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Evaluation of Green Microalgae Biodiversity in the Alpine Ecosystem Adeline Stewart

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Evaluation of green microalgae biodiversity in the alpine ecosystem Adeline Stewart To cite this version: Adeline Stewart. Evaluation of green microalgae biodiversity in the alpine ecosystem. Vegetal Biology. Université Grenoble Alpes [2020-..], 2021. English. NNT : 2021GRALV012. tel-03261557 HAL Id: tel-03261557 https://tel.archives-ouvertes.fr/tel-03261557 Submitted on 15 Jun 2021 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. THÈSE Pour obtenir le grade de DOCTEUR DE L’UNIVERSITE GRENOBLE ALPES Spécialité : Biologie Végétale Arrêté ministériel : 25 mai 2016 Présentée par Adeline STEWART Thèse dirigée par Eric MARECHAL, DR1, CNRS, et codirigée par Eric COISSAC, MCF, UGA et par Jean-Gabriel VALAY, PR, UGA préparée au sein du Laboratoire d’Ecologie Alpine et au Laboratoire de Physiologie Cellulaire et Végétale avec le soutien de l’unité mixte de service Lautaret dans l'École Doctorale de Chimie Sciences du Vivant Evaluation de la biodiversité des microalgues vertes dans l'écosystème alpin Thèse soutenue publiquement le 3 Mars 2021, devant le jury composé de : Madame, Christelle BRETON Professeur, Université Grenoble Alpes, Présidente du jury Madame, Stéphanie MANEL Professeur, EPHE, Rapportrice Madame, Yonghua LI-BEISSON Directeur de recherches, CEA Cadarache, Rapportrice Monsieur, Stéphane RAVANEL Directeur de recherches, INRAE, LPCV, Examinateur Madame, Nathalie SIMON Maître de Conférences, Sorbonne Université, Examinatrice Madame, Christiane GALLET Professeur, Université Savoie Mont-Blanc, Examinatrice 1 Acknowledgements There are many people who have made this possible, and I can not thank them enough. First and foremost, I want to thank my amazing thesis jury: the thesis reviewers, Yonghua Li- Beisson and Stéphanie Manel, and the jury members, Christelle Breton, Natalie Simon, Stéphane Ravanel and Christiane Gallet. Thank you for accepting to review this work and for accepting to be present at my PhD defense, physically or virtually, especially in these complicated times. I look forward to our exchange; it will be an honor to discuss this project with you. Second, I want to thank the three most important people for this project, as they created it, my three PhD directors: Eric Maréchal, Eric Coissac and Jean-Gabriel Valay. You have taken me to a completely new level in science. You greatly encouraged me to participate in many scientific activities outside of experiments, which I am very grateful for, as it exposed me to so much I never thought I would love. Beyond science, all three of you have taught me very valuable life lessons which have made me that much stronger. Thank you for trusting me with this amazing project. I want to give an extra thanks to Eric Maréchal, who has given so much to this project, he was the leader it needed, the one admittedly everyone relied on, and who had a hand in every single part of this project and my scientific education during my thesis. I also want to thank the IDEX Glyco@Alps, who financed this project. Beyond that, Glyco@Alps meant much more to me, it was like a family, it made me feel surrounded and supported. I am grateful for the so many wonderful opportunities that a PhD student rarely gets anywhere else, and the chance to get to know scientists from all different backgrounds and places. I especially want to thank Ferielle, Anne and Christelle, who are at the heart of Glyco@Alps. I also want to thank all the other PhD students involved, especially Marie, Rubal, François and Juliette; your friendship has meant more to me than you know, you were there during difficult times, especially in the beginning, and you got me through, thank you so much. A warm thank you to Isabelle Domaizon and Frederic Beisson, for participating in both of my thesis committees (CSI) and for all the help and advice they have given me. I want to thank Isabelle especially, for the lake DNA samples and a very interesting collaboration on that study. I have also had help from the ISTerre platform for snow composition analysis with the wonderful Delphine Tisserand and Sarah Bureau. Thank you so much for this collaboration, I learned so much with you! I also had the pleasure of working with the MeteoFrance Centre d'Études de la Neige with Marie Dumont during sampling. I want to thank her for her advice and time, and for coming with us sampling snow algae, it was an enriching experience and collaboration. I want to thank everyone at LECA for making my time at the lab vividly memorable. The LECA is full of interesting personalities, discovered during long conversations in the break room and during runs on the trails at lunch. I thank Marc, Irene, Amélie, Céline, Fred, Monica, 2 Julien, Marius, Sylvie and Clément for their precious help and sympathy. Thank you so much to Delphine Rioux and Christian Miquel for their help on métabar experiments! I am grateful to my intern Auria Kallend, it was amazing to work on metabarcoding data with someone so efficient and that has her own ideas despite being still at the beginning of her science career. Her work and the help of Aurélie lead to Chapter 7 happening, so thanks to the both of you! Aurélie Bonin is one of my ultimate favorite people from LECA. I am so grateful for the help you gave me, I won’t forget it! I am also very grateful to François Pompanon, our lab director, for his enthusiasm and much needed help when I came to talk about projects and other matters. I have great respect for him as a labhead, a PI and a teacher. I also want to thank Stephane Reynaud, whose support was very deeply appreciated. Good luck being the new lab director! I also thank Florence, Agnès, Delphine and the rest of the admin staff who have come and gone, you make everything we do possible, thank you so much for everything! At LECA, I found some remarkable friends: Marie Usal, Joaquim Germain, Laure Denoyelle and Charlotte Her. I don't think I would've made it without you guys, you were and still are, my biggest sources of comfort and help at work and outside. You guys are my friends for life now, so I hope you are not tired of shameless Harry Potter references and non-stop nagging to go for runs with me. I want to thank everyone at LPCV. I will start with Melissa Conte, Alberto Amato and Etienne Deragon, who always got on board with my ideas and are probably the nicest people one can ever meet. You are the real MVPs of this project, experimentally. Thank you so much to Juliette Jouhet, our fearless team leader, a wonderful person; Big thanks to Dimitrios Petroutsos for help with NPQ experiments and for your kindness, encouragements and advice for my science career! Thank you to Giovanni Finazzi and for all the photosynthesis and light- stress related experiments; Thanks to Sassia, Valérie, Juliette Salvaing, Denis, Fabrice, Claude, Catherine, Mathilde for all your wonderful help on various things, thanks to Véronique for the FACS experiments, and Marcel Kuntz for the HPLC pigment experiments. And thank you to everyone else at PCV! You are all incredible people, you are a big part of the reason PCV is one of the best labs, and I will miss you all greatly. I want to give huge thanks to the PCV staff Tiffany, Sophie and Alexandre, you already know this but you are amazing, nothing would get done without you! I have made some wonderful friends here, too. Stéphanie, Nolwenn & Greg especially, but also Sebastien, Cecile, Natacha, Chrispi, Benoît… you were always there when I needed it the most and I won’t ever forget that. I want to thank the SAJF –now Jardin du Lautaret- team for all the help with the sampling campaign, especially Pascal, and with help organizing events. I also want to thank Rolland for trusting me to give plant biology classes to his students, it was a very rewarding experience! I had the amazing opportunity to go to the Flora Course at the Roscoff Marine Station, and I want to thank all the teachers and the other students there. It was an unforgettable adventure that I cherish and will never forget. I also want to thank the ‘R in Grenoble’ team, for moments of pure R coding joy, so much support and super interesting R sessions. On the same note, I want to thank Dr. Marc de Boissieu, the organizing team of the Scientific Game Jam and its participants. It was my favorite event, I met so many wonderful people there, it was a true highlight of my thesis. 3 I also want to thank all the teaching and admin staff at Université Grenoble Alpes for an incredible, rewarding experience. I especially want to thank Dr. Corinne Mercier, a true source of inspiration. She introduced me to parasitology and Toxoplasma gondii, my first love in science, which lead me to study lipids and plants. Thank you so, so much for everything you do! In the same line, I want to thank my previous supervisors during my Master's because they were also incredibly inspiring and contributed to my career so much. Dr. Yoshiki Yamaryo- Botté for her contagious love of plant lipids and her hours-long presentation preparation sessions, Dr.
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  • Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses

    Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses

    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts.