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8 results on '"Bittner, Lucie"'

1. Clade-specific diversification dynamics of marine diatoms since the Jurassic.

Author

Lewitus E, Bittner L, Malviya S, Bowler C, and Morlon H

Subjects
Carbon Dioxide chemistry, Climate Change, DNA Barcoding, Taxonomic, Microbial Interactions, Oceans and Seas, Phytoplankton classification, Silicon Dioxide chemistry, Biodiversity, Diatoms classification, Phylogeny, Phytoplankton physiology
Abstract

Diatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and the Earth's biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of variation in carbon dioxide partial pressure (pCO 2 ) on early diatom diversification, followed by a major burst of diversification in the late Eocene epoch, after which diversification is chiefly affected by sea level, an influx of silica availability and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favour some clades at the expense of others.

Published
2018
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2. Patterns of rare and abundant marine microbial eukaryotes.

Author

Logares R, Audic S, Bass D, Bittner L, Boutte C, Christen R, Claverie JM, Decelle J, Dolan JR, Dunthorn M, Edvardsen B, Gobet A, Kooistra WH, Mahé F, Not F, Ogata H, Pawlowski J, Pernice MC, Romac S, Shalchian-Tabrizi K, Simon N, Stoeck T, Santini S, Siano R, Wincker P, Zingone A, Richards TA, de Vargas C, and Massana R

Subjects
Atlantic Ocean, Base Sequence, Cluster Analysis, Europe, High-Throughput Nucleotide Sequencing, Mediterranean Sea, Molecular Sequence Data, North Sea, Population Density, RNA, Ribosomal, 18S genetics, Species Specificity, Biodiversity, Eukaryota genetics, Eukaryota physiology, Marine Biology statistics & numerical data, Microbiota genetics, Phylogeny
Abstract

Background: Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions., Results: Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change., Conclusions: We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Published
2014
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5. 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

6. 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

7. 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, de Vargas, Colomban, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), 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), The Natural History Museum [London] (NHM), University of Exeter, Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], University of Oslo (UiO), Diversité et Interactions au sein du Plancton Océanique (DIPO), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-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), Stazione Zoologica Anton Dohrn (SZN), Kyoto University, Université de Genève = University of Geneva (UNIGE), Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Kyoto University [Kyoto], University of Geneva [Switzerland], Dynamiques de l'Environnement Côtier (DYNECO), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
Geologic Sediments, Base Sequence, fungi, Fungi, High-Throughput Nucleotide Sequencing, Biodiversity, Sequence Analysis, DNA, Plankton, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Europe, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Alveolata, RNA, Ribosomal, 18S, Seawater, Ecosystem, Phylogeny, Stramenopiles
Abstract

International audience; Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.

Published
2015

8. Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes

Author

Bittner, Lucie, Payri, Claude E., Maneveldt, Gavin W., Couloux, Arnaud, Cruaud, Corinne, de Reviers, Bruno, and Le Gall, Line

Subjects
*CORALLINE algae, *MITOCHONDRIAL DNA, *BIOLOGICAL classification, *MOLECULAR biology, *PHYLOGENY, *GENETIC markers, *MAXIMUM likelihood statistics, *CYTOCHROME oxidase
Abstract

Abstract: Systematics of the red algal order Corallinales has a long and convoluted history. In the present study, molecular approaches were used to assess the phylogenetic relationships based on the analyses of two datasets: a large dataset of SSU sequences including mainly sequences from GenBank; and a combined dataset including four molecular markers (two nuclear: SSU, LSU; one plastidial: psbA; and one mitochondrial: COI). Phylogenetic analyses of both datasets re-affirmed the monophyly of the Corallinales as well as the two families (Corallinaceae and Hapalidiaceae) currently recognized within the order. Three of the four subfamilies of the Corallinaceae (Corallinoideae, Lithophylloideae, Metagoniolithoideae) were also resolved as a monophyletic lineage whereas members of the Mastophoroideae were resolved as four distinct lineages. We therefore propose to restrict the Mastophoroideae to the genera Mastophora, Metamastophora, and possibly Lithoporella in the aim of rendering this subfamily monophyletic. In addition, our phylogenies resolved the genus Hydrolithon in two unrelated lineages, one containing the generitype Hydrolithon reinboldii and the second containing Hydrolithon onkodes, which used to be the generitype of the now defunct genus Porolithon. We therefore propose to resurrect the genus Porolithon for the second lineage encompassing those species with primarily monomerous thalli, and trichocyte arrangements in large pustulate horizontal rows. Moreover, our phylogenetic analyses revealed the presence of cryptic diversity in several taxa, shedding light on the need for further studies to better circumscribe species frontiers within the diverse order Corallinales, especially in the genera Mesophyllum and Neogoniolithon. [Copyright &y& Elsevier]

Published
2011
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