Affiliation(s)
- Karen J Wang
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, 02912, USA.
- Institute at Brown for Environment and Society, Brown University, Providence, RI, 02912, USA.
| | - Yongsong Huang
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, 02912, USA.
- Institute at Brown for Environment and Society, Brown University, Providence, RI, 02912, USA.
| | - Tyler Kartzinel
- Institute at Brown for Environment and Society, Brown University, Providence, RI, 02912, USA
- Department of Ecology, Evolution, and Organismal Biology, Brown University, Providence, RI, 02912, USA
| | - Markus Majaneva
- Norwegian Institute for Nature Research (NINA), NO-7485, Trondheim, Norway
| | - Nora Richter
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, 02912, USA
- Institute at Brown for Environment and Society, Brown University, Providence, RI, 02912, USA
- Department of Marine Microbiology & Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1790 AB, Den Burg, The Netherlands
| | - Sian Liao
- Institute at Brown for Environment and Society, Brown University, Providence, RI, 02912, USA
- Department of Chemistry, Brown University, Providence, RI, 02912, USA
| | - Camilla S Andresen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Øster Voldgade 10, 1350, Copenhagen K, Denmark
| | - Flor Vermassen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Øster Voldgade 10, 1350, Copenhagen K, Denmark
- Department of Geological Sciences, Stockholm University, 106 91, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, 106 91, Stockholm, Sweden
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2
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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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3
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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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Chin Chwan Chuong JJ, Rahman M, Ibrahim N, Heng LY, Tan LL, Ahmad A. Harmful Microalgae Detection: Biosensors versus Some Conventional Methods. SENSORS 2022; 22:s22093144. [PMID: 35590834 PMCID: PMC9103738 DOI: 10.3390/s22093144] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/10/2022]
Abstract
In the last decade, there has been a steady stream of information on the methods and techniques available for detecting harmful algae species. The conventional approaches to identify harmful algal bloom (HAB), such as microscopy and molecular biological methods are mainly laboratory-based and require long assay times, skilled manpower, and pre-enrichment of samples involving various pre-experimental preparations. As an alternative, biosensors with a simple and rapid detection strategy could be an improvement over conventional methods for the detection of toxic algae species. Moreover, recent biosensors that involve the use of nanomaterials to detect HAB are showing further enhanced detection limits with a broader linear range. The improvement is attributed to nanomaterials’ high surface area to volume ratio, excellent biological compatibility with biomolecules, and being capable of amplifying the electrochemical signal. Hence, this review presents the potential usage of biosensors over conventional methods to detect HABs. The methods reported for the detection of harmful algae species, ranging from conventional detection methods to current biosensor approaches will be discussed, along with their respective advantages and drawbacks to indicate the future prospects of biosensor technology for HAB event management.
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Affiliation(s)
- Jeremy Jason Chin Chwan Chuong
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia; (J.J.C.C.C.); (N.I.); (L.L.T.)
| | - Mahbubur Rahman
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia;
- Department of General Educational Development (GED), Faculty of Science & Information Technology, Daffodil International University, Dhaka 1341, Bangladesh
| | - Nadiah Ibrahim
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia; (J.J.C.C.C.); (N.I.); (L.L.T.)
| | - Lee Yook Heng
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia;
- Correspondence: ; Tel.: +60-3-8921-3356; Fax: +60-3-8921-5410
| | - Ling Ling Tan
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia; (J.J.C.C.C.); (N.I.); (L.L.T.)
| | - Asmat Ahmad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor Darul Ehsan, Malaysia;
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Nuisance Algae in Ballast Water Facing International Conventions. Insights from DNA Metabarcoding in Ships Arriving in Bay of Biscay. WATER 2020. [DOI: 10.3390/w12082168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ballast water is one of the main vectors of transport of nuisance species among marine ports. Neither treatment nor interchange completely reduces the risk of ballast water containing DNA from harmful species, being a signal of potential threat. However, although there are some efficient treatments, they are not available on all ships and there might be some technological/economical constrains for their active and routine usage. Understanding what routes lead to a higher risk of contamination is important for designing targeted surveillance. We analysed ballast water from seven ships arriving in Gijon port (south Bay of Biscay, Spain). DNA metabarcoding was employed for identification of exotic species and harmful algae. One ship carried DNA of 20 risk species in the ballast water. Three ships contained DNA of only one risk species, and three ships had none. Seventy two algae species were found, 22.2% are exotic to the Bay of Biscay and 11.1% are catalogued as harmful. The results demonstrated the importance of continuous surveillance of ballast water.
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6
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Lekang K, Lanzén A, Jonassen I, Thompson E, Troedsson C. Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments. MARINE POLLUTION BULLETIN 2020; 154:111102. [PMID: 32319925 DOI: 10.1016/j.marpolbul.2020.111102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Increased exploitation of resources in sensitive marine ecosystems emphasizes the importance of knowledge regarding ecological impacts. However, current bio-monitoring practices are limited in terms of target-organisms and temporal resolution. Hence, developing new technologies is vital for enhanced ecosystem understanding. In this study, we have applied a prototype version of a phylogenetic microarray to assess the eukaryote community structures of marine sediments from an area with ongoing oil and gas drilling activity. The results were compared with data from both sequencing (metabarcoding) and morphology-based monitoring to evaluate whether microarrays were capable of detecting ecosystem disturbances. A significant correlation between microarray data and chemical pollution indicators, as well as sequencing-based results, was demonstrated, and several potential indicator organisms for pollution-associated parameters were identified, among them a large fraction of microorganisms not covered by traditional morphology-based monitoring. This suggests that microarrays have a potential in future environmental monitoring.
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Affiliation(s)
- Katrine Lekang
- Department of Biology, University of Bergen, Bergen, Norway; Department of Pharmacy, University of Oslo, Norway.
| | - Anders Lanzén
- AZTI-Tecnalia, Marine Research Division, Pasaia, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Eric Thompson
- Department of Biology, University of Bergen, Bergen, Norway; Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway; NORCE, Bergen, Norway
| | - Christofer Troedsson
- Department of Biology, University of Bergen, Bergen, Norway; NORCE, Bergen, Norway; Ocean Bergen AS, Bergen, Norway
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7
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Konkel R, Toruńska-Sitarz A, Cegłowska M, Ežerinskis Ž, Šapolaitė J, Mažeika J, Mazur-Marzec H. Blooms of Toxic Cyanobacterium Nodularia spumigena in Norwegian Fjords During Holocene Warm Periods. Toxins (Basel) 2020; 12:toxins12040257. [PMID: 32326551 PMCID: PMC7232221 DOI: 10.3390/toxins12040257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/03/2020] [Accepted: 04/13/2020] [Indexed: 01/08/2023] Open
Abstract
In paleoecological studies, molecular markers are being used increasingly often to reconstruct community structures, environmental conditions and ecosystem changes. In this work, nodularin, anabaenopeptins and selected DNA sequences were applied as Nodularia spumigena markers to reconstruct the history of the cyanobacterium in the Norwegian fjords. For the purpose of this study, three sediment cores collected in Oslofjorden, Trondheimsfjorden and Balsfjorden were analyzed. The lack of nodularin in most recent sediments is consistent with the fact that only one report on the sporadic occurrence and low amounts of the cyanobacterium in Norwegian Fjords in 1976 has been published. However, analyses of species-specific chemical markers in deep sediments showed that thousands of years ago, N. spumigena constituted an important component of the phytoplankton community. The content of the markers in the cores indicated that the biomass of the cyanobacterium increased during the warmer Holocene periods. The analyses of genetic markers were less conclusive; they showed the occurrence of microcystin/nodularin producing cyanobacteria of Nostocales order, but they did not allow for the identification of the organisms at a species level.
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Affiliation(s)
- Robert Konkel
- University of Gdańsk, Faculty of Oceanography and Geography, Division of Marine Biotechnology, Marszałka J. Piłsudskiego 46, PL-81-378 Gdynia, Poland; (R.K.); (A.T.-S.)
| | - Anna Toruńska-Sitarz
- University of Gdańsk, Faculty of Oceanography and Geography, Division of Marine Biotechnology, Marszałka J. Piłsudskiego 46, PL-81-378 Gdynia, Poland; (R.K.); (A.T.-S.)
| | - Marta Cegłowska
- Institute of Oceanology, Polish Academy of Science, Powstańców Warszawy 55, PL-81-712 Sopot, Poland;
| | - Žilvinas Ežerinskis
- Mass Spectrometry Laboratory, Center for Physical Sciences and Technology, LT-10257 Vilnius, Lithuania; (Ž.E.); (J.Š.)
| | - Justina Šapolaitė
- Mass Spectrometry Laboratory, Center for Physical Sciences and Technology, LT-10257 Vilnius, Lithuania; (Ž.E.); (J.Š.)
| | - Jonas Mažeika
- Laboratory of nuclear geophysics and radioecology, Nature research Centre Akademijos Str. 2, LT-08412 Vilnius, Lithuania;
| | - Hanna Mazur-Marzec
- University of Gdańsk, Faculty of Oceanography and Geography, Division of Marine Biotechnology, Marszałka J. Piłsudskiego 46, PL-81-378 Gdynia, Poland; (R.K.); (A.T.-S.)
- Correspondence: ; Tel.: +48-585-236-621
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8
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Chambouvet A, Monier A, Maguire F, Itoïz S, del Campo J, Elies P, Edvardsen B, Eikreim W, Richards TA. Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi. Curr Biol 2019; 29:4093-4101.e4. [DOI: 10.1016/j.cub.2019.09.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/12/2019] [Accepted: 09/30/2019] [Indexed: 11/29/2022]
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9
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Kremp A, Hansen PJ, Tillmann U, Savela H, Suikkanen S, Voß D, Barrera F, Jakobsen HH, Krock B. Distributions of three Alexandrium species and their toxins across a salinity gradient suggest an increasing impact of GDA producing A. pseudogonyaulax in shallow brackish waters of Northern Europe. HARMFUL ALGAE 2019; 87:101622. [PMID: 31349884 DOI: 10.1016/j.hal.2019.101622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 06/10/2023]
Abstract
Blooms of Alexandrium spp. are a well-known phenomenon in Northern European waters. While A. tamarense/catenella, and A. pseudogonyaulax have been reported from marine waters, high densities of A. ostenfeldii are mainly observed at lower salinities in North Sea estuaries and the Baltic Sea, suggesting salinity as a driver of Alexandrium species composition and toxin distribution. To investigate this relationship, an oceanographic expedition through a natural salinity gradient was conducted in June 2016 along the coasts of Denmark. Besides hydrographic data, phytoplankton and sediment samples were collected for analyses of Alexandrium spp. cell and cyst abundances, for toxin measurement and cell isolation. Plankton data revealed the predominance of A. pseudogonyaulax at all transect stations while A. ostenfeldii and A. catenella generally contributed a minor fraction to the Alexandrium community. High abundances of A. pseudogonyaulax in the shallow enclosed Limfjord were accompanied by high amounts of goniodomin A (GDA). This toxin was also detected at low abundances along with A. pseudogonyaulax in the North Sea and the Kattegat. Genetic and morphological characterization of established strains showed high similarity of the Northern European population to distant geographic populations. Despite low cell abundances of A. ostenfeldii, different profiles of cycloimines were measured in the North Sea and in the Limfjord. This field survey revealed that salinity alone does not determine Alexandrium species and toxin distribution, but emphasizes the importance of habitat conditions such as proximity to seed banks, shelter, and high nutrient concentrations. The results show that A. pseudogonyaulax has become a prominent member of the Alexandrium spp. community over the past decade in the study area. Analyses of long term monitoring data from the Limfjord confirmed a recent shift to A. pseudogonyaulax dominance. Cyst and toxin records of the species in Kiel Bight suggest a spreading potential into the brackish Baltic Sea, which might lead to an expansion of blooms under future climate conditions.
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Affiliation(s)
- Anke Kremp
- Leibniz Institut für Ostseeforschung Warnemünde, Seestr. 15, 18119 Rostock, Germany; Finnish Environment Institute, Marine Research Centre, Agnes Sjöbergin katu 2, 00790 Helsinki, Finland.
| | - Per Juel Hansen
- University of Copenhagen, Marine Biological Section, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Urban Tillmann
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany
| | - Henna Savela
- Finnish Environment Institute, Marine Research Centre, Agnes Sjöbergin katu 2, 00790 Helsinki, Finland; Department of Biochemistry/Biotechnology, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Sanna Suikkanen
- Finnish Environment Institute, Marine Research Centre, Agnes Sjöbergin katu 2, 00790 Helsinki, Finland
| | - Daniela Voß
- Institut für Chemie und Biologie des Meeres (ICBM), Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Facundo Barrera
- Departamento de Química Ambiental, Facultad de Ciencias. Centro de Investigación en Biodiversidad y Ambientes Sustentables. Universidad Católica de la Santísima Concepción. Alonso de Ribera 2850, 4090541, Concepción, Chile
| | - Hans Henrik Jakobsen
- University of Århus, Institute for Bioscience, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Bernd Krock
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570 Bremerhaven, Germany
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10
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Gran‐Stadniczeñko S, Egge E, Hostyeva V, Logares R, Eikrem W, Edvardsen B. Protist Diversity and Seasonal Dynamics in Skagerrak Plankton Communities as Revealed by Metabarcoding and Microscopy. J Eukaryot Microbiol 2019; 66:494-513. [PMID: 30414334 PMCID: PMC6587730 DOI: 10.1111/jeu.12700] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 02/03/2023]
Abstract
Protist community composition and seasonal dynamics are of major importance for the production of higher trophic levels, such as zooplankton and fish. Our aim was to reveal how the protist community in the Skagerrak changes through the seasons by combining high-throughput sequencing and microscopy of plankton collected monthly over two years. The V4 region of the 18S rRNA gene was amplified by eukaryote universal primers from the total RNA/cDNA. We found a strong seasonal variation in protist composition and proportional abundances, and a difference between two depths within the euphotic zone. Highest protist richness was found in late summer-early autumn, and lowest in winter. Temperature was the abiotic factor explaining most of the variation in diversity. Dinoflagellates was the most abundant and diverse group followed by ciliates and diatoms. We found about 70 new taxa recorded for the first time in the Skagerrak. The seasonal pattern in relative read abundance of major phytoplankton groups was well in accordance with microscopical biovolumes. This is the first metabarcoding study of the protist plankton community of all taxonomic groups and through seasons in the Skagerrak, which may serve as a baseline for future surveys to reveal effects of climate and environmental changes.
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Affiliation(s)
| | - Elianne Egge
- Department of BiosciencesUniversity of OsloP. O. Box 1066 Blindern0316OsloNorway
| | | | - Ramiro Logares
- Department of Marine Biology and OceanographyInstitut de Ciències del Mar (CSIC)08003BarcelonaCataloniaSpain
| | - Wenche Eikrem
- Department of BiosciencesUniversity of OsloP. O. Box 1066 Blindern0316OsloNorway
- Norwegian Institute for Water ResearchGaustadalléen 210349OsloNorway
| | - Bente Edvardsen
- Department of BiosciencesUniversity of OsloP. O. Box 1066 Blindern0316OsloNorway
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11
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Danchenko S, Fragoso B, Guillebault D, Icely J, Berzano M, Newton A. Harmful phytoplankton diversity and dynamics in an upwelling region (Sagres, SW Portugal) revealed by ribosomal RNA microarray combined with microscopy. HARMFUL ALGAE 2019; 82:52-71. [PMID: 30928011 DOI: 10.1016/j.hal.2018.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
The study region in Sagres, SW Portugal, is subject to natural eutrophication of coastal waters by wind-driven upwelling, which stimulates high primary productivity facilitating the recent economic expansion of bivalve aquaculture in the region. However, this economic activity is threatened by harmful algal blooms (HAB) caused by the diatoms Pseudo-nitzschia spp., Dinophysis spp. and other HAB dinoflagellates, all of which can produce toxins, that can induce Amnesic Shellfish Poisoning (ASP), Diarrhetic Shellfish Poisoning (DSP) and Paralytic Shellfish Poisoning (PSP). This study couples traditional microscopy with 18S/28S rRNA microarray to improve the detection of HAB species and investigates the relation between HAB and the specific oceanographic conditions in the region. Good agreement was obtained between microscopy and microarray data for diatoms of genus Pseudo-nitzschia and dinoflagellates Dinophysis spp., Gymnodinium catenatum and raphidophyte Heterosigma akashiwo, with less effective results for Prorocentrum. Microarray provided detection of flagellates Prymnesium spp., Pseudochattonella spp., Chloromorum toxicum and the important HAB dinoflagellates of the genera Alexandrium and Azadinium, with the latter being one of the first records from the study region. Seasonality and upwelling induced by northerly winds were found to be the driving forces of HAB development, with Pseudo-nitzschia spp. causing the risk of ASP during spring and summer upwelling season, and dinoflagellates causing the risk of DSP and PSP during upwelling relaxation, mainly in summer and autumn. The findings were in agreement with the results from toxicity monitoring of shellfish by the Portuguese Institute for Sea and Atmosphere and confirm the suitability of the RNA microarray method for HABs detection and aquaculture management applications.
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Affiliation(s)
- Sergei Danchenko
- CIMA - Centre for Marine and Environmental Research, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; Facultad de Ciencias del Mar y Ambientales, University of Cadiz, Campus de Puerto Real, Polígono San Pedro s/n, Puerto Real, 11510, Cadiz, Spain.
| | - Bruno Fragoso
- CIMA - Centre for Marine and Environmental Research, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; Facultad de Ciencias del Mar y Ambientales, University of Cadiz, Campus de Puerto Real, Polígono San Pedro s/n, Puerto Real, 11510, Cadiz, Spain; Sagremarisco Lda., Apartado 21, Vila do Bispo, 8650-999, Portugal
| | | | - John Icely
- CIMA - Centre for Marine and Environmental Research, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; Sagremarisco Lda., Apartado 21, Vila do Bispo, 8650-999, Portugal
| | - Marco Berzano
- Polytechnic University of Marche, Piazza Roma, 22, 60121 Ancona, AN, Italy
| | - Alice Newton
- FCT - University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; NILU-IMPEC, Box 100, 2027 Kjeller, Norway
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12
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Mazzega E, Beran A, Cabrini M, de Marco A. In vitro isolation of nanobodies for selective Alexandrium minutum recognition: A model for convenient development of dedicated immuno-reagents to study and diagnostic toxic unicellular algae. HARMFUL ALGAE 2019; 82:44-51. [PMID: 30928010 DOI: 10.1016/j.hal.2019.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 06/09/2023]
Abstract
At the present, the identification of planktonic species in coastal water is still a time intensive process performed by highly trained personnel that relies either on qPCR or on light microscopy observation and in vitro culturing. Furthermore, the increasing danger represented by Harmful Algal Blooms (HABs) inside phytoplankton community and the recent implementation of the legislation on ballast water management to prevent the introduction of HABs and NIS (Non Indigenous Species) urge the development of faster and reliable diagnostic methods. Immuno-based approaches could fulfil this need provided that the costs for antibody selection and production will be reduced. In this work it is demonstrated for the first time the feasibility to recover nanobodies (VHHs) selective for native surface epitopes of Alexandrium minutum by direct whole cell bio-panning using a pre-immune phage display library. The recombinant nature of VHHs enabled their rapid engineering into eGFP fluorescent reagents (fluobodies) that were produced recombinantly in bacteria and are directly suitable for fluorescence microscopy and flow cytometry. Immune-detection identified also cysts and anti-Alexandrium fluobodies showed no cross-reactivity with indigenous not-toxic phytoplankton microalgae belonging to different geni. The fluobodies were able to bind selectively to the target cells in both fixed and fresh samples with minimal processing.
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Affiliation(s)
- Elisa Mazzega
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia
| | - Alfred Beran
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Trieste, Italy
| | - Marina Cabrini
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), Trieste, Italy
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Slovenia.
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13
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Diatom diversity through HTS-metabarcoding in coastal European seas. Sci Rep 2018; 8:18059. [PMID: 30584235 PMCID: PMC6305388 DOI: 10.1038/s41598-018-36345-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 11/16/2018] [Indexed: 11/30/2022] Open
Abstract
Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community. Almost all metabarcodes (99.6%) were assigned to known genera (121) and species (236), the most abundant of which were those already known from classic studies and coincided with those seen in light microscopy. rDNA and rRNA showed comparable patterns for the dominant taxa, but rRNA revealed a much higher diversity particularly in the sediment communities. Peculiar to diatoms is a tight bentho-pelagic coupling, with many benthic or planktonic species colonizing both water column and sediments and the dominance of planktonic species in both habitats. Overall metabarcoding results reflected the marked specificity of diatoms compared to other protistan groups in terms of morphological and ecological characteristics, at the same time confirming their great potential in the description of protist communities.
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14
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Development and testing of an 18S rRNA phylogenetic microarray for marine sediments. J Microbiol Methods 2018; 154:95-106. [DOI: 10.1016/j.mimet.2018.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/09/2018] [Accepted: 10/08/2018] [Indexed: 11/22/2022]
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15
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Engesmo A, Strand D, Gran-Stadniczeñko S, Edvardsen B, Medlin LK, Eikrem W. Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae). HARMFUL ALGAE 2018; 75:105-117. [PMID: 29778220 DOI: 10.1016/j.hal.2018.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
Blooms of ichthyotoxic microalgae pose a great challenge to the aquaculture industry world-wide, and there is a need for fast and specific methods for their detection and quantification in monitoring programs. In this study, quantitative real-time PCR (qPCR) assays for the detection and enumeration of three ichthyotoxic flagellates: the dinoflagellate Karenia mikimotoi (Miyake & Kominami ex Oda) Hansen & Moestrup and the two raphidophytes Heterosigma akashiwo (Hada) Hada ex Hara & Chihara and Fibrocapsa japonica Toriumi & Takano were developed. Further, a previously published qPCR assay for the dinoflagellate Karlodinium veneficum (Ballantine) Larsen was used. Monthly samples collected for three years (Aug 2009-Jun 2012) in outer Oslofjorden, Norway were analysed, and the results compared with light microscopy cell counts. The results indicate a higher sensitivity and a lower detection limit (down to 1 cell L-1) for both qPCR assays. Qualitative and semi-quantitative results were further compared with those obtained by environmental 454 high throughput sequencing (HTS, metabarcoding) and scanning electron microscopy (SEM) examination from the same samplings. All four species were detected by qPCR and HTS and/or SEM in outer Oslofjorden (Aug 2009-Jun 2012); Karlodinium veneficum was present year-round, whereas Karenia mikimotoi, Heterosigma akashiwo and Fibrocapsa japonica appeared mainly during the autumn in all three years. This is the first observation of Fibrocapsa japonica in Norwegian coastal waters. This species has previously been recorded off the Swedish west coast and German Bight, which may suggest a northward dispersal.
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Affiliation(s)
- Anette Engesmo
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway.
| | - David Strand
- Norwegian Veterinary Institute, P.O. box 750 Sentrum, 0106, Oslo, Norway.
| | | | - Bente Edvardsen
- University of Oslo, Department of Biosciences, P. O. box 1066 Blindern, 0316, Oslo, Norway.
| | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, Pl1 2PB, United Kingdom.
| | - Wenche Eikrem
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway; University of Oslo, Department of Biosciences, P. O. box 1066 Blindern, 0316, Oslo, Norway.
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16
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Kurt O, Özdal-Kurt F, Akçora CM, Özkut M, Tuğlu MI. Neurotoxic, cytotoxic, apoptotic and antiproliferative effects of some marine algae extracts on the NA2B cell line. Biotech Histochem 2018; 93:59-69. [PMID: 29388476 DOI: 10.1080/10520295.2017.1381992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Oxidative stress contributes to cancer pathologies and to apoptosis. Marine algae exhibit cytotoxic, antiproliferative and apoptotic effects; their metabolites have been used to treat many types of cancer. We investigated in culture extracts of Petalonia fascia, Jania longifurca and Halimeda tuna to determine their effects on mouse neuroblastoma cell line, NA2B. NA2B cells were treated with algae extracts, and the survival and proliferation of NA2B cells were assessed using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The effects of algae extracts on oxidative stress in NA2B cells also were investigated using nitric oxide synthase (NOS) immunocytochemistry and apoptosis was assessed using terminal deoxynucleotidyl transferase dUTP nick end labeling. We observed significant neurite inhibition with moderate damage by the neurotoxicity-screening test (NST) at IC50 dilutions of the extracts. MTT demonstrated that J. longifurca extracts were more toxic than P. fascia and H. tuna extracts. We found an increase of endothelial and inducible NOS immunostaining for oxidative stress and TUNEL analysis revealed increased apoptosis after application of extract. Our findings suggest that the algae we tested may have potential use for treatment of cancer.
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Affiliation(s)
- O Kurt
- a Faculty of Sciences and Literature, Department of Biology , Manisa Celal Bayar University , Yunusemre/Manisa , Turkey
| | - F Özdal-Kurt
- a Faculty of Sciences and Literature, Department of Biology , Manisa Celal Bayar University , Yunusemre/Manisa , Turkey
- b Department of Molecular, Cell and Systems Biology, Stem Cell Center , College of Natural and Agricultural Sciences, University of California Riverside , Riverside , CA
| | - C M Akçora
- a Faculty of Sciences and Literature, Department of Biology , Manisa Celal Bayar University , Yunusemre/Manisa , Turkey
| | - M Özkut
- c Department of Histology and Embryology, Faculty of Medicine , Manisa Celal Bayar University , Yunusemre/Manisa , Turkey
| | - M I Tuğlu
- c Department of Histology and Embryology, Faculty of Medicine , Manisa Celal Bayar University , Yunusemre/Manisa , Turkey
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17
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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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18
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Orozco J, Villa E, Manes CL, Medlin LK, Guillebault D. Electrochemical RNA genosensors for toxic algal species: enhancing selectivity and sensitivity. Talanta 2016; 161:560-566. [PMID: 27769448 DOI: 10.1016/j.talanta.2016.08.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/18/2016] [Accepted: 08/28/2016] [Indexed: 10/21/2022]
Abstract
Harmful algal blooms (HABs) are becoming more frequent as climate changes, with tropical species moving northward. Monitoring programs detecting the presence of toxic algae before they bloom are of paramount importance to protect aquatic ecosystems, aquaculture, human health and local economies. Rapid and reliable species identification methods using molecular barcodes coupled to biosensor detection tools have received increasing attention over the past decade as an alternative to the impractical standard microscopic counting-based techniques. This work reports on a PCR amplification-free electrochemical genosensor for the enhanced selective and sensitive detection of RNA from multiple Mediterranean toxic algal species. For a sandwich hybridization (SHA), we designed longer capture and signal probes for more specific target discrimination against a single base-pair mismatch from closely related species and for reproducible signals. We optimized experimental conditions, viz., minimal probe concentration in the SHA on a screen-printed gold electrode and selected the best electrochemical mediator. Probes from 13 Mediterranean dinoflagellate species were tested under optimized conditions and the format further tested for quantification of RNA from environmental samples. We not only enhanced the selectivity and sensitivity of the state-of-the-art toxic algal genosensors but also increased the repertoire of toxic algal biosensors in the Mediterranean, towards an integral and automatic monitoring system.
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Affiliation(s)
- Jahir Orozco
- Microbia Environnement Observatoire Océanologique, Banyuls/mer, F-66651 France.
| | - Elisa Villa
- Microbia Environnement Observatoire Océanologique, Banyuls/mer, F-66651 France
| | - Carmem-Lara Manes
- Microbia Environnement Observatoire Océanologique, Banyuls/mer, F-66651 France
| | - Linda K Medlin
- Microbia Environnement Observatoire Océanologique, Banyuls/mer, F-66651 France
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19
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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: 26] [Impact Index Per Article: 2.9] [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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20
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Zhang C, Chen G, Ma C, Wang Y, Zhang B, Wang G. Parallel detection of harmful algae using reverse transcription polymerase chain reaction labeling coupled with membrane-based DNA array. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:4565-4575. [PMID: 24338073 DOI: 10.1007/s11356-013-2416-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/27/2013] [Indexed: 06/03/2023]
Abstract
Harmful algal blooms (HABs) are a global problem, which can cause economic loss to aquaculture industry's and pose a potential threat to human health. More attention must be made on the development of effective detection methods for the causative microalgae. The traditional microscopic examination has many disadvantages, such as low efficiency, inaccuracy, and requires specialized skill in identification and especially is incompetent for parallel analysis of several morphologically similar microalgae to species level at one time. This study aimed at exploring the feasibility of using membrane-based DNA array for parallel detection of several microalgae by selecting five microaglae, including Heterosigma akashiwo, Chaetoceros debilis, Skeletonema costatum, Prorocentrum donghaiense, and Nitzschia closterium as test species. Five species-specific (taxonomic) probes were designed from variable regions of the large subunit ribosomal DNA (LSU rDNA) by visualizing the alignment of LSU rDNA of related species. The specificity of the probes was confirmed by dot blot hybridization. The membrane-based DNA array was prepared by spotting the tailed taxonomic probes onto positively charged nylon membrane. Digoxigenin (Dig) labeling of target molecules was performed by multiple PCR/RT-PCR using RNA/DNA mixture of five microalgae as template. The Dig-labeled amplification products were hybridized with the membrane-based DNA array to produce visible hybridization signal indicating the presence of target algae. Detection sensitivity comparison showed that RT-PCR labeling (RPL) coupled with hybridization was tenfold more sensitive than DNA-PCR-labeling-coupled with hybridization. Finally, the effectiveness of RPL coupled with membrane-based DNA array was validated by testing with simulated and natural water samples, respectively. All of these results indicated that RPL coupled with membrane-based DNA array is specific, simple, and sensitive for parallel detection of microalgae which shows promise for monitoring natural samples in the future.
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Affiliation(s)
- Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, People's Republic of China
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21
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Dittami SM, Riisberg I, Edvardsen B. Molecular probes for the detection and identification of ichthyotoxic marine microalgae of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6824-6837. [PMID: 23361173 DOI: 10.1007/s11356-012-1402-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 12/03/2012] [Indexed: 06/01/2023]
Abstract
Phytoflagellates of the genus Pseudochattonella (Dictyochophyceae, Ochrophyta) form blooms in marine coastal waters in northern Europe, Japan, and New Zealand that at times cause fish kills with severe losses for the aquaculture industry. The aim of this study was to develop molecular probes for the detection and identification of Pseudochattonella at the genus and species level. A variety of probes were developed and applied to either dot blot hybridization, (q)PCR, or microarray format. In the dot blot hybridization assay, five different oligonucleotide probes targeting the small subunit (SSU) rDNA were tested against DNA from 18 microalgal strains and shown to be specific to the genus Pseudochattonella. A genus-specific PCR assay was developed by identifying an appropriate primer pair in the SSU-internal transcribed spacer 1 (ITS1) rDNA region. Its specificity was tested by screening against both target and non-target strains, and the assay was used to confirm the presence or absence of Pseudochattonella species in environmental samples. In order to distinguish between the two species of the genus, two PCR primer pairs each biased towards one of the species were designed in the large subunit (LSU) rDNA D1 domain and used for quantitative real-time PCR. Five selected probes (three SSU and two LSU rDNA) were adapted for the use on microarrays and included on a prototype multi-species microarray for the detection of harmful algae ( http://www.midtal.com ). Finally, microarrays and qPCR were used for the monthly monitoring of a sampling site in outer Oslofjorden during a 1-year period. Members of Pseudochattonella are difficult to identify by light microscopy in Lugol's preserved samples, and the two species Pseudochattonella verruculosa and Pseudochattonella farcimen can be morphologically distinguished only by transmission electron microscopy. The molecular probes designed in this study will be a valuable asset to microscopical detection methods in the monitoring of harmful algae and for biogeographical and ecological studies of this genus.
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Affiliation(s)
- Simon M Dittami
- Department of Biology, Marine Biology, University of Oslo, P.O. Box 1066, Blindern, 0316, Oslo, Norway
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22
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Edvardsen B, Dittami SM, Groben R, Brubak S, Escalera L, Rodríguez F, Reguera B, Chen J, Medlin LK. Molecular probes and microarrays for the detection of toxic algae in the genera Dinophysis and Phalacroma (Dinophyta). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6733-6750. [PMID: 23263760 PMCID: PMC3782643 DOI: 10.1007/s11356-012-1403-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/03/2012] [Indexed: 06/01/2023]
Abstract
Dinophysis and Phalacroma species containing diarrheic shellfish toxins and pectenotoxins occur in coastal temperate waters all year round and prevent the harvesting of mussels during several months each year in regions in Europe, Chile, Japan, and New Zealand. Toxicity varies among morphologically similar species, and a precise identification is needed for early warning systems. Molecular techniques using ribosomal DNA sequences offer a means to identify and detect precisely the potentially toxic species. We designed molecular probes targeting the 18S rDNA at the family and genus levels for Dinophysis and Phalacroma and at the species level for Dinophysis acuminata, Dinophysis acuta, and Dinophysis norvegica, the most commonly occurring, potentially toxic species of these genera in Western European waters. Dot blot hybridizations with polymerase chain reaction (PCR)-amplified rDNA from 17 microalgae were used to demonstrate probe specificity. The probes were modified along with other published fluorescence in situ hybridization and PCR probes and tested for a microarray platform within the MIDTAL project ( http://www.midtal.com ). The microarray was applied to field samples from Norway and Spain and compared to microscopic cell counts. These probes may be useful for early warning systems and monitoring and can also be used in population dynamic studies to distinguish species and life cycle stages, such as cysts, and their distribution in time and space.
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Affiliation(s)
- Bente Edvardsen
- Marine Biology, Department of Biology, University of Oslo, P.O. Box 1066, 0316, Oslo, Norway,
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23
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Testing a Microarray to Detect and Monitor Toxic Microalgae in Arcachon Bay in France. MICROARRAYS 2013; 2:1-23. [PMID: 27605178 PMCID: PMC5003436 DOI: 10.3390/microarrays2010001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/24/2013] [Accepted: 02/26/2013] [Indexed: 11/16/2022]
Abstract
Harmful algal blooms (HABs) occur worldwide, causing health problems and economic damages to fisheries and tourism. Monitoring agencies are therefore essential, yet monitoring is based only on time-consuming light microscopy, a level at which a correct identification can be limited by insufficient morphological characters. The project MIDTAL (Microarray Detection of Toxic Algae)—an FP7-funded EU project—used rRNA genes (SSU and LSU) as a target on microarrays to identify toxic species. Furthermore, toxins were detected with a newly developed multiplex optical Surface Plasmon Resonance biosensor (Multi SPR) and compared with an enzyme-linked immunosorbent assay (ELISA). In this study, we demonstrate the latest generation of MIDTAL microarrays (version 3) and show the correlation between cell counts, detected toxin and microarray signals from field samples taken in Arcachon Bay in France in 2011. The MIDTAL microarray always detected more potentially toxic species than those detected by microscopic counts. The toxin detection was even more sensitive than both methods. Because of the universal nature of both toxin and species microarrays, they can be used to detect invasive species. Nevertheless, the MIDTAL microarray is not completely universal: first, because not all toxic species are on the chip, and second, because invasive species, such as Ostreopsis, already influence European coasts.
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