List of scientific publications

(Last update : March 2014)

Submitted (4 papers)

Forster D, Bittner L, Karkar S, Dunthorn M, Romac S, Audic S, Lopez P, Stoeck T, Bapteste E. (2014). Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic patterns as multicellular organisms. ISME. Submitted.

Glücksman E, Cavalier-Smith T, Santini S, Bass D (2014). Novel diversity of sulcozoan ciliary gliding protists (Apusomonadida, Planomonadida, Mantamonadida) and ecological patterns revealed by targeted probes, large-scale data mining, and metagenomics. Environmental Microbiology.  Submitted

Mahé, F., Rognes, T., Quince, C., de Vargas., C. & Dunthorn, M. 2014. Swarm: robust and fast clustering method for amplicon-based studies. Nature Methods. Submitted.

Nanjappa, D., S. Audic, S. Romac, W. H. C. F. Kooistra, and A. Zingone. 2014: Mining metagenomic databases for the assessment of species diversity and distribution in an ancient diatom lineage. Plos One. Submitted.

2014 - In press (5 papers)

Bendif, E. M., I. Probert, M. Carmichael, S. Romac, K. Hagino, and C. de Vargas. 2014: Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta). Journal of Phycology 50:140–148.

Chambouvet, A., C. Berney, S. Romac, S. Audic, F. Maguire, C. de Vargas, and T. A. Richards. 2014: Diverse molecular signatures for ribosomally “active” Perkinsea in marine sediments. BMC Microbiology in press.

Dunthorn, M., J. Otto, S. a Berger, A. Stamatakis, F. Mahé, S. Romac, C. de Vargas, S. Audic, B. Consortium, A. Stock, F. Kauff, and T. Stoeck. 2014: Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context. Molecular biology and evolution. In press.

Hartikainen, H., O. S. Ashford, C. Berney, B. Okamura, S. W. Feist, C. Baker-Austin, G. D. Stentiford, and D. Bass. 2014: Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians. The ISME journal 8:177–186.

Logares, R., S. Audic, D. Bass, L. Bittner, R. Christen, J. Claverie, J. Decelle, J. R. Dolan, M. Dunthorn, B. Edvardsen, A. Gobet, W. H. C. F. Kooistra, F. Mahé, F. Not, H. Ogata, J. Pawlowski, C. Massimo, S. Romac, K. Shalchian-tabrizi, N. Simon, S. Santini, R. Siano, P. Wincker, A. Zingone, T. A. Richards, C. de Vargas, and R. Massana. 2014: Patterns of Rare and Abundant Marine Microbial Eukaryotes. Current Biology in press.

2013 (14 papers)

André, A., A. Weiner, R. Aurahs, C. J. Douady, T. De Garidel-thoron, G. Escarguel, C. de Vargas, M. Kucera, F. Quillévéré, R. Morard, and T. de Garidel-Thoron. 2013: The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer. Paleobiology 39:21–39.

Bendif, E. M., I. Probert, D. . Schroeder, and C. de Vargas. 2013a: On the description of Tisochrysis lutea gen . nov . sp . nov . and Isochrysis nuda sp. nov. in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta). Journal of Applied Phycology.

Bendif, E., M. Al-Kandari, I. Probert, and D. . Schroeder. 2013b: Microalgae systematics : can we still fit a square peg in a round hole when new evidence says it is a triangle ? The Marine Biologist 1:15–17.

Berney, C., S. Romac, F. Mahé, S. Santini, R. Siano, and D. Bass. 2013: Vampires in the oceans: predatory cercozoan amoebae in marine habitats. The ISME journal:2387–2399.

Bittner, L., A. Gobet, S. Audic, S. Romac, E. S. Egge, S. Santini, H. Ogata, I. Probert, B. Edvardsen, and C. de Vargas. 2013a: Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Molecular ecology 22:87–101.

Del Campo, J., F. Not, I. Forn, M. E. Sieracki, and R. Massana. 2013a: Taming the smallest predators of the oceans. The ISME journal 7:351–358.

Del Campo, J., V. Balagué, I. Forn, I. Lekunberri, and R. Massana. 2013b: Culturing bias in marine heterotrophic flagellates analyzed through seawater enrichment incubations. Microbial ecology 66:489–499.

Egge, E., L. Bittner, T. Andersen, S. Audic, C. de Vargas, and B. Edvardsen. 2013: 454 Pyrosequencing To Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: a Test for Marine Haptophytes. PloS one 8:e74371.

Guillou, L., D. Bachar, S. Audic, D. Bass, C. Berney, L. Bittner, C. Boutte, G. Burgaud, C. de Vargas, J. Decelle, J. Del Campo, J. R. Dolan, M. Dunthorn, B. Edvardsen, M. Holzmann, W. H. C. F. Kooistra, E. Lara, N. Le Bescot, R. Logares, F. Mahé, R. Massana, M. Montresor, R. Morard, F. Not, J. Pawlowski, I. Probert, A.-L. Sauvadet, R. Siano, T. Stoeck, D. Vaulot, P. Zimmermann, and R. Christen. 2013: The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic acids research 41:D597–604.

Hingamp, P., N. Grimsley, S. G. Acinas, C. Clerissi, L. Subirana, J. Poulain, I. Ferrera, H. Sarmento, E. Villar, G. Lima-Mendez, K. Faust, S. Sunagawa, J.-M. Claverie, H. Moreau, Y. Desdevises, P. Bork, J. Raes, C. de Vargas, E. Karsenti, S. Kandels-Lewis, O. Jaillon, F. Not, S. Pesant, P. Wincker, and H. Ogata. 2013: Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. The ISME journal 7:1678–1695.

Percopo, I., R. Siano, R. Rossi, V. Soprano, D. Sarno, and A. Zingone. 2013: A new potentially toxic Azadinium species (Dinophyceae) from the Mediterranean Sea, A. dexteroporum sp. nov. Journal of Phycology 966:n/a–n/a.

Pernice, M. C., R. Logares, L. Guillou, and R. Massana. 2013: General patterns of diversity in major marine microeukaryote lineages. PloS one 8:e57170.

Roy, A.-S., S. M. Gibbons, H. Schunck, S. Owens, J. G. Caporaso, M. Sperling, J. I. Nissimov, S. Romac, L. Bittner, M. Mühling, U. Riebesell, J. LaRoche, and J. a. Gilbert. 2013: Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Biogeosciences 10:555–566.

Sperling, M., J. Piontek, G. Gerdts, a. Wichels, H. Schunck, a.-S. Roy, J. La Roche, J. Gilbert, J. I. Nissimov, L. Bittner, S. Romac, U. Riebesell, and a. Engel. 2013: Effect of elevated CO2 on the dynamics of particle-attached and free-living bacterioplankton communities in an Arctic fjord. Biogeosciences 10:181–191.

2012 (10 papers)

Bass, D., A. Yabuki, S. Santini, S. Romac, and C. Berney. 2012: Reticulamoeba is a long-branched Granofilosean (Cercozoa) that is missing from sequence databases. PloS one 7:e49090.

Logares, R., S. Audic, S. Santini, M. C. Pernice, C. de Vargas, and R. Massana. 2012: Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. The ISME journal 6:1823–1833.

Massana, R., and R. Logares. 2012: Eukaryotic versus prokaryotic marine picoplankton ecology. Environmental microbiology 15:1254–1261.

Nissimov, J. I., C. a Worthy, P. Rooks, J. a Napier, S. a Kimmance, M. R. Henn, H. Ogata, and M. J. Allen. 2012a: Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. Journal of virology 86:2896–2897.

Nissimov, J. I., C. a Worthy, P. Rooks, J. a Napier, S. a Kimmance, M. R. Henn, H. Ogata, and M. J. Allen. 2012b: Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. Journal of virology 86:2380–2381.

Ota, S., W. Eikrem, and B. Edvardsen. 2012: Ultrastructure and molecular phylogeny of thaumatomonads (Cercozoa) with emphasis on Thaumatomastix salina from Oslofjorden, Norway. Protist 163:560–573.

Pawlowski, J., S. Audic, S. Adl, D. Bass, L. Belbahri, C. Berney, S. S. Bowser, I. Cepicka, J. Decelle, M. Dunthorn, A. M. Fiore-Donno, G. H. Gile, M. Holzmann, R. Jahn, M. Jirků, P. J. Keeling, M. Kostka, A. Kudryavtsev, E. Lara, J. Lukeš, D. G. Mann, E. a D. Mitchell, F. Nitsche, M. Romeralo, G. W. Saunders, A. G. B. Simpson, A. V Smirnov, J. L. Spouge, R. F. Stern, T. Stoeck, J. Zimmermann, D. Schindel, and C. de Vargas. 2012: CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS biology 10:e1001419.

Richards, T. a., M. D. M. Jones, G. Leonard, and D. Bass. 2012: Marine Fungi: Their Ecology and Molecular Diversity. Annual Review of Marine Science 4:495–522.

Rodríguez-Martínez, R., G. Rocap, R. Logares, S. Romac, and R. Massana. 2012: Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4). Molecular biology and evolution 29:1393–1406.

Ujiié, Y., T. Asami, T. de Garidel-Thoron, H. Liu, Y. Ishitani, and C. de Vargas. 2012: Longitudinal differentiation among pelagic populations in a planktic foraminifer. Ecology and evolution 2:1725–1737.

2011 (14 papers)

Bass, D., and T. a. Richards. 2011: Three reasons to re-evaluate fungal diversity “on Earth and in the ocean.”Fungal Biology Reviews 25:159–164.

Beaufort, L., I. Probert, T. de Garidel-Thoron, E. M. Bendif, D. Ruiz-Pino, N. Metzl, C. Goyet, N. Buchet, P. Coupel, M. Grelaud, B. Rost, R. E. M. Rickaby, and C. de Vargas. 2011: Sensitivity of coccolithophores to carbonate chemistry and ocean acidification. Nature 476:80–83.

Del Campo, J., and R. Massana. 2011: Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys. Protist 162:435–448.

Hagino, K., E. M. Bendif, J. R. Young, K. Kogame, I. Probert, Y. Takano, T. Horiguchi, C. de Vargas, and H. Okada. 2011: New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliania huxleyi (Prymnesiophyceae) from the Cox1b-ATP4 genes. Journal of Phycology 47:1164–1176.

Jones, M. D. M., I. Forn, C. Gadelha, M. J. Egan, D. Bass, R. Massana, and T. a Richards. 2011: Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:200–203.

Lepere, C., M. Demura, M. Kawachi, S. Romac, I. Probert, and D. Vaulot. 2011: Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations. FEMS microbiology ecology 76:513–523.

Massana, R. 2011: Eukaryotic picoplankton in surface oceans. Annual review of microbiology 65:91–110.

Massana, R., M. Pernice, J. a Bunge, and J. del Campo. 2011: Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean. The ISME journal 5:184–195.

Nissimov, J. I., C. a Worthy, P. Rooks, J. a Napier, S. a Kimmance, M. R. Henn, H. Ogata, and M. J. Allen. 2011a: Draft genome sequence of the coccolithovirus EhV-84. Standards in genomic sciences 5:1–11.

Nissimov, J. I., C. a Worthy, P. Rooks, J. a Napier, S. a Kimmance, M. R. Henn, H. Ogata, and M. J. Allen. 2011b: Draft genome sequence of the Coccolithovirus Emiliania huxleyi virus 203. Journal of virology 85:13468–13469.

Ogata, H., J. Ray, K. Toyoda, R.-A. Sandaa, K. Nagasaki, G. Bratbak, and J.-M. Claverie. 2011: Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. The ISME journal 5:1143–1151.

Pillet, L., C. de Vargas, and J. Pawlowski. 2011: Molecular identification of sequestered diatom chloroplasts and kleptoplastidy in foraminifera. Protist 162:394–404.

Yoshida, T., J.-M. Claverie, and H. Ogata. 2011: Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids. Virology journal 8:427.

2010 (2 papers)

Siano, R., M. Montresor, I. Probert, F. Not, and C. de Vargas. 2010: Pelagodinium gen. nov. and P. béii comb. nov., a dinoflagellate symbiont of planktonic foraminifera. Protist 161:385–399.

Stoeck, T., D. Bass, M. Nebel, R. Christen, M. D. M. Jones, H.-W. Breiner, and T. a Richards. 2010: Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular ecology 19 Suppl 1:21–31.

Behnke, A., M. Engel, R. Christen, M. Nebel, R. R. Klein, and T. Stoeck. 2010: Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environmental microbiology 13:340–349.

In prep :

Audic, S., Garet-Delmas, M.J., Romac, S., de Vargas, C., et al.  Reverse taxonomy to assess unknown protistan biodiversity. In prep.

Bass, D., Hartikainen, H., Del Campo, J., Ruiz-Trillo, I., & et al. . DRIP clade (Ichthyosporea) - lineage-specific approach, probing biomarks samples; In prep.

Berney, C. et al. . Novel eukaryotic lineages and the invisible protistan biosphere. In prep.

Bittner, L. and the BioMarKs consortium. Is everything everywhere in coastal marine protists? In prep.

Bjorbækmo, M., & Al., E. . Diversity of marine parasites. In prep.

Cabello, A.-M., & et al. . Increasing chrysophyte diversity using group-specific primers against the V4 region. In prep.

Cabello, A.-M., & et al. Exploring population genetics of pelagophytes with ITS rDNA barcodes. In prep.

Chambouvet A., Leonard G., Mahé F., Romac S., Audic S., Maguire F., de Vargas C. and Richards T.A. Multi-provenance biodiversity signatures for fungi in european marine environment. Fungal diversity. In prep.

Del Campo, J., & et al. . Phylogenetic analysis of unicellular opisthokonta (excluding metazoa and fungi). In prep.

Edvardsen, B., Bittner, L., Egge, E. S., Zingone, A., Eikrem, W., Romac, S., Audic, S., de Vargas, C., et al. Haptophyte diversity in European coastal waters as revealed by 454 pyrosequencing. In prep.

Egge, E. S., Bittner, L., Edvardsen, B., Eikrem, W., &  et al. Diversity and dynamics of haptophytes in outer Oslofjorden revealed by 454-pyrosequencing. In prep.

Egge, E. S., Edvardsen, B., Eikrem, W., & et al. Deep-branching novel lineages of haptophytes in Oslofjorden uncovered by 454 pyrosequencing. In prep.

Eikrem, W., Hostyeva, Ota, S. Egge, E. S., & et al. . Seasonal dynamics of planktonic protists in outer Oslofjord as revealed by light and electron microscopy. In prep.

Gobet, A., Massana, R., Logares, R., Romac, S., Audic, S., de Vargas, C., and the BioMarKs consortium. Disentangling marine protistan activity from its apparent diversity. In prep.

Gran, S., Egge, E. S., Andersen, T., Eikrem, W., Edvardsen, B., & et al. . Seasonal dynamics of pico- and nanoplanktonic protists in outer Oslofjord as revealed by 454-pyrosequencing. In prep.

Mahé, F., & et al. DNA versus RNA-based metabarcoding of a global eukaryotic mock community. In prep.

Massana, R., & the BioMarKs consortium. NGS assessment of protistan biodiversity in EU marine coastal waters and sediments. In prep.

Ota, S., Eikrem, W., Edvardsen, B., & et al. Distribution and identification of Azadinium species (Dinophyceae) in European coastal waters. In prep.

Pawlowski, J., Reo, M., Lejzerowicz, F., & the BioMarKs consortium. Metabarcoding reveals massive planktonic dispersal of coastal benthic foraminifera. In prep.

Piredda, R.,  Zingone, A., Kooistra, WHCF,  Sarno, D.  Montresor, M.  and the BioMarKs consortium: SSU rDNA metabarcodind of diatom diversity across European seas (in preparation)

Rodriguez-Giner, C., & et al. Exploring populations genetics of MAST-4 using ITS1 rDNA barcodes. In prep.

Rodriguez-Giner, C., et al. NGS versus FISH quantification of picoeukaryotes relative abundances. In prep.

Rodriguez-Giner, C., et al. Seasonality of marine picoeukaryotes in Blanes Bay (4 years at the V4 region) - Taxonomic and community comparison. In prep.

Stoeck, T., and the BioMarKs consortium. Molecular ecology of coastal marine protists: water column versus sediments versus terrestrial biomes. In prep.

Vaulot, D., Lopes, A., Audic, S., Romac, S., de Vargas & et al. . Green phytoplankton (Chlorophyta) in european coastal waters from SSU rRNA V4 tags. In prep.