Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization

Available genomic data for the toxic, bloom-forming, benthic Ostreopsis spp. are traditionally obtained from isolates rather than from individuals originally present in environmental samples. Samples from the final phase of the first reported Ostreopsis bloom in European North Atlantic waters (Algar...

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Published in:Toxins
Main Authors: Vitor Ramos, Daniele Salvi, João Paulo Machado, Micaela Vale, Joana Azevedo, Vitor Vasconcelos
Format: Article in Journal/Newspaper
Language:English
Published: MDPI AG 2015
Subjects:
HAB
R
Online Access:https://doi.org/10.3390/toxins7072514
https://doaj.org/article/39a2a38842bf4030ab56187607c8915a
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spelling ftdoajarticles:oai:doaj.org/article:39a2a38842bf4030ab56187607c8915a 2023-05-15T17:36:27+02:00 Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization Vitor Ramos Daniele Salvi João Paulo Machado Micaela Vale Joana Azevedo Vitor Vasconcelos 2015-06-01T00:00:00Z https://doi.org/10.3390/toxins7072514 https://doaj.org/article/39a2a38842bf4030ab56187607c8915a EN eng MDPI AG http://www.mdpi.com/2072-6651/7/7/2514 https://doaj.org/toc/2072-6651 2072-6651 doi:10.3390/toxins7072514 https://doaj.org/article/39a2a38842bf4030ab56187607c8915a Toxins, Vol 7, Iss 7, Pp 2514-2533 (2015) Ostreopsis HAB culture-independent approach phylogeny ITS2 secondary structure NE Atlantic Portugal environmental samples Medicine R article 2015 ftdoajarticles https://doi.org/10.3390/toxins7072514 2022-12-30T20:36:23Z Available genomic data for the toxic, bloom-forming, benthic Ostreopsis spp. are traditionally obtained from isolates rather than from individuals originally present in environmental samples. Samples from the final phase of the first reported Ostreopsis bloom in European North Atlantic waters (Algarve, south coast of Portugal) were studied and characterized, using a culture-independent approach. In the first instance, a microscopy-based analysis revealed the intricate complexity of the samples. Then, we evaluated the adequacy of commonly used molecular tools (i.e., primers and nuclear ribosomal markers) for the study of Ostreopsis diversity in natural samples. A PCR-based methodology previously developed to identify/detect common Ostreopsis species was tested, including one new combination of existing PCR primers. Two sets of environmental rRNA sequences were obtained, one of them (1052 bp) with the newly tested primer set. These latter sequences encompass both the ITS1-5.8S-ITS2 region and the D1/D2 domain of the LSU rRNA gene, leading us to an accurate identification of ITS2. In turn, this allowed us to predict and show for the first time the ITS2 secondary structure of Ostreopsis. With 92 bp in length and a two-helix structure, the ITS2 of this genus revealed to be unique among the dinoflagellates. Both the PCR approach as the phylogenetic analyses allowed to place the Ostreopsis cells observed in the samples within the O. cf. ovata phylospecies’ complex, discarding the presence of O. cf. siamensis. The (phylo)genetic results point out a certain level of nucleotide sequence divergence, but were inconclusive in relation to a possible geographic origin of the O. cf. ovata population from the Algarve’s bloom. Article in Journal/Newspaper North Atlantic Directory of Open Access Journals: DOAJ Articles Toxins 7 7 2514 2533
institution Open Polar
collection Directory of Open Access Journals: DOAJ Articles
op_collection_id ftdoajarticles
language English
topic Ostreopsis
HAB
culture-independent approach
phylogeny
ITS2 secondary structure
NE Atlantic
Portugal
environmental samples
Medicine
R
spellingShingle Ostreopsis
HAB
culture-independent approach
phylogeny
ITS2 secondary structure
NE Atlantic
Portugal
environmental samples
Medicine
R
Vitor Ramos
Daniele Salvi
João Paulo Machado
Micaela Vale
Joana Azevedo
Vitor Vasconcelos
Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization
topic_facet Ostreopsis
HAB
culture-independent approach
phylogeny
ITS2 secondary structure
NE Atlantic
Portugal
environmental samples
Medicine
R
description Available genomic data for the toxic, bloom-forming, benthic Ostreopsis spp. are traditionally obtained from isolates rather than from individuals originally present in environmental samples. Samples from the final phase of the first reported Ostreopsis bloom in European North Atlantic waters (Algarve, south coast of Portugal) were studied and characterized, using a culture-independent approach. In the first instance, a microscopy-based analysis revealed the intricate complexity of the samples. Then, we evaluated the adequacy of commonly used molecular tools (i.e., primers and nuclear ribosomal markers) for the study of Ostreopsis diversity in natural samples. A PCR-based methodology previously developed to identify/detect common Ostreopsis species was tested, including one new combination of existing PCR primers. Two sets of environmental rRNA sequences were obtained, one of them (1052 bp) with the newly tested primer set. These latter sequences encompass both the ITS1-5.8S-ITS2 region and the D1/D2 domain of the LSU rRNA gene, leading us to an accurate identification of ITS2. In turn, this allowed us to predict and show for the first time the ITS2 secondary structure of Ostreopsis. With 92 bp in length and a two-helix structure, the ITS2 of this genus revealed to be unique among the dinoflagellates. Both the PCR approach as the phylogenetic analyses allowed to place the Ostreopsis cells observed in the samples within the O. cf. ovata phylospecies’ complex, discarding the presence of O. cf. siamensis. The (phylo)genetic results point out a certain level of nucleotide sequence divergence, but were inconclusive in relation to a possible geographic origin of the O. cf. ovata population from the Algarve’s bloom.
format Article in Journal/Newspaper
author Vitor Ramos
Daniele Salvi
João Paulo Machado
Micaela Vale
Joana Azevedo
Vitor Vasconcelos
author_facet Vitor Ramos
Daniele Salvi
João Paulo Machado
Micaela Vale
Joana Azevedo
Vitor Vasconcelos
author_sort Vitor Ramos
title Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization
title_short Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization
title_full Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization
title_fullStr Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization
title_full_unstemmed Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization
title_sort culture-independent study of the late-stage of a bloom of the toxic dinoflagellate ostreopsis cf. ovata: preliminary findings suggest genetic differences at the sub-species level and allow its2 structure characterization
publisher MDPI AG
publishDate 2015
url https://doi.org/10.3390/toxins7072514
https://doaj.org/article/39a2a38842bf4030ab56187607c8915a
genre North Atlantic
genre_facet North Atlantic
op_source Toxins, Vol 7, Iss 7, Pp 2514-2533 (2015)
op_relation http://www.mdpi.com/2072-6651/7/7/2514
https://doaj.org/toc/2072-6651
2072-6651
doi:10.3390/toxins7072514
https://doaj.org/article/39a2a38842bf4030ab56187607c8915a
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container_title Toxins
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