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Wu G, Liu F, Chen G, Wang Y, Wang Y, Zhang C. Establishment of a multiplex polymerase chain reaction detection assay for three common harmful microalgae in the East China Sea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:60500-60513. [PMID: 37036653 DOI: 10.1007/s11356-023-26821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/31/2023] [Indexed: 04/11/2023]
Abstract
It is urgent to develop techniques that can simultaneously detect multiple microalgae, due to the diversity of harmful algal blooms (HABs)-forming algal species. The target algae species in this study are Heterosigma akashiwo, Prorocentrum donghaiense and Karenia mikimotoi. These algae are the dominant species that cause HABs in the East China Sea, and the multiple detection technique focusing on these three algae is not common. Therefore, this study established a multiplex polymerase chain reaction(mPCR) to diagnose the three algae, which is simple and low cost. First, the corresponding specific primers were designed based on the D1-D2 region of the large subunit (LSU) ribosomal DNA sequence. Then, mPCR was established and the reaction conditions were optimized. And the specificity, sensitivity, and stability of mPCR were evaluated. The result of specificity test showed that the established mPCR had good specificity for the target microalgae and did not cross-react with eighteen non-target microalgae. The sensitivity of experiment was 3.3 × 10-1 ng μL-1, and the established mPCR was not affected by the interfering microalgae. Moreover, the practicability evaluation of mPCR by using the simulated natural water samples showed that the detection limit of target microalgae was 100 cells mL-1, which could meet the demand for early warning of HABs. In summary, the established mPCR is characterized by strong specificity, good stability, and multiple analysis to detect H. akashiwo, P. donghaiense, and K. mikimotoi.
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Affiliation(s)
- Ganlin Wu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Yihan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, Shandong Province, People's Republic of China.
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Farhat A, Elleuch J, Ben Amor F, Barkallah M, Smith KF, Ben Neila I, Abdelkafi S, Fendri I. A fast and accurate method for specific detection and quantification of the bloom-forming microalgae Karlodinium veneficum in the marine environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:88699-88709. [PMID: 35836051 DOI: 10.1007/s11356-022-21667-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Karlodinium veneficum is a toxic benthic globally distributed dinoflagellate which has direct impacts on human health and the environment. Early and accurate detection of this harmful algal bloom-forming species could be useful for potential risks monitoring and management. In the present work, a real-time PCR targeting the internal transcribed spacer ribosomal DNA region for the specific detection and absolute quantification of K. veneficum was designed. Then, the assay conditions were adjusted and validated. The developed qPCR was highly specific for the target species and displayed no cross-reactivity with closely related dinoflagellates and/or other microalgal species commonly distributed along the Tunisian coast. Its lowest detection limit was 5 rDNA copies per reaction, which is often considered satisfying. qPCR assay enumeration accuracy was evaluated using artificially inoculated environmental samples. The comparison of the cell abundance estimates obtained by qPCR assay with the theoretical estimates showed no statistically significant difference across a range of concentrations. We suggest that the qPCR approach developed in the present study may be a valuable tool to investigate the distribution and seasonal dynamics of K. veneficum in marine environments.
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Affiliation(s)
- Ameny Farhat
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Sciences of Sfax, University of Sfax, B.P. 1171, 3000, 3029, Sfax, Tunisia
| | - Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Faten Ben Amor
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson, 7042, New Zealand
| | | | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Imen Fendri
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Sciences of Sfax, University of Sfax, B.P. 1171, 3000, 3029, Sfax, Tunisia.
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Liu F, Zhang C, Wang Y, Chen G. A review of the current and emerging detection methods of marine harmful microalgae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152913. [PMID: 34999066 DOI: 10.1016/j.scitotenv.2022.152913] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
In recent years, the scale and frequency of outbreaks of harmful algal blooms (HABs) have increased year by year due to the intensification of seawater eutrophication and global climate change. HABs have become a global marine ecological and environmental problem, which poses a serious threat to human health, marine ecological security, and economic development. The establishment of detection technology for harmful microalgae is fundamental to the early warning and prevention of HABs. To date, several detection methods have been developed for harmful microalgae, they however lack a unified classification standard. It is difficult to use a reasonable mix of all the developed methods to improve the accuracy of detection results. Here, all of the established detection methods for harmful microalgae were reviewed, including morphological structure-based detection methods, cytochrome-based detection techniques, immunoassays, and nucleic acid-based detection methods. The principles, advantages, and weaknesses of these methods were highlighted. Their application in the detection of harmful microalgae was summarized. Overall, different detection methods are suitable for different purposes. Further development of more accurate, cost-effective, efficient, and rapid detection technology is required in the future. This review is expected to provide a reference for research related to the monitoring of marine environment, early warning of HABs, and the molecular identification of harmful microalgae.
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Affiliation(s)
- Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo 315211, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai 264209, PR China.
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Elleuch J, Barkallah M, Smith KF, Ben Neila I, Fendri I, Abdelkafi S. Quantitative PCR assay for the simultaneous identification and enumeration of multiple Karenia species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:36889-36899. [PMID: 32577959 DOI: 10.1007/s11356-020-09739-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Quantitative PCR (qPCR) is the method of choice for specific detection and quantification of harmful algal bloom (HAB) species. Development of qPCR assay for simultaneous enumeration of species that frequently co-exist in HABs is required. A high sensitivity TaqMan qPCR assay, using probe and primers, located at ITS1-5.8S-ITS2 rDNA region, detecting, specifically, Karenia selliformis, K. bidigitata, and K. mikimotoi, was designed. ITS1-5.8S-ITS2 rDNA region copy numbers per Karenia cell genome were estimated to 217.697 ± 67.904, allowing cell quantification. An application of the designed methodology in field samples has been conducted, and it showed high sensitivity (detection of around 10-1 cell/100 mg of bivalve mollusk tissue, equivalent to about 20 copies of the target sequence). We suggest that the optimized method could contribute to early detection of three closely related Karenia species in seafood cultivating areas to promote control quality, guarantee a fast and effective intervention, and improve public health prevention.
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Affiliation(s)
- Jihen Elleuch
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia.
| | - Mohamed Barkallah
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson, 7042, New Zealand
| | | | - Imen Fendri
- Laboratory of Plant Biotechnology Applied to the Improvement of Cultures, Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Slim Abdelkafi
- Laboratoire de Génie Enzymatique et Microbiologie, Equipe Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, Sfax, Tunisia
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Qin Y, Zhang C, Liu F, Chen Q, Yang Y, Wang Y, Chen G. Establishment of double probes rolling circle amplification combined with lateral flow dipstick for rapid detection of Chattonella marina. HARMFUL ALGAE 2020; 97:101857. [PMID: 32732057 DOI: 10.1016/j.hal.2020.101857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
Chattonella marina is one of the main algae that could cause harmful algal blooms. It has killed a large number of cultured fish in coastal areas of many countries, causing serious economic losses. Therefore, it is necessary to establish a method that can specifically detect C. marina at pre-bloom abundance, so that timely measures can be taken before this alga causes harm. In this study, a long probe, a short probe and a pair of amplification primers were first designed by using the internal transcribed spacer (ITS) sequence of C. marina as the target gene and using the CD74 gene of a distant species Gallus gallus as the base sequence. The double probes rolling circle amplification (dpRCA) system was then established with the designed probes and amplification primers. A novel detection protocol referred to as dpRCA-LFD by combining the dpRCA products and lateral flow dipstick (LFD) was finally established, which can make the detection results visible to the naked eyes. The reaction conditions of dpRCA were optimized and the optimal conditions were as follows: cycle number of ligation reaction, 12; ligation temperature, 58 °C; amplification temperature, 60 °C; and amplification time, 60 min. The specificity test that was performed using the optimized dpRCA conditions indicated that dpRCA-LFD was exclusively specific for the target alga. The tests with the genomic DNA of C. marina and the recombinant plasmid containing the ITS sequence of C. marina showed that the sensitivity of dpRCA-LFD was 100 times higher than that of conventional PCR. The detection limit (DL) for the genomic DNA was 8.3 × 10-3 ng µL-1 (8.3 × 10-3 ng per reaction), and the DL for the recombinant plasmid DNA was 7.8 copies µL-1 (7.8 copies per reaction). The practicality of the developed dpRCA-LFD was further validated by test with the spiked samples containing C. marina and field samples. The simulative test showed that the dpRCA-LFD has a DL of 10 cells mL-1. The dpRCA-LFD could successfully recognize the target cells from the field samples. In summary, the dpRCA-LFD established in this study has advantages of good specificity, high sensitivity, and easily visible detection results, and therefore is promising for the analysis of C. marina in field samples.
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Affiliation(s)
- Yue Qin
- College of Oceanology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, Shandong Province 264209, PR China
| | - Chunyun Zhang
- College of Oceanology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, Shandong Province 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China.
| | - Fuguo Liu
- College of Oceanology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, Shandong Province 264209, PR China
| | - Qixin Chen
- College of Oceanology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, Shandong Province 264209, PR China
| | - Yuchen Yang
- College of Oceanology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, Shandong Province 264209, PR China
| | - Yuanyuan Wang
- College of Oceanology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, Shandong Province 264209, PR China
| | - Guofu Chen
- College of Oceanology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, Shandong Province 264209, PR China.
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Danchenko S, Fragoso B, Guillebault D, Icely J, Berzano M, Newton A. Harmful phytoplankton diversity and dynamics in an upwelling region (Sagres, SW Portugal) revealed by ribosomal RNA microarray combined with microscopy. HARMFUL ALGAE 2019; 82:52-71. [PMID: 30928011 DOI: 10.1016/j.hal.2018.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/07/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
The study region in Sagres, SW Portugal, is subject to natural eutrophication of coastal waters by wind-driven upwelling, which stimulates high primary productivity facilitating the recent economic expansion of bivalve aquaculture in the region. However, this economic activity is threatened by harmful algal blooms (HAB) caused by the diatoms Pseudo-nitzschia spp., Dinophysis spp. and other HAB dinoflagellates, all of which can produce toxins, that can induce Amnesic Shellfish Poisoning (ASP), Diarrhetic Shellfish Poisoning (DSP) and Paralytic Shellfish Poisoning (PSP). This study couples traditional microscopy with 18S/28S rRNA microarray to improve the detection of HAB species and investigates the relation between HAB and the specific oceanographic conditions in the region. Good agreement was obtained between microscopy and microarray data for diatoms of genus Pseudo-nitzschia and dinoflagellates Dinophysis spp., Gymnodinium catenatum and raphidophyte Heterosigma akashiwo, with less effective results for Prorocentrum. Microarray provided detection of flagellates Prymnesium spp., Pseudochattonella spp., Chloromorum toxicum and the important HAB dinoflagellates of the genera Alexandrium and Azadinium, with the latter being one of the first records from the study region. Seasonality and upwelling induced by northerly winds were found to be the driving forces of HAB development, with Pseudo-nitzschia spp. causing the risk of ASP during spring and summer upwelling season, and dinoflagellates causing the risk of DSP and PSP during upwelling relaxation, mainly in summer and autumn. The findings were in agreement with the results from toxicity monitoring of shellfish by the Portuguese Institute for Sea and Atmosphere and confirm the suitability of the RNA microarray method for HABs detection and aquaculture management applications.
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Affiliation(s)
- Sergei Danchenko
- CIMA - Centre for Marine and Environmental Research, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; Facultad de Ciencias del Mar y Ambientales, University of Cadiz, Campus de Puerto Real, Polígono San Pedro s/n, Puerto Real, 11510, Cadiz, Spain.
| | - Bruno Fragoso
- CIMA - Centre for Marine and Environmental Research, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; Facultad de Ciencias del Mar y Ambientales, University of Cadiz, Campus de Puerto Real, Polígono San Pedro s/n, Puerto Real, 11510, Cadiz, Spain; Sagremarisco Lda., Apartado 21, Vila do Bispo, 8650-999, Portugal
| | | | - John Icely
- CIMA - Centre for Marine and Environmental Research, University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; Sagremarisco Lda., Apartado 21, Vila do Bispo, 8650-999, Portugal
| | - Marco Berzano
- Polytechnic University of Marche, Piazza Roma, 22, 60121 Ancona, AN, Italy
| | - Alice Newton
- FCT - University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal; NILU-IMPEC, Box 100, 2027 Kjeller, Norway
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Bates SS, Hubbard KA, Lundholm N, Montresor M, Leaw CP. Pseudo-nitzschia, Nitzschia, and domoic acid: New research since 2011. HARMFUL ALGAE 2018; 79:3-43. [PMID: 30420013 DOI: 10.1016/j.hal.2018.06.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 05/11/2023]
Abstract
Some diatoms of the genera Pseudo-nitzschia and Nitzschia produce the neurotoxin domoic acid (DA), a compound that caused amnesic shellfish poisoning (ASP) in humans just over 30 years ago (December 1987) in eastern Canada. This review covers new information since two previous reviews in 2012. Nitzschia bizertensis was subsequently discovered to be toxigenic in Tunisian waters. The known distribution of N. navis-varingica has expanded from Vietnam to Malaysia, Indonesia, the Philippines and Australia. Furthermore, 15 new species (and one new variety) of Pseudo-nitzschia have been discovered, bringing the total to 52. Seven new species were found to produce DA, bringing the total of toxigenic species to 26. We list all Pseudo-nitzschia species, their ability to produce DA, and show their global distribution. A consequence of the extended distribution and increased number of toxigenic species worldwide is that DA is now found more pervasively in the food web, contaminating new marine organisms (especially marine mammals), affecting their physiology and disrupting ecosystems. Recent findings highlight how zooplankton grazers can induce DA production in Pseudo-nitzschia and how bacteria interact with Pseudo-nitzschia. Since 2012, new discoveries have been reported on physiological controls of Pseudo-nitzschia growth and DA production, its sexual reproduction, and infection by an oomycete parasitoid. Many advances are the result of applying molecular approaches to discovering new species, and to understanding the population genetic structure of Pseudo-nitzschia and mechanisms used to cope with iron limitation. The availability of genomes from three Pseudo-nitzschia species, coupled with a comparative transcriptomic approach, has allowed advances in our understanding of the sexual reproduction of Pseudo-nitzschia, its signaling pathways, its interactions with bacteria, and genes involved in iron and vitamin B12 and B7 metabolism. Although there have been no new confirmed cases of ASP since 1987 because of monitoring efforts, new blooms have occurred. A massive toxic Pseudo-nitzschia bloom affected the entire west coast of North America during 2015-2016, and was linked to a 'warm blob' of ocean water. Other smaller toxic blooms occurred in the Gulf of Mexico and east coast of North America. Knowledge gaps remain, including how and why DA and its isomers are produced, the world distribution of potentially toxigenic Nitzschia species, the prevalence of DA isomers, and molecular markers to discriminate between toxigenic and non-toxigenic species and to discover sexually reproducing populations in the field.
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Affiliation(s)
- Stephen S Bates
- Fisheries and Oceans Canada, Gulf Fisheries Centre, P.O. Box 5030, Moncton, New Brunswick, E1C 9B6, Canada.
| | - Katherine A Hubbard
- Fish and Wildlife Research Institute (FWRI), Florida Fish and Wildlife Conservation Commission (FWC), 100 Eighth Avenue SE, St. Petersburg, FL 33701 USA; Woods Hole Center for Oceans and Human Health, Woods Hole Oceanographic Institution, 266 Woods Hole Road, Woods Hole, MA, 02543 USA
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, DK-1307 Copenhagen K, Denmark
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
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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. ENVIRONMENTAL MONITORING AND ASSESSMENT 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] [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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9
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Molecular Techniques for the Detection of Organisms in Aquatic Environments, with Emphasis on Harmful Algal Bloom Species. SENSORS 2017; 17:s17051184. [PMID: 28531156 PMCID: PMC5470929 DOI: 10.3390/s17051184] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 05/18/2017] [Accepted: 05/20/2017] [Indexed: 02/08/2023]
Abstract
Molecular techniques to detect organisms in aquatic ecosystems are being gradually considered as an attractive alternative to standard laboratory methods. They offer faster and more accurate means of detecting and monitoring species, with respect to their traditional homologues based on culture and microscopic counting. Molecular techniques are particularly attractive when multiple species need to be detected and/or are in very low abundance. This paper reviews molecular techniques based on whole cells, such as microscope-based enumeration and Fluorescence In-Situ Hybridization (FISH) and molecular cell-free formats, such as sandwich hybridization assay (SHA), biosensors, microarrays, quantitative polymerase chain reaction (qPCR) and real time PCR (RT-PCR). Those that combine one or several laboratory functions into a single integrated system (lab-on-a-chip) and techniques that generate a much higher throughput data, such as next-generation systems (NGS), were also reviewed. We also included some other approaches that enhance the performance of molecular techniques. For instance, nano-bioengineered probes and platforms, pre-concentration and magnetic separation systems, and solid-phase hybridization offer highly pre-concentration capabilities. Isothermal amplification and hybridization chain reaction (HCR) improve hybridization and amplification techniques. Finally, we presented a study case of field remote sensing of harmful algal blooms (HABs), the only example of real time monitoring, and close the discussion with future directions and concluding remarks.
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McCoy GR, Touzet N, Fleming GTA, Raine R. Evolution of the MIDTAL microarray: the adaption and testing of oligonucleotide 18S and 28S rDNA probes and evaluation of subsequent microarray generations with Prymnesium spp. cultures and field samples. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:9704-9716. [PMID: 25631743 DOI: 10.1007/s11356-015-4152-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/19/2015] [Indexed: 06/04/2023]
Abstract
The toxic microalgal species Prymnesium parvum and Prymnesium polylepis are responsible for numerous fish kills causing economic stress on the aquaculture industry and, through the consumption of contaminated shellfish, can potentially impact on human health. Monitoring of toxic phytoplankton is traditionally carried out by light microscopy. However, molecular methods of identification and quantification are becoming more common place. This study documents the optimisation of the novel Microarrays for the Detection of Toxic Algae (MIDTAL) microarray from its initial stages to the final commercial version now available from Microbia Environnement (France). Existing oligonucleotide probes used in whole-cell fluorescent in situ hybridisation (FISH) for Prymnesium species from higher group probes to species-level probes were adapted and tested on the first-generation microarray. The combination and interaction of numerous other probes specific for a whole range of phytoplankton taxa also spotted on the chip surface caused high cross reactivity, resulting in false-positive results on the microarray. The probe sequences were extended for the subsequent second-generation microarray, and further adaptations of the hybridisation protocol and incubation temperatures significantly reduced false-positive readings from the first to the second-generation chip, thereby increasing the specificity of the MIDTAL microarray. Additional refinement of the subsequent third-generation microarray protocols with the addition of a poly-T amino linker to the 5' end of each probe further enhanced the microarray performance but also highlighted the importance of optimising RNA labelling efficiency when testing with natural seawater samples from Killary Harbour, Ireland.
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Affiliation(s)
- Gary R McCoy
- The Ryan Institute, National University of Ireland, Galway, Martin Ryan Building, Galway, Ireland,
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Detection of emerging and re-emerging pathogens in surface waters close to an urban area. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:5505-27. [PMID: 26006125 PMCID: PMC4454982 DOI: 10.3390/ijerph120505505] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 04/30/2015] [Accepted: 05/18/2015] [Indexed: 12/02/2022]
Abstract
Current knowledge about the spread of pathogens in aquatic environments is scarce probably because bacteria, viruses, algae and their toxins tend to occur at low concentrations in water, making them very difficult to measure directly. The purpose of this study was the development and validation of tools to detect pathogens in freshwater systems close to an urban area. In order to evaluate anthropogenic impacts on water microbiological quality, a phylogenetic microarray was developed in the context of the EU project µAQUA to detect simultaneously numerous pathogens and applied to samples from two different locations close to an urban area located upstream and downstream of Rome in the Tiber River. Furthermore, human enteric viruses were also detected. Fifty liters of water were collected and concentrated using a hollow-fiber ultrafiltration approach. The resultant concentrate was further size-fractionated through a series of decreasing pore size filters. RNA was extracted from pooled filters and hybridized to the newly designed microarray to detect pathogenic bacteria, protozoa and toxic cyanobacteria. Diatoms as indicators of the water quality status, were also included in the microarray to evaluate water quality. The microarray results gave positive signals for bacteria, diatoms, cyanobacteria and protozoa. Cross validation of the microarray was performed using standard microbiological methods for the bacteria. The presence of oral-fecal transmitted human enteric-viruses were detected using q-PCR. Significant concentrations of Salmonella, Clostridium, Campylobacter and Staphylococcus as well as Hepatitis E Virus (HEV), noroviruses GI (NoGGI) and GII (NoGII) and human adenovirus 41 (ADV 41) were found in the Mezzocammino site, whereas lower concentrations of other bacteria and only the ADV41 virus was recovered at the Castel Giubileo site. This study revealed that the pollution level in the Tiber River was considerably higher downstream rather than upstream of Rome and the downstream location was contaminated by emerging and re-emerging pathogens.
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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] [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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