Journal of Genomics Genome Sequence of Kordia Sp. Strain
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THÈSE DE DOCTORAT DE SORBONNE UNIVERSITÉ Spécialité Écologie Microbienne Marine École Doctorale 227 « Sciences de la Nature et de l’Homme : Écologie et Évolution » Par Laure ARSENIEFF En vue de l’obtention du grade de Docteur de Sorbonne Université PARASITISME ET CONTRÔLE DES BLOOMS DE DIATOMÉES EN MANCHE OCCIDENTALE Thèse soutenue le 14 Décembre 2018, devant un jury composé de : Dr. Claire GACHON……………………………………………………………………………………………… ..Rapporteur Maître de conférences, The Scottish Association for Marine Science Dr. Kay BIDLE………………………………………………………………………………………………………… Rapporteur Professeur, Rutgers University Dr. Télesphore SIME-NGANDO …........................................................... ..................Examinateur Directeur de recherche, Laboratoire Microorganismes : Génome et Environnement, UMR CNRS Dr. Éric THIEBAUT……………………………………………………………………………………………… ..Examinateur Professeur, Station Biologique de Roscoff, Sorbonne Université, CNRS Dr. Anne-Claire BAUDOUX …................................................... .................Co-directrice de Thèse Chargée de recherche, Station Biologique de Roscoff, Sorbonne Université, CNRS Dr. Nathalie SIMON ………………………………………………………………………………Co -directrice de Thèse Maître de conférences, Station Biologique de Roscoff, Sorbonne Université, CNRS Station Biologique de Roscoff UMR7144 Adaptation et Diversité en Milieu Marin Équipe Diversité et Interactions au sein du Plancton Océanique – Groupe Plancton Projet DynaMO Interactions durables et contrôle des blooms et successions de diatomées en Manche -
Ecological and Functional Capabilities of an Uncultured Kordia
1 2 3 4 5 6 7 Ecological and functional capabilities of an uncultured 8 Kordia sp. 9 10 Royo-Llonch M1,4, Sánchez P1, González JM2, Pedrós-Alió C3, Acinas SG1* 11 12 _____________________________________________________________________ 13 14 1 Department oF Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), 15 CSIC, Barcelona, Spain. 16 2 Department oF Microbiology, University oF La Laguna, La Laguna, Spain 17 3 Systems Biology Program, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain 18 4 Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma 19 de Barcelona, Bellaterra, Spain 20 21 *Correspondence: 22 Dr. Silvia G. Acinas 23 [email protected]; 24 25 Keywords: SAG , Kordia, co-assembly, photoheterotrophy, metagenomics 26 1 27 Abstract 28 Cultivable bacteria are only a Fraction oF the diversity in microbial communities. However, 29 the oFFicial procedures For classiFication and characterization of a novel prokaryotic 30 species still rely on isolates. Thanks to Single Cell Genomics, it is possible to retrieve 31 genomes From environmental samples by sequencing them individually, and to assign 32 speciFic genes to a speciFic taxon, regardless oF their ability to grow in culture. In this 33 study, we perFormed a complete description oF the uncultured Kordia sp. 34 TARA_039_SRF, a proposed novel species within the genus Kordia, using culture- 35 independent techniques. The type material was a high-quality draFt genome (94.97% 36 complete, 4.65% gene redundancy) co-assembled using 10 nearly identical Single 37 AmpliFied Genomes (SAGs) From surFace seawater in the North Indian Ocean from the 38 Tara Oceans expedition. -
Genome Characteristics of Kordia Antarctica IMCC3317T And
www.nature.com/scientificreports OPEN Genome characteristics of Kordia antarctica IMCC3317T and comparative genome analysis of the genus Kordia Yeonjung Lim1, Ilnam Kang2* & Jang‑Cheon Cho1* The genus Kordia is one of many genera afliated with the family Flavobacteriaceae of the phylum Bacteroidetes, well known for its degradation of high molecular weight organic matters. The genus Kordia currently comprises eight species, type strains of which have been isolated from a diverse range of marine environments. As of this report, four genome sequences have been submitted for cultured strains of Kordia, but none are complete nor have they been analyzed comprehensively. In this study, we report the complete genome of Kordia antarctica IMCC3317T, isolated from coastal seawater of the Antarctic Peninsula. The complete genome of IMCC3317T consists of a single circular chromosome with 5.5 Mbp and a 33.2 mol% of G+C DNA content. The IMCC3317T genome showed features typical of chemoheterotrophic marine bacteria and similar to other Kordia genomes, such as complete gene sets for the Embden–Meyerhof–Parnas glycolysis pathway, tricarboxylic acid cycle and oxidative phosphorylation. The genome also encoded many carbohydrate-active enzymes, some of which were clustered into approximately seven polysaccharide utilization loci, thereby demonstrating the potential for polysaccharide utilization. Finally, a nosZ gene encoding nitrous oxide reductase, an T enzyme that catalyzes the reduction of N2O to N2 gas, was also unique to the IMCC3317 genome. Te phylum Bacteroidetes is among the most abundant phyla in the ocean, accounting for an average of approxi- mately 10% of marine surface bacterioplankton cells1,2. Marine Bacteroidetes specializes in the utilization of particulate and high molecular weight organic matter predominately from micro- or macroalgae3, and many studies have shown that Bacteroidetes increases in abundance during phytoplankton blooms in coastal waters, occupying more than 50% of the bacterial community at certain times4,5. -
Exploring Microdiversity in Novel Kordia Sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean Via Single Amplified Genomes
Research Collection Journal Article Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes Author(s): Royo-Llonch, Marta; Ferrera, Isabel; Cornejo-Castillo, Francisco M.; Sánchez, Pablo; Salazar Guiral, Guillem; Stepanauskas, Ramunas; González, José M.; Sieracki, Michael E.; Speich, Sabrina; Stemmann, Lars; Pedrós-Alió, Carlos; Acinas, Silvia G. Publication Date: 2017-07 Permanent Link: https://doi.org/10.3929/ethz-b-000371229 Originally published in: Frontiers in Microbiology 8, http://doi.org/10.3389/fmicb.2017.01317 Rights / License: Creative Commons Attribution 4.0 International This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library fmicb-08-01317 July 21, 2017 Time: 15:22 # 1 ORIGINAL RESEARCH published: 25 July 2017 doi: 10.3389/fmicb.2017.01317 Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes Marta Royo-Llonch1, Isabel Ferrera1, Francisco M. Cornejo-Castillo1, Pablo Sánchez1, Guillem Salazar1, Ramunas Stepanauskas2, José M. González3, Michael E. Sieracki4, Sabrina Speich5, Lars Stemmann6, Carlos Pedrós-Alió7 and Silvia G. Acinas1,8* 1 Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Edited by: Científicas, Barcelona, Spain, 2 Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United -
Exploring Microdiversity in Novel Kordia Sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean Via Single Amplified Genomes
ORIGINAL RESEARCH published: 25 July 2017 doi: 10.3389/fmicb.2017.01317 Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes Marta Royo-Llonch 1, Isabel Ferrera 1, Francisco M. Cornejo-Castillo 1, Pablo Sánchez 1, Guillem Salazar 1, Ramunas Stepanauskas 2, José M. González 3, Michael E. Sieracki 4, Sabrina Speich 5, Lars Stemmann 6, Carlos Pedrós-Alió 7 and Silvia G. Acinas 1,8 * 1 Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Edited by: Científicas, Barcelona, Spain, 2 Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States, 3 Department of Roland Hatzenpichler, Microbiology, University of La Laguna, La Laguna, Spain, 4 National Science Foundation, Arlington, VA, United States, Montana State University, 5 École Normale Supérieure, Département de Géosciences, Laboratoire de Météorologie Dynamique, UMR 8539 United States ENS-CNRS- École Polytechnique, Paris, France, 6 Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire 7 Reviewed by: d’Océanographie de Villefranche (LOV) UMR7093, Observatoire Océanologique, Villefranche-sur-Mer, France, Systems Jayashree Ray, Biology Program, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas, Madrid, Spain, 8 Lawrence Berkeley National Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain Laboratory, United States Christian Rinke, Marine Bacteroidetes constitute a very abundant bacterioplankton group in the The University of Queensland, Australia oceans that plays a key role in recycling particulate organic matter and includes Albert Leopold Mueller, several photoheterotrophic members containing proteorhodopsin. Relatively few marine Stanford University, United States Bacteroidetes species have been described and, moreover, they correspond to cultured *Correspondence: Silvia G.