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Page De Garde V3 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 Occidentale Je tiens à remercier la région Bretagne et Sorbonne Université (Université Pierre et Marie Curie au moment de mon inscription) pour avoir financé ce travail de thèse. Je remercie également l’ANR CALYPSO ( ANR-15-CE01-0009) et le projet EC2CO CNRS-INSU CYCBLOS pour avoir financé mes expérimentations et mes derniers mois de thèse. Au lieu d’attendre les éclaircie s, Il faut mieux apprendre à danser sous la pluie Remerciements Un an auparavant à la retraite phytopk, je vous disais « Dans un an tout est fini ! », vous m’aviez ri au nez et répondu « Mais non ! On a le temps ! ».. Alors ça y est, nous y voilà, un an après, voici venu le temps des remerciements… Je tiens à remercier mon jury, Claire Gachon, Kay Bidle, Télesphore Sime-Ngando et Eric Thiébaut d’avoir accepté de lire et d’évaluer ce travail de thèse. Merci également à mon comité de thèse, Diana Sa rno, Yvan Bettarel, Télesphore et Christophe Destombe pour m’avoir conseillée, mais aussi d’avoir point é les forces et les faiblesses de ce travail. Et tout naturellement, merci à vous Nathalie et Anne-Claire. Merci de m’avoir fait confiance, il y a 3 ans , lorsque je passais l’entretien, d’avoir cru en moi, en mes capacités, mais surtout de m’avoir donné l’opportunité de travailler sur ce projet, de m’avoir donné l’occasion de me développer, de combler mes lacunes, de m’avoir laissée m’exprimer et de m’avo ir donné tant de liberté. Grâce à vous, j’ai reçu une formation de qualité, des échanges scientifiques intenses, où j’ai appris que rigueur et prudence valent mieux que grosse production sans précision. Merci pour votre patience, votre écoute et votre sens critique. Merci d’avoir été là dans ces derniers moments pas très évidents. Merci pour les belles expériences auxquelles j’ai pu participer grâce à vous, comme la Croatie, le Canada, les USA ou encore Camaret-sur-Mer. Vous êtes le duo de choc, complémentaires dans vos recherches et dans vos idées. Vos qualités humaines sont ce qui vous caractérise, grandement nécessaires dans le monde de la recherche. Je vous souhaite une très belle continuation dans vos carrières respectives, ainsi que toute la reconnaissance que vous méritez. Christian, il y a un an et demi, tu as vu le potentiel bactérien dans mes cultures et à partir de là, notre petite collaboration a démarré. C’était une expérience enrichissante de confronter nos deux domaines et d’essayer de jongler avec les compétences et les attentes de l’autre. J’ai beaucoup apprécié d’avoir une autre vision du système et de pousser un peu plus loin mes connaissances. Notamment, tu as eu l’idée d’intégrer Raphaël Lami dans ce projet, apportant alors une toute autre dimension (le quorum sensing, quèsaco ?). Raphaël, merci pour ces nombreux échanges, appels et corrections. D’une façon générale Christian, merci pour cela, et aussi pour les nombreuses discussions, je sais maintenant que tu les aimes les potins ! Quand je pense à ma thèse et à ces trois années, je pense aussi à toi Fabienne, mon petit couple. Tu as été là dans les tout premiers moments, et tu es restée jusqu’au bout. Merci pour ton soutien, pour tes conseils, pour ton aide et pour tout reste. Je pense aussi à toi Florence. Petite pépite découverte au cours du temps. D’une bonne humeur sans faille au quotidien, voilà qui a de quoi nous faire tenir les jours de grisaille ! Merci aussi à Momo, tornade de folie, et à Pris, que je n’ai découvert que trop tard à mon goût ! Toujours à l’écoute, le sourire aux lèvres et dynamiques, même quand il y en a RLB ! Merci aussi à Sarah et à Estelle. Chacune de vous les filles m’a aidée et conseillée lors de cette thèse. Quelle aurait été cette aventure sans vous ?! Une chose est sûre, elle aurait été plus fade. De façon générale, je tiens à remercier toute l’équipe phytoplankton (incluant la RCC bien sûr !), pour votre accueil il y a quelques années. Ça a été un vrai plaisir de travailler à vos côtés et de partager ce quotidien. Petite dédicace particulière à Laurence, ton regard de maman et tes visites de fin de journée vont me manquer. Prends grand soin d’Ulysse ! Dans ce projet de thèse, j’ai eu l’occasion de travailler avec beaucoup de personnes. Merci à chacune d’entre elles d’avoir apporté leurs expertises et leurs connaissances. Les travaux sont plus solides scientifiquement grâce à vous mais aussi plus intéressants et pertinents. Notamment, Alexandre. Tu as débuté tes premiers pas dans la recherche avec Nathalie et moi, j’espère que ce stage t’aura plu. Merci pour ton travail, je te souhaite une belle continuation. Également, je tiens à remercier les marins et l’équipe chimie marine. Echantillonner à vos côtés était un vrai régal ! Surtout quand il y avait du foie de lotte ! Adriana, Martina, Hugo et Ulysse, avoir partagé ce si grand espace avec vous était un vrai plaisir. Ulysse, un grand merci pour ces dernières semaines. Et ces longues soirées ! On retiendra qu’il faut être souple pour réussir dans la recherche ;) Merci les copains. Merci les anciens. Merci les nouveaux. Certains vous appelleront piliers de bar, je vous appellerai murs porteurs ! Doriane, Tristan, Valoch, Théophile, Juju, Hugo, Laura, Alexis, Thibaut, Marine, Peche, Charles, Victor, Camille, Ulysse, Eloïse, Damien, Flo, Jérémy, Mariana, Martin, Mathilde, Léna, et tous les autres ! Merci d’avoir été là, pour un verre, pour un bon moment ou pour plus ! Thanks folks! Le temps breton me paraissait moins rude grâce à vous. Par contre la note au Ty Pi erre… ! Je vous souhaite à tous d’être heureux, dans vos vies et dans ce que vous faites, et de ne rien regretter. Hugo et Ambre, merci pour cette JJC2016, un vrai régal de l’organiser avec vous. J’en garde de très bons souvenirs. Laura, merci de m’avoir enseigné l’art de Word et de la mise en page, grâce à toi, une belle crise a été évitée. Eloïse ma belle, merci pour la Crocro et ces belles années, on finit ensemble à quelques jours d’intervalle cette expérience. Prends soin de toi. Peche, we don’t need l ong conversation between you and I. Just thank you. You know the rest. I don’t wish you all the best, you don’t need it. Merci à vous, Christophe, Jean, Thierry, et Céline (vous remarquerez, j’omets vos petits surnoms). Pour ces repas, ces moments de déte ntes et d’humour (souvent salace) mais aussi de conversations plus sérieuses. Merci d’être passés au -delà de la différence d’âge et de niveau « hiérarchique ». Plus de gens comme vous sont nécessaires. Merci pour ce moment ;) Merci à toutes les personnes q ue j’ai côtoyées durant ma thèse, et que malheureusement la fatigue me fait oublier. Venir travailler dans de telles conditions tous les jours était un privilège ! Aux amis en dehors de la station, votre soutien parfois à travers les frontières a été sans égal ! Anaïs, Aurélien et tous les autres ! Petite pensée pour toi ma Lau, merci pour tes nombreuses visites dans ce petit village de charme qu’est Roscoff et ces skypes qui ont permis de m’évader quelques instants. Et enfin, merci à ma famille. De m’av oir soutenue depuis toutes ces années, sans jamais plier. Je m’excuse pour la distance que je nous ai imposé, et aux appels manqués, surtout ces derniers mois.. Merci pour tout. Contents INTRODUCTION ................................................................................................................ 1 Implications du parasitisme dans l’écologie et l’évolution du phytoplancton .................. 3 Les diatomées, groupe majeur du phytoplancton ........................................................... 12 Les parasites de diatomées .............................................................................................. 19 1. Les virus associés aux diatomées ......................................................................... 19 2. Les parasites eucaryotes ...................................................................................... 26 3. Les bactéries marines algicides ............................................................................ 38 OBJECTIFS DE THÈSE ......................................................................................................
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