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Around the Black Queen Hypothesis

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Around the Black Queen Hypothesis ANNÉE 2017 THÈSE / UNIVERSITÉ DE RENNES 1 sous le sceau de l’Université Bretagne Loire pour le grade de DOCTEUR DE L’UNIVERSITÉ DE RENNES 1 Mention : Biologie Ecole doctorale Écologie Géosciences Agronomie Alimentation Alix Mas Préparée à l’unité de recherche 6553 ECOBIO Écosystèmes, Biodiversité, Évolution Observatoire des Sciences de Univers de Rennes Thèse rapportée par : Forecasting evolution of Sara MITRI Assistant Professor, Université de Lausanne, Département de Microbiologie Fondamentale (DMF) bacteria in a George KOWALCHUK Professor Doctor, Universiteit Utrecht, Ecology and Biodiveristy Department specialization context: et soutenue à Rennes le 27 novembre 2017 a functional approach devant le jury composé de : in George KOWALCHUK combining modeling, Professor Doctor, Universiteit Utrecht, Ecology and Biodiveristy Department / Rapporteur vitro Samuel CHAFFRON experiments and Chargé de Recherche, CNRS Nantes, LS2N UMR 6004 / Examinateur genomic analyses. Thomas POMMIER Chargé de Recherche, Ecologie Microbienne UMR 5557, INRA Lyon / Examinateur Yvan LAGADEUC Professeur, Université de Rennes 1, ECOBIO UMR 6553 / Directeur de thèse Philippe VANDENKOORNHUYSE Professeur, Université de Rennes 1, ECOBIO UMR 6553 / Co-directeur de thèse Des étoiles plein la vie, Du soleil et de la lune aussi Remerciements Thanks Remerciements First of all, I would like to sincerely thank the jury members for their interest in this Ph.D work and the time spent examining it. It is an honor for me to have your names here. Merci Sara Mitri, Merci George Kowalchuk, Merci Samuel Chaffron, Merci Thomas Pommier. ∗ La recherche, C’est un peu là ou nos rêves et le réel se confrontent, et parfois se rejoignent. J’ai commencé à y apprendre la patience, J’y ai ressenti de l’excitation; et de la frustration, J’ai regardé les choses avec les yeux, les oreilles et l’esprit grand ouvert. J’ai appris à accepter l’imperfection, car la vie l’est, imparfaite. J’ai continué à rêver, par-delà les contraintes, pour ne pas laisser place à la résig- nation. J’ai eu la sensation de baigner dans la synergie des pensées, des volontés et des rêves virevoltants de chacun. Ces trois années furent un vrai chemin de vie, Et je souhaite remercier, du fond du cœur, les gens qui m’ont accompagnés sur ce bout de chemin. Les personnes qui ont été présentes sur la course de fond, et les personnes qui ont été présentes sur le sprint de fin, qui m’ont apporté leur soutien au quotidien ou aux moments difficiles. J’ai de la chance de vous avoir auprès de moi. Pour toujours, mes parents et ma famille. Vous êtes une ressource sans fin pour moi, un équilibre, un bonheur. Je vous embrasse de tout mon cœur. Et spécialement, Merci Mam, je pourrais écrire une thèse entière rien que pour te remercier, de ta bienveillance, de ton soutien et du don de toi-même. Merci à tous les gens qui ont eu foi en moi, et qui ont maintenu à flot la jauge si labile de ma confiance-en-soi. Philippe, ton enthousiasme pour la Science est sans prix. Merci de ta présence continue, de tes encouragements, et de ta confiance. Merci aussi de m’avoir par- Remerciements fois ramené les pieds sur terre ("non mais t’as les fils qui se touchent là Alix!"), fait découvrir le vin (et accessoirement la recherche, hehe). Je suis contente d’avoir été un de tes pioupious. (le favori, mais on le dira pas à Nathan) Yvan, merci pour ton encadrement et ta confiance depuis le master, et de m’avoir permis de parfois mieux comprendre le ’behind the scene’ de la recherche. A quand la balade à poney?! Merci Nathan et Kevin, qui avez su accepter et rire avec moi de l’ampleur de ma bulle, et de ma concentration "papillonnante"! Merci aussi pour l’aide en stats, vos encouragements, les discussions scientifiques, et les moments de haute voltige intellectuelle (’ouhhhou c’est qui le patron?!!’) Nathan merci aussi pour les nombreuses musiques partagées (et d’avoir failli me casser un bras un jour, sisi, j’avais un bleu même). Et Nivek, merci d’avoir presque réparé mes freins de vélo:), de m’avoir tiré à 30km en roller (record!) et pour ton soutien en fin de thèse. (et les brownies! mnomnomnom) Merci Eve et Lorine, d’avoir rejoint le 216 un peu plus tard, et permit de rééquili- brer la part féminine de ce bureau (0,5 femme c’était pas assez)! Je vous souhaite une bonne fin de thèse les filles! C’était chouette, ces quelques années tous en- semble! Et bien sûr merci à tous les quatre pour les poissons d’anniversaire! - devant lesquels j’ai parfois scotché de longues minutes.. Merci aux personnes de ma vie, Merci Titi, de me faire rire, de me réconforter, d’être une âme-sœur(-cousine) qui est là depuis toujours. Merci Flifloof pour tes lettres, tes petites attentions, et ta belle philosophie de vie. Merci aussi à mes amies proches, les fifilles, c’est toujours ressourçant de partager du temps avec vous, et ces fou-rires comme j’en ai rarement ailleurs! Merci Anne, pour ces années partagées (avec Gros Cookie) à l’appartement rue de Toulouse, je m’y suis sentie bien, j’ai aimé nos discussions, et ton soutien, empreint de réalisme qui m’a souvent fait aller de l’avant. Sarah, tu es partie depuis un moment mais tu as été une vrai ressource quand j’étais une bébé thésard, nos longues discussions étaient toujours apaisantes ou fructueuses, et j’admirerai toujours ta force et ta persévérance! (Guèppendorf!) Didi, tu es un vrai souffle de sympathie, de simplicité et d’énergie! C’est un plaisir à chaque fois que l’on se voit. Merci pour ton amitié, la virée en Italie, les chocolats italiens, les cafés, les discussions de tout et de rien partagées! Merci Pampli, d’avoir apporté quelques temps un bel équilibre à ma vie, de Remerciements m’avoir permis de voir les choses avec d’autres yeux. A côté de combien de blagues ironiques suis-je passées?! -telle une poule devant une fourchette! Merci Mewena, Guylaine, pour cette rencontre et ce lien particulier. Je suis heureuse de vous connaître. Des pensées pour mes chères Paulines, je vous adore, et j’ai hâte de repartir en voyage avec vous! Laure, Manue, merci de votre présence dans la dernière période bien difficile traversée. Merci Fa, pour les moments partagés en fin de thèse, ça m’a permis de garder la tête hors de l’eau. Merci Marie et Benji pour votre accueil chaleureux et ressourçant, je suis si ex- citée de partir voir les PPMR! A dream about to come true! Gorenka, thanks girl, for those insightful evening pep-talks that helped much lately. I hope we keep in touch :) Des pensées particulières aussi pour les personnes avec qui j’ai grimpé, couru, fais du yoga (merci Léa!), du roller, du hip-hop etc, qui sont devenus des ami(e)s au cours de ces trois ans. Finalement, Merci aux chercheurs ayant participé à mes comités de thèse, Julie Jacquiery, Eric Petit, Alexis Dufresne, Damien Eveillard, Yvan Le Bras, Fab- rice Not, Pierre Peterlongo et Achim Quaiser. Merci Pietro de Anna, Marko Budinich, Shahrad Jashmidi, Erwan Corre et Xi Liu, Wesley Delage, Victoria Potdevin, Jean Coquet, et toutes les personnes avec qui j’ai pu travailler, longtemps ou ponctuellement, et avec qui j’ai aussi souvent partagé de nombreux moments sympathiques. Merci à l’ensemble du laboratoire d’Ecobio, à ses chouettes doctorants, et no- tamment aux personnes qui ont pris part à la mise en place et à la dynamique des RJSE. Jolie expérience, comme tout le reste de cette thèse! Et d’après une analyse statistique approfondie, il semblerait que je puisse aussi remercier Lindt pour les 360 tablettes de chocolat consommées au cours de ces trois années! Oups. Bonne lecture! Alix MAS Forecasting evolution of bacteria in a specialization context: A functional approach combining metabolic modeling, in vitro experiments and genomic analyses. Contents I Opening Section: Thesis’Background, Rationale and Ob- jectives 1 1 A background synthesis of Evolution 3 1.1 History and theory of Evolution . 5 1.1.1 History of Evolution . 5 1.1.2 Concepts underlying Evolution . 7 1.1.3 Forces at stake in Evolution . 11 1.1.4 Relevant complementary theories of Evolution . 18 1.1.5 The study of evolution . 20 1.2 Evolution and the Bacterial World . 24 1.2.1 Advantage for the study of evolution . 24 1.2.2 Evolutionary mechanisms distinction . 25 2 Rationale of the predictive approach developed 27 2.1 Introduction . 29 2.2 The Unpredictability of Evolution . 30 2.2.1 Mutations’ randomness and effects . 30 2.2.2 Phenotypes Complexity and Neutral Theory . 32 2.2.3 The Environment of Evolution . 33 2.2.4 The Chaotic Dynamics of Biological Systems . 33 2.3 A door ajar on the predictability of evolution . 35 2.3.1 Convergence of Phenotypic features . 35 2.3.2 Predictability in the evolution of genomes? . 36 2.3.3 Evolution, a process constrained at several levels . 38 2.4 A Metabolic approach to Predict evolution in a specialization context 40 2.4.1 Metabolic Constraints . 40 2.4.2 Reductive environment and Specialization . 40 2.4.3 Forecasting metabolism and evolution during Specializa- tion . 41 I 2.5 What a (R)evolution! . 44 3 Thesis Context and Objectives 47 II Forecasting Population and Community Evolution based on Metabolic Interactions: Around the Black Queen Hypothe- sis 53 1 Beyond the Black Queen Hypothesis 55 1.1 Introduction . 58 1.2 Material and Methode .
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