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Daniel Vaulot - One of the best experts on this subject based on the ideXlab platform.
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Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula
Scientific Reports, 2021Co-Authors: Nicole Trefault, Dominique Marie, Adriana Lopes Dos Santos, Catherine Gérikas Ribeiro, Rodrigo De La Iglesia, Mario Moreno-pino, Génesis Parada-pozo, Antonia Cristi, Daniel VaulotAbstract:Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris , which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.
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No evidence of phago-mixotropy in Micromonas polaris (Mamiellophyceae), the dominant picophytoplankton species in the Arctic.
Journal of phycology, 2021Co-Authors: Valeria Jimenez, Florence Le Gall, John A. Burns, Fabrice Not, Daniel VaulotAbstract:In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phagomixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.
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Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula.
2020Co-Authors: N. Trefaut, Dominique Marie, Rodrigo De La Iglesia, Mario Moreno-pino, Antonia Cristi, A. Lopes Dos Santos, C. Gerikas Ribeiro, Daniel VaulotAbstract:Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Prymnesiophyceae and Cryptophyceae. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to but clearly distinct from M. polaris, which potentially represent a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.
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Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high arctic
Journal of Phycology, 2019Co-Authors: Sheree Yau, Herve Moreau, Sara Balzano, Priscillia Gourvil, Wenche Eikrem, Marie-line Escande, Adriana Lopes Dos Santos, Catherine Gérikas Ribeiro, Daniel VaulotAbstract:Members of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet, polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella. ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis. Both species have round green cells with diameter between 3 and 5 μm, one long flagellum and a short flagellum (~1 μm) and are covered by spiderweb‐like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding data sets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic, while no environmental barcode matches M. baffinensis. Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice‐adapted Mantoniella species.
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Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.
Scientific Reports, 2019Co-Authors: Margot Tragin, Daniel VaulotAbstract:Mamiellophyceae (unicellular green algae) are a key phytoplankton group in coastal waters. Although extensively studied over the last 20 years, the overall oceanic distribution of the major species/clades is still poorly known. To address this problem, we analyzed the 2014 Ocean Sampling Day (OSD) metabarcoding dataset providing sequences from the V4 hypervariable region of the 18S rRNA gene for 157 samples collected at 143 mostly coastal stations. Mamiellophyceae were found at nearly all OSD stations and represented 55% of the green microalgae (Chlorophyta) reads. We performed phylogenetic analyses of unique OSD metabarcodes (amplicon single variants, ASVs) and GenBank reference sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45% of the Mamiellophyceae reads), Micromonas (34%), Bathycoccus (10%) and Mantoniella (8.7%). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) was the second most represented clade after Ostreococcus “lucimarinus”. Micromonas could be separated into nine clades, exceeding the six species and candidate species already described. Finally, we found two new environmental clades within Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.
Herve Moreau - One of the best experts on this subject based on the ideXlab platform.
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The medium-size noncoding RNA transcriptome of Ostreococcus tauri, the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies
NAR Genomics and Bioinformatics, 2020Co-Authors: Laurie Bousquet, Herve Moreau, Nigel Grimsley, Klaas Vandepoele, Claire Hemon, Paul Malburet, François Bucchini, Manuel EcheverriaAbstract:Abstract The small nucleolar RNAs (snoRNAs), essential for ribosome biogenesis, constitute a major family of medium-size noncoding RNAs (mncRNAs) in all eukaryotes. We present here, for the first time in a marine unicellular alga, the characterization of the snoRNAs family in Ostreococcus tauri, the smallest photosynthetic eukaryote. Using a transcriptomic approach, we identified 131 O. tauri snoRNAs (Ot–snoRNA) distributed in three classes: the C/D snoRNAs, the H/ACA snoRNAs and the MRP RNA. Their genomic organization revealed a unique combination of both the intronic organization of animals and the polycistronic organization of plants. Remarkably, clustered genes produced Ot–snoRNAs with unusual structures never previously described in plants. Their abundances, based on quantification of reads and northern blots, showed extreme differences in Ot–snoRNA accumulation, mainly determined by their differential stability. Most of these Ot–snoRNAs were predicted to target rRNAs or snRNAs. Seventeen others were orphan Ot–snoRNAs that would not target rRNA. These were specific to O. tauri or Mamiellophyceae and could have functions unrelated to ribosome biogenesis. Overall, these data reveal an ‘evolutionary response’ adapted to the extreme compactness of the O. tauri genome that accommodates the essential Ot–snoRNAs, developing multiple strategies to optimize their coordinated expression with a minimal cost on regulatory circuits.
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Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high arctic
Journal of Phycology, 2019Co-Authors: Sheree Yau, Herve Moreau, Sara Balzano, Priscillia Gourvil, Wenche Eikrem, Marie-line Escande, Adriana Lopes Dos Santos, Catherine Gérikas Ribeiro, Daniel VaulotAbstract:Members of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet, polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella. ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis. Both species have round green cells with diameter between 3 and 5 μm, one long flagellum and a short flagellum (~1 μm) and are covered by spiderweb‐like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding data sets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic, while no environmental barcode matches M. baffinensis. Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice‐adapted Mantoniella species.
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Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol.
Genes, 2019Co-Authors: Frédéric Sanchez, Herve Moreau, Sheree Yau, Solène Geffroy, Manon Norest, Nigel GrimsleyAbstract:Ostreococcus tauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20–40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome.
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Mantoniella beaufortii and Mantoniella baffinensis sp. now. (Mamiellales, Mamiellophyceae), two new green algal species from the high Arctic
2018Co-Authors: Sheree Yau, Catherine Gérikas Ribeiro, Adriana Lopes Dos Santos, Herve Moreau, Sara Balzano, Priscillia Gourvil, Wenche Eikrem, Marie-line Escande, Daniel VaulotAbstract:Members of the class Mamiellophyceae comprise species that can dominate picophytoplankton diversity in polar waters. Yet polar species are often morphologically indistinguishable from temperate species, although clearly separated by molecular features. Here we examine four Mamiellophyceae strains from the Canadian Arctic. The 18S rRNA and Internal Transcribed Spacer 2 (ITS2) gene phylogeny place these strains within the family Mamiellaceae (Mamiellales, Mamiellophyceae) in two separate clades of the genus Mantoniella . ITS2 synapomorphies support their placement as two new species, Mantoniella beaufortii and Mantoniella baffinensis . Both species have round green cells with diameter between 3-5 μm, one long flagellum and a short reduced flagellum (≈1 μm) and are covered by spiderweb-like scales, making both species similar to other Mantoniella species. Morphologically, M. beaufortii and M. baffinensis are most similar to the cosmopolitan M. squamata with only minor differences in scale structure distinguishing them. Screening of global marine metabarcoding datasets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic while no environmental barcode matches M. baffinensis . Like other Mamiellophyceae genera that have distinct polar and temperate species, the polar distribution of these new species suggests they are cold or ice-adapted Mantoniella species.
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marinobacter dominates the bacterial community of the ostreococcus tauri phycosphere in culture
Frontiers in Microbiology, 2016Co-Authors: Josselin Lupette, Marc Krasovec, Herve Moreau, Nigel Grimsley, Raphaël LamiAbstract:Microalgal–bacterial interactions are commonly found in marine environments and are well known in diatom cultures maintained in laboratory. These interactions also exert strong effects on bacterial and algal diversity in the oceans. Small green eukaryote algae of the class Mamiellophyceae (Chlorophyta) are ubiquitous and some species, such as Ostreococcus spp., are particularly important in Mediterranean coastal lagoons, and are observed as dominant species during phytoplankton blooms in open sea. Despite this, little is known about the diversity of bacteria that might facilitate or hinder O. tauri growth. We show, using rDNA 16S sequences, that the bacterial community found in O. tauri RCC4221 laboratory cultures is dominated by γ-proteobacteria from the Marinobacter genus, regardless of the growth phase of O. tauri RCC4221, the photoperiod used, or the nutrient conditions (limited in nitrogen or phosphorous) tested. Several strains of Marinobacter algicola were detected, all closely related to strains found in association with taxonomically distinct organisms, particularly with dinoflagellates and coccolithophorids. These sequences were more distantly related to M. adhaerens, M. aquaeoli and bacteria usually associated to euglenoids. This is the first time, to our knowledge, that distinct Marinobacter strains have been found to be associated with a green alga in culture.
Yves Desdevises - One of the best experts on this subject based on the ideXlab platform.
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revision of the genus micromonas manton et parke chlorophyta Mamiellophyceae of the type species m pusilla butcher manton parke and of the species m commoda van baren bachy and worden and description of two new species based on the genetic and phenot
Protist, 2017Co-Authors: Nathalie Simon, Elodie Foulon, Yves Desdevises, Marie Latimier, Evelyne Derelle, Florence Le Gall, Daphne Grulois, Margot Tragin, Aude Houdan, Fabien JouenneAbstract:The green picoalgal genus Micromonas is broadly distributed in estuaries, coastal marine habitats and open oceans, from the equator to the poles. Phylogenetic, ecological and genomic analyses of culture strains and natural populations have suggested that this cosmopolitan genus is composed of several cryptic species corresponding to genetic lineages. We performed a detailed analysis of variations in morphology, pigment content, and sequences of the nuclear-encoded small-subunit rRNA gene and the second internal transcribed spacer (ITS2) from strains isolated worldwide. A new morphological feature of the genus, the presence of tip hairs at the extremity of the hair point, was discovered and subtle differences in hair point length were detected between clades. Clear non-homoplasious synapomorphies were identified in the small-subunit rRNA gene and ITS2 spacer sequences of five genetic lineages. These findings lead us to provide emended descriptions of the genus Micromonas, of the type species M. pusilla, and of the recently described species M. commoda, as well as to describe 2 new species, M. bravo and M. polaris. By clarifying the status of the genetic lineages identified within Micromonas, these formal descriptions will facilitate further interpretations of large-scale analyses investigating ecological trends in time and space for this widespread picoplankter.
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Revision of the Genus Micromonas Manton et Parke (Chlorophyta, Mamiellophyceae), of the Type Species M. pusilla (Butcher) Manton & Parke and of the Species M. commoda van Baren, Bachy and Worden and Description of Two New Species Based on the Genetic
Protist, 2017Co-Authors: Nathalie Simon, Elodie Foulon, Yves Desdevises, Marie Latimier, Daphne Grulois, Margot Tragin, Aude Houdan, Florence Le Gall, Evelyne DerelleAbstract:The green picoalgal genus Micromonas is broadly distributed in estuaries, coastal marine habitats and open oceans, from the equator to the poles. Phylogenetic, ecological and genomic analyses of culture strains and natural populations have suggested that this cosmopolitan genus is composed of several cryptic species corresponding to genetic lineages. We performed a detailed analysis of variations in morphology, pigment content, and sequences of the nuclear-encoded small-subunit rRNA gene and the second internal transcribed spacer (ITS2) from strains isolated worldwide. A new morphological feature of the genus, the presence of tip hairs at the extremity of the hair point, was discovered and subtle differences in hair point length were detected between clades. Clear non-homoplasious synapomorphies were identified in the small-subunit rRNA gene and ITS2 spacer sequences of five genetic lineages. These findings lead us to provide emended descriptions of the genus Micromonas, of the type species M. pusilla, and of the recently described species M. commoda, as well as to describe 2 new species, M. bravo and M. polaris. By clarifying the status of the genetic lineages identified within Micromonas, these formal descriptions will facilitate further interpretations of large-scale analyses investigating ecological trends in time and space for this widespread picoplankter.
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Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes
Environmental Microbiology Reports, 2015Co-Authors: Camille Clerissi, Yves Desdevises, Stephane Audic, Sarah Romac, Colomban De Vargas, Silvia G Acinas, Raffaela Casotti, Julie Poulain, Patrick Wincker, Pascal HingampAbstract:High-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey–predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction.
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unveiling of the diversity of prasinoviruses phycodnaviridae in marine samples by using high throughput sequencing analyses of pcr amplified dna polymerase and major capsid protein genes
Applied and Environmental Microbiology, 2014Co-Authors: Camille Clerissi, Nigel Grimsley, Julie Poulain, Pascal Hingamp, Hiroyuki Ogata, Yves DesdevisesAbstract:Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.
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Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, O. mediterraneus sp. nov. (Mamiellales, Mamiellophyceae).
Protist, 2013Co-Authors: Lucie Subirana, Yves Desdevises, Evelyne Derelle, Gwenael Piganeau, Birger Marin, Bérangère Péquin, Stephanie Michely, Marie-line Escande, Julie Meilland, Herve MoreauAbstract:Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 μm diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species’ descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species’ divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus , we purified >30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov. , previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.
Margot Tragin - One of the best experts on this subject based on the ideXlab platform.
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Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding.
Scientific Reports, 2019Co-Authors: Margot Tragin, Daniel VaulotAbstract:Mamiellophyceae (unicellular green algae) are a key phytoplankton group in coastal waters. Although extensively studied over the last 20 years, the overall oceanic distribution of the major species/clades is still poorly known. To address this problem, we analyzed the 2014 Ocean Sampling Day (OSD) metabarcoding dataset providing sequences from the V4 hypervariable region of the 18S rRNA gene for 157 samples collected at 143 mostly coastal stations. Mamiellophyceae were found at nearly all OSD stations and represented 55% of the green microalgae (Chlorophyta) reads. We performed phylogenetic analyses of unique OSD metabarcodes (amplicon single variants, ASVs) and GenBank reference sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45% of the Mamiellophyceae reads), Micromonas (34%), Bathycoccus (10%) and Mantoniella (8.7%). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) was the second most represented clade after Ostreococcus “lucimarinus”. Micromonas could be separated into nine clades, exceeding the six species and candidate species already described. Finally, we found two new environmental clades within Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.
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Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding
bioRxiv, 2018Co-Authors: Margot Tragin, Daniel VaulotAbstract:The Ocean Sampling Day (OSD) project provided metabarcoding data for the V4 hyper-variable regions of the 18S rRNA gene from 157 samples collected at 143 mostly coastal stations. In this paper we focus on the class Mamiellophyceae, which was found at nearly all OSD stations and represented 55 % of the green microalgae (Chlorophyta) reads in the 2014 OSD dataset. We performed phylogenetic analyses of unique OSD metabarcodes (ASV, amplicon single variants) and reference GenBank sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45 % of the Mamiellophyceae reads), Micromonas (34 %), Bathycoccus (10 %) and Mantoniella (8.7 %). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) with 2 very clear base pair differences compared to the oceanic clade B in the V4 region was the second most represented clade after the coastal Ostreococcus 9lucimarinus9. Within Micromonas, ten clades were found exceeding the 4 species and 2 candidate species already described. Finally, we found 2 new environmental clades of Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.
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Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset
Scientific Reports, 2018Co-Authors: Margot Tragin, Daniel VaulotAbstract:The ecology and distribution of green phytoplankton (Chlorophyta) in the ocean is poorly known because most studies have focused on groups with large cell size such as diatoms or dinoflagellates that are easily recognized by traditional techniques such as microscopy. The Ocean Sampling Day (OSD) project sampled surface waters quasi-simultaneously at 141 marine locations, mostly in coastal waters. The analysis of the 18S V4 region OSD metabarcoding dataset reveals that Chlorophyta are ubiquitous and can be locally dominant in coastal waters. Chlorophyta represented 29% of the global photosynthetic reads (Dinoflagellates excluded) and their contribution was especially high at oligotrophic stations (up to 94%) and along the European Atlantic coast. Mamiellophyceae dominated most coastal stations. At some coastal stations, they were replaced by Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae or Chlorophyceae as the dominating group, while oligotrophic stations were dominated either by Chloropicophyceae or the uncultured prasinophytes clade IX. Several Chlorophyta classes showed preferences in terms of nitrate concentration, distance to the coast, temperature and salinity. For example, Chlorophyceae preferred cold and low salinity coastal waters, and prasinophytes clade IX warm, high salinity, oligotrophic oceanic waters.
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Towards an atlas of green microalgae (Chlorophyta) in the ocean
2017Co-Authors: Margot TraginAbstract:The green lineage that dominates on land is represented by Chlorophyta which account in average for 25% of photosynthetic sequences (Dinoflagellates excluded) in global marine molecular inventories. Although Chlorophyta are major keys for ecological understanding of the ocean, as well as the evolutionary story understanding of land plants, their diversity and distribution in marine waters has been understudied. This thesis aims at investigating the environmental diversity of marine Chlorophyta and describing their distributions based on available large scale metabarcoding datasets. First, a reference database of publicly available 18S rRNA sequences of Chlorophyta was assembled and critically curated. Next, the Ocean Sampling Day (OSD) 18S metabarcode datasets were analysed. Chlorophyta diversity was compared for a limited sample set based on two regions of the 18S rRNA: the V4 and V9 regions. Then, Chlorophyta distribution was studied using the full OSD V4 dataset. Careful taxonomic investigations using both automatic and hand checked assignation of OTUs using alignments and phylogenies allowed to confirm the existence of new environmental prasinophytes clades and to confirme, that the Mamiellophyceae were the major group in coastal waters, while prasinophytes Clade VII and IX were dominating the oceanic oligotrophic stations. Comparing V4 and V9 regions illustrated the influence of the reference database on diversity. Moreover, the taxonomic investigation highlighted the diversity gaps between reference databases and environmental datasets. This work emphasizes the neglected importance of Chlorophyta in marine waters and provides some suggestions for future research.
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Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta.
Environmental microbiology, 2017Co-Authors: Margot Tragin, Adriana Zingone, Daniel VaulotAbstract:Summary We compared the composition of eukaryotic communities using two genetic markers (18S rRNA V4 and V9 regions) at 27 sites sampled during Ocean Sampling Day 2014, with a focus on photosynthetic groups and, more specifically green algae (Chlorophyta). Globally, the V4 and V9 regions of the 18S rRNA gene provided similar images of alpha diversity and ecological patterns. However, V9 provided 20% more OTUs built at 97% identity than V4. 34% of the genera were found with both markers and, of the remnant, 22% were found only with V4 and 44% only with V9. For photosynthetic groups, V4 and V9 performed equally well to describe global communities at different taxonomic levels from the division to the genus and provided similar Chlorophyta distribution patterns. However, at lower taxonomic level, the V9 dataset failed for example to describe the diversity of Dolichomastigales (Chlorophyta, Mamiellophyceae) emphasizing the lack of V9 sequences for this group and the importance of the reference database for metabarcode analysis. We conclude that in order to address questions regarding specific groups (e.g., a given genus), it is necessary to choose the marker based not only on the genetic divergence within this group but also on the existence of reference sequences in databases.
Alexey V. Troitsky - One of the best experts on this subject based on the ideXlab platform.
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The pico-sized Mamiellophyceae and a novel Bathycoccus clade from the summer plankton of Russian Arctic Seas and adjacent waters.
FEMS microbiology ecology, 2020Co-Authors: T A Belevich, Irina A Milyutina, Galina Anatolievna Abyzova, Alexey V. TroitskyAbstract:Global climate changes and anthropogenic activity greatly impact Arctic marine biodiversity including phytoplankton which contribute greatly to atmospheric oxygen production. Thus the study of microalgae has rising topicality. Class Mamiellophyceae is an important component of phototrophic picoplankton. To get more knowledge about Mamiellophyceae distribution and diversity special study were performed in such remote areas as the Russian Arctic seas. A metabarcoding of pico-sized Mamiellophyceae was undertaken by high-throughput sequencing of the 18S rRNA gene sequence V4 region from samples collected in July-September 2017 in the Barents, Kara, and Laptev seas, and in the adjacent waters of the Norwegian Sea. Our study is the first to show that Mamiellophyceae among the summer picoplankton of Russian Arctic seas are diverse and represented by 16 algae species/phylotypes. We discovered a new candidate species of Bathycoccus assigned to a new Bathycoccus clade A-uncultured Bathycoccus Kara 2017. It was found that several Micromonas species can co-exist, with M. polaris dominating north of 72°N. The presence of Ostreococcus tauri, O. lucimarinus and O. mediterraneus at high latitudes beyond 65°N was documented for the first time, similar to findings for some other taxa. Our results will be important for obtaining a global view of Mamiellophyceae community dynamics.
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Photosynthetic Picoeukaryotes Diversity in the Underlying Ice Waters of the White Sea, Russia
Diversity, 2020Co-Authors: T A Belevich, L. V. Ilyash, Maria D Logacheva, Irina A Milyutina, Alexey V. TroitskyAbstract:The White Sea is a unique basin combining features of temperate and arctic seas. The current state of its biocenoses can serve as a reference point in assessing the expected desalination of the ocean as a result of climate change. A metagenomic study of under-ice ice photosynthetic picoeukaryotes (PPEs) was undertaken by Illumina high-throughput sequencing of the 18S rDNA V4 region from probes collected in March 2013 and 2014. The PPE biomass in samples was 0.03–0.17 µg C·L−1 and their abundance varied from 10 cells·mL−1 to 140 cells·mL−1. There were representatives of 16 algae genera from seven classes and three supergroups, but Chlorophyta, especially Mamiellophyceae, dominated. The most represented genera were Micromonas and Mantoniella. For the first time, the predominance of Mantoniella (in four samples) and Bolidophyceae (in one sample) was observed in under-ice water. It can be assumed that a change in environmental conditions will lead to a considerable change in the structure of arctic PPE communities.
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Photosynthetic Picoeukaryotes in the Land-Fast Ice of the White Sea, Russia
Microbial Ecology, 2018Co-Authors: T A Belevich, L. V. Ilyash, Maria D Logacheva, D V Goryunov, Irina A Milyutina, Alexey V. TroitskyAbstract:The White Sea is a unique marine environment combining features of temperate and Arctic seas. The composition and abundance of photosynthetic picoeukaryotes (PPEs) were investigated in the land-fast ice of the White Sea, Russia, in March 2013 and 2014. High-throughput tag sequencing (Illumina MiSeq system) of the V4 region of the 18S rRNA gene was used to reveal the diversity of PPE ice community. The integrated PPE abundance varied from 11 × 10^6 cells/m^2 to 364 × 10^6 cells/m^2; the integrated biomass ranged from 0.02 to 0.26 mg С/m^2. The composition of sea-ice PPEs was represented by 16 algae genera belonging to eight classes and three super-groups. Chlorophyta, especially Mamiellophyceae, dominated among ice PPEs. The detailed analysis revealed the latent diversity of Micromonas and Mantоniella . Micromonas clade E2 revealed in the subarctic White Sea ice indicates that the area of distribution of this species is wider than previously thought. We suppose there exists a new Micromonas clade F. Micromonas clade C and Minutocellulus polymorphus were first discovered in the ice and extend the modern concept of sympagic communities’ diversity generally and highlights the importance of further targeting subarctic sea ice for microbial study.
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Phototrophic picoeukaryotes of Onega Bay, the White Sea: Abundance and species composition
Moscow University Biological Sciences Bulletin, 2017Co-Authors: T A Belevich, L. V. Ilyash, Maria D Logacheva, Irina A Milyutina, Alexey V. TroitskyAbstract:The abundance, biomass, and composition of phototrophic picoeukaryotes (PPE, cell size less than 3 μm) were studied in Onega Bay of the White Sea in June 2015. The highest PPE abundance and biomass were registered in the 0–5-m water layer. In the bay, in the 0–5-m water layer, the average abundance and biomass varied from 0 to 36.8 × 10^4 cell/L and from 0 to 117 μg С/m^3, respectively. The Illumina sequencing of V4 region of 18S rRNA gene revealed eight classes of PPE. Mamiellophyceae dominated both by number of reads and by operational taxonomic units. The green algae Bathycoccus prasinos, Ostreococcus tauri , and Micromonas pusila , as well as diatoms Skeletonema marinoi and Minidiscus trioculatus , were identified to the species level.
