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Directeur de recherche CNRS

Scientific Director of the Roscoff Culture Collection

I have been working at the Station Biologique of Roscoff since 1985.
I am focusing on the diversity and ecology of eukaryotic picophytoplankton, more specifically the green algae, but also of other groups like bolidophytes and haptophytes involved in symbioses with cyanobacteria.
I am also the scientific director of the Roscoff Culture Collection.

Major current research projects
 

  • Diversity and oceanic distribution of marine green algae, with a focus on oceanic prasinophytes from clade VII
  • Diversity and distribution of Bolidophytes and Parmales (collaboration with A. Kuwata, Japan)
  • Analysis of eukaryotic communities using metabarcoding of the 18S rRNA gene, especially on populations sorted by flow cytometry (cooperation with USP, São Paulo, Brazil)
  • Polar picoplankton communities (projects GreenEdge and MicroPolar, cooperation with Chile) and their adapatation to the long winter polar night (ANR PhytoPol)

 

Current Postdocs and students
 

  • Adriana Lopes dos Santos, post-doctorante : diversity and distribution of prasinophytes clade VII and bolidophytes
  • Margot Tragin, PhD student (2014-2017) : global oceanic distribution of green algae with a focus on polar ecosystems
  • Catherine Ribeiro-Gerikas, PhD student Universidade de São Paulo: symbioses between eukaryotes and N2 fixing cyanobacteria on the continental shelf of Brazil

 

Collaborations
 

  • Akira Kuwata, Sendai, Japan
  • Bente Edvardsen and Wenche Eikrem, Oslo, Norway
  • Rodrigo de la Iglesia and Nicole Trefaut, Santiago, Chile
  • Marcel Babin, Takuvik, Québec
  • Hervé Moreau, Banyuls, France

Past PhD students
 

  • 2005-2009 Sylvie Masquelier, Université de Paris 6 PhD
  • 2004-2007 Manon Viprey, Université de Paris 6 PhD
  • 1999-2003 Isabelle Mary, Université de Rennes PhD
  • 1996-1999 Stéphan Jacquet, Université de Paris 6, PhD
  • 1995-1998 Laure Guillou, Université de Paris 6, PhD
  • 1991-1995 Nathalie Simon, Université de Paris 6, PhD
  • 1986-1988 Frederic Partensky, Université de Paris 6, PhD

 

Past post-docs

  •     2009-2012 Sergio Balzano, Post doc
  •     2008-2009 Shuhei Ota, Post doc
  •     2008-2009 Cécile Lepère, Post doc
  •     2006-2008 Xiaoli Shi, Post doc
  •     2006-2008 Fabien Jouenne, Post doc
  •     2002-2004 Francisco Rodriguez (post-doc co-direction with L. Guillou)
  •     2002-2003 Fei Zhu (post-doc)
  •     2002-2003 Agnès Groisillier (post-doc)
  •     2000-2002 Khadidja Romari, Université de Montpellier (post-doc)
  •     1997-1999 Michael Rappé, Oregon State University (post-doc)
  •     1996-1997 Seung-Yeo Moon, University of Seoul (post-doc)

 

Publications

You can see the full list and download reprints from Research Gate.

Submitted papers

  • Magalhães, K., Vaulot, D., and Oliveira, M.C. (2018) Hemiselmis aquamarina sp . nov . (Cryptomonadales , Cryptophyceae), a cryptomonad with a novel phycobiliprotein type (Cr-PC 564). Protist submitted:
  • Cabello, A.M., Logares, R., Rodríguez-Martínez, R., Romac, S., Vaulot, D., and Massana, R. (2018) Pelagophyte assemblages of the global ocean display low intraspecific diversity. ISME J. submitted:
  • Partensky, F., Six, C., Ratin, M., Garczarek, L., Vaulot, D., Grébert, T., et al. (2018) The cyanobacterium Acaryochloris thomasi sp. nov. contains Chlorophyll a and b but no Chlorophyll d. ISME J. submitted:
  • Stern, R., Kraberg, A., Bresnan, E., Kooistra, W.H.C.F., Lovejoy, C., Montresor, M., et al. (2018) Can molecular tools enhance long-term monitoring of marine protists? J. Plankton Res. submitted:
  • Kuwata, A., Yamada, K., Lopes dos Santos, A., Tragin, M., Ichinomiya, M., Yoshikawa, S., and Vaulot, D. (2018) Biology and ecology of Parmales (Bolidophyceae), a picophytoplankton group, sister of diatoms. Front. Microbiol. submitted:

Diversity and taxonomy of phytoplankton

  • Lopes dos Santos, A., Pollina, T., Gourvil, P., Corre, E., Marie, D., Garrido, J. L., et al. (2017). Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Sci. Rep. 7, 14019. doi:10.1038/s41598-017-12412-5.
  • Simon, N., Foulon, E., Grulois, D., Six, C., Latimier, M., Desdevises, Y., et al. (2017). 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. Protist in press. doi:10.1016/j.protis.2017.09.002.
  • Marie D, Le Gall F, Edern R, Gourvil P, Vaulot D. (2017). Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry. J Phycol 53: 271–282.
  • Lopes dos Santos A, Gourvil P, Tragin M, Noël M-H, Decelle J, Romac S, et al. (2017). Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. ISME J 11: 512–528.
  • Tragin M, Lopes dos Santos A, Christen R, Vaulot D. (2016). Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. Perspect Phycol 3: 141–154.
  • Edvardsen B, Egge ES, Vaulot D. (2016). Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. Perspect Phycol 3: 77–91.
  • Ichinomiya M, dos Santos AL, Gourvil P, Yoshikawa S, Kamiya M, Ohki K, et al. (2016). Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. ISME J 10: 2419–2434.
  • Lopes dos Santos A, Gourvil P, Rodriguez-Hernandez F, Garrido JL, Vaulot D. (2016). Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII. J Phycol 52: 148–155..
  • Not F, Probert I, Gerikas-Ribeiro C, Crenn K, Guillou L, Jeanthon C, et al. (2016). Photosymbiosis in marine pelagic environments. In:The marine microbiome – an untold resource of biodiversity and biotechnological potential, Stal, LJ, Cretoiu, SM (eds), Springer, in press.
  • Ichinomiya, M., Lopes dos Santos, A., Gourvil, P., Yoshikawa, S., Kamiya, M., Ohki, K., Audic, S. et al. 2015. Diversity and oceanic distribution of Parmales and Bolidophyceae, a picoplankton group closely related to diatoms. ISME J. 
  • Lopes dos Santos, A., Gourvil, P., Rodriguez-Hernandez, F., Garrido, J.L. & Vaulot, D. 2016. Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII. J. Phycol. 52 : 148-155.
  • Jouenne, F., Eikrem, W., Le Gall, F., Johnsen, G. & Vaulot, D. 2011. Prasinoderma singularis sp. nov., a solitary coccoid prasinophyte from the South East Pacific Ocean. Protist. 162:70–84.

Polar ecosystems

  • Balzano S, Percopo I, Siano R, Gourvil P, Chanoine M, Marie D, et al. (2017). Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex Wood M (ed). J Phycol 53: 161–187.
  • Egas C, Henríquez-Castillo C, Delherbe N, Molina E, Dos Santos AL, Lavin P, et al. (2017). Short timescale dynamics of phytoplankton in Fildes Bay, Antarctica. Antarct Sci in press: 1–12.
  • Percopo I, Ruggiero MV, Balzano S, Gourvil P, Lundholm N, Siano R, et al. (2016). Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex Mock T (ed). J Phycol 52: 184–199.
  • Balzano, S., Marie, D., Gourvil, P. & Vaulot, D. 2012. Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples. ISME J. 6:1480–98.

Tropical and sub-tropical ecosystems

  • Gérikas Ribeiro, C., Lopes dos Santos, A., Marie, D., Brandini, P., and Vaulot, D. (2018) Small eukaryotic phytoplankton communities off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria. ISME J. in press:
  • Gérikas Ribeiro C, Lopes dos Santos A, Marie D, Helena Pellizari V, Pereira Brandini F, Vaulot D. (2016). Pico and nanoplankton abundance and carbon stocks along the Brazilian Bight. PeerJ 4: e2587.
  • Gérikas Ribeiro C, Marie D, Lopes dos Santos A, Pereira Brandini F, Vaulot D. (2016). Estimating microbial populations by flow cytometry: Comparison between instruments. Limnol Oceanogr Methods 14: 750–758.
  • Man-Aharonovich, D., Philosof, A., Kirkup, B.C., Le Gall, F., Yogev, T., Berman-Frank, I., Polz, M.F. et al. 2010. Diversity of active marine picoeukaryotes in the eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME J. 4:1044–52.
  • Shi, X.L., Lepère, C., Scanlan, D.J. & Vaulot, D. 2011. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean. PLoS One. 6:e18979.
  • Shi, X.L., Marie, D., Jardillier, L., Scanlan, D.J. & Vaulot, D. 2009. Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS One. 4:e7657.

Metabarcoding

  • Tragin, M., Zingone, A., and Vaulot, D. (2017). Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta. Environ. Microbiol. in press, 1–41. doi:10.1111/1462-2920.13952.
  • Massana, R., Gobet, A., Audic, S., Bass, D., Bittner, L., Boutte, C., Chambouvet, A. et al. 2015. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environ. Microbiol. 17:4035-4049.
  • Forster D, Dunthorn M, Mahé F, Dolan JR, Audic S, Bass D, et al. (2016). Benthic protists: the under-charted majority Olson J (ed). FEMS Microbiol Ecol 92: fiw120.

Metagenomics

  • Vannier, T., Leconte, J., Seeleuthner, Y., Mondy, S., Pelletier, E., Aury, J.-M., de Vargas, C. et al. 2016. Survey of the green picoalga Bathycoccus genomes in the global ocean. Sci. Rep. 6:37900.
  • Vaulot, D., Lepère, C., Toulza, E., de la Iglesia, R., Poulain, J., Gaboyer, F., Moreau, H. et al. 2012. Metagenomes of the Picoalga Bathycoccus from the Chile coastal upwelling. PLoS One. 7:e39648.
  • Thompson, A.W., Foster, R.A., Krupke, A., Carter, B.J., Musat, N., Vaulot, D., Kuypers, M.M.M. et al. 2012. Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga. Science. 337:1546–50.
  • Roux, S., Enault, F., Bronner, G., Vaulot, D., Forterre, P. & Krupovic, M. 2013. Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses. Nat. Commun. 4.
  • Plominsky, A.M., Delherbe, N., Ugalde, J.A., Allen, E.E., Blanchet, M., Ikeda, P., Santibañez, F. et al. 2014. Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at Cáhuil Lagoon, Chile. Genome Announc. 2:e01172–14.

Databases

  • Mordret, S., Piredda, R., Vaulot, D., Montresor, M., Kooistra, W.H.C.F., and Sarno, D. (2018) DinoREF: a curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol. Ecol. Resour. in press:
  • Decelle, J., Romac, S., Stern, R.F., Bendif, E.M., Zingone, A., Audic, S., Guiry, M.D. et al. 2015. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol. Ecol. Resour. in press.
  • Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small SubUnit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597–604.
  • Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V. et al. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 12:e1001889.