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256 results on '"Audic, Stéphane"'

1. Mimivirus and the emerging concept of 'giant' virus

Author

Claverie, Jean-Michel, Ogata, Hiroyuki, Audic, Stéphane, Abergel, Chantal, Fournier, Pierre-Edouard, and Suhre, Karsten

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The recently discovered Acanthamoeba polyphaga Mimivirus is the largest known DNA virus. Its particle size (>400 nm), genome length (1.2 million bp) and large gene repertoire (911 protein coding genes) blur the established boundaries between viruses and parasitic cellular organisms. In addition, the analysis of its genome sequence identified new types of genes not expected to be seen in a virus, such as aminoacyl-tRNA synthetases and other central components of the translation machinery. In this article, we examine how the finding of a giant virus for the first time overlapping with the world of cellular organisms in terms of size and genome complexity might durably influence the way we look at microbial biodiversity, and force us to fundamentally revise our classification of life forms. We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which make them closer to small parasitic prokaryotes than to regular viruses., Comment: Submitted to Virus Research

Published
2005

2. Mimivirus Gene Promoters Exhibit an Unprecedented Conservation among all Eukaryotes

Author

Suhre, Karsten, Audic, Stéphane, and Claverie, Jean-Michel

Subjects
Quantitative Biology - Genomics
Abstract

The initial analysis of the recently sequenced genome of Acanthamoeba polyphaga Mimivirus, the largest known double-stranded DNA virus, predicted a proteome of size and complexity more akin to small parasitic bacteria than to other nucleo-cytoplasmic large DNA viruses, and identified numerous functions never before described in a virus. It has been proposed that the Mimivirus lineage could have emerged before the individualization of cellular organisms from the 3 domains of life. An exhaustive in silico analysis of the non-coding moiety of all known viral genomes, now uncovers the unprecedented perfect conservation of a AAAATTGA motif in close to 50% of the Mimivirus genes. This motif preferentially occurs in genes transcribed from the predicted leading strand and is associated with functions required early in the viral infectious cycle, such as transcription and protein translation. A comparison with the known promoter of unicellular eukaryotes, in particular amoebal protists, strongly suggests that the AAAATTGA motif is the structural equivalent of the TATA box core promoter element. This element is specific to the Mimivirus lineage, and may correspond to an ancestral promoter structure predating the radiation of the eukaryotic kingdoms. This unprecedented conservation of core promoter regions is another exceptional features of Mimivirus, that again raises the question of its evolutionary origin.

Published
2005
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4. The 1.2-Megabase Genome Sequence of Mimivirus

Author

Raoult, Didier, Audic, Stéphane, Robert, Catherine, Abergel, Chantal, Renesto, Patricia, Ogata, Hiroyuki, La Scola, Bernard, Suzan, Marie, and Claverie, Jean-Michel

Published
2004

11. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Author

Massana, Ramon, Gobet, Angélique, Audic, Stéphane, Bass, David, Bittner, Lucie, Boutte, Christophe, Chambouvet, Aurélie, Christen, Richard, Claverie, Jean-Michel, Decelle, Johan, Dolan, John R., Dunthorn, Micah, Edvardsen, Bente, Forn, Irene, Forster, Dominik, Guillou, Laure, Jaillon, Olivier, Kooistra, Wiebe H. C. F., Logares, Ramiro, Mahé, Frédéric, Not, Fabrice, Ogata, Hiroyuki, Pawlowski, Jan, Pernice, Massimo C., Probert, Ian, Romac, Sarah, Richards, Thomas, Santini, Sébastien, Shalchian-Tabrizi, Kamran, Siano, Raffaele, Simon, Nathalie, Stoeck, Thorsten, Vaulot, Daniel, Zingone, Adriana, and de Vargas, Colomban

Published
2015
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13. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author

Guillou, Laure, Bachar, Dipankar, Audic, Stéphane, Bass, David, Berney, Cédric, Bittner, Lucie, Boutte, Christophe, Burgaud, Gaétan, de Vargas, Colomban, Decelle, Johan, del Campo, Javier, Dolan, John R., Dunthorn, Micah, Edvardsen, Bente, Holzmann, Maria, Kooistra, Wiebe H.C.F., Lara, Enrique, Le Bescot, Noan, Logares, Ramiro, Mahé, Frédéric, Massana, Ramon, Montresor, Marina, Morard, Raphael, Not, Fabrice, Pawlowski, Jan, Probert, Ian, Sauvadet, Anne-Laure, Siano, Raffaele, Stoeck, Thorsten, Vaulot, Daniel, Zimmermann, Pascal, and Christen, Richard

Published
2013
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16. A Giant Virus in Amoebae

Author

La Scola, Bernard, Audic, Stéphane, Robert, Catherine, Jungang, Liang, de Lamballerie, Xavier, Drancourt, Michel, Birtles, Richard, Claverie, Jean-Michel, and Raoult, Didier

Published
2003

18. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

Author

Claverie Jean-Michel, Lescot Magali, Audic Stéphane, Cloeckaert Axel, and Zygmunt Michel S

Subjects
Brucella, Bacterial Genome Evolution, Comparative Genomics, Evolution, QH359-425
Abstract

Abstract Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups.

Published
2011
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19. Brucella microti: the genome sequence of an emerging pathogen

Author

Scholz Holger C, Claverie Jean-Michel, Lescot Magali, and Audic Stéphane

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Using a combination of pyrosequencing and conventional Sanger sequencing, the complete genome sequence of the recently described novel Brucella species, Brucella microti, was determined. B. microti is a member of the genus Brucella within the Alphaproteobacteria, which consists of medically important highly pathogenic facultative intracellular bacteria. In contrast to all other Brucella species, B. microti is a fast growing and biochemically very active microorganism with a phenotype more similar to that of Ochrobactrum, a facultative human pathogen. The atypical phenotype of B. microti prompted us to look for genomic differences compared to other Brucella species and to look for similarities with Ochrobactrum. Results The genome is composed of two circular chromosomes of 2,117,050 and 1,220,319 base pairs. Unexpectedly, we found that the genome sequence of B. microti is almost identical to that of Brucella suis 1330 with an overall sequence identity of 99.84% in aligned regions. The most significant structural difference between the two genomes is a bacteriophage-related 11,742 base pairs insert only present in B. microti. However, this insert is unlikely to have any phenotypical consequence. Only four protein coding genes are shared between B. microti and Ochrobactrum anthropi but impaired in other sequenced Brucella. The most noticeable difference between B. microti and other Brucella species was found in the sequence of the 23S ribosomal RNA gene. This unusual variation could have pleiotropic effects and explain the fast growth of B. microti. Conclusion Contrary to expectations from the phenotypic analysis, the genome sequence of B. microti is highly similar to that of known Brucella species, and is remotely related to the one of O. anthropi. How the few differences in gene content between B. microti and B. suis 1330 could result in vastly different phenotypes remains to be elucidated. This unexpected finding will complicate the task of identifying virulence determinants in the Brucella genus. The genome sequence of B. microti will serve as a model for differential expression analysis and complementation studies. Our results also raise some concerns about the importance given to phenotypical traits in the definition of bacterial species.

Published
2009
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20. Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction

Author

Audic Stéphane, Parola Philippe, Socolovschi Cristina, Renesto Patricia, Giumelli Bernadette, Robert Catherine, Leroy Quentin, El Karkouri Khalid, Fournier Pierre-Edouard, and Raoult Didier

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The Rickettsia genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent R. prowazekii, which causes epidemic typhus and kills its arthropod host, to the mild pathogen R. africae, the agent of African tick-bite fever, which does not affect the fitness of its tick vector. Results We evaluated the clonality of R. africae in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 bp including a tra operon and an unstable 12,377-bp plasmid. To study the genetic characteristics associated with virulence, we compared this species to R. prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii have, respectively, the less and most decayed genomes. Eighteen genes are present only in R. africae including one with a putative protease domain upregulated at 37°C. Conclusion Based on these data, we speculate that a loss of regulatory genes causes an increase of virulence of rickettsial species in ticks and mammals. We also speculate that in Rickettsia species virulence is mostly associated with gene loss. The genome sequence was deposited in GenBank under accession number [GenBank: NZ_AAUY01000001].

Published
2009
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22. UniEuk: Time to Speak a Common Language in Protistology!

Author

Berney, Cédric, Ciuprina, Andreea, Bender, Sara, Brodie, Juliet, Edgcomb, Virginia, Kim, Eunsoo, Rajan, Jeena, Wegener Parfrey, Laura, Adl, Sina, Audic, Stéphane, Bass, David, Caron, David A., Cochrane, Guy, Czech, Lucas, Dunthorn, Micah, and Geisen, Stefan

Subjects
Diversity, EukMap, EukBank, Eukaryotes, EukRef, Community expertise, Laboratory of Nematology, PE&RC, Laboratorium voor Nematologie, Taxonomy
Abstract

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes.

Published
2017

26. First Tara Oceans V9 rDNA metabarcoding dataset

Author

de Vargas, Colomban, Audic, Stéphane, Henry, Nicolas, Decelle, Johan, Mahé, Frédéric, Logares, Ramiro, Lara, Enrique, Berney, Cédric, Le Bescot, Noan, Probert, Ian, Carmichael, Margaux, Poulain, Julie, Romac, Sarah, Colin, Sébastien, Aury, Jean-Marc, Bittner, Lucie, Chaffron, Samuel, Dunthorn, Micah, Engelen, Stefan, Flegontova, Olga, Guidi, Lionel, Horák, Aleš, Jaillon, Olivier, Lima-Mendez, Gipsi, Lukeš, Julius, Malviya, Shruti, Morard, Raphael, Mulot, Matthieu, Scalco, Eleonora, Siano, Raffaele, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans Coordinators, Acinas, Silvia G., Bork, Peer, Bowler, Chris, Gorsky, Gabriel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Raes, Jeroen, Sieracki, Mike, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Weissenbach, Jean, Wincker, Patrick, and Karsenti, Eric

Subjects
14. Life underwater
Abstract

Accompanying material, text, data and figures for the article de Vargas et al., 'Eukaryotic plankton diversity in the sunlit ocean', Science 348, 1261605 (2015), doi: 10.1126/science.1261605 &nbsp

Published
2015
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27. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, and Iudicone, Daniele

Subjects
fungi
Abstract

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic., プランクトンの世界 : 新しいフロンティア -タラ海洋探査からの最新情報-. 京都大学プレスリリース. 2015-05-22.

Published
2015

28. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

Author

de Vargas, Colomban, Audic, Stéphane, Henry, Nicolas, Decelle, Johan, Mahé, Frédéric, Logares, Ramiro, Lara, Enrique, Berney, Cédric, Le Bescot, Noan, Probert, Ian, Carmichael, Margaux, Poulain, Julie, Romac, Sarah, Colin, Sébastien, Aury, Jean-Marc, Bittner, Lucie, Chaffron, Samuel, Dunthorn, Micah, Engelen, Stefan, Flegontova, Olga, Guidi, Lionel, Horak, Ales, Jaillon, Olivier, Lima-Mendez, Gipsi, Lukeš, Julius, Malviya, Shruti, Morard, Raphael, Mulot, Matthieu, Scalco, Eleonora, Siano, Raffaele, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Acinas, Silvia G, Bork, Peer, Bowler, Chris, Gorsky, Gabriel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Sieracki, Michael E, Speich, Sabrina, Stemmann, Lars, Tara Oceans coordinators, Department of Bio-engineering Sciences, and Microbiology

Subjects
Oceans and Seas, fungi, plankton, Sunlight, Animals, DNA Barcoding, Taxonomic, Eukaryota, natural sciences, Sequence Analysis, DNA, phylogeny, DNA, Ribosomal, Ribosomes, biodiversity
Abstract

Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

Published
2015

29. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

Author

von Dassow, Peter, John, Uwe, Ogata, Hiroyuki, Probert, Ian, Bendif, El Mahdi, Kegel, Jessica U, Audic, Stéphane, Wincker, Patrick, da Silva, Corinne, Claverie, Jean-Michel, Doney, Scott, Glover, David M, Mella-Flores, Daniella, Herrera, Yeritza, Lescot, Magali, Garet-Delmas, Marie-José, de Vargas, Colomban, Instituto Milenio de Oceanografia (IMO), Pontificia Universidad Católica de Chile (UC), Evolutionary Biology and Ecology of Algae (EBEA), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Kyoto University, Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Marine Biological Association of the UK, The Laboratory, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Woods Hole Oceanographic Institution (WHOI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Pontificia Universidad Católica de Chile (UC), and Kyoto University [Kyoto]

Subjects
fungi, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microbiology, Ecology, Evolution, Behavior and Systematics
Abstract

Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers., Supplementary Information accompanies this paper on The ISME Journal website (http://www.nature.com/ismej)

Published
2015

30. Ocean plankton. Determinants of community structure in the global plankton interactome

Author

Lima-Mendez, Gipsi, Faust, Karoline, Henry, Nicolas, Decelle, Johan, Colin, Sébastien, Carcillo, Fabrizio, Chaffron, Samuel, Ignacio-Espinosa, J Cesar, Roux, Simon, Vincent, Flora, Bittner, Lucie, Darzi, Youssef, Wang, Jun, Audic, Stéphane, Berline, Léo, Bontempi, Gianluca, Cabello, Ana M, Coppola, Laurent, Cornejo-Castillo, Francisco M, d'Ovidio, Francesco, De Meester, Luc, Ferrera, Isabel, Garet-Delmas, Marie-José, Guidi, Lionel, Lara, Elena, Pesant, Stéphane, Royo-Llonch, Marta, Salazar, Guillem, Sánchez, Pablo, Sebastian, Marta, Souffreau, Caroline, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Gorsky, Gabriel, Not, Fabrice, Ogata, Hiroyuki, Speich, Sabrina, Stemmann, Lars, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Sunagawa, Shinichi, Bork, Peer, Sullivan, Matthew B, Karsenti, Eric, Bowler, Chris, de Vargas, Colomban, Raes, Jeroen, Tara Oceans coordinators, Department of Bio-engineering Sciences, Faculty of Economic and Social Sciences and Solvay Business School, Faculty of Sciences and Bioengineering Sciences, Hydrology and Hydraulic Engineering, and Microbiology

Subjects
Food Chain, Platyhelminths, Oceans and Seas, fungi, plankton, Sunlight, Animals, viruses, phylogeny, Host Specificity, symbiosis
Abstract

Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.

Published
2015

31. PFR²: a curated database of planktonic Foraminifera18S ribosomal DNA as a resource for studies of plankton ecology, biogeography, and evolution

Author

Morard, Raphaël, Darling, Kate F, Mahé, Frédéric, Audic, Stéphane, Ujiié, Yurika, Weiner, Agnes K.F., André, Aurore, Seears, Heidi, Wade, Chris M, Quillévéré, Frédéric, Douady, Christophe Jean, Escarguel, Gilles, De Garidel-Thoron, Thibault, Siccha, Michael, Kucera, Michal, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), School of Geography and Geosciences [St Andrews], University of St Andrews [Scotland], School of Geosciences [Edinburgh], University of Edinburgh, Department of ecology, Technische Universität Kaiserslautern (TU Kaiserslautern), Department of biology, Shinshu University [Nagano], URCA - UFR Sciences exactes et naturelles (URCA UFR SEN), Université de Reims Champagne-Ardenne (URCA), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Department of Biological Sciences [Bethlehem], Lehigh University, School of life sciences, University of Nottingham, UK (UON), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, planktonic foraminifera, 18S ribosomal DNA, fungi, [SDE]Environmental Sciences, sequence database, genetic diversity, molecular taxonomy, molecular ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract

International audience; Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR2, the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR2 website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent.

Published
2015

33. Benthic protists: the under-charted majority

Author

Forster, Dominik, primary, Dunthorn, Micah, additional, Mahé, Fréderic, additional, Dolan, John R., additional, Audic, Stéphane, additional, Bass, David, additional, Bittner, Lucie, additional, Boutte, Christophe, additional, Christen, Richard, additional, Claverie, Jean-Michel, additional, Decelle, Johan, additional, Edvardsen, Bente, additional, Egge, Elianne, additional, Eikrem, Wenche, additional, Gobet, Angélique, additional, Kooistra, Wiebe H.C.F., additional, Logares, Ramiro, additional, Massana, Ramon, additional, Montresor, Marina, additional, Not, Fabrice, additional, Ogata, Hiroyuki, additional, Pawlowski, Jan, additional, Pernice, Massimo C., additional, Romac, Sarah, additional, Shalchian-Tabrizi, Kamran, additional, Simon, Nathalie, additional, Richards, Thomas A., additional, Santini, Sébastien, additional, Sarno, Diana, additional, Siano, Raffaele, additional, Vaulot, Daniel, additional, Wincker, Patrick, additional, Zingone, Adriana, additional, de Vargas, Colomban, additional, and Stoeck, Thorsten, additional

Published
2016
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34. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms

Author

Ichinomiya, Mutsuo, primary, dos Santos, Adriana Lopes, additional, Gourvil, Priscillia, additional, Yoshikawa, Shinya, additional, Kamiya, Mitsunobu, additional, Ohki, Kaori, additional, Audic, Stéphane, additional, de Vargas, Colomban, additional, Noël, Mary-Hélène, additional, Vaulot, Daniel, additional, and Kuwata, Akira, additional

Published
2016
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37. CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

Author

Pawlowski , Jan, Audic , Stéphane, Adl , Sina, Bass , David, Belbahri , Lassaâd, Berney , Cédric, Bowser , Samuel S., Cepicka , Ivan, Decelle , Johan, Dunthorn , Micah, Fiore-Donno , Anna Maria, Gile , Gillian H., Holzmann , Maria, Jahn , Regine, Jirků , Miloslav, Keeling , Patrick J., Kostka , Martin, Kudryavtsev , Alexander, Lara , Enrique, Lukeš , Julius, Mann , David G., Mitchell , Edward A. D., Nitsche , Frank, Romeralo , Maria, Saunders , Gary W., Simpson , Alastair G. B., Smirnov , Alexey V., Spouge , John L., Stern , Rowena F., Stoeck , Thorsten, Zimmermann , Jonas, Schindel , David, Department of genetics and evolution, University of Geneva [Switzerland], Evolution des Protistes et Ecosystèmes Pélagiques ( EPEP ), Adaptation et diversité en milieu marin ( ADMM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), University of Saskatchewan [Saskatoon] ( U of S ), Department of life sciences, The Natural History Museum [London], Laboratory of Soil Biology, University of Neuchatel, Wadsworth Center, Department of Zoology, University of Kaiserslautern [Kaiserslautern], Institute of Botany and Landscape Ecology, University of Greifswald, Department of Biochemistry and Molecular Biology, Department of Evolutionary Genetics, Botanischer Garten und Botanischer Museum Berlin-Dahlem, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Canadian Institute for Advanced Research ( CIAR ), Université de Montréal, Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University ( SPSPU ) -Saint Petersburg State Polytechnical University ( SPSPU ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Royal Botanical Garden Edinburgh, Royal Botanical Garden, Universität zu Köln, Department of Systematic Biology [Uppsala], Evolutionary Biology Centre ( EBC ), Uppsala University-Uppsala University, University of New Brunswick ( UNB ), Department of Biology - Life Sciences Centre, Department of Invertebrate Zoology, National Center for Biotechnology Information ( NCBI ), Sir AlisterHardyFoundationforOceanScience, TheLaboratory,CitadelHill,PlymouthPL12PB,UK, Dept of Ecology, University of Kaiserslautern, Smithsonian Institution National Museum of Natural History ( NMNH ), Consortium for the Barcoding of Life, European ERA-net program BiodivErsA under the BioMarKs project, French ANR project [09-BLAN-0348 POSEIDON], and Swiss National Science Foundation [31003A-140766]

Subjects
[ SDE ] Environmental Sciences, [ SDV ] Life Sciences [q-bio], fungi
Abstract

International audience; Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth.

Published
2012

39. PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution

Author

Morard, Raphaël, primary, Darling, Kate F., additional, Mahé, Frédéric, additional, Audic, Stéphane, additional, Ujiié, Yurika, additional, Weiner, Agnes K. M., additional, André, Aurore, additional, Seears, Heidi A., additional, Wade, Christopher M., additional, Quillévéré, Frédéric, additional, Douady, Christophe J., additional, Escarguel, Gilles, additional, de Garidel‐Thoron, Thibault, additional, Siccha, Michael, additional, Kucera, Michal, additional, and de Vargas, Colomban, additional

Published
2015
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40. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Author

Decelle, Johan, primary, Romac, Sarah, additional, Stern, Rowena F., additional, Bendif, El Mahdi, additional, Zingone, Adriana, additional, Audic, Stéphane, additional, Guiry, Michael D., additional, Guillou, Laure, additional, Tessier, Désiré, additional, Le Gall, Florence, additional, Gourvil, Priscillia, additional, Dos Santos, Adriana L., additional, Probert, Ian, additional, Vaulot, Daniel, additional, de Vargas, Colomban, additional, and Christen, Richard, additional

Published
2015
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43. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton

Author

von Dassow, Peter, primary, John, Uwe, additional, Ogata, Hiroyuki, additional, Probert, Ian, additional, Bendif, El Mahdi, additional, Kegel, Jessica U, additional, Audic, Stéphane, additional, Wincker, Patrick, additional, Da Silva, Corinne, additional, Claverie, Jean-Michel, additional, Doney, Scott, additional, Glover, David M, additional, Flores, Daniella Mella, additional, Herrera, Yeritza, additional, Lescot, Magali, additional, Garet-Delmas, Marie-José, additional, and de Vargas, Colomban, additional

Published
2014
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44. Patterns of Rare and Abundant Marine Microbial Eukaryotes

Author

Logares, Ramiro, primary, Audic, Stéphane, additional, Bass, David, additional, Bittner, Lucie, additional, Boutte, Christophe, additional, Christen, Richard, additional, Claverie, Jean-Michel, additional, Decelle, Johan, additional, Dolan, John R., additional, Dunthorn, Micah, additional, Edvardsen, Bente, additional, Gobet, Angélique, additional, Kooistra, Wiebe H.C.F., additional, Mahé, Frédéric, additional, Not, Fabrice, additional, Ogata, Hiroyuki, additional, Pawlowski, Jan, additional, Pernice, Massimo C., additional, Romac, Sarah, additional, Shalchian-Tabrizi, Kamran, additional, Simon, Nathalie, additional, Stoeck, Thorsten, additional, Santini, Sébastien, additional, Siano, Raffaele, additional, Wincker, Patrick, additional, Zingone, Adriana, additional, Richards, Thomas A., additional, de Vargas, Colomban, additional, and Massana, Ramon, additional

Published
2014
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48. Phyto REF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

Author

Decelle, Johan, Romac, Sarah, Stern, Rowena F., Bendif, El Mahdi, Zingone, Adriana, Audic, Stéphane, Guiry, Michael D., Guillou, Laure, Tessier, Désiré, Le Gall, Florence, Gourvil, Priscillia, Dos Santos, Adriana L., Probert, Ian, Vaulot, Daniel, Vargas, Colomban, and Christen, Richard

Subjects
EUKARYOTES, NUCLEOTIDE sequencing, GENETIC barcoding, PHOTOSYNTHESIS, PHYTOPLANKTON, RIBOSOMAL RNA
Abstract

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the Phyto REF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the Phyto REF sequences) and freshwater taxa were also included to broaden the applicability of Phyto REF to different aquatic and terrestrial habitats. Phyto REF, accessible via a web interface (), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing. [ABSTRACT FROM AUTHOR]

Published
2015
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49. PFR2: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.

Author

Morard, Raphaël, Darling, Kate F., Mahé, Frédéric, Audic, Stéphane, Ujiié, Yurika, Weiner, Agnes K. M., André, Aurore, Seears, Heidi A., Wade, Christopher M., Quillévéré, Frédéric, Douady, Christophe J., Escarguel, Gilles, Garidel‐Thoron, Thibault, Siccha, Michael, Kucera, Michal, and Vargas, Colomban

Subjects
FORAMINIFERA, ECOLOGY of plankton, RIBOSOMAL DNA, MOLECULAR ecology, TAXONOMY
Abstract

Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S r DNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR2, the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S r DNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR2 website, available at , allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
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50. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author

Guillou, Laure, primary, Bachar, Dipankar, additional, Audic, Stéphane, additional, Bass, David, additional, Berney, Cédric, additional, Bittner, Lucie, additional, Boutte, Christophe, additional, Burgaud, Gaétan, additional, de Vargas, Colomban, additional, Decelle, Johan, additional, del Campo, Javier, additional, Dolan, John R., additional, Dunthorn, Micah, additional, Edvardsen, Bente, additional, Holzmann, Maria, additional, Kooistra, Wiebe H.C.F., additional, Lara, Enrique, additional, Le Bescot, Noan, additional, Logares, Ramiro, additional, Mahé, Frédéric, additional, Massana, Ramon, additional, Montresor, Marina, additional, Morard, Raphael, additional, Not, Fabrice, additional, Pawlowski, Jan, additional, Probert, Ian, additional, Sauvadet, Anne-Laure, additional, Siano, Raffaele, additional, Stoeck, Thorsten, additional, Vaulot, Daniel, additional, Zimmermann, Pascal, additional, and Christen, Richard, additional

Published
2012
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