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Comparative Genomics of Closely Related Thermococcus Isolates, a Genus of Hyperthermophilic Archaea

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Thèse&préparée&à&l'Université&de&Bretagne&Occidentale& pour obtenir le diplôme de DOCTEUR&délivré&de&façon&partagée&par& présentée par L'Université&de&Bretagne&Occidentale&et&l'Université&de&Bretagne&Loire& ! Damien Courtine Spécialité):)Microbiologie) ) Préparée au Laboratoire de Microbiologie des École!Doctorale!Sciences!de!la!Mer!et!du!Littoral! Environnements Extrêmes (LM2E) UMR6197, UBO – Ifremer – CNRS – Génomique comparative Thèse!soutenue!le!19!Décembre!2017! devant le jury composé de : d'isolats Anna?Louise!REYSENBACH!! Professeur, Université de Portland (USA) / Rapporteur) phylogénétiquement Simonetta!GRIBALDO! proches appartenant au Directrice de Recherche, Institut Pasteur / Rapporteur) genre Thermococcus, une Dominique!LAVENIER!! Directeur de Recherche, CNRS Rennes / Examinateur) archée hyperthermophile Karine!ALAIN!! Chargée de recherche, CNRS Brest / Directrice)de)thèse) Loïs!MAIGNIEN! Maître de Conférence, Université de Bretagne Occidentale / Co9 encadrant) A.!Murat!EREN! Maître de conférence, Université de Chicago (USA) / Co9encadrant) Yann!MOALIC! Enseignant Chercheur, Université de Bretagne Occidentale / Invité Acknowledgements This thesis work was carried out at the Laboratoire de Microbiologie des Environnements Extrêmes (LM2E) at the Institut Universitaire Européen de la Mer (IUEM). It was financed by the Région Bretagne (Brittany Region) and Labex MER. I thank Mohamed Jebbar, Anne Godfroy and Didier Flament for welcoming me in this laboratory. First of all, I would like to sincerely thank the members of the jury who agreed to evaluate this work. I would like to thank Anna-Louise Reysenbach, Professor at the Portland University, and Simoneta Gribaldo, Research director at the Institut Pasteur, for agreeing to review this thesis. I would also like to thank DominiQue Lavenier, Research Director at the CNRS, and Yann Moalic, Researcher at the Université de Bretagne Occidentale, for reviewing this work. I would like to thank Karine Alain for her support, availability and kindness. Many thanks to Lois Maignien, for his guidance; this work could not have taken place without his advices and its availability. I would also like to thank A. Murat Eren (aka Meren) for its advices, for allowing me to sequence more genomes in this project, and also for hosted me for 1 month in his lab at the University of Chicago. This visit was a very enriching experience. donner accès à des données génomiques supplémentaires, et égalem leUn séQuençage merci particulier de génomes à Patrick via Forterre, Jacques Oberto et Violette Da Cunha de mavoir ent davoir finalisé Je remercie Myriam Georges pourlERC toute EVOMOB)L. son aide apportée lors des manips de bio-mol et pour tous les autres moments. e, et des Thermococcales. MerciUn merci Stéphanie, également pour tonà Nadège aide et taBienvenu bienveillance pour aulutilisation quotidien. de la souchothèqu MerciStéphane à toutes L(aridon les personnes pour ses ayantnombreux participé conseils de près en culture ou de loin à ce travail. du LM2E pour leur disponibilité et leur gentillesse. UnMerci remerciement à lensemble particulierdes membres à la team EcoGenomics, Florian, Clarisse et la nouvelle recrue Blandine, pour toutes les discussions, les réunions du lundi, merci pour ces moments. des thésards, passés, présents, futurs, pour toutes les discussions, soutiens, et bons moments passés ensemble, en commençant par les anciens,Également Gaëlle, à lensemble Sandrine, Matthieu, Simon, Coraline; la génération 2014: Mélanie, Charlène, Vincent, Gwenn et Tiphaine; Les prochains sur la liste: Sébastien, Yang, Caroline, Clarisse, et Florian (encore toi?!); les « jeunes »: Sarah, Jordan, Pierre et les derniers arrivés, Marc, Blandine et David. Je souhaite adresser un sincère merci au FEIRI, et plus particulièrement à Sandy, Frédéric de informatiQue apportée : les debugs de Penduick, Quand . et Emmanuel, pour toute lai Margane, bien Quele mactu sois ne veutpartie plus du démarrer…labo peu après Merci mon arrivée, un grand merci pour tous les bons moments ! Je voudr faire cette thèse. ais également adresser un merci à )van, qui ma longuement aidé et poussé à Enfin je voudrais remercier ma famille, Maman, Papa, Steph, Brigitte, Mathis, Mémé, À ma moitié, pour avoir enduré mes crises et être à mes côtés tous les jours, dans les bonsdavoir et crules autresen moi, moments, je nen serais je ne pas te remercierai là sans vous. jamais assez. Table of contents Acknowledgements List of figures List of tables List of abbreviations Chapter I: Introduction.......................................................................................... 1 I) Introduction of deep-sea hydrothermal vents .................................................... 1 1) Generalities about deep-sea hydrothermal vents ........................................................... 1 2) Deep-sea hydrothermal vent ecology .................................................................................. 4 3) Extremophiles ............................................................................................................................... 7 II) The third domain of life: Archaea ........................................................................... 9 1) Generalities .................................................................................................................................... 9 2) The order Thermococcales ..................................................................................................... 11 III) Ordering microbial diversity in cohesive units ............................................. 17 1) The necessity to classify microorganisms ........................................................................ 17 a) Historical motivations ..................................................................................................... 17 b) Classification of living beings ....................................................................................... 17 2) The actual definition of a microbial species .................................................................... 19 a) The definition ..................................................................................................................... 19 b) How are species delineated? ........................................................................................ 19 i) Sequence similarity .................................................................................................. 19 x DNA-DNA sequence similarity ....................................................................... 19 x Average Nucleotide Identity ........................................................................... 22 ii) Phenotype ................................................................................................................... 23 iii) Additional methods ............................................................................................... 23 c) The lacking parameters: Ecology ................................................................................ 24 i) Species as a group of ecologically coherent isolates ................................... 24 d) Why species definition is still the same? ................................................................. 24 3) What about a new species definition in the genomic era? ......................................... 25 a) Currently, definition does not integrate ecology .................................................. 25 b) How incorporate ecology and genomic data in a more cohesive model? ... 25 4) Instead of thinking species, think population ................................................................. 26 a) Definition of a population .............................................................................................. 26 b) Genomic units: how to cluster genomes? ................................................................ 26 i) Sequence similarity .................................................................................................. 26 ii) Genetic units .............................................................................................................. 27 c) A population is not static ................................................................................................ 27 d) Different models exist ..................................................................................................... 28 i) Based on recombination/selection ratio ......................................................... 28 5) Examples of natural populations ......................................................................................... 31 a) Vibrio ...................................................................................................................................... 31 b) Sulfolobus ............................................................................................................................. 32 IV) Objectives of the thesis ............................................................................................ 33 Chapter II: Materials and Methods .................................................................. 34 I) The LM2E culture collection: UBOCC .................................................................... 34 1) Culture of hyperthermophilic and anaerobic isolates ................................................. 34 a) Preparation of culture media ....................................................................................... 35 b) Sterilization steps ............................................................................................................
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