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The Influence of Bacteria on the Adaptation to Changing Environments in Ectocarpus : a Systems Biology Approach Hetty Kleinjan

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The Influence of Bacteria on the Adaptation to Changing Environments in Ectocarpus : a Systems Biology Approach Hetty Kleinjan The influence of bacteria on the adaptation to changing environments in Ectocarpus : a systems biology approach Hetty Kleinjan To cite this version: Hetty Kleinjan. The influence of bacteria on the adaptation to changing environments in Ectocar- pus : a systems biology approach. Molecular biology. Sorbonne Université, 2018. English. NNT : 2018SORUS267. tel-02868508 HAL Id: tel-02868508 https://tel.archives-ouvertes.fr/tel-02868508 Submitted on 15 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Sorbonne Université ED 227 - Sciences de la Nature et de l'Homme : écologie & évolution Laboratoire de Biologie Intégrative des Modèles Marins Equipe Biologie des algues et interactions avec l'environnement The influence of bacteria on the adaptation to changing environments in Ectocarpus: a systems biology approach Par Hetty KleinJan Thèse de doctorat en Biologie Marine Dirigée par Simon Dittami et Catherine Boyen Présentée et soutenue publiquement le 24 septembre 2018 Devant un jury composé de : Pr. Ute Hentschel Humeida, Rapportrice GEOMAR, Kiel, Germany Dr. Suhelen Egan, Rapportrice UNSW Sydney, Australia Dr. Fabrice Not, Examinateur Sorbonne Université – CNRS Dr. David Green, Examinateur SAMS, Oban, UK Dr. Aschwin Engelen, Examinateur CCMAR, Faro, Portugal Dr. Catherine Boyen, Directrice de thèse Sorbonne Université – CNRS Dr. Simon Dittami, Co-directeur de thèse Sorbonne Université – CNRS To my sister, the biggest hero of all time Acknowledgments All good things must come to end and today, although I hardly believe it and I don’t dare to say it out loud yet, is the end of my thesis, or at least the writing of it. I hereby wish to express my gratitude to everyone who has contributed to this work, or to the process of getting here in any other way. First and foremost, I wish to thank my supervisors, Simon and Catherine, for giving me the opportunity to start the PhD, and also for their continued support until this very moment. Special thanks to Simon, for putting faith in me as a person and as a scientist. I could not have wished for anyone more kind, more motivating, or more efficient in proofreading ;-) I would like to thank the members of my thesis committee, Thomas Wichard, Christian Jeanthon, and Christophe Destombe, for their valuable input and scientific guidance throughout the three years. Also a pre-thank you (if you can say that) for the members of my jury, Fabrice Not, Suhelen Egan, Ute Hentschel Humeida, David Green, and Aschwin Engelen. I hope you enjoy reading the manuscript! A great thanks to all collaborators in this project. Thomas Wichard, who let me work in his laboratory to do metabolomics. Christian Jeanthon, who helped during the cultivation experiments in the first year of my thesis, and introduced me to the challenges of marine microbiology. Thanks to Eileen Bresnan and Kevin MacKenzie for their hospitality and warm welcome when I arrived in Aberdeen earlier this year. I will never forget how excited we all were about the fusilli-shaped bacteria! Thanks to Anne Siegel, Clémence Frioux and Enora Fremy for their computational expertise and know-how on metabolic networks especially towards the end of the thesis (sorry for letting you wait for the data!). Thanks to everyone at the ABiMs platform for letting me use the server and for solving all technical issues related to that. Special thanks to Erwan Corre for his input regarding the transcriptomic/metagenomic work and for making this project work from an informatic point of view. I want to thank Laurence Dartevelle for her advice on how to best culture Ectocarpus with and without bacteria and for her help in the laboratory. It is very much appreciated! A special thanks to Bertille Burgunter-Delamare for her enthusiasm and passion for her master project, which was truly amazing. The work you accomplished is very impressive and I’m very convinced you’ll do great in your PhD! I want to thank everyone in the ALFF consortium, and all supervisors, for putting together such a nice group of PhD students :-) I am very grateful to have met so many new people, from so many different places. The first post-PhD student meeting is already arranged, and I am convinced we will keep meeting each other, be it in an academic setting or just for fun (hopefully the latter of course). In particular, I want to thank Gianmaria Califano for always seeing the bright side of things (I truly need that!), and also for helping me with the analysis of the metabolite data. Finally, I want to thank my friends who helped me take my mind off the thesis from time to time. Miriam, who has been a great friend since the very first moment we met in Bonn and was always there when I needed someone to talk to. Svenja, Martina, Margot, and Zujaila for making me laugh all the time :-). Nick and Jaro for playing soccer and games and for always being in for fun. Nick also for making me appreciate napping time!! Yao for sharing food and thoughts with me in the office. Simon B. for always being friendly in the morning and teaching me some very handy Unix tricks. Josselin, for just being there :D. Djoyce, who helped me realize that the even the tiniest steps will make you move forward. Martine, who made me apply to this project three years ago. Wiebren, for following me on this journey and for sticking around until the end. Merci! Bedankt! Thank you! Table of contents ACKNOWLEDGMENTS ...................................................................................................................................... 3 TABLE OF CONTENTS ........................................................................................................................................ 5 GLOSSARY ........................................................................................................................................................ 7 GENERAL INTRODUCTION .............................................................................................................................. 10 HOLOBIONTS IN MULTICELLULAR EUKARYOTES - CHALLENGES & KEY QUESTIONS ................................................................ 10 HOLOBIONTS IN TERRESTRIAL MODELS ....................................................................................................................... 12 HOLOBIONTS IN BROWN MACROALGAE - A UNIQUE GROUP OF MULTICELLULAR EUKARYOTES ................................................ 13 FACTORS THAT SHAPE THE ALGAL HOLOBIONT ............................................................................................................. 16 MACROALGAL HOLOBIONTS IN A CHANGING ENVIRONMENT ........................................................................................... 23 THESIS SUBJECT: THE RESPONSE OF ECTOCARPUS HOLOBIONTS TO CHANGING SALINITY ....................................................... 24 CHAPTER 1. EXPLORING THE CULTIVABLE ECTOCARPUS MICROBIOME .......................................................... 28 ABSTRACT ............................................................................................................................................................ 29 INTRODUCTION ..................................................................................................................................................... 30 MATERIAL AND METHODS ....................................................................................................................................... 31 RESULTS .............................................................................................................................................................. 38 DISCUSSION ......................................................................................................................................................... 44 CONFLICT OF INTEREST ........................................................................................................................................... 50 AUTHOR CONTRIBUTIONS ....................................................................................................................................... 50 FUNDING ............................................................................................................................................................. 50 ACKNOWLEDGMENTS ............................................................................................................................................. 50 CHAPTER 2. CULTIVABLE BACTERIA FROM THE ECTOCARPUS SURFACE – APPLICATIONS ............................... 52 INTRODUCTION ..................................................................................................................................................... 52 I. THE IMPACT OF CULTIVABLE BACTERIAL SYMBIONTS ON THE FRESHWATER RESPONSE IN ECTOCARPUS SUBULATUS FRESHWATER STRAIN .............................................................................................................................................. 54 II. SPECIFICITY OF CROSS-LINEAGE CROSS-TALK: DO ECTOCARPUS-DERIVED BACTERIA INTERACT WITH
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