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Mora D, Schlüsener M, Fischer H, Kleinteich J, Schulz M, Ternes T, Thiel J, Wick A, Krenek S. From genes to toxins: Profiling Prymnesium parvum during a riverine harmful algal bloom. HARMFUL ALGAE 2024; 136:102644. [PMID: 38876525 DOI: 10.1016/j.hal.2024.102644] [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: 01/17/2024] [Revised: 04/19/2024] [Accepted: 05/12/2024] [Indexed: 06/16/2024]
Abstract
Blooms of Prymnesium parvum, a unicellular alga globally distributed in marine and brackish environments, frequently result in massive fish kills due to the production of toxins called prymnesins by this haptophyte. In August 2022, a harmful algal bloom (HAB) of this species occurred in the lower Oder River (Poland and Germany), which caused mass mortalities of fish and other organisms. This HAB was linked to low discharge of the Oder and mining activities that caused a significant increase in salinity. In this context, we report on the molecular detection and screening of this haptophyte and its toxins in environmental samples and clonal cultures derived thereof. Both conventional PCR and droplet digital PCR assays reliably detected P. parvum in environmental samples. eDNA metabarcoding using the V4 region of the 18S rRNA gene revealed a single Prymnesium sequence variant, but failed to identify it to species level. Four clonal cultures established from environmental samples were unambiguously identified as P. parvum by molecular phylogenetics (near full-length 18S rRNA gene) and light microscopy. Phylogenetic analysis (ITS1-5.8S-ITS2 marker region) placed the cultured phylotype within a clade containing other P. parvum strains known to produce B-type prymnesins. Toxin-screening of the cultures using liquid chromatography-electrospray ionization - time of flight mass spectrometry identified B-type prymnesins, which were also detected in extracts of filter residues from water samples of the Oder collected during the HAB. Overall, our investigation provides a detailed characterization of P. parvum, including their prymnesins, during this HAB in the Oder River, contributing valuable insights into this ecological disaster. In addition, the droplet digital PCR assay established here will be useful for future monitoring of low levels of P. parvum on the Oder River or any other salt-impacted and brackish water bodies.
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Affiliation(s)
- Demetrio Mora
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany; Current address: Observatory for Climate, Environment and Biodiversity (OCEB), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Michael Schlüsener
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Helmut Fischer
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Julia Kleinteich
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Manoj Schulz
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Thomas Ternes
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Joana Thiel
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Sascha Krenek
- Federal Institute of Hydrology (BfG), Am Mainzer Tor 1, 56068 Koblenz, Germany.
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Sildever S, Nishi N, Inaba N, Asakura T, Kikuchi J, Asano Y, Kobayashi T, Gojobori T, Nagai S. Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.79471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful algal bloom (HAB) species. In this study, the presence of HAB species and their appearance patterns were investigated by employing molecular and light microscopy-based monitoring in Tokyo Bay, Japan. The potential co-appearance patterns between the HAB species, as well as with other eukaryotes and prokaryotes were investigated using correlation and association rule-based time-series analysis. In total, 40 unique HAB species were detected, including 12 toxin-producing HAB species previously not reported from the area. More than half of the HAB species were present throughout the sampling season (summer to autumn) and no structuring or succession patterns associated with the environmental conditions could be detected. Statistically significant (p < 0.05, rS ranging from −0.88 to 0.90) associations were found amongst the HAB species and other eukaryotic and prokaryotic species, including genera containing growth-limiting bacteria. However, significant correlations between species differed amongst the years, indicating that variability in environmental conditions between the years may have a stronger influence on the microalgal community structure and interspecies interactions than the variability during the sampling season. The association rule-based time-series analysis allowed the detection of a previously reported negative relationship between Synechococcus sp. and Skeletonema sp. in nature. Overall, the results support the applicability of metabarcoding and HTS-based microalgae monitoring, as it facilitates more precise species identification compared to light microscopy, as well as provides input for investigating potential interactions amongst different species/groups through simultaneous detection of multiple species/genera.
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Wagstaff BA, Pratscher J, Rivera PPL, Hems ES, Brooks E, Rejzek M, Todd JD, Murrell JC, Field RA. Assessing the Toxicity and Mitigating the Impact of Harmful Prymnesium Blooms in Eutrophic Waters of the Norfolk Broads. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:16538-16551. [PMID: 34882392 DOI: 10.1021/acs.est.1c04742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Prymnesium parvum is a toxin-producing microalga, which causes harmful algal blooms globally, frequently leading to massive fish kills that have adverse ecological and economic implications for natural waterways and aquaculture alike. The dramatic effects observed on fish are thought to be due to algal polyether toxins, known as the prymnesins, but their lack of environmental detection has resulted in an uncertainty about the true ichthyotoxic agents. Using qPCR, we found elevated levels of P. parvum and its lytic virus, PpDNAV-BW1, in a fish-killing bloom on the Norfolk Broads, United Kingdom, in March 2015. We also detected, for the first time, the B-type prymnesin toxins in Broads waterway samples and gill tissue isolated from a dead fish taken from the study site. Furthermore, Norfolk Broads P. parvum isolates unambiguously produced B-type toxins in laboratory-grown cultures. A 2 year longitudinal study of the Broads study site showed P. parvum blooms to be correlated with increased temperature and that PpDNAV plays a significant role in P. parvum bloom demise. Finally, we used a field trial to show that treatment with low doses of hydrogen peroxide represents an effective strategy to mitigate blooms of P. parvum in enclosed water bodies.
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Affiliation(s)
- Ben A Wagstaff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Jennifer Pratscher
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Peter Paolo L Rivera
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Edward S Hems
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Elliot Brooks
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
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4
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Feist SM, Lance RF. Genetic detection of freshwater harmful algal blooms: A review focused on the use of environmental DNA (eDNA) in Microcystis aeruginosa and Prymnesium parvum. HARMFUL ALGAE 2021; 110:102124. [PMID: 34887004 DOI: 10.1016/j.hal.2021.102124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Recurrence and severity of harmful algal blooms (HABs) are increasing due to a number of factors, including human practices and climate change. Sensitive and robust methods that allow for early and expedited HAB detection across large landscape scales are needed. Among the suite of HAB detection tools available, a powerful option exists in genetics-based approaches utilizing environmental sampling, also termed environmental DNA (eDNA). Here we provide a detailed methodological review of three HAB eDNA approaches (quantitative PCR, high throughput sequencing, and isothermal amplification). We then summarize and synthesize recently published eDNA applications covering a variety of HAB surveillance and research objectives, all with a specific emphasis in the detection of two widely problematic freshwater species, Microcystis aeruginosa and Prymnesium parvum. In our summary and conclusion we build on this literature by discussing ways in which eDNA methods could be advanced to improve HAB detection. We also discuss ways in which eDNA data could be used to potentially provide novel insight into the ecology, mitigation, and prediction of HABs.
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Affiliation(s)
- Sheena M Feist
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States.
| | - Richard F Lance
- Environmental Lab, United States Army Corps of Engineers Research and Development Center, Vicksburg, MS, 39180, United States
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5
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Sildever S, Laas P, Kolesova N, Lips I, Lips U, Nagai S. Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.72371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods.
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Castelli G, Bruno F, Reale S, Catanzaro S, Valenza V, Vitale F. Molecular Diagnosis of Leishmaniasis: Quantification of Parasite Load by a Real-Time PCR Assay with High Sensitivity. Pathogens 2021; 10:pathogens10070865. [PMID: 34358015 PMCID: PMC8308825 DOI: 10.3390/pathogens10070865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/21/2022] Open
Abstract
Real-time PCR was developed to quantify Leishmania infantum kinetoplast DNA and optimized to achieve a sensitivity of 1 parasite/mL. For this purpose, we cloned the conserved kDNA fragment of 120 bp into competent cells and correlated them with serial dilutions of DNA extracted from reference parasite cultures calculating that a parasite cell contains approximately 36 molecules of kDNA. This assay was applied to estimate parasite load in clinical samples from visceral, cutaneous leishmaniasis patients and infected dogs and cats comparing with conventional diagnosis. The study aimed to propose a real-time PCR for the detection of Leishmania DNA from clinical samples trying to solve the diagnostic problems due to the low sensitivity of microscopic examination or the low predictive values of serology and resolve problems related to in vitro culture. The quantitative PCR assay in this study allowed detection of Leishmania DNA and quantification of considerably low parasite loads in samples that had been diagnosed negative by conventional techniques. In conclusion, this quantitative PCR can be used for the diagnosis of both human, canine and feline Leishmaniasis with high sensitivity and specificity, but also for evaluating treatment and the endpoint determination of leishmaniasis.
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Affiliation(s)
- Germano Castelli
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy; (G.C.); (S.C.); (V.V.); (F.V.)
| | - Federica Bruno
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy; (G.C.); (S.C.); (V.V.); (F.V.)
- Correspondence: ; Tel.: +39-0916565368
| | - Stefano Reale
- Laboratorio di Tecnologie Diagnostiche Innovative (TDI), Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy;
| | - Simone Catanzaro
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy; (G.C.); (S.C.); (V.V.); (F.V.)
| | - Viviana Valenza
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy; (G.C.); (S.C.); (V.V.); (F.V.)
| | - Fabrizio Vitale
- Centro di Referenza Nazionale per le Leishmaniosi (C.Re.Na.L.), OIE Leishmania Reference Laboratory, Istituto Zooprofilattico Sperimentale della Sicilia, Via Gino Marinuzzi 3, 90129 Palermo, Italy; (G.C.); (S.C.); (V.V.); (F.V.)
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Nagai S, Chen H, Kawakami Y, Yamamoto K, Sildever S, Kanno N, Oikawa H, Yasuike M, Nakamura Y, Hongo Y, Fujiwara A, Kobayashi T, Gojobori T. Monitoring of the toxic dinoflagellate Alexandrium catenella in Osaka Bay, Japan using a massively parallel sequencing (MPS)-based technique. HARMFUL ALGAE 2019; 89:101660. [PMID: 31672234 DOI: 10.1016/j.hal.2019.101660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/10/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Since 2002, blooms of Alexandrium catenella sensu Fraga et al. (2015) and paralytic shellfish toxicity events have occurred almost yearly in Osaka Bay, Japan. To better understand the triggers for reoccurring A. catenella blooms in Osaka Bay, phytoplankton community was monitored during the spring seasons of 2012-2015. Monitoring was performed using massively parallel sequencing (MPS)-based technique on amplicon sequences of the 18S rRNA gene. Dense blooms of A. catenella occurred every year except in 2012, however, there was no significant correlation with the environmental parameters investigated. Plankton community diversity decreased before and middle of the A. catenella blooms, suggesting that the decline in diversity could be an indicator for the bloom occurrence. The yearly abundance pattern of A. catenella cells obtained by morphology-based counting coincided with the relative sequence abundances, which supports the effectiveness of MPS-based phytoplankton monitoring.
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Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan.
| | - Hungyen Chen
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Yoko Kawakami
- AXIOHELIX Co. Ltd, -12-17 Kandaizumicho, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 2926-1 Tanigawa, Misaki, Sen-Nan, Osaka, 599-0311, Japan
| | - Sirje Sildever
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Hiroshi Oikawa
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Motoshige Yasuike
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Yuki Hongo
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Atushi Fujiwara
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia
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Sildever S, Kawakami Y, Kanno N, Kasai H, Shiomoto A, Katakura S, Nagai S. Toxic HAB species from the Sea of Okhotsk detected by a metagenetic approach, seasonality and environmental drivers. HARMFUL ALGAE 2019; 87:101631. [PMID: 31349888 DOI: 10.1016/j.hal.2019.101631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/30/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
During recent decades, the distribution of harmful algal bloom (HAB) species has expanded worldwide together with the increase of blooms and toxicity events. In this study, the presence of toxic HAB species in the Sea of Okhotsk was investigated based on metagenetic data collected during 6 years of weekly monitoring. Operational taxonomic units (OTUs) associated with the toxic HAB species were detected based on amplifying 18S V7-V9 and 28S D1 rRNA gene regions. In total, 43 unique OTUs associated with toxic HAB species were revealed, with 26 of those previously not reported from the Sea of Okhotsk. More OTUs belonging to dinoflagellates were detected by 18S, whereas a similar number of OTUs associated with dinoflagellates and diatoms were detected by targeting the 28S region. Species belonging to genera Alexandrium, Karenia and Karlodinium were mainly associated with OTUs under Dinophyceae, whereas Bacillariophyceae was represented by the species belonging to genus Pseudo-nitzschia. From the detected OTUs, 22 showed a clear seasonal pattern with the majority of those appearing during summer-autumn. For Alexandrium pacificum, Aureococcus anophagefferens, and Pseudo-nitzschia pungens, the seasonal pattern was detected based on both rRNA regions. Additionally, 14 OTUs were detected during all seasons and two OTUs appeared sporadically. OTUs associated with the toxic species had low relative read abundances, which together with other factors such as similar and variable morphology as well as usage of fixatives, may explain why those species have previously not been detected by light microscopy. Environmental parameters, especially water temperature, significantly (<0.05) influenced the variability in OTU relative abundances and displayed significant (<0.05) correlations with the unique OTUs. The results of this study demonstrate the usefulness of the metagenetic approach for phytoplankton monitoring, which is especially relevant for detecting toxic HAB species.
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Affiliation(s)
- Sirje Sildever
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan
| | - Yoko Kawakami
- AXIOHELIX Co. Ltd, Chiyoda-ku, Tokyo, 101-0024, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan
| | - Hiromi Kasai
- Hokkaido National Fisheries Research Institute, Kushiro, Hokkaido, 085-0802, Japan
| | | | | | - Satoshi Nagai
- National Research Institute of Fisheries Science, Yokohama Kanagawa, 236-8648, Japan.
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9
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Hems ES, Nepogodiev SA, Rejzek M, Field RA. Synthesis of glyceryl glycosides related to A-type prymnesin toxins. Carbohydr Res 2018; 463:14-23. [PMID: 29698849 PMCID: PMC5999359 DOI: 10.1016/j.carres.2018.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 11/23/2022]
Abstract
A suite of glycosylated glycerol derivatives representing various fragments of the glycosylated ichthyotoxins called prymnesins were chemically synthesised. Glycerol was used to represent a small fragment of the prymnesin backbone, and was glycosylated at the 2° position with the sugars currently reported to be present on prymnesin toxins. Neighbouring group participation was utilised to synthesise 1,2-trans-glycosides. SnCl2-promoted glycosylation with furanosyl fluorides gave 1,2-cis-furanosides with moderate stereocontrol, whilst TMSOTf promoted glycosylation with a furanosyl imidate gave a 1,2-cis-furanoside with good stereocontrol. The chemical synthesis of two larger glyceryl diglycoside fragments of prymnesin-1, glycosylated with α-ʟ-arabinopyranose and α-ᴅ-ribofuranose, is also described. As the stereochemistry of the prymnesin backbones at this region is undefined, both the 2R- and 2S- glycerol isomers were synthesised. The separated diastereoisomers were distinguished by comparing NOESY NMR with computational models.
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Affiliation(s)
- Edward S Hems
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sergey A Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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10
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Engesmo A, Strand D, Gran-Stadniczeñko S, Edvardsen B, Medlin LK, Eikrem W. Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae). HARMFUL ALGAE 2018; 75:105-117. [PMID: 29778220 DOI: 10.1016/j.hal.2018.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
Blooms of ichthyotoxic microalgae pose a great challenge to the aquaculture industry world-wide, and there is a need for fast and specific methods for their detection and quantification in monitoring programs. In this study, quantitative real-time PCR (qPCR) assays for the detection and enumeration of three ichthyotoxic flagellates: the dinoflagellate Karenia mikimotoi (Miyake & Kominami ex Oda) Hansen & Moestrup and the two raphidophytes Heterosigma akashiwo (Hada) Hada ex Hara & Chihara and Fibrocapsa japonica Toriumi & Takano were developed. Further, a previously published qPCR assay for the dinoflagellate Karlodinium veneficum (Ballantine) Larsen was used. Monthly samples collected for three years (Aug 2009-Jun 2012) in outer Oslofjorden, Norway were analysed, and the results compared with light microscopy cell counts. The results indicate a higher sensitivity and a lower detection limit (down to 1 cell L-1) for both qPCR assays. Qualitative and semi-quantitative results were further compared with those obtained by environmental 454 high throughput sequencing (HTS, metabarcoding) and scanning electron microscopy (SEM) examination from the same samplings. All four species were detected by qPCR and HTS and/or SEM in outer Oslofjorden (Aug 2009-Jun 2012); Karlodinium veneficum was present year-round, whereas Karenia mikimotoi, Heterosigma akashiwo and Fibrocapsa japonica appeared mainly during the autumn in all three years. This is the first observation of Fibrocapsa japonica in Norwegian coastal waters. This species has previously been recorded off the Swedish west coast and German Bight, which may suggest a northward dispersal.
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Affiliation(s)
- Anette Engesmo
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway.
| | - David Strand
- Norwegian Veterinary Institute, P.O. box 750 Sentrum, 0106, Oslo, Norway.
| | | | - Bente Edvardsen
- University of Oslo, Department of Biosciences, P. O. box 1066 Blindern, 0316, Oslo, Norway.
| | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, Pl1 2PB, United Kingdom.
| | - Wenche Eikrem
- Norwegian Institute for Water Research, Gaustadallèen 21, 0349, Oslo, Norway; University of Oslo, Department of Biosciences, P. O. box 1066 Blindern, 0316, Oslo, Norway.
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11
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Abstract
Prymnesium parvum is a toxin-producing microalga that causes harmful algal blooms globally, which often result in large-scale fish kills that have severe ecological and economic implications. Although many toxins have previously been isolated from P. parvum, ambiguity still surrounds the responsible ichthyotoxins in P. parvum blooms and the biotic and abiotic factors that promote bloom toxicity. A major fish kill attributed to P. parvum occurred in Spring 2015 on the Norfolk Broads, a low-lying set of channels and lakes (Broads) found on the East of England. Here, we discuss how water samples taken during this bloom have led to diverse scientific advances ranging from toxin analysis to discovery of a new lytic virus of P. parvum, P. parvum DNA virus (PpDNAV-BW1). Taking recent literature into account, we propose key roles for sialic acids in this type of viral infection. Finally, we discuss recent practical detection and management strategies for controlling these devastating blooms.
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12
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Eckford-Soper LK, Daugbjerg N. Interspecific Competition Study Between Pseudochattonella farcimen and P. verruculosa (Dictyochophyceae)-Two Ichthyotoxic Species that Co-occur in Scandinavian Waters. MICROBIAL ECOLOGY 2017; 73:259-270. [PMID: 27645137 DOI: 10.1007/s00248-016-0856-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
The genus Pseudochattonella has become a frequent component of late winter-early spring phytoplankton community in Scandinavian waters, causing extensive fish kills and substantial economic losses. One of currently two recognised species, P. farcimen, is often abundant prior to the diatom spring bloom. Recent field studies have revealed that P. farcimen and P. verruculosa have a period of overlap in their temperature ranges and thus their seasonal occurrences. Using laboratory cultures, we investigated the seasonal succession and growth of P. farcimen and P. verruculosa in both mono- and mixed-culture using the recently developed Pseudochattonella 'qPCR subtraction method', which for the first time allowed the simultaneous enumeration of these morphologically indistinguishable species in mixed assemblages. We examined how these species interacted over four different temperatures (5, 8, 11 and 15 °C). The observed growth rates and cell yields varied with temperature revealing their preferred temperature optima. P. farcimen was able to achieve positive net growth over all temperatures, while P. verruculosa failed to grow below 11 °C. Growth responses were statistically different between mono- and mixed-cultures with the outcome of these interactions being temperature-dependent. Nutrients (nitrate and phosphate) and pH levels were also measured throughout the growth experiments to better understand how these factors influenced growth of both species. P. verruculosa was shown to be less sensitive to high pH as growth ceased at pH 9.1, whereas P. farcimen stopped growing at pH 8.4. Understanding the influence of abiotic factors (e.g. temperature, pH and competition) on growth rates allows for a better understanding and prediction of phytoplankton community dynamics.
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Affiliation(s)
- Lisa K Eckford-Soper
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen Ø, Denmark.
| | - Niels Daugbjerg
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen Ø, Denmark
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Eckford-Soper LK, Daugbjerg N. A quantitative real-time PCR assay for identification and enumeration of the occasionally co-occurring ichthyotoxic Pseudochattonella farcimen and P. verruculosa (Dictyochophyceae) and analysis of variation in gene copy numbers during the growth phase of single and mixed cultures. JOURNAL OF PHYCOLOGY 2016; 52:174-83. [PMID: 27037583 DOI: 10.1111/jpy.12389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/27/2015] [Indexed: 05/28/2023]
Abstract
The ichthyotoxic genus Pseudochattonella forms recurrent extensive blooms in coastal waters in Japan, New Zealand and Northern Europe. It comprises of two morphologically similar species, P. verruculosa and P. farcimen, which complicates visual species identification and enumeration of live and fixed material. Primers designed previously could not quantitatively distinguish species in mixed assemblages. To address this issue we developed two primer sets: one revealed itself to be genus specific for Pseudochattonella and the other species-specific for P. verruculosa. By subtracting cell estimates for P. verruculosa from combined results we could calculate cell numbers for P. farcimen. This approach has overcome the challenges posed by the very limited sequence availability and low gene variability between the two species. The qPCR assay was extensively tested for specificity, efficiency and sensitivity over an entire growth cycle in both single and mixed assemblages. Comparison of cell abundance estimates obtained by qPCR assay and microscopy showed no statistically significant difference until stationary and death phases. The assay was also tested on environmental samples collected during a small Pseudochattonella bloom in Denmark in March-April 2015. It was impossible to distinguish P. farcimen and P. verruculosa by light microscopy but qPCR showed both species were present. The two methods provided nearly identical cell numbers but the assay provided discrimination and enumeration of both species.
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Affiliation(s)
- Lisa K Eckford-Soper
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen Ø, DK-2100, Denmark
| | - Niels Daugbjerg
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen Ø, DK-2100, Denmark
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Eckford-Soper LK, Daugbjerg N. Development of a multiplex real-time qPCR assay for simultaneous enumeration of up to four marine toxic bloom-forming microalgal species. HARMFUL ALGAE 2015; 48:37-43. [PMID: 29724474 DOI: 10.1016/j.hal.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/30/2015] [Accepted: 06/30/2015] [Indexed: 06/08/2023]
Abstract
Harmful algal blooms (HAB) pose serious economic and health risks worldwide. Current methods of identification require high levels of taxonomic skill and can be highly time-consuming thus limiting sample throughput. So, new rapid and reliable methods for detection and enumeration of HAB species are required. Here we describe a high-throughput, multiplex-qPCR (M-qPCR) method using hydrolysis probe technology for the simultaneous detection of four HAB species commonly found in many coastal areas worldwide: Alexandrium tamarense, Karenia mikimotoi, Karlodinium veneficum and Prymnesium parvum. Primers and probes were species-specific and highly efficient when tested in simplex. Species were then added in succession and the assay conditions adjusted until all four species could be quantitatively evaluated simultaneously. Enumeration accuracy of the M-qPCR assay as a monitoring tool was evaluated using spiked natural environmental samples from Danish coastal waters. Comparison of estimates of cell abundances obtained by the M-qPCR technique with those obtained by light microscopy (Sedgwick Rafter technique) showed no statistically significant difference across a range of concentrations. We were also able to identify and enumerate target cells that would be below the detection limit of light microscopy making this a suitable method for early bloom detection or for low biomass species. With the development of molecular probes for a greater number of algal species M-qPCR will be of great benefit to phytoplankton monitoring programmes and the aquaculture industry worldwide.
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Affiliation(s)
- Lisa K Eckford-Soper
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100 Copenhagen Ø, Denmark.
| | - Niels Daugbjerg
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100 Copenhagen Ø, Denmark
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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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Approaches for the detection of harmful algal blooms using oligonucleotide interactions. Anal Bioanal Chem 2014; 407:95-116. [PMID: 25381608 DOI: 10.1007/s00216-014-8193-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/02/2014] [Accepted: 09/15/2014] [Indexed: 01/14/2023]
Abstract
Blooms of microscopic algae in our waterways are becoming an increasingly important environmental concern. Many are sources of harmful biotoxins that can lead to death in humans, marine life and birds. Additionally, their biomass can cause damage to ecosystems such as oxygen depletion, displacement of species and habitat alteration. Globally, the number and frequency of harmful algal blooms has increased over the last few decades, and monitoring and detection strategies have become essential for managing these events. This review discusses developments in the use of oligonucleotide-based 'molecular probes' for the selective monitoring of algal cell numbers. Specifically, hybridisation techniques will be a focus.
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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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Penna A, Galluzzi L. The quantitative real-time PCR applications in the monitoring of marine harmful algal bloom (HAB) species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6851-62. [PMID: 23247526 PMCID: PMC3782655 DOI: 10.1007/s11356-012-1377-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/29/2012] [Indexed: 05/15/2023]
Abstract
In the last decade, various molecular methods (e.g., fluorescent hybridization assay, sandwich hybridization assay, automatized biosensor detection, real-time PCR assay) have been developed and implemented for accurate and specific identification and estimation of marine toxic microalgal species. This review focuses on the recent quantitative real-time PCR (qrt-PCR) technology developed for the control and monitoring of the most important taxonomic phytoplankton groups producing biotoxins with relevant negative impact on human health, the marine environment, and related economic activities. The high specificity and sensitivity of the qrt-PCR methods determined by the adequate choice of the genomic target gene, nucleic acid purification protocol, quantification through the standard curve, and type of chemical detection method make them highly efficient and therefore applicable to harmful algal bloom phenomena. Recent development of qrt-PCR-based assays using the target gene of toxins, such as saxitoxin compounds, has allowed more precise quantification of toxigenic species (i.e., Alexandrium catenella) abundance. These studies focus only on toxin-producing species in the marine environment. Therefore, qrt-PCR technology seems to offer the advantages of understanding the ecology of harmful algal bloom species and facilitating the management of their outbreaks.
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Affiliation(s)
- Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, Pesaro, Italy,
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Battocchi C, Totti C, Vila M, Masó M, Capellacci S, Accoroni S, Reñé A, Scardi M, Penna A. Monitoring toxic microalgae Ostreopsis (dinoflagellate) species in coastal waters of the Mediterranean Sea using molecular PCR-based assay combined with light microscopy. MARINE POLLUTION BULLETIN 2010; 60:1074-1084. [PMID: 20188383 DOI: 10.1016/j.marpolbul.2010.01.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 01/19/2010] [Accepted: 01/25/2010] [Indexed: 05/28/2023]
Abstract
A molecular PCR-based assay was developed and applied to macrophyte and seawater samples containing mixed microphytobenthic and phytoplanktonic assemblages, respectively, in order to detect toxic Ostreopsis species in Mediterranean Sea. The specificity and sensitivity of the molecular PCR assay were assessed with both plasmidic and genomic DNA of the target genus or species using taxon-specific primers in the presence of background macrophyte DNA. The PCR molecular technique allowed rapid detection of the Ostreopsis cells, even at abundances undetectable within the resolution limit of the microscopy technique. Species-specific identification of Ostreopsis was determined only by PCR-based assay, due to the inherent difficulty of morphological identification in field samples. In the monitoring of the toxic Ostreopsis blooms PCR-based methods proved to be effective tools complementary to microscopy for rapid and specific detection of Ostreopsis and other toxic dinoflagellates in marine coastal environments.
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Affiliation(s)
- Cecilia Battocchi
- Dipartimento di Scienze Biomolecolari, Sez. Biol. Amb., Università di Urbino, Viale Trieste 296, 61100 Pesaro, Italy
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Manning SR, La Claire JW. Prymnesins: toxic metabolites of the golden alga, Prymnesium parvum Carter (Haptophyta). Mar Drugs 2010; 8:678-704. [PMID: 20411121 PMCID: PMC2857367 DOI: 10.3390/md8030678] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/09/2010] [Accepted: 03/10/2010] [Indexed: 11/16/2022] Open
Abstract
Increasingly over the past century, seasonal fish kills associated with toxic blooms of Prymnesium parvum have devastated aquaculture and native fish, shellfish, and mollusk populations worldwide. Protracted blooms of P. parvum can result in major disturbances to the local ecology and extensive monetary losses. Toxicity of this alga is attributed to a collection of compounds known as prymnesins, which exhibit potent cytotoxic, hemolytic, neurotoxic and ichthyotoxic effects. These secondary metabolites are especially damaging to gill-breathing organisms and they are believed to interact directly with plasma membranes, compromising integrity by permitting ion leakage. Several factors appear to function in the activation and potency of prymnesins including salinity, pH, ion availability, and growth phase. Prymnesins may function as defense compounds to prevent herbivory and some investigations suggest that they have allelopathic roles. Since the last extensive review was published, two prymnesins have been chemically characterized and ongoing investigations are aimed at the purification and analysis of numerous other toxic metabolites from this alga. More information is needed to unravel the mechanisms of prymnesin synthesis and the significance of these metabolites. Such work should greatly improve our limited understanding of the physiology and biochemistry of P. parvum and how to mitigate its blooms.
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Affiliation(s)
- Schonna R Manning
- Section of MCD Biology, The University of Texas at Austin, 1 University Station, A6700, Austin, Texas 78712, USA.
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Albuquerque P, Mendes MV, Santos CL, Moradas-Ferreira P, Tavares F. DNA signature-based approaches for bacterial detection and identification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2009; 407:3641-51. [PMID: 19062077 DOI: 10.1016/j.scitotenv.2008.10.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 10/21/2008] [Accepted: 10/23/2008] [Indexed: 05/17/2023]
Abstract
During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.
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Affiliation(s)
- Pedro Albuquerque
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
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PCR Techniques as Diagnostic Tools for the Identification and Enumeration of Toxic Marine Phytoplankton Species. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8480-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
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