DOCTORAL THESIS 2020 PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez DOCTORAL THESIS 2020 Doctoral Programme of Environmental and Biomedical Microbiology PHYLOGENOMICS OF BACTEROIDETES; HALOPHILIC BACTEROIDETES AS AN EXAMPLE ON HOW THEIR GENOMES INTERACT WITH THE ENVIRONMENT Raúl Muñoz Jiménez Thesis Supervisor: Ramon Rosselló Móra Thesis Supervisor: Rudolf Amann Thesis tutor: Elena I. García-Valdés Pukkits Doctor by the Universitat de les Illes Balears Publications resulted from this thesis Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Systematic and Applied Microbiology, 39(5), 281–296 Munoz, R., Rosselló-Móra, R., & Amann, R. (2016). Corrigendum to “Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov.” [Syst. Appl. Microbiol. 39 (5) (2016) 281–296]. Systematic and Applied Microbiology, 39, 491–492. Munoz, R., Amann, R., & Rosselló-Móra, R. (2019). Ancestry and adaptive radiation of Bacteroidetes as assessed by comparative genomics. Systematic and Applied Microbiology, 43(2), 126065. Dr. Ramon Rosselló Móra, of the Institut Mediterrani d’Estudis Avançats, Esporles and Dr. Rudolf Amann, of the Max-Planck-Institute für Marine Mikrobiologie, Bremen WE DECLARE: That the thesis titled Phylogenomics of Bacteroidetes; halophilic Bacteroidetes as an example on how their genomes interact with the environment, presented by Raúl Muñoz Jiménez to obtain a doctoral degree, has been completed under our supervision and meets the requirements to opt for an International Doctorate. For all intents and purposes, we hereby sign this document. Signatures Esporles, May the 15th 2020 Bremen, May the 15th 2020 A mis padres, que para dar lo mejor a sus hijos se dedicaron a cocer pan y fregar suelos. Sin saberlo cultivaban y mataban microorganismos. Ni se imaginaban que una generación más tarde esos bichos darían para tanto. Gracias por acompañarme hasta aquí. 5 Acknowledgments This research was funded by the Max Planck Society, the Spanish Ministry of Economy and Competitivity projects CGL2012-39627-C03-03, CLG2015-66686-C3-1-P and PGC2018-096956- B-C41 that also supported the work with European Regional Development Fund (FEDER) funds, the preparatory phase of the Microbial Resource Research Infrastructure (MIRRI) funded by the EU (grant number 312251), and the financial support of Deep Blue Sea Enterprise S.L. The PhD candidate would like to thank the MPI for Marine Microbiology in Bremen for their support and welcoming during this research. The IMEDEA for the facilitating their premises and resources. The UIB for providing with the appropriate environment for my education. Also the SEM (Spanish Society of Microbiology) for awarding the presentation of the bacteroidetal phylogeny of Bacteroidetes as the best oral presentation in their 2016 congress. And specially the REDEX (The Spanish Network on Extremophiles), since it has brilliantly promoted the excellence in microbial research while created strong bonds between young talents in the years of my membership. Many thanks, of course, to my directors. The experience of fulfilling a thesis would not be completed without some bumps and bruises, but I was lucky to count with two individuals that happen to be excellent people in and out academia. Thank you ever so much for depositing your trust in me and carry on no matter what. It was a tight end but we made it. Thank you Dr. Rudolf Amann for your perspectives and appraisals. And thanks to Dr. Ramon Rosselló-Móra for everything, the good and the bad, the whole roller-coaster. I have learned a lot from you and not only about science. Above all, I have learned about caring for what you do and caring for the people you depend on. Many thanks to Dr. Hanno Teeling. We have personally met in too few occasions due to contrary events, but your presence in the last period of this research has been invaluable. Your detailed input and empathy has caused a deep impact on me. I only wish I can become a little like you someday. In this group, despite he has not co-authored any of the presented research, I would like to include Dr. Pablo Yarza, who introduced me to the management of databases and curation of the All-Species Living Tree Project. It all started there and then at the Marine Microbiology Group (MMG). The terminal command line, the ARB graphic user interface, the cumbersome data collection. Thank you Pablo. Also from the MMG I would like to thank Dr. Arantxa López, the person who spotted me out of a class of over 30 pupils to tell Ramon I could lend a good hand at the lab. You are responsible for this thesis in first term. Thanks to senior PhD candidates in the MMG like Dr. Jocelyn Brito and Dr. Ana Suarez for your leading. Special thanks to Dr. Ana Suarez, you kept reaching out for me, during your post-doctoral contract you invited me at Newcastle University to present my first research, and furthermost, you kept reaching out as a close friend. Also thanks to Dr. Ana Cifuentes, another reference during my MMG days, you rocked it hard, you made me think, opened my mind and taught me we could agree or not but still understand each other. Thanks to the ‘next generation MMG’. It has been fun and educating to share the lab routines with you: Dr. Bartomeu Viver, Xisca Font, Joan Gago and Sara Díaz. Let me thank personally to Carlota Alejandre, my ‘verruguita’, my ally, confident, and MPI-grant fellow. We will laugh over a glass of wine telling ours stories. Also personal thanks to Dr. Merit Mora (de-la-Mo-ra), my princess, and Dr. Carlos Diaz my second ‘extremeño’. When two talents like you collided the bond had to be covalent. Gracias Princess por tantos y tantos momentos de risa descontrolada, lágrima empoderada y humor punzante. Gracias Carlos por sumar tanto. And finally, a very emotional acknowledgment to ‘The Rock’ and ‘The Mom’ in the MMG, Mercedes Urdiain. Sobra decir lo buena profesional que eres y gran soporte técnico que nos ofreces, pero hay que destacar tu calidad humana y tu 6 enorme corazón. Me apena que Pepón no lea estas líneas. Es de recibo agradecerle a él también lo que nos ha cuidado y enseñado. Brindo por él mientras escribo estas líneas aunque no sea con un Lagavulin de 18 años. Y brindo por ti y por lo que está por venir. During my working years in the MMG I was also honored to meet people who stayed for a limited time and contributed to both my microbial knowledge and professional growth; Neus, Roberto, Diego, Luis, Bai. And above all Dr. Pablo Gallardo and Dr. Nayaret Chamorro, my two favorite Chilean people and soul mates in good and evil. Les amo weones. Many thanks to the Microbiology teaching board at the UIB that shed light to my understanding and satiated my thirst for knowledge; Dr. Jorge Lalucat and Dr. Elena García-Galmés, tutors of this thesis, Dr. Balbina Nogales, Dr. Rafael Bosch, Dr. Antoni Bennasar, Dr. Margarita Gomila and Dr. Arantxa Peña. Also thanks to Dr. Eduardo Pastor from the CAB (Centro de Astrobiología) at INTA, Madrid. It was my pleasure to work with you in the previous years to this thesis research and coinciding in some academic events. Somehow, I could relate to you and learn that a person like me had a voice in the crowded academic world. Thank you so much for being so genuine and sharing. Last in the microbiology-related list of acknowledgments, I would like to thank everyone at the Microbiology department at the West Hertforshire NHS Trust, United Kingdom. I was 20 when I left Spain pursuing an independent lifestyle and English proficiency, quiting my biology degree at which I felt I was not competent enough. Lucky me, I happened to get a job as an administrative clerk at the Microbiology lab at Watford General Hospital. You observed me, you noticed I was curious about those little bugs, and offered me the chance of my life: a promoting grant with full education to become a biomedical lab technician. My life turned left and I returned to Spain with unfinished academic training. But I came back a 24 year-old Spaniard with a fine practical training in classic microbiological techniques and skills, sure of his vocational job. You made me fall in love with microbiology. Special thanks to my mentors Dr. Deborah Surridge and Dr. Phillip Spears. And of course to my dearest Gillian Adlington-Graham, who was and still is there to remind me not to wear my heart on my sleeve. Last, from Hemel Hempstead General Hospital, I would like to include Dr. Deborah Nolan and Dr. Jeanette Allen to my list of acknowledgements for boosting up my self-esteem as a scientist. And from St. Albans City Hospital Dr. Asunya Padayachee, for her life-coaching and complicity. Acknowledgments in English are closured with massive thanks to Jennifer McNish, my ‘English Mom’ and serious nominee to International Hosting Mom to be awarded by the United Nations someday. I remember arriving to Oakland College in St. Albans and being assigned guest to a widow lady with two cats. I felt shivers down my spine. I was ever so wrong to judge a book by its cover. You hosted, cared for, taught and even fed me when I needed it, welcoming to your family for ever. And it was funny enough that was you who warned me about the position at Watford General Hospital’s Microbiology Lab, encouraged me to apply and even got the application form, threw it on top of the dinner table and told me: ‘do it, you never know’.