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Guillebault D, Medlin LK. Application of the μAqua microarray for pathogenic organisms across a marine/freshwater interface. Harmful Algae 2020; 92:101703. [PMID: 32113605 DOI: 10.1016/j.hal.2019.101703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/26/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Monitoring drinking water quality is an important public health issue and pathogenic organisms present a particularly serious health hazard in freshwater bodies. However, many pathogenic bacteria, including cyanobacteria, and pathogenic protozoa can be swept into coastal lagoons and into near-shore marine environments where they continue to grow and pose a health threat to marine mammals and invertebrates. In this study, we tested the suitability of a phylochip (microarray for species detection) developed for freshwater pathogenic organisms to be applied to samples taken across a marine/freshwater interface at monthly intervals for two years. Toxic cyanobacteria and pathogenic protozoa were more numerous in a coastal lagoon than at the freshwater or marine site, indicating that this microarray can be used to detect the presence of these pathogens across a marine/freshwater interface and thus the potential for toxicity to occur within the entire watershed.
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Affiliation(s)
- Delphine Guillebault
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, F-66650, Banyuls sur Mer, France
| | - Linda K Medlin
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes LBBM, F-66650, Banyuls sur Mer, France.
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Van de Waal DB, Guillebault D, Alfonso A, Rodríguez I, Botana LM, Bijkerk R, Medlin LK. Molecular detection of harmful cyanobacteria and expression of their toxin genes in Dutch lakes using multi-probe RNA chips. Harmful Algae 2018; 72:25-35. [PMID: 29413382 DOI: 10.1016/j.hal.2017.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 06/08/2023]
Abstract
Harmful cyanobacterial blooms are a major threat to water quality and human health. Adequate risk assessment is thus required, which relies strongly on comprehensive monitoring. Here, we tested novel multi-probe RNA chips developed in the European project, μAqua, to determine the abundance of harmful cyanobacterial species and expression of selected toxin genes in six Dutch lakes. All of the targeted cyanobacterial genera, except for Planktothrix, were detected using the microarray, with predominance of Dolichospermum and Microcystis signals, of which the former was found across all sites and detected by the probes for Anabaena where it was formerly placed. These were confirmed by microscopic cell counts at three sites, whereas at the other sites, microscopic cell counts were lower. Probe signals of Microcystis showed larger variation across sites but also matched microscopic counts for three sites. At the other sites, microscopic counts were distinctly higher. We detected anatoxin-a in the water at all sites, but unfortunately no genes for this toxin were on this generation of the toxin array. For microcystins, we found none or low concentrations in the water, despite high population densities of putative microcystin producers (i.e. Microcystis, Dolichospermum). The described method requires further testing with a wider range of cyanobacterial communities and toxin concentrations before implementation into routine cyanobacterial risk assessment. Yet, our results demonstrate a great potential for applying multi-probe RNA chips for species as well as toxins to eutrophic waters with high cyanobacterial densities as a routine monitoring tool and as a predictive tool for toxin potential.
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Affiliation(s)
- Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Post Office Box 50, 6700 AB Wageningen, The Netherlands.
| | | | - Amparo Alfonso
- Department of Pharmacology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus Universitario, 27002 Lugo, Spain
| | - Inés Rodríguez
- Department of Pharmacology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus Universitario, 27002 Lugo, Spain
| | - Luis M Botana
- Department of Pharmacology, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus Universitario, 27002 Lugo, Spain
| | - Ronald Bijkerk
- Koeman & Bijkerk B.V., Post Office Box 111, 9750 AC Haren, The Netherlands
| | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, PL1 2PB, UK
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Akçaalan R, Albay M, Koker L, Baudart J, Guillebault D, Fischer S, Weigel W, Medlin LK. Seasonal dynamics of freshwater pathogens as measured by microarray at Lake Sapanca, a drinking water source in the north-eastern part of Turkey. Environ Monit Assess 2017; 190:42. [PMID: 29273852 DOI: 10.1007/s10661-017-6314-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
Monitoring drinking water quality is an important public health issue. Two objectives from the 4 years, six nations, EU Project μAqua were to develop hierarchically specific probes to detect and quantify pathogens in drinking water using a PCR-free microarray platform and to design a standardised water sampling program from different sources in Europe to obtain sufficient material for downstream analysis. Our phylochip contains barcodes (probes) that specifically identify freshwater pathogens that are human health risks in a taxonomic hierarchical fashion such that if species is present, the entire taxonomic hierarchy (genus, family, order, phylum, kingdom) leading to it must also be present, which avoids false positives. Molecular tools are more rapid, accurate and reliable than traditional methods, which means faster mitigation strategies with less harm to humans and the community. We present microarray results for the presence of freshwater pathogens from a Turkish lake used drinking water and inferred cyanobacterial cell equivalents from samples concentrated from 40 into 1 L in 45 min using hollow fibre filters. In two companion studies from the same samples, cyanobacterial toxins were analysed using chemical methods and those dates with highest toxin values also had highest cell equivalents as inferred from this microarray study.
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Affiliation(s)
- Reyhan Akçaalan
- Faculty of Aquatic Sciences, Istanbul University, Ordu cad. No:8 34134, Laleli, Istanbul, Turkey
| | - Meric Albay
- Faculty of Aquatic Sciences, Istanbul University, Ordu cad. No:8 34134, Laleli, Istanbul, Turkey
| | - Latife Koker
- Faculty of Aquatic Sciences, Istanbul University, Ordu cad. No:8 34134, Laleli, Istanbul, Turkey
| | - Julia Baudart
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
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5
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Baudart J, Guillebault D, Mielke E, Meyer T, Tandon N, Fischer S, Weigel W, Medlin LK. Erratum to: Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters. Appl Microbiol Biotechnol 2016; 101:887. [PMID: 27966050 DOI: 10.1007/s00253-016-8040-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Julia Baudart
- Sorbonne Universités, UPMC University Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, (LBBM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | | | - Erik Mielke
- MariLim Aquatic Research, GmbH Heinrich-Wöhlk-Str. 14, 24232, Kiel, Germany
| | - Thomas Meyer
- MariLim Aquatic Research, GmbH Heinrich-Wöhlk-Str. 14, 24232, Kiel, Germany
| | | | | | | | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, PL1 2PB, UK.
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6
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Baudart J, Guillebault D, Mielke E, Meyer T, Tandon N, Fischer S, Weigel W, Medlin LK. Microarray (phylochip) analysis of freshwater pathogens at several sites along the Northern German coast transecting both estuarine and freshwaters. Appl Microbiol Biotechnol 2016; 101:871-886. [PMID: 27872997 DOI: 10.1007/s00253-016-7937-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/02/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Monitoring the quality of drinking water is an important issue for public health. Two of the main objectives of the European Project μAQUA were (i) the development of specific probes to detect and quantify pathogens in drinking water and (ii) the design of standardized sampling programs of water from different sources in Europe in order to obtain sufficient material for downstream analysis. Our phylochip contains barcodes that specifically identify freshwater pathogens for enabling the detection of organisms that can be risks for human health. Monitoring for organisms with molecular tools is rapid, more accurate and more reliable than traditional methods. Rapid detection means that mitigation strategies come into play faster with less harm to the community and to humans. Samples were collected from several waters in France, Germany, Ireland, Italy and Turkey over 2 years. We present microarray results for the presence of freshwater pathogens from brackish and freshwater sites in Northern Germany, and cyanobacterial cell numbers inferred from these sites. In a companion study from the same samples, cyanobacterial toxins were analyzed using two methods and those sites with highest toxin values also had highest cell numbers as inferred from this microarray study.
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Affiliation(s)
- Julia Baudart
- Sorbonne Universités, UPMC University Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, (LBBM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | | | - Erik Mielke
- MariLim Aquatic Research, GmbH Heinrich-Wöhlk-Str.14, 24232, Kiel, Germany
| | - Thomas Meyer
- MariLim Aquatic Research, GmbH Heinrich-Wöhlk-Str.14, 24232, Kiel, Germany
| | | | | | | | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, PL1 2PB, UK.
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7
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Kegel JU, Guillebault D, Medlin LK. Application of microarrays (phylochips) for analysis of community diversity by species identification. ACTA ACUST UNITED AC 2016. [DOI: 10.1127/pip/2016/0048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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D'Ugo E, Marcheggiani S, Fioramonti I, Giuseppetti R, Spurio R, Helmi K, Guillebault D, Medlin LK, Simeonovski I, Boots B, Breitenbach U, Koker L, Albay M, Mancini L. Detection of Human Enteric Viruses in Freshwater from European Countries. Food Environ Virol 2016; 8:206-214. [PMID: 27117764 DOI: 10.1007/s12560-016-9238-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
The transmission of water-borne pathogens typically occurs by a faecal-oral route, through inhalation of aerosols, or by direct or indirect contact with contaminated water. Previous molecular-based studies have identified viral particles of zoonotic and human nature in surface waters. Contaminated water can lead to human health issues, and the development of rapid methods for the detection of pathogenic microorganisms is a valuable tool for the prevention of their spread. The aims of this work were to determine the presence and identity of representative human pathogenic enteric viruses in water samples from six European countries by quantitative polymerase chain reaction (q-PCR) and to develop two quantitative PCR methods for Adenovirus 41 and Mammalian Orthoreoviruses. A 2-year survey showed that Norovirus, Mammalian Orthoreovirus and Adenoviruses were the most frequently identified enteric viruses in the sampled surface waters. Although it was not possible to establish viability and infectivity of the viruses considered, the detectable presence of pathogenic viruses may represent a potential risk for human health. The methodology developed may aid in rapid detection of these pathogens for monitoring quality of surface waters.
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Affiliation(s)
- Emilio D'Ugo
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy.
| | - Stefania Marcheggiani
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Ilaria Fioramonti
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Giuseppetti
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Spurio
- School of Biosciences and Veterinary Medicine, University of Camerino, Ascoli Piceno, Italy
| | - Karim Helmi
- Veolia Rechercheur & Innovation, Saint-Maurice, France
| | | | - Linda K Medlin
- Microbia Environnement, Observatoire Océanologique, 66650, Banyuls/Mer, France
| | - Ivan Simeonovski
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Bas Boots
- UCD School of Biosystems Engineering, Agriculture and Food Science Centre, Dublin, Ireland
| | | | - Latife Koker
- Fisheries Faculty, Istanbul University, Istanbul, Turkey
| | - Meric Albay
- Fisheries Faculty, Istanbul University, Istanbul, Turkey
| | - Laura Mancini
- Quality and Fishfarm Unit, Department Environmental Environment & Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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McNamee SE, Medlin LK, Kegel J, McCoy GR, Raine R, Barra L, Ruggiero MV, Kooistra WHCF, Montresor M, Hagstrom J, Blanco EP, Graneli E, Rodríguez F, Escalera L, Reguera B, Dittami S, Edvardsen B, Taylor J, Lewis JM, Pazos Y, Elliott CT, Campbell K. Distribution, occurrence and biotoxin composition of the main shellfish toxin producing microalgae within European waters: A comparison of methods of analysis. Harmful Algae 2016; 55:112-120. [PMID: 28073524 DOI: 10.1016/j.hal.2016.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 06/06/2023]
Abstract
Harmful algal blooms (HABs) are a natural global phenomena emerging in severity and extent. Incidents have many economic, ecological and human health impacts. Monitoring and providing early warning of toxic HABs are critical for protecting public health. Current monitoring programmes include measuring the number of toxic phytoplankton cells in the water and biotoxin levels in shellfish tissue. As these efforts are demanding and labour intensive, methods which improve the efficiency are essential. This study compares the utilisation of a multitoxin surface plasmon resonance (multitoxin SPR) biosensor with enzyme-linked immunosorbent assay (ELISA) and analytical methods such as high performance liquid chromatography with fluorescence detection (HPLC-FLD) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) for toxic HAB monitoring efforts in Europe. Seawater samples (n=256) from European waters, collected 2009-2011, were analysed for biotoxins: saxitoxin and analogues, okadaic acid and dinophysistoxins 1/2 (DTX1/DTX2) and domoic acid responsible for paralytic shellfish poisoning (PSP), diarrheic shellfish poisoning (DSP) and amnesic shellfish poisoning (ASP), respectively. Biotoxins were detected mainly in samples from Spain and Ireland. France and Norway appeared to have the lowest number of toxic samples. Both the multitoxin SPR biosensor and the RNA microarray were more sensitive at detecting toxic HABs than standard light microscopy phytoplankton monitoring. Correlations between each of the detection methods were performed with the overall agreement, based on statistical 2×2 comparison tables, between each testing platform ranging between 32% and 74% for all three toxin families illustrating that one individual testing method may not be an ideal solution. An efficient early warning monitoring system for the detection of toxic HABs could therefore be achieved by combining both the multitoxin SPR biosensor and RNA microarray.
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Affiliation(s)
- Sara E McNamee
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Stranmillis Road, Belfast BT9 5AG, UK
| | - Linda K Medlin
- Marine Biological Association of UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Jessica Kegel
- Marine Biological Association of UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Gary R McCoy
- Martin Ryan Institute, National University of Ireland, Galway, Ireland
| | - Robin Raine
- Martin Ryan Institute, National University of Ireland, Galway, Ireland
| | - Lucia Barra
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | | | | | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Johannes Hagstrom
- Linnaeus University, Marine Ecology Department, SE-39182 Kalmar, Sweden
| | - Eva Perez Blanco
- Linnaeus University, Marine Ecology Department, SE-39182 Kalmar, Sweden
| | - Edna Graneli
- Linnaeus University, Marine Ecology Department, SE-39182 Kalmar, Sweden
| | - Francisco Rodríguez
- Instituto Español de Oceanografía, Subida a Radio Faro 50, 36390 Vigo, Spain
| | - Laura Escalera
- Instituto Español de Oceanografía, Subida a Radio Faro 50, 36390 Vigo, Spain
| | - Beatriz Reguera
- Instituto Español de Oceanografía, Subida a Radio Faro 50, 36390 Vigo, Spain
| | - Simon Dittami
- University of Oslo, Department of Biosciences, 0316 Oslo, Norway
| | - Bente Edvardsen
- University of Oslo, Department of Biosciences, 0316 Oslo, Norway
| | - Joe Taylor
- Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK
| | - Jane M Lewis
- Faculty of Science and Technology, University of Westminster, London W1W 6UW, UK
| | - Yolanda Pazos
- INTECMAR, Peirao de Vilaxoán, Villagarcía de Arosa 36611, Spain
| | - Christopher T Elliott
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Stranmillis Road, Belfast BT9 5AG, UK
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Stranmillis Road, Belfast BT9 5AG, UK.
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Greer B, McNamee SE, Boots B, Cimarelli L, Guillebault D, Helmi K, Marcheggiani S, Panaiotov S, Breitenbach U, Akçaalan R, Medlin LK, Kittler K, Elliott CT, Campbell K. A validated UPLC-MS/MS method for the surveillance of ten aquatic biotoxins in European brackish and freshwater systems. Harmful Algae 2016; 55:31-40. [PMID: 28073545 DOI: 10.1016/j.hal.2016.01.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Revised: 01/14/2016] [Accepted: 01/14/2016] [Indexed: 05/26/2023]
Abstract
Over the past few decades, there has been an increased frequency and duration of cyanobacterial Harmful Algal Blooms (HABs) in freshwater systems globally. These can produce secondary metabolites called cyanotoxins, many of which are hepatotoxins, raising concerns about repeated exposure through ingestion of contaminated drinking water or food or through recreational activities such as bathing/swimming. An ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) multi-toxin method has been developed and validated for freshwater cyanotoxins; microcystins-LR, -YR, -RR, -LA, -LY and -LF, nodularin, cylindrospermopsin, anatoxin-a and the marine diatom toxin domoic acid. Separation was achieved in around 9min and dual SPE was incorporated providing detection limits of between 0.3 and 5.6ng/L of original sample. Intra- and inter-day precision analysis showed relative standard deviations (RSD) of 1.2-9.6% and 1.3-12.0% respectively. The method was applied to the analysis of aquatic samples (n=206) from six European countries. The main class detected were the hepatotoxins; microcystin-YR (n=22), cylindrospermopsin (n=25), microcystin-RR (n=17), microcystin-LR (n=12), microcystin-LY (n=1), microcystin-LF (n=1) and nodularin (n=5). For microcystins, the levels detected ranged from 0.001 to 1.51μg/L, with two samples showing combined levels above the guideline set by the WHO of 1μg/L for microcystin-LR. Several samples presented with multiple toxins indicating the potential for synergistic effects and possibly enhanced toxicity. This is the first published pan European survey of freshwater bodies for multiple biotoxins, including two identified for the first time; cylindrospermopsin in Ireland and nodularin in Germany, presenting further incentives for improved monitoring and development of strategies to mitigate human exposure.
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Affiliation(s)
- Brett Greer
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, UK
| | - Sara E McNamee
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, UK
| | - Bas Boots
- University College Dublin, National University of Ireland, Dublin, Ireland
| | - Lucia Cimarelli
- Laboratory of Genetics, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, MC 62032, Italy
| | | | - Karim Helmi
- Veolia Environnement Recherche et Innovation SNC, France
| | | | - Stefan Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia 1504, Bulgaria
| | | | | | | | - Katrin Kittler
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Christopher T Elliott
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, UK
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Stranmillis Road, Belfast BT9 5AG, UK.
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12
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Herrera-Sepúlveda A, Medlin LK, Murugan G, Sierra-Beltrán AP, Cruz-Villacorta AA, Hernández-Saavedra NY. Are Prorocentrum hoffmannianum and Prorocentrum belizeanum (DINOPHYCEAE, PROROCENTRALES), the same species? An integration of morphological and molecular data. J Phycol 2015; 51:173-188. [PMID: 26986267 DOI: 10.1111/jpy.12265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/05/2014] [Indexed: 06/05/2023]
Abstract
The taxonomic assignment of Prorocentrum species is based on morphological characteristics; however, morphological variability has been found for several taxa isolated from different geographical regions. In this study, we evaluated species boundaries of Prorocentrum hoffmannianum and Prorocentrum belizeanum based on morphological and molecular data. A detailed morphological analysis was done, concentrating on the periflagellar architecture. Molecular analyses were performed on partial Small Sub-Unit (SSU) rDNA, partial Large Sub-Unit (LSU) rDNA, complete Internal Transcribed Spacer Regions (ITS1-5.8S-ITS2), and partial cytochrome b (cob) sequences. We concatenated the SSU-ITS-LSU fragments and constructed a phylogenetic tree using Bayesian Inference (BI) and maximum likelihood (ML) methods. Morphological analyses indicated that the main characters, such as cell size and number of depressions per valve, normally used to distinguish P. hoffmannianum from P. belizeanum, overlapped. No clear differences were found in the periflagellar area architecture. Prorocentrum hoffmannianum and P. belizeanum were a highly supported monophyletic clade separated into three subclades, which broadly corresponded to the sample collection regions. Subtle morphological overlaps found in cell shape, size, and ornamentation lead us to conclude that P. hoffmanianum and P. belizeanum might be considered conspecific. The molecular data analyses did not separate P. hoffmannianum and P. belizeanum into two morphospecies, and thus, we considered them to be the P. hoffmannianum species complex because their clades are separated by their geographic origin. These geographic and genetically distinct clades could be referred to as ribotypes: (A) Belize, (B) Florida-Cuba, (C1) India, and (C2) Australia.
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Affiliation(s)
- Angélica Herrera-Sepúlveda
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, PL1 2BP, UK
| | - Gopal Murugan
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Arturo P Sierra-Beltrán
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Ariel A Cruz-Villacorta
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Norma Y Hernández-Saavedra
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
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McCoy GR, Kegel JU, Touzet N, Fleming GTA, Medlin LK, Raine R. An assessment of RNA content in Prymnesium parvum, Prymnesium polylepis, cf. Chattonella sp. and Karlodinium veneficum under varying environmental conditions for calibrating an RNA microarray for species detection. FEMS Microbiol Ecol 2014; 88:140-59. [PMID: 24392749 DOI: 10.1111/1574-6941.12277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/06/2013] [Accepted: 12/22/2013] [Indexed: 10/25/2022] Open
Abstract
Traditional methods of identification and enumeration can be somewhat ambiguous when identifying phytoplankton that requires electron microscopic examination to verify specific morphological features. Members of the genus Prymnesium (division Haptophyta), members of the Raphidophyceae and naked dinoflagellates are examples of such phytoplankton whose identification can be difficult. One alternative to traditional microscopy-based methods of identification is to use molecular protocols to detect target species. Methods that measure cellular DNA and RNA content can be used to estimate the number of cells present in a sample. This study investigated the variation of RNA yields in Prymnesium parvum, P. polylepis, cf. Chattonella sp. and Karlodinium veneficum cells grown under different light, temperature, salinity and inorganic nutrient conditions. This information was used to calibrate the signal intensity of a variety of oligonucleotide probes spotted onto the microarrays for the detection of toxic algae (MIDTAL), which is being developed to aid national monitoring agencies and to provide a faster means of identifying and quantifying harmful phytoplankton in water column samples.
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Affiliation(s)
- Gary R McCoy
- The Ryan Institute, National University of Ireland, Galway, Ireland
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Medlin LK. Evolution of the Diatoms: VIII. Re-Examination of the SSU-Rrna Gene Using Multiple Outgroups and a Cladistic Analysis of Valve Features. ACTA ACUST UNITED AC 2014. [DOI: 10.4172/2376-0214.1000129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Orozco J, Medlin LK. Review: advances in electrochemical genosensors-based methods for monitoring blooms of toxic algae. Environ Sci Pollut Res Int 2013; 20:6838-6850. [PMID: 23097073 DOI: 10.1007/s11356-012-1258-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 10/09/2012] [Indexed: 05/28/2023]
Abstract
Harmful algal blooms (HABs), which have expanded worldwide in their occurrence and frequency, are a serious menace to aquatic ecosystems and humans. The development of rapid, accurate and cost-effective detection systems for toxic algal monitoring in aquatic environments is urgently required. Although many efforts have been devoted to develop reliable tools to monitor the entire spectrum of existing toxic algae, a portable semi-automated system that enables HAB monitoring at a low cost is still not available for general purchase. This work reviews the challenges and opportunities in translating the remarkable progress of electrochemical genosensors-based methods towards practical in situ HAB monitoring applications. It is specifically focused on reviewing the optimised methods for a detection system based on a sandwich hybridisation assay (SHA) performed over transducer platforms of different materials, geometries and dimensions and presenting the diverse advantages and disadvantages among them. Probe design and specificity and optimisation of the genosensor in terms of hybridisation conditions and electrochemical signal are discussed as well as their long-term stability and storage and semi-automation attempts. With continuous innovation and attention to key challenges, we expect semi-automatic devices containing DNA-based electrochemical biosensors to have an important impact upon monitoring of serious HAB events.
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Affiliation(s)
- Jahir Orozco
- Department of Nanoengineering, University of California-San Diego, La Jolla, CA, 92093, USA,
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Dittami SM, Pazos Y, Laspra M, Medlin LK. Microarray testing for the presence of toxic algae monitoring programme in Galicia (NW Spain). Environ Sci Pollut Res Int 2013; 20:6778-6793. [PMID: 23660802 DOI: 10.1007/s11356-012-1295-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/29/2012] [Indexed: 06/02/2023]
Abstract
Rapid and reliable detection of harmful algae in coastal areas and shellfish farms is an important requirement of monitoring programmes. Monitoring of toxic algae by means of traditional methods, i.e., light microscopy, can be time consuming when many samples have to be routinely analysed. Reliable species identification requires expensive equipment and trained personnel to carry out the analyses. However, all techniques for the monitoring of harmful algae usually require transportation of samples to specialised laboratories. In many monitoring laboratories, results are usually obtained within five working days after receiving the sample and therefore preventative measures are not always possible. Molecular technologies are rapidly improving the detection of phytoplankton and their toxins and the speed at which the results can be obtained. Assays are based on the discrimination of the genetic differences of the different species and species-specific probes can be designed. Such probes have been adapted to a microarray or phylochip format and assessed in several EU monitoring sites. Microarray results are presented for 1 year of field samples validated with cell counts from concentrated samples taken during toxic events from the weekly sampling of the Galician Monitoring Programme done by INTECMAR. The Galician monitoring laboratory does their own counting and their results are posted on their web site within 24 h. There was good correlation between cells present and microarray signals. In the few cases of false negatives, these can be attributed to poor RNA extraction of the target species, viz. Prorocentrum or Dinophysis. Where potential false positives were encountered, the smaller volume taken for cell counts as compared to the upto 300 times more volume taken for RNA extraction for the microarray is likely the cause for these differences, making the microarray more sensitive. The microarray was able to provide better species resolution in Alexandrium and Pseudo-nitzschia. In all cases, the toxins recovered by the toxin array were matched by target species in the array or in the cell counts.
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Affiliation(s)
- Simon M Dittami
- Department of Biology, University of Oslo, P.O. Box 1066, Blindern, 0316, Oslo, Norway
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Medlin LK. Note: steps taken to optimise probe specificity and signal intensity prior to field validation of the MIDTAL (Microarray for the Detection of Toxic Algae). Environ Sci Pollut Res Int 2013; 20:6686-6689. [PMID: 23636588 DOI: 10.1007/s11356-012-1450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 12/18/2012] [Indexed: 06/02/2023]
Abstract
A microarray for the detection of toxic algal species was developed in the European Union 7th Framework project MIDTAL. We initially tested all available fluorescence in situ hybridisation probes for toxic algae, which are normally designed to a length of 18 nt, and found that in most cases the signal was rather weak or all probes designed from the second half of the molecule were inaccessible in a microarray format because of secondary structure of the ribosomal RNA molecule We modified the length of the probes, the fragmentation of the rRNA, the stringency of the washing buffers and the length of the spacer molecules linking the probes to the glass surface of the microarray. Because of the secondary structure of the rRNA molecule, regions of the molecule can be difficult to access by the probes. Each of these modifications has improved probe accessibility and probe specificity to reduce false positives.
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Affiliation(s)
- Linda K Medlin
- Marine Biological Association of the UK, The Laboratory, Plymouth, PL1 2 PB, UK,
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Herrera-Sepúlveda A, Hernandez-Saavedra NY, Medlin LK, West N. Capillary electrophoresis finger print technique (CE-SSCP): an alternative tool for the monitoring activities of HAB species in Baja California Sur Costal. Environ Sci Pollut Res Int 2013; 20:6863-6871. [PMID: 22744160 DOI: 10.1007/s11356-012-1033-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/07/2012] [Indexed: 05/28/2023]
Abstract
In Mexican waters, there is no a formal and well-established monitoring program of harmful algal blooms (HAB) events. Until now, most of the work has been focused on the characterization of organisms present in certain communities. Therefore, the development of new techniques for the rapid detection of HAB species is necessary. Capillary electrophoresis finger print technique (CE-SSCP) is a fingerprinting technique based on the identification of different conformers dependent of its base composition. This technique, coupled with capillary electrophoresis, has been used to compare and identify different conformers. The aim of this study was to determine if CE-SSCP analysis of ribosomal RNA (rRNA) gene fragments could be used for a rapid identification of toxic and harmful HAB species to improve monitoring activities along the coasts of Baja California Sur, Mexico.Three different highly variable regions of the 18S and 28S rRNA genes were chosen and their suitability for the discrimination of different dinoflagellate species was assessed by CE-SSCP.The CE-SSCP results obtained for the LSU D7 fragment has demonstrated that this technique with this gene region could be useful for the identification of the ten dinoflagellates species of different genera.We have shown that this method can be used to discriminate species and the next step will be to apply it to natural samples to achieve our goal of molecular monitoring for toxic algae in Mexican waters. This strategy will offer an option to improve an early warning system of HAB events for coastal BCS, allowing the possible implementation of mitigation strategies. A monitoring program of HAB species using molecular methods will permit the analysis of several samples in a short period of time, without the pressure of counting with a taxonomic expert in phytoplankton taxonomy.
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Affiliation(s)
- Angélica Herrera-Sepúlveda
- Centro de Investigaciones Biológicas del Noroeste S. C., Instituto Politécnico Nacional No. 195, La Paz, BCS 23090, Mexico
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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). Environ Sci Pollut Res Int 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Seenivasan R, Sausen N, Medlin LK, Melkonian M. Picomonas judraskeda gen. et sp. nov.: the first identified member of the Picozoa phylum nov., a widespread group of picoeukaryotes, formerly known as 'picobiliphytes'. PLoS One 2013; 8:e59565. [PMID: 23555709 PMCID: PMC3608682 DOI: 10.1371/journal.pone.0059565] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 02/19/2013] [Indexed: 01/21/2023] Open
Abstract
In 2007, a novel, putatively photosynthetic picoeukaryotic lineage, the ‘picobiliphytes’, with no known close eukaryotic relatives, was reported from 18S environmental clone library sequences and fluorescence in situ hybridization. Although single cell genomics later showed these organisms to be heterotrophic rather than photosynthetic, until now this apparently widespread group of pico-(or nano-)eukaryotes has remained uncultured and the organisms could not be formally recognized. Here, we describe Picomonas judraskeda gen. et sp. nov., from marine coastal surface waters, which has a ‘picobiliphyte’ 18S rDNA signature. Using vital mitochondrial staining and cell sorting by flow cytometry, a single cell-derived culture was established. The cells are biflagellate, 2.5–3.8×2–2.5 µm in size, lack plastids and display a novel stereotypic cycle of cell motility (described as the “jump, drag, and skedaddle”-cycle). They consist of two hemispherical parts separated by a deep cleft, an anterior part that contains all major cell organelles including the flagellar apparatus, and a posterior part housing vacuoles/vesicles and the feeding apparatus, both parts separated by a large vacuolar cisterna. From serial section analyses of cells, fixed at putative stages of the feeding cycle, it is concluded that cells are not bacterivorous, but feed on small marine colloids of less than 150 nm diameter by fluid-phase, bulk flow endocytosis. Based on the novel features of cell motility, ultrastructure and feeding, and their isolated phylogenetic position, we establish a new phylum, Picozoa, for Picomonas judraskeda, representing an apparently widespread and ecologically important group of heterotrophic picoeukaryotes, formerly known as ‘picobiliphytes’.
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Affiliation(s)
- Ramkumar Seenivasan
- Department of Botany, Cologne Biocenter, University of Cologne, Cologne, Germany.
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21
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Ebenezer V, Medlin LK, Ki JS. Molecular detection, quantification, and diversity evaluation of microalgae. Mar Biotechnol (NY) 2012; 14:129-142. [PMID: 22200918 DOI: 10.1007/s10126-011-9427-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 12/02/2011] [Indexed: 05/31/2023]
Abstract
This study reviews the available molecular methods and new high-throughput technologies for their practical use in the molecular detection, quantification, and diversity assessment of microalgae. Molecular methods applied to other groups of organisms can be adopted for microalgal studies because they generally detect universal biomolecules, such as nucleic acids or proteins. These methods are primarily related to species detection and discrimination among various microalgae. Among current molecular methods, some molecular tools are highly valuable for small-scale detection [e.g., single-cell polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), and biosensors], whereas others are more useful for large-scale, high-throughput detection [e.g., terminal restriction length polymorphism, isothermal nucleic acid sequence-based amplification, loop-mediated isothermal amplification, microarray, and next generation sequencing (NGS) techniques]. Each molecular technique has its own strengths in detecting microalgae, but they may sometimes have limitations in terms of detection of other organisms. Among current technologies, qPCR may be considered the best method for molecular quantification of microalgae. Metagenomic microalgal diversity can easily be achieved by 454 pyrosequencing rather than by the clone library method. Current NGS, third and fourth generation technologies pave the way for the high-throughput detection and quantification of microalgal diversity, and have significant potential for future use in field monitoring.
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Affiliation(s)
- Vinitha Ebenezer
- Department of Green Life Science, College of Convergence, Sangmyung University, Seoul 110-743, South Korea
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Barker GLA, Green JC, Hayes PK, Medlin LK. Preliminary results using the rapd analysis to screen bloom populations ofEmiliania huxleyi(Haptophyta). ACTA ACUST UNITED AC 2012. [DOI: 10.1080/00364827.1994.10413562] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Aggarwal RK, Allainguillaume J, Bajay MM, Barthwal S, Bertolino P, Chauhan P, Consuegra S, Croxford A, Dalton DL, den Belder E, Díaz-Ferguson E, Douglas MR, Drees M, Elderson J, Esselink GD, Fernández-Manjarrés JF, Frascaria-Lacoste N, Gäbler-Schwarz S, Garcia de Leaniz C, Ginwal HS, Goodisman MAD, Guo B, Hamilton MB, Hayes PK, Hong Y, Kajita T, Kalinowski ST, Keller L, Koop BF, Kotzé A, Lalremruata A, Leese F, Li C, Liew WY, Martinelli S, Matthews EA, Medlin LK, Messmer AM, Meyer EI, Monteiro M, Moyer GR, Nelson RJ, Nguyen TTT, Omoto C, Ono J, Pavinato VAC, Pearcy M, Pinheiro JB, Power LD, Rawat A, Reusch TBH, Sanderson D, Sannier J, Sathe S, Sheridan CK, Smulders MJM, Sukganah A, Takayama K, Tamura M, Tateishi Y, Vanhaecke D, Vu NV, Wickneswari R, Williams AS, Wimp GM, Witte V, Zucchi MI. Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010. Mol Ecol Resour 2011; 11:219-22. [PMID: 21429127 DOI: 10.1111/j.1755-0998.2010.02944.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.
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Affiliation(s)
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- Centre for Cellular and Molecular Biology (CSIR), Hyderabad 500007, India
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Medlin LK, Kaczmarska I. Corrigendum to “Letter to the Editor Correctly assigning original discoveries to original authors” [Mol. Phylogenet. Evol. 50 (2009) 407–408]. Mol Phylogenet Evol 2010. [DOI: 10.1016/j.ympev.2010.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Medlin LK, Kaczmarska I. Correctly assigning original discoveries to original authors. Mol Phylogenet Evol 2009; 50:407-8; author reply 409-10. [DOI: 10.1016/j.ympev.2008.08.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 08/28/2008] [Indexed: 10/21/2022]
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Medlin LK, Sato S, Mann DG, Kooistra WHCF. MOLECULAR EVIDENCE CONFIRMS SISTER RELATIONSHIP OF ARDISSONEA, CLIMACOSPHENIA, AND TOXARIUM WITHIN THE BIPOLAR CENTRIC DIATOMS (BACILLARIOPHYTA, MEDIOPHYCEAE), AND CLADISTIC ANALYSES CONFIRM THAT EXTREMELY ELONGATED SHAPE HAS ARISEN TWICE IN THE DIATOMS(1). J Phycol 2008; 44:1340-1348. [PMID: 27041731 DOI: 10.1111/j.1529-8817.2008.00560.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
With the use of a new kit from Qiagen to amplify total genome quantity, DNA was bulked up from two diatoms that are difficult to grow (Ardissonea and Climacosphenia), and the nuclear SSU rRNA gene was successfully amplified. Results of Bayesian analyses showed that these diatoms are sister to Toxarium and belong to the bi- and multipolar centric diatoms. The results indicate that extremely elongate shape has arisen at least twice in diatoms, in the true pennates, and in the bipolar centrics. The two lateral pattern centers of Ardissonea and Climacosphenia likely represent a modified annulus that subtends ribs internally as well as externally. Studies of sexual reproduction are needed to determine whether Ardissonea, Climacosphenia, and Toxarium achieve their elongate shape by similar means to each other and to true pennates, that is, by controlling the expansion of the auxospores by sequential addition of silicified bands (to form a properizonium or perizonium).
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Affiliation(s)
- Linda K Medlin
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UKAlfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, GermanyRoyal Botanic Garden, Edinburgh EH3 5LR, Scotland, UKStazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Shinya Sato
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UKAlfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, GermanyRoyal Botanic Garden, Edinburgh EH3 5LR, Scotland, UKStazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - David G Mann
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UKAlfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, GermanyRoyal Botanic Garden, Edinburgh EH3 5LR, Scotland, UKStazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Wiebe H C F Kooistra
- Marine Biological Association of the UK, Citadel Hill, Plymouth PL1 2PB, UKAlfred-Wegener-Institute for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, GermanyRoyal Botanic Garden, Edinburgh EH3 5LR, Scotland, UKStazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
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Diercks S, Metfies K, Medlin LK. Development and adaptation of a multiprobe biosensor for the use in a semi-automated device for the detection of toxic algae. Biosens Bioelectron 2008; 23:1527-33. [PMID: 18294835 DOI: 10.1016/j.bios.2008.01.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 12/06/2007] [Accepted: 01/09/2008] [Indexed: 10/22/2022]
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Medlin LK. If everything is everywhere, do they share a common gene pool? Gene 2007; 406:180-3. [DOI: 10.1016/j.gene.2007.09.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Revised: 08/10/2007] [Accepted: 09/06/2007] [Indexed: 11/30/2022]
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Not F, Valentin K, Romari K, Lovejoy C, Massana R, Töbe K, Vaulot D, Medlin LK. Picobiliphytes: A Marine Picoplanktonic Algal Group with Unknown Affinities to Other Eukaryotes. Science 2007; 315:253-5. [PMID: 17218530 DOI: 10.1126/science.1136264] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Environmental sequencing has revealed unimagined diversity among eukaryotic picoplankton. A distinct picoplanktonic algal group, initially detected from 18S ribosomal DNA (rDNA) sequences, was hybridized with rRNA λ-targeted (rRNA-targeted) probes, detected by tyramide signal amplification–fluorescent in situ hybridization, and showed an organelle-like body with orange fluorescence indicative of phycobilins. Using this fluorescence signal, cells were sorted by flow cytometry and probed. Hybridized cells contained a 4′,6′-diamidino-2-phenylindole–stained organelle resembling a plastid with a nucleomorph. This suggests that they may be secondary endosymbiotic algae. Pending the isolation of living cells and their formal description, these algae have been termed picobiliphytes.
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Affiliation(s)
- Fabrice Not
- Station Biologique de Roscoff, UMR 7144 CNRS and Université Pierre et Marie Curie, Boîte Postale 74, 29682 Roscoff Cedex, France.
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Medlin LK, Metfies K, Mehl H, Wiltshire K, Valentin K. Picoeukaryotic plankton diversity at the Helgoland time series site as assessed by three molecular methods. Microb Ecol 2006; 52:53-71. [PMID: 16703447 DOI: 10.1007/s00248-005-0062-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Accepted: 07/08/2005] [Indexed: 05/09/2023]
Abstract
We analyzed picoeukaryote assemblages in the German Bight at the Helgoland time series site by sequencing cloned eukaryotic 18S rRNA genes in six genetic libraries plus one library from the Orkney Islands from a cruise of opportunity. The libraries were constructed from environmental samples collected at different periods of the year. The same samples were also analyzed using a fingerprinting technique, single-strand conformational polymorphism (SSCP), and DNA microarrays with class-level oligonucleotide probes. One hundred unique clones were analyzed from each library, thus insuring over 85% coverage of the library. The V4 region of the 18S rRNA gene was sequenced from each of these clones, thus providing the most discrimination among the clones. The nonphotosynthetic picoeukaryotic component dominated over the photosynthetic one and was represented by the ciliates at 45% and group II alveolates at 42%. Prasinophytes dominated the photosynthetic group at 40%, but other picoplankton groups, such as bolidomonads and chrysophytes, were also present. Totally novel groups were found in the cryptomonads and in the dinoflagellates. A new algal group sister to the cryptophyte nuclear gene and the glaucocystophytes was also found. These three groups have been found in other picoeukaryotic planktonic clone libraries. SSCP analyses at closer time intervals suggest that clone libraries should be made at weekly intervals if succession in the picoeukaryotic plankton community is to be monitored accurately. A comparison of annual samples suggests thatthere appears to be an annual cycle with regard to species composition. Microarray analysis supported the clone library data and offered a faster means of community analysis, which can be performed with similar accuracy and with higher throughput for a more in-depth analysis.
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Affiliation(s)
- L K Medlin
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, D-27570, Bremerhaven, Germany.
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Kopp M, Doucette GJ, Kodama M, Gerdts G, Schütt C, Medlin LK. Phylogenetic analysis of selected toxic and non-toxic bacterial strains isolated from the toxic dinoflagellate Alexandrium tamarense. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00442.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Kühn SF, Medlin LK. The Systematic Position of the Parasitoid Marine Dinoflagellate Paulsenella vonstoschii (Dinophyceae) Inferred from Nuclear-Encoded Small Subunit Ribosomal DNA. Protist 2005; 156:393-8. [PMID: 16310744 DOI: 10.1016/j.protis.2005.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Revised: 07/15/2005] [Accepted: 07/15/2005] [Indexed: 11/16/2022]
Abstract
Members of the genus Paulsenella Chatton are marine phagotrophic dinoflagellates that specifically attack marine diatoms. In this phylogenetic study, we show that Paulsenella groups with Amyloodinium ocellatum (Brown) Brown et Hovasse, Pfiesteria piscicida Steidinger et Burkholder (Dinophyceae), Pfiesteria shumwayae Glasgow et Burkholder, and the cryptoperidiniopsoids, all members of the order Peridiniales. In the phylogenetic tree, Paulsenella diverged after Amyloodinium ocellatum but prior to Pfiesteria and the cryptoperidiniopsoids. This suggests that Paulsenella also belongs to the order Peridiniales and its earlier description as gymnodinioid and athecate has to be revised.
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Affiliation(s)
- Stefanie F Kühn
- Department of Marine Botany (FB2), University of Bremen, Leobener Strasse/NW2, D-28359 Bremen, Germany
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Beszteri B, Acs E, Medlin LK. Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity. Protist 2005; 156:317-33. [PMID: 16325544 DOI: 10.1016/j.protis.2005.07.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Accepted: 07/15/2005] [Indexed: 11/24/2022]
Abstract
Cyclotella meneghiniana Kützing is one of the most commonly found and intensively studied freshwater diatom species. However, it is considered taxonomically problematic because of its unusually wide ecological range and large frustule ultrastructural variation. As part of a study of morphological and genetic variation in this morphospecies, we surveyed nucleotide variation in the hypervariable D1/D2 regions of the 28S rDNA, in the ribosomal internal transcribed spacer region (containing ITS1, the 5.8S rDNA and ITS2) and in the 18S rDNA in a collection of 20 sympatric strains. High genetic variability and strong indications of genetic structure among the Cyclotella meneghiniana strains were found. Representatives of four genetically distinct--apparently reproductively isolated--groups were revealed among them. The random distribution of ITS variation within these four groups indicated that the genetic structure in Cyclotella meneghiniana can probably be explained by the presence of cryptic sexual species rather than by the lack of allogamous sexual reproduction. The morphological features traditionally used for species identification in this group cannot distinguish these putative cryptic species.
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MESH Headings
- Animals
- Biodiversity
- DNA, Ribosomal Spacer/genetics
- DNA, Ribosomal Spacer/isolation & purification
- Diatoms/classification
- Diatoms/genetics
- Genetic Variation
- Germany
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/isolation & purification
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/isolation & purification
- Recombination, Genetic
- Sequence Alignment
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Bánk Beszteri
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
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Metfies K, Huljic S, Lange M, Medlin LK. Electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii with a DNA-biosensor. Biosens Bioelectron 2005; 20:1349-57. [PMID: 15590289 DOI: 10.1016/j.bios.2004.05.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2003] [Revised: 05/19/2004] [Accepted: 05/20/2004] [Indexed: 11/21/2022]
Abstract
The steady rise of observations of harmful or toxic algal blooms throughout the world in the past decades constitute a menace for coastal ecosystems and human interests. As a consequence, a number of programs have been launched to monitor the occurrence of harmful and toxic algae. However, the identification is currently done by microscopic examination, which requires a broad taxonomic knowledge, expensive equipment and is very time consuming. In order to facilitate the identification of toxic algae, an inexpensive and easy-to-handle DNA-biosensor has been adapted for the electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii. The detection of the toxic algae is based on a sandwich hybridisation, which is carried out on a disposable sensor chip. A set of two probes for the species-specific identification of A. ostenfeldii was developed. The specificity of the probes could be shown in dot-blot hybridisations and with the DNA-biosensor. The sensitivity of the DNA-biosensor was optimised with respect to hybridisation temperature and NaCl-concentration and a significant increase of the sensitivity of the DNA-biosensor could be obtained by a fragmentation of the rRNA prior to the hybridisation and by adding a helper oligonucleotide, which binds in close proximity to the probes to the hybridisation.
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Affiliation(s)
- Katja Metfies
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
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John U, Fensome RA, Medlin LK. The application of a molecular clock based on molecular sequences and the fossil record to explain biogeographic distributions within the Alexandrium tamarense "species complex" (Dinophyceae). Mol Biol Evol 2003; 20:1015-27. [PMID: 12716990 DOI: 10.1093/molbev/msg105] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The cosmopolitan dinoflagellate genus Alexandrium, and especially the A. tamarense species complex, contain both toxic and nontoxic strains. An understanding of their evolution and paleogeography is a necessary precursor to unraveling the development and spread of toxic forms. The inclusion of more strains into the existing phylogenetic trees of the Alexandrium tamarense species complex from large subunit rDNA sequences has confirmed that geographic distribution is consistent with the molecular clades but not with the three morphologically defined species that constitute the complex. In addition, a new clade has been discovered, representing Mediterranean nontoxic strains. The dinoflagellates fossil record was used to calibrate a molecular clock: key dates used in this calibration are the origins of the Peridiniales (estimated at 190 MYA), Gonyaulacaceae (180 MYA), and Ceratiaceae (145 MYA). Based on the data set analyzed, the origin of the genus Alexandrium was estimated to be around late Cretaceous (77 MYA), with its earliest possible origination in the mid Cretaceous (119 MYA). The A. tamarense species complex potentially diverged around the early Neogene (23 MYA), with a possible first appearance in the late Paleogene (45 MYA). A paleobiogeographic scenario for Alexandrium is based on (1) the calculated possible ages of origination for the genus and its constituent groups; (2) paleogeographic events determined by plate movements, changing ocean configurations and currents, as well as climatic fluctuations; and (3) the present geographic distribution of the various clades of the Alexandrium tamarense species complex.
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Affiliation(s)
- Uwe John
- Alfred-Wegener-Institut für Polar- und Meeresforschung, Bremerhaven, Germany
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Abstract
Coccolithophores are a group of calcifying unicellular algae that constitute a major fraction of oceanic primary productivity, play an important role in the global carbon cycle, and are key biostratigraphic marker fossils. Their taxonomy is primarily based on the morphology of the minute calcite plates, or coccoliths, covering the cell. These are diverse and include widespread fine scale variation, of which the biological/taxonomic significance is unknown. Do they represent phenotypic plasticity, genetic polymorphisms, or species-specific characters? Our research on five commonly occurring coccolithophores supports the hypothesis that such variation represents pseudocryptic speciation events, occurring between 0.3 and 12.9 million years ago from a molecular clock estimation. This finding suggests strong stabilizing selection acting on coccolithophorid phenotypes. Our results also provide strong support for the use of fine scale morphological characters of coccoliths in the fossil record to improve biostratigraphic resolution and paleoceanographic data retrieval.
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Affiliation(s)
- Alberto G Saez
- Alfred Wegener Institute for Polar and Marine Biology, Department of Biological Oceanography, Am Handelshafen 12, D-27570 Bremerhaven, Germany.
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Affiliation(s)
- Wiebe H Kooistra
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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Iglesias-Rodriguez MD, Saez AG, Groben R, Edwards KJ, Batley J, Medlin LK, Hayes PK. Polymorphic microsatellite loci in global populations of the marine coccolithophorid Emiliania huxleyi. ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2002.00289.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Oligonucleotide probes provide rapid, easy identification of species difficult to identify by more traditional means, e.g. light microscopy. Phaeocystis is a difficult genus to identify as a unicell and thus presents a good candidate for probe development. Hybridisation using PCR products or cell lysates rather than whole cells as targets provides access to more highly variable regions of the genome, such as non-coding spacer regions of the ribosomal operon for detection of fine scale molecular variation not available in the coding regions. The ITS region is an excellent region of the genome to discriminate between Phaeocystis species. PCR amplified ITS-1 sequence from one Phaeocystis antarctica strain was labelled with digoxigenin and hybridised to total nucleic acids from 35 Phaeocystis strains, the prymnesiophyte Emiliania huxleyi, the diatom Cylindrotheca closterium, the rhodophyte Phycodrys austrogeorgia, the phaeophyte Desmarestia aculeata and the chlorophyte Acrosiphonia arcta. Strong signals were observed in all cold water species, i.e. Phaeocystis antarctica and Phaeocystis pouchetii, whereas other warm-water Phaeocystis spp. were not labelled or only weakly labelled with the ITS-1 probe. No hybridisations were observed in all other genera. A short oligonucleotide probe for all cold-water Phaeocystis spp. and for Phaeocystis pouchetii was designed from the ITS-1. Both probes were labelled with digoxigenin and tested in a dot blot analysis against PCR products from 23 Phaeocystis species. Only the two cold water species or Phaeocystis pouchetii were, respectively, labelled by their specific probe.
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Affiliation(s)
- Martin Lange
- State Education and Research Center for Agriculture, Viticulture and Horticulture, Germany
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Groben R, Medlin LK. Meeting report: EU workshop "Analysis of Single Cells in the Marine Phytoplankton" (ASCMAP), Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany, April 15-21, 2002. Protist 2002; 153:193-5. [PMID: 12389810 DOI: 10.1078/1434-4610-00097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Eschbach E, Scharsack JP, John U, Medlin LK. Improved erythrocyte lysis assay in microtitre plates for sensitive detection and efficient measurement of haemolytic compounds from ichthyotoxic algae. J Appl Toxicol 2001; 21:513-9. [PMID: 11746200 DOI: 10.1002/jat.797] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Haemolytic substances produced by ichthyotoxic algae often are unknown in molecular structure or specific mechanism of toxicity. Detection and quantification of such substances are dependent on bioassays, using markers that are sensitive for haemolytic impairment and generation of a recordable response. The erythrocyte lysis assay (ELA) represents an advantageous bioassay in this respect, because the lytic response can be measured photometrically by the amount of released haemoglobin. The aim of the present study was to establish an improved assay based on the ELA principle, for sensitive determination of haemolytic substances of microalgae and for high sample throughput. For this purpose we adapted the ELA to a 96-well microtitre plate format, which significantly reduced the sample volumes and allowed rapid processing of samples. Further improvement was achieved by measuring absorption of lysed erythrocytes at 414 nm, which significantly increased the sensitivity of the ELA compared to the measurements at 540 nm that are usually applied in this type of assay. Using carp (Cyprinus carpio) erythrocytes it was possible to detect haemolysis induced by 4 microg ml(-1) of saponin and as little as two haemolytic Alexandrium tamarense cells. It is suggested that this improved ELA in microtitre plates be used as a low-cost monitoring tool for detection and analysis of potential harmful algae. Furthermore, this ELA can be useful as a sensitive screening system for substances of pharmacological interest, e.g. selectively acting cytolytic antibiotics.
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Affiliation(s)
- E Eschbach
- Alfred-Wegener-Institute for Polar and Marine Research, Section of Biological Oceanography, Bremerhaven, Germany.
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Eschbach E, Reckermann M, John U, Medlin LK. A simple and highly efficient fixation method for Chrysochromulina polylepis (Prymnesiophytes) for analytical flow cytometry. Cytometry 2001; 44:126-32. [PMID: 11378863 DOI: 10.1002/1097-0320(20010601)44:2<126::aid-cyto1091>3.0.co;2-n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND To study the fragile Prymnesiophyte species Chrysochromulina polylepis by flow cytometry (FC), we needed an effective fixation method. This method must guarantee a high yield of fixed cells to achieve acceptable measurement times by FC and to allow quick processing of many samples. Moreover, we wanted a method that allows for storage of fixed samples when FC analysis cannot be done immediately. METHODS Different aldehydes and methanol were tested at different final concentrations. Gravity sedimentation and centrifugation were applied to achieve higher cell concentrations. Storage of fixed samples was tested under different conditions. RESULTS 0.25% glutaraldehyde (GA) fixation yielded a recovery rate of about 90%. The signals obtained by FC analysis were excellent. It is possible to centrifuge GA-fixed cells and to store them for several weeks. CONCLUSIONS GA is the fixative of choice for FC analysis of C. polylepis (and possibly other small delicate species) because it yielded highly significant recovery rates and high-quality FC signals. Cells can be centrifuged to increase the cell concentration, thereby achieving short measurement times with FC. The possibility of long-term storage of fixed cells presents an additional advantage if FC analysis cannot be done immediately.
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Affiliation(s)
- E Eschbach
- Alfred-Wegener-Institute for Polar and Marine Research, Section of Biological Oceanography, Bremerhaven, Germany.
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Abstract
The systematic position of the genus Cryothecomonas has been determined from an analysis of the nuclear-encoded small subunit ribosomal RNA gene of Cryothecomonas longipes and two strains of Cryothecomonas aestivalis. Our phylogenetic trees inferred from maximum likelihood, distance and maximum parsimony methods robustly show that the genus Cryothecomonas clusters within the phylum Cercozoa, and is related to the sarcomonad flagellate Heteromita globosa. Morphological data supporting the taxonomic placement of Cryothecomonas near the sarcomonad flagellates has been compiled from the literature. The high number of nucleotide substitutions found between two morphologically indistinguishable strains of Cryothecomonas aestivalis suggests the possibility of cryptic species within Cryothecomonas aestivalis.
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Affiliation(s)
- S Kühn
- University of Bremen, Marine Botany, Bremen, Germany
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Simon N, Campbell L, Ornolfsdottir E, Groben R, Guillou L, Lange M, Medlin LK. Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J Eukaryot Microbiol 2000; 47:76-84. [PMID: 10651300 DOI: 10.1111/j.1550-7408.2000.tb00014.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Photosynthetic pico- and nanoplankton dominate phytoplankton biomass and primary production in the oligotrophic open ocean. Species composition, community structure, and dynamics of the eukaryotic components of these size classes are poorly known primarily because of the difficulties associated with their preservation and identification. Molecular techniques utilizing 18S rRNA sequences offer a number of new and rapid means of identifying the picoplankton. From the available 18S rRNA sequence data for the algae, we designed new group-specific oligonucleotide probes for the division Chlorophyta, the division Haptophyta, and the class Pelagophyceae (division Heterokonta). Dot blot hybridization with polymerase chain reaction amplified target rDNA and whole-cell hybridization assays with fluorescence microscopy and flow cytometry were used to demonstrate probe specificity. Hybridization results with representatives from seven algal classes supported the phylogenetic affinities of the cells. Such group- or taxon-specific probes will be useful in examining community structure, for identifying new algal isolates, and for in situ detection of these three groups, which are thought to be the dominant algal taxa in the oligotrophic regions of the ocean.
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Affiliation(s)
- N Simon
- Department of Oceanography, Texas A&M University, College Station 77843-3146, USA
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47
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Groben R, Colijn F, Medlin LK. Meeting report: aquatic flow cytometry: achievements and prospects, Research- and Technology Centre Westcoast (FTZ), Büsum, Germany, October 15-16, 1998. Protist 1999; 150:7-10. [PMID: 10724513 DOI: 10.1016/s1434-4610(99)70003-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Medlin LK, Lange M, Wellbrock U, Donner G, Elbrächter M, Hummert C, Luckas B. Sequence comparisons link toxic European isolates of Alexandrium tamarense from the Orkney Islands to toxic North American stocks. Eur J Protistol 1998. [DOI: 10.1016/s0932-4739(98)80060-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chesnick JM, Kooistra WH, Wellbrock U, Medlin LK. Ribosomal RNA analysis indicates a benthic pennate diatom ancestry for the endosymbionts of the dinoflagellates Peridinium foliaceum and Peridinium balticum (Pyrrhophyta). J Eukaryot Microbiol 1997; 44:314-20. [PMID: 9225445 DOI: 10.1111/j.1550-7408.1997.tb05672.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The establishment of chloroplasts as cellular organelles in the dinoflagellate, heterokont (stramenopile), haptophyte, and cryptophyte algae is widely accepted to have been the result of secondary endosymbiotic events, that is, the uptake of a photosynthetic eukaryote by a phagotrophic eukaryote. However, the circumstances that promote such associations between two phylogenetically distinct organisms and result in the integration of their genomes to form a single functional photosynthetic cell is unclear. The dinoflagellates Peridinium foliaceum and Peridinium balticum are unusual in that each contains a membrane-bound eukaryotic heterokont endosymbiont. These symbioses have been interpreted, through data derived from ultrastructural and biochemical investigations, to represent an intermediate stage of secondary endosymbiotic chloroplast acquisition. In this study we have examined the phylogenetic origin of the P. foliaceum and P. balticum heterokont endosymbionts through analysis of their nuclear small subunit ribosomal RNA genes. Our analyses clearly demonstrate both endosymbionts are pennate diatoms belonging to the family Bacillariaceae. Since members of the Bacillariaceae are usually benthic, living on shallow marine sediments, the manner in which establishment of a symbiosis between a planktonic flagellated dinoflagellate and a bottom-dwelling diatom is discussed. In particular, specific environmentally-associated life strategy stages of the host and symbiont, coupled with diatom food preferences by the dinoflagellate, may have been vital to the formation of this association.
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Affiliation(s)
- J M Chesnick
- Biology Department, Lafayette College, Easton, Pennsylvania 18042, USA.
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Kooistra WH, Medlin LK. Evolution of the diatoms (Bacillariophyta). IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record. Mol Phylogenet Evol 1996; 6:391-407. [PMID: 8975694 DOI: 10.1006/mpev.1996.0088] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Small subunit ribosomal RNA (ssu rRNA) coding regions from 30 diatoms, 3 oomycetes, and 6 pelagophytes were used to construct linearized trees, maximum-likelihood trees, and neighbor-joining trees inferred from both unweighted and weighted distances. Stochastic accumulation of sequence substitutions among the diatoms was assessed with relative rate tests. Pennate diatoms evolved relatively slowly but within the limits set by a stochastic model; centric diatoms exceeded those limits. A rate distribution test was devised to identify those taxa showing an aberrant distribution of base substitutions within the ssu rRNA coding region. First appearance dates of diatom taxa from the fossil record were regressed against their corresponding branch lengths to infer the average and earliest possible age for the origin of the diatoms, the pennate diatoms, and the centric diatom order Thalassiosirales. Our most lenient age estimate (based on the median-evolving diatom taxon in the maximum-likelihood tree or on the average branch length in a linearized tree) suggests that their average age is approximately 164-166 Ma, which is close to their earliest fossil record. Both calculations suggest that it is unlikely that diatoms existed prior to 238-266 Ma. Rate variation among the diatoms' ssu rRNA coding regions and uncertainties associated with the origin of extant taxa in the fossil record contribute significantly to the variation in age estimates obtained. Different evolutionary models and the exclusion of fast or slow evolving taxa did not significantly affect age estimates; however, the inclusion of aberrantly fast evolving taxa did. Our molecular clock calibrations indicate that the rRNA coding regions in the diatoms are evolving at approximately 1% per 18 to 26 Ma, which is the fastest substitution rate reported in any pro- or eukaryotic group of organisms to date.
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Affiliation(s)
- W H Kooistra
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
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