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UNIVERSITÉ DE STRASBOURG Pauline UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ UMR 7156 Génétique Moléculaire Génomique, Microbiologie THÈSE présentée par : Pauline CHAIGNAUD soutenue le : 29 Juin 2016 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline : Sciences du vivant Spécialité : Aspects moléculaires et cellulaires de la biologie Le rôle des bactéries dans le filtrage du chlorométhane, un gaz destructeur de la couche d’ozone – des souches modèles aux communautés microbiennes de sols forestiers Bacteria as chloromethane sinks – from model strains to forest soil communities THÈSE dirigée par : Mme. BRINGEL Françoise Directrice de recherche, Université de Strasbourg, France M. KOLB Steffen Docteur, Leibnizzentrum für Agrarlandschaftsforschung (ZALF) und Universität Bayreuth, Allemagne RAPPORTEURS : Mme. LAUGA Béatrice Professeure, Université de Pau, France M. HORN Marcus Docteur, Universität Bayreuth, Allemagne AUTRES MEMBRES DU JURY : M. POTIER Serge Professeur, Université de Strasbourg, France Mme. KNIEF Claudia Professeure, Universität Bonn, Allemagne Ce travail de thèse est une cotutelle entre l’Université de Strasbourg et l’Université de Bayreuth. Il a été réalisé respectivement dans l’équipe AIME dirigée par le Professeur Stéphane Vuilleumier au sein du laboratoire de Génétique Moléculaire, Génomique et Microbiologie, ainsi qu’au sein du département d’écologie microbienne (EMIC) dirigé par le Professeur Harold Drake à Bayreuth. Je tiens à remercier les membres de mon jury de thèse ; le Pr. Serge Potier, Dr. Marcus Horn, Pr. Béatrice Lauga et le Pr. Claudia Knief, d’avoir accepté d’évaluer mon travail. Je remercie également mes 2 directeurs de thèse pour leur encadrement, le Dr. Françoise Bringel et le Dr. Steffen Kolb. Françoise, merci pour tes nombreuses remarques et critiques qui m’ont permis d’avancer et d’aller au bout de mon cursus universitaire. Steffen, merci pour ton accueil à Bayreuth et pour ton aide dans la réalisation de ce projet. Merci aux membres de l’équipe AIME pour son soutien tout au long de ma thèse et d’autant plus ces derniers mois. Stéphane, merci de m’avoir fait confiance lors de mon stage de master, et montré que je pouvais me dépasser. Sans ce stage, je n’en serai pas là aujourd’hui. Cette expérience n’aurait pas été possible sans ton aide, ton écoute, et ton soutien à toute épreuve. Un grand merci à Thierry pour m’avoir proposé de faire mon stage de master au sein de l’équipe. Merci pour ta disponibilité, tes conseils et les nombreuses corrections de mon mémoire. Tes blagues sur mon choix de partir en thèse vont me manquer ! Christelle, je ne te remercierai jamais assez pour tout surtout pour tes blagues et clichés sur Lille et le Nord… Je pourrai faire un chapitre complet de remerciements ! Merci à Yousra, ton grain de folie, tes chansons chantées en yaourt et tes prises de kung-fu au milieu de couloir me feront toujours rire ! Merci aux post-docs, et thésards rencontrés pendant toutes ces années dans l’équipe. Sabrina, ma compatriote du Nord, merci pour ton aide, ton écoute et ta bonne humeur. Merci de m’avoir permis de me remémorer des monuments de la chanson française injustement oubliés ; Larusso, Ophélie Winter…. Merci à Bruno, pour ta présence au quotidien (et le soir à table). Qui va te saouler, maintenant, avec des débats qui se terminent toujours en monologue ?! Merci pour ta disponibilité et ton aide. Ludo, merci pour ton aide et surtout ton sourire qui illuminait notre bureau tous les jours… Merci également aux « anciens » thésards de l’équipe, Fahran et Omniae pour leurs conseils et Louis, Panyu, Elova (et ses Elovades…) ainsi qu’à Emmanuel. Merci également à Jackson, Jean-Seb, Christian, David et Julien pour leur aide, soutien et les bières après le labo. Merci à toute l’équipe EMIC pour son accueil et sa bienveillance. Un merci tout particulier à Mareen, pour son aide, ses conseils et sa disponibilité lors des expériences de SIP. Merci aussi à Adam et Sindy pour avoir pris le temps de me faire visiter la ville de Bayreuth. Enfin, merci à mes proches pour leur présence ces dernières années, mes parents, Charlotte, Antoine, Caro, Brigitte, Lucile et Sophie sans vous je n’en serai pas là aujourd’hui. Diese Diplomarbeit entstand mit der Unterstützung der Universität Straßburg und der Universität Bayreuth . Sie wurde realisiert durch das AIME Team von dem Professor des Labors für molekulare Genetik, Genomik und Mikrobiologie Stephane Vuilleumier, sowie Professor Harold Drake, Leiter der Abteilung für mikrobielle Ökologie ( EMIC ) in Bayreuth. Ich möchte den Mitgliedern meines Bewertungskomitees danken; Professor Serge Potier, Doktor Marcus Horn, Professor Béatrice Lauga und Professor Claudia Knief, die sich bereiterklärt haben meine Arbeit zu bewerten. Ich danke auch meinen beiden Betreuern für ihre Führung, Doktor Françoise Bringel und Doktor Steffen Kolb. Françoise, danke für die vielen Kommentare und die Kritik, die mich weitergebracht haben und es mir ermöglicht haben meinen Studiengang an der Universität zu beenden. Steffen, vielen Dank mich in Bayreuth willkommen geheißen zu haben und für deine Hilfe an diesem Projekt. Vielen Dank an die Mitglieder des AIME Teams für ihre Unterstützung während meiner Diplomarbeit und vor allem in den letzten Monaten. Stéphane, danke für dein Vertrauen in mich während meiner Masterarbeit, das mir zeigte mich selbst zu übertreffen. Ohne dieses Referendariat wäre ich heute nicht hier. Diese Erfahrung wäre nicht möglich gewesen ohne deine Hilfe, dein aufmerksames Ohr und deine unermüdliche Unterstützung. Ein großes Dankeschön an Thierry für die Einladung meinen Master innerhalb des Teams abzuleisten. Vielen Dank für deine Verfügbarkeit, deine Beratung und zahlreiches „auf die Sprünge helfen“ meines Gedächtnisses. Deine Witze über meine Wahl eine Diplomarbeit zu schreiben werden mir fehlen. Christelle, ich könnte dir niemals genug danken vor allem für deine Witze und Klischees über Lille und den Norden ... Ich könnte ein ganzes Kapitel mit Danksagungen vollschreiben! Vielen Dank an Yousra, deine Verrücktheit, deine in Joghurt gesungen Lieder und deine Kung-Fu- Vorstellungen inmitten des Flurs, die mich immer zum Lachen bringen werden! Vielen Dank an die „Post-Docs“ und Doktoranden, die sich all die Jahre im Team trafen. Sabrina, meine Kollegin des Nordens, vielen Dank für deine Hilfe, dein Ohr und deine gute Laune. Vielen Dank, mich an die zu Unrecht vergessenen, französischen Lieder erinnert zu haben ; Larusso, Ophélie Winter .... Vielen Dank an Bruno für deine tägliche Anwesenheit (und Abends am Tisch). Wer wird dich jetzt mit Diskussionen nerven, die immer im Monolog enden? Vielen Dank für deine Verfügbarkeit und deine Hilfe. Ludo, ich danke dir für deine Hilfe und vor allem dein Lächeln, das unser Büro jeden Tag erleuchtete. Vielen Dank an das "alte" Team von Doktoranden, Farhan und Omniae für ihre Beratung und Louis, Panyu, EloVA (und seine Elovades ...), sowie Emmanuel. Danke auch an Jackson, Jean-Seb, Christian, David und Julian für ihre Hilfe, Unterstützung und das Bier nach der Arbeit im Labor. Vielen Dank an das EMIC Team für ihre Gastfreundschaft und Freundlichkeit. Ein ganz besonderer Dank an Mareen, für ihre Hilfe, Beratung und Verfügbarkeit bei SIP-Experimenten. Vielen Dank ebenfalls an Adam und Sindy, die sich die Zeit genommen haben, mir die Stadt Bayreuth zu zeigen. Abschließend danke Ich meiner Familie für ihre Anwesenheit in den letzten Jahren, meinen Eltern, Charlotte, Anthony, Caro, Brigitte, Lucile und Sophie. Ohne euch würde ich heute nicht hier stehen. Table of contents Table of contents List of abbreviations ............................................................................................................ 5 List of figures ....................................................................................................................... 7 List of tables ...................................................................................................................... 11 Chapter 1. Introduction (in English) .................................................................................. 15 1. Chlorinated methanes ....................................................................................................... 15 2. Chloromethane ................................................................................................................. 18 2.1. Sources of chloromethane ........................................................................................ 18 2.1.1. Abiotic production ................................................................................................. 19 2.1.2. Biotic production ................................................................................................... 20 2.2. Chloromethane sinks ................................................................................................. 27 2.2.1. Abiotic degradation of chloromethane ................................................................. 27 2.2.2. Biotic degradation of chloromethane ................................................................... 27 2.3. Global chloromethane balance in soil ....................................................................... 30 3. Methylotrophy .................................................................................................................. 32 3.1. Methylotrophic pathways ......................................................................................... 33 3.2. Bacterial degradation of dichloromethane
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