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Daniel Vaulot - One of the best experts on this subject based on the ideXlab platform.

  • Plastid 16S rRNA Gene Diversity among Eukaryotic Picophytoplankton Sorted by Flow Cytometry from the South Pacific Ocean
    2015
    Co-Authors: Xiao Li Shi, David J. Scanlan, Daniel Vaulot
    Abstract:

    The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA

  • Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.
    PLoS ONE, 2011
    Co-Authors: Xiao Li Shi, Cécile Lepère, David J. Scanlan, Daniel Vaulot
    Abstract:

    The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

  • Groups without Cultured Representatives Dominate Eukaryotic Picophytoplankton in the Oligotrophic South East Pacific Ocean
    PLoS ONE, 2009
    Co-Authors: Xiao Li Shi, David J. Scanlan, Dominique Marie, Ludwig Jardillier, Daniel Vaulot
    Abstract:

    Background: Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 mm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone. Methodology/Principal Findings: In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated. Conclusions/Significance: Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups.

  • Eukaryotic picoplankton communities of the Mediterranean Sea in summer assessed by molecular approaches (DGGE, TTGE, QPCR)
    FEMS microbiology ecology, 2006
    Co-Authors: Dominique Marie, Fei Zhu, Vanessa Balagué, Josephine Ras, Daniel Vaulot
    Abstract:

    The composition and abundance of eukaryotic picoplankton (defined here as cells smaller than 3 μm) was investigated in the Morocco upwelling and throughout the Mediterranean Sea in late summer using flow cytometry and molecular methods (gradient gel electrophoresis and quantitative PCR). The picoplankton displayed characteristics typical of oligotrophic oceanic areas with concentrations down to 1000 cells mL−1 in the Eastern Basin. The most abundant eukaryotic sequences recovered by gradient gel electrophoresis were related to uncultivated marine groups: alveolates I (16%) and II (26%) and a newly discovered group (env Nansha, 17%) for which sequences have been recently obtained from the South China Sea and that could be related to Acantharians. Prasinophyceae (photosynthetic green algae) accounted for 10% of the sequences, whereas Cercozoa, Stramenopiles, Polycystinea, dinoflagellates and ciliates provided minor contributions. The use of quantitative PCR coupled with taxon-specific primers allowed us to estimate the relative abundance of several taxa belonging to the Prasinophyceae. Of the three genera assessed, Bathycoccus appeared as the most abundant, forming localized maxima at depth.

  • ecotype diversity in the marine picoeukaryote ostreococcus chlorophyta Prasinophyceae
    Environmental Microbiology, 2005
    Co-Authors: Francisco Rodriguez, Daniel Vaulot, Evelyne Derelle, Laure Guillou, Florence Le Gall, Herve Moreau
    Abstract:

    Summary The importance of the cyanobacteria Prochlorococ- cus and Synechococcus in marine ecosystems in terms of abundance and primary production can be partially explained by ecotypic differentiation. Despite the dominance of eukaryotes within photosynthetic picoplankton in many areas a similar differentiation has never been evidenced for these organisms. Here we report distinct genetic (rDNA 18S and internal tran- scribed spacer (ITS) sequencing), karyotypic (pulsed- field gel electrophoresis), phenotypic (pigment composition) and physiological (light-limited growth rates) traits in 12 Ostreococcus strains (Prasino- phyceae) isolated from various marine environments and depths, which suggest that the concept of ecotype could also be valid for eukaryotes. Internal transcribed spacer phylogeny grouped together four deep strains isolated between 90 m and 120 m depth from different geographical origins. Three deep strains displayed larger chromosomal bands, differ- ent chromosome hybridization patterns, and an addi- tional chlorophyll (chl) c -like pigment. Furthermore, growth rates of deep strains show severe photo- inhibition at high light intensities, while surface strains do not grow at the lowest light intensities. These features strongly suggest distinct adaptation to environmental conditions encountered at surface and the bottom of the oceanic euphotic zone, remi- niscent of that described in prokaryotes.

Christian Wilhelm - One of the best experts on this subject based on the ideXlab platform.

  • The investigation of violaxanthin de-epoxidation in the primitive green alga Mantoniella squamata (Prasinophyceae) indicates mechanistic differences in xanthophyll conversion to higher plants
    Phycologia, 2012
    Co-Authors: Susann Schaller, Christian Wilhelm, Dariusz Latowski, Małgorzata Jemioła-rzemińska, Theresa Quaas, Kazimierz Strzałka, Reimund Goss
    Abstract:

    Schaller S., Latowski D., JemioŁa-Rzeminska M., Quaas T., Wilhelm C., StrzaŁka K. and Goss R. 2012. The investigation of violaxanthin de-epoxidation in the primitive green alga Mantoniella squamata (Prasinophyceae) indicates mechanistic differences in xanthophyll conversion to higher plants. Phycologia 51: 359–370. DOI: 10.2116/11-127.1 The violaxanthin (Vx) de-epoxidation of the green alga Mantoniella squamata (Prasinophyceae) was investigated in thylakoid membranes and in enzyme assays with the isolated Vx de-epoxidase (VDE), where pure Vx or purified light-harvesting complexes of M. squamata (MLHC) or spinach (LHCII) were used. The detailed analysis of the VDE amino acid sequences of prasinophycean algae and higher plants suggests that structural differences of the M. squamata VDE are responsible for the slow conversion of Ax to Zx that is typical for this alga. The present experiments further demonstrate that the availability of the substrate Vx has a strong impact on the overall de-epoxidation reacti...

  • THE LIGHT‐HARVESTING SYSTEM OF THE UNICELLULAR ALGA Mantoniella squamata (Prasinophyceae): EVIDENCE FOR THE LACK OF A PHOTOSYSTEM I‐SPECIFIC ANTENNA COMPLEX
    Photochemistry and Photobiology, 1993
    Co-Authors: A. Schmitt, A. Herold, C. Welte, Aloysius Wild, Christian Wilhelm
    Abstract:

    The light-harvesting complexes (LHC) were isolated from the unicellular alga Mantoniella squamata (Prasinophyceae) by sucrose-density centrifugation. Beside the major LHC (II), a photosystem I complex was obtained that could be dissociated into a photosystem I core complex and an associated LHC I. In contrast to other chlorophyll b-containing antennae, both LHC II as well as LHC I were observed to be identical with respect to the following features: the molecular weights, the isoelectric points and the retention behavior on anion-exchange chromatography of the apoproteins, the pigment content and the absorption and fluorescence spectra

  • the light harvesting system of the unicellular alga mantoniella squamata Prasinophyceae evidence for the lack of a photosystem i specific antenna complex
    Photochemistry and Photobiology, 1993
    Co-Authors: A. Schmitt, A. Herold, C. Welte, Aloysius Wild, Christian Wilhelm
    Abstract:

    The light-harvesting complexes (LHC) were isolated from the unicellular alga Mantoniella squamata (Prasinophyceae) by sucrose-density centrifugation. Beside the major LHC (II), a photosystem I complex was obtained that could be dissociated into a photosystem I core complex and an associated LHC I. In contrast to other chlorophyll b-containing antennae, both LHC II as well as LHC I were observed to be identical with respect to the following features: the molecular weights, the isoelectric points and the retention behavior on anion-exchange chromatography of the apoproteins, the pigment content and the absorption and fluorescence spectra

Nathalie Simon - One of the best experts on this subject based on the ideXlab platform.

  • A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel
    Applied and Environmental Microbiology, 2004
    Co-Authors: Fabrice Not, Thierry Cariou, Mikel Latasa, Daniel Vaulot, Dominique Marie, Nathalie Simon
    Abstract:

    The class Prasinophyceae (Chlorophyta) contains several photosynthetic picoeukaryotic species described from cultured isolates. The ecology of these organisms and their contributions to the picoeukaryotic community in aquatic ecosystems have received little consideration. We have designed and tested eight new 18S ribosomal DNA oligonucleotide probes specific for different Prasinophyceae clades, genera, and species. Using fluorescent in situ hybridization associated with tyramide signal amplification, these probes, along with more general probes, have been applied to samples from a marine coastal site off Roscoff (France) collected every 2 weeks between July 2000 and September 2001. The abundance of eukaryotic picoplankton remained high (>10(3) cells ml(-1)) during the sampling period, with maxima in summer (up to 2 X 10(4) cells ml(-1)), and a single green algal species, Micromonas pusilla (Prasinophyceae), dominated the community all year round. Members of the order Prasinococcales and the species Bathycoccus prasinos (Mamiellales) displayed sporadic occurrences, while the abundances of all other Prasinophyceae groups targeted remained negligible

Dominique Marie - One of the best experts on this subject based on the ideXlab platform.

  • Groups without Cultured Representatives Dominate Eukaryotic Picophytoplankton in the Oligotrophic South East Pacific Ocean
    PLoS ONE, 2009
    Co-Authors: Xiao Li Shi, David J. Scanlan, Dominique Marie, Ludwig Jardillier, Daniel Vaulot
    Abstract:

    Background: Photosynthetic picoeukaryotes (PPE) with a cell size less than 3 mm play a critical role in oceanic primary production. In recent years, the composition of marine picoeukaryote communities has been intensively investigated by molecular approaches, but their photosynthetic fraction remains poorly characterized. This is largely because the classical approach that relies on constructing 18S rRNA gene clone libraries from filtered seawater samples using universal eukaryotic primers is heavily biased toward heterotrophs, especially alveolates and stramenopiles, despite the fact that autotrophic cells in general outnumber heterotrophic ones in the euphotic zone. Methodology/Principal Findings: In order to better assess the composition of the eukaryotic picophytoplankton in the South East Pacific Ocean, encompassing the most oligotrophic oceanic regions on earth, we used a novel approach based on flow cytometry sorting followed by construction of 18S rRNA gene clone libraries. This strategy dramatically increased the recovery of sequences from putative autotrophic groups. The composition of the PPE community appeared highly variable both vertically down the water column and horizontally across the South East Pacific Ocean. In the central gyre, uncultivated lineages dominated: a recently discovered clade of Prasinophyceae (IX), clades of marine Chrysophyceae and Haptophyta, the latter division containing a potentially new class besides Prymnesiophyceae and Pavlophyceae. In contrast, on the edge of the gyre and in the coastal Chilean upwelling, groups with cultivated representatives (Prasinophyceae clade VII and Mamiellales) dominated. Conclusions/Significance: Our data demonstrate that a very large fraction of the eukaryotic picophytoplankton still escapes cultivation. The use of flow cytometry sorting should prove very useful to better characterize specific plankton populations by molecular approaches such as gene cloning or metagenomics, and also to obtain into culture strains representative of these novel groups.

  • Eukaryotic picoplankton communities of the Mediterranean Sea in summer assessed by molecular approaches (DGGE, TTGE, QPCR)
    FEMS microbiology ecology, 2006
    Co-Authors: Dominique Marie, Fei Zhu, Vanessa Balagué, Josephine Ras, Daniel Vaulot
    Abstract:

    The composition and abundance of eukaryotic picoplankton (defined here as cells smaller than 3 μm) was investigated in the Morocco upwelling and throughout the Mediterranean Sea in late summer using flow cytometry and molecular methods (gradient gel electrophoresis and quantitative PCR). The picoplankton displayed characteristics typical of oligotrophic oceanic areas with concentrations down to 1000 cells mL−1 in the Eastern Basin. The most abundant eukaryotic sequences recovered by gradient gel electrophoresis were related to uncultivated marine groups: alveolates I (16%) and II (26%) and a newly discovered group (env Nansha, 17%) for which sequences have been recently obtained from the South China Sea and that could be related to Acantharians. Prasinophyceae (photosynthetic green algae) accounted for 10% of the sequences, whereas Cercozoa, Stramenopiles, Polycystinea, dinoflagellates and ciliates provided minor contributions. The use of quantitative PCR coupled with taxon-specific primers allowed us to estimate the relative abundance of several taxa belonging to the Prasinophyceae. Of the three genera assessed, Bathycoccus appeared as the most abundant, forming localized maxima at depth.

  • A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel
    Applied and Environmental Microbiology, 2004
    Co-Authors: Fabrice Not, Thierry Cariou, Mikel Latasa, Daniel Vaulot, Dominique Marie, Nathalie Simon
    Abstract:

    The class Prasinophyceae (Chlorophyta) contains several photosynthetic picoeukaryotic species described from cultured isolates. The ecology of these organisms and their contributions to the picoeukaryotic community in aquatic ecosystems have received little consideration. We have designed and tested eight new 18S ribosomal DNA oligonucleotide probes specific for different Prasinophyceae clades, genera, and species. Using fluorescent in situ hybridization associated with tyramide signal amplification, these probes, along with more general probes, have been applied to samples from a marine coastal site off Roscoff (France) collected every 2 weeks between July 2000 and September 2001. The abundance of eukaryotic picoplankton remained high (>10(3) cells ml(-1)) during the sampling period, with maxima in summer (up to 2 X 10(4) cells ml(-1)), and a single green algal species, Micromonas pusilla (Prasinophyceae), dominated the community all year round. Members of the order Prasinococcales and the species Bathycoccus prasinos (Mamiellales) displayed sporadic occurrences, while the abundances of all other Prasinophyceae groups targeted remained negligible

A. Schmitt - One of the best experts on this subject based on the ideXlab platform.