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Structuring Factors of Microbial Communities in the Atmospheric Boundary Layer Romie Tignat-Perrier

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Structuring Factors of Microbial Communities in the Atmospheric Boundary Layer Romie Tignat-Perrier Structuring factors of microbial communities in the atmospheric boundary layer Romie Tignat-Perrier To cite this version: Romie Tignat-Perrier. Structuring factors of microbial communities in the atmospheric boundary layer. Ocean, Atmosphere. Université Grenoble Alpes, 2019. English. NNT : 2019GREAU034. tel-02496882 HAL Id: tel-02496882 https://tel.archives-ouvertes.fr/tel-02496882 Submitted on 3 Mar 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. THÈSE Pour obtenir le grade de DOCTEUR DE LA COMMUNAUTE UNIVERSITE GRENOBLE ALPES Spécialité : Sciences de la Terre et Univers, Environnement Arrêté ministériel : 25 mai 2016 Présentée par Romie TIGNAT-PERRIER Thèse dirigée par Aurélien DOMMERGUE, Maître de Conférences, Institut des Géosciences de l’Environnement, Université Grenoble Alpes, et Catherine LAROSE, Chargée de Recherche, Laboratoire Ampère de l’Ecole Centrale de Lyon Thèse préparée au sein de l’Institut des Géosciences de l’Environnement à Grenoble dans l'École Doctorale Terre Univers Environnement Facteurs de structuration des communautés microbiennes de la couche limite atmosphérique Thèse soutenue publiquement le 22 novembre 2019, devant le jury composé de : Dr. Viviane DESPRES HDR, Max Planck Institute for Chemistry Biochemistry Department – Mainz (Allemagne), Rapportrice Dr. Andrea FRANZETTI HDR, University of Milano Department of Earth and Environmental Sciences – Milan (Italie), Rapporteur Dr. Barbara D’ANNA Directrice de Recherche, Laboratoire Chimie Environnement Université Aix Marseille – Marseille (France), Examinatrice Dr. Pierre AMATO Chargé de Recherche, Institut de Chimie de Clermont-Ferrand – Clermont-Ferrand (France), Examinateur Dr. Jean MARTINS Directeur de Recherche, Institut des Géosciences de l’Environnement Université Grenoble Alpes – Grenoble (France), Président du jury Pr. Timothy M. VOGEL Professeur, Laboratoire Ampère Université Lyon 1 – Lyon (France), Examinateur Dr. Catherine LAROSE Chargée de Recherche, Laboratoire Ampère Ecole Centrale de Lyon – Lyon (France), Directrice de thèse Dr. Aurélien DOMMERGUE Maître de conférences, Institut des Géosciences de l’Environnement Université Grenoble Alpes – Grenoble (France), Directeur de thèse PHD THESIS Toward the title of DOCTOR OF SCIENCE OF THE GRENOBLE ALPES UNIVERSITY COMMUNITY Speciality: Earth and Universe Sciences Arrêté ministériel : 25 mai 2016 Presented by Romie TIGNAT-PERRIER PhD thesis supervised by Aurélien DOMMERGUE, Maître de Conférences, Institut des Géosciences de l’Environnement, Université Grenoble Alpes and Catherine LAROSE, Chargée de Recherche, Laboratoire Ampère de l’Ecole Centrale de Lyon PhD thesis prepared in the Institut des Géosciences de l’Environnement in Grenoble and the Terre Univers Environnement doctoral school Structuring factors of microbial communities in the atmospheric boundary layer PhD defense on the 22th of November, 2019, in Grenoble In front of the following jury members: Dr. Viviane DESPRES HDR, Max Planck Institute for Chemistry Biochemistry Department – Mainz (Germany), Reviewer Dr. Andrea FRANZETTI HDR, University of Milano Department of Earth and Environmental Sciences – Milan (Italy), Reviewer Dr. Barbara D’ANNA DR, Laboratoire Chimie Environnement Université Aix Marseille – Marseille (France), Examinator Dr. Pierre AMATO CR, Institut de Chimie de Clermont-Ferrand – Clermont-Ferrand (France), Examinator Dr. Jean MARTINS DR, Institut des Géosciences de l’Environnement Université Grenoble Alpes – Grenoble (France), President of the jury Pr. Timothy M. VOGEL Professor, Laboratoire Ampère Université Lyon 1 – Lyon (France), Examinator Dr. Catherine LAROSE Chargée de Recherche, Laboratoire Ampère Ecole Centrale de Lyon – Lyon (France), Supervisor Dr. Aurélien DOMMERGUE Maître de conférences, Institut des Géosciences de l’Environnement Université Grenoble Alpes – Grenoble (France), Supervisor Acknowledgements First of all, I wish to thank my supervisors Catherine Larose and Aurélien Dommergue, as well as my adviser Timothy M. Vogel. I thank you Tim for being one of my best university lecturer. I am grateful to you for telling me about this project on atmospheric microbial communities. Thank you Cath and Aurélien for being supporting and trusting me. I loved discussing with you three about my work, I thank you for everything I learnt from you. These three years have been intense and the PhD a real training work where I developed many skills. I really appreciated to have the opportunity to teach at the University of Lyon 1, to supervise a master student (Myriam Spajer), to do oral and poster presentations in international conferences and to develop English oral and written skills. I would like to thank the members of my annual comities, i.e. Pierre Amato (Institut de Chimie de Clermont-Ferrand), Barbara d’Anna (LCE de Marseille), Alexandre Poulain (University of Ottawa) and Eric Bapteste (IBPS de Paris) for having accepted to discuss about my work and for giving me advices. I thank the members of my PhD jury, Jean Martins (IGE Grenoble), Barbara d’Anna, Pierre Amato, Andrea Franzetti (University of Milano, Italy) and Viviane Després (Max Planck Institute for Chemistry in Mainz, Germany) for having accepted to evaluate my work. I thank the Région Auvergne-Rhône Alpes for having financed my PhD. I thank the team of the IGE in Grenoble for having welcomed me. I thank particularly Jean-Luc Jaffrezo, Jean Martins and the PhD student Abdoulaye for our discussions on atmospheric chemistry and atmospheric microorganisms. It was nice to be in regular contact with you Abdoulaye. I could really not have hoped for better coworkers at the Laboratoire Ampère, Ecole Centrale de Lyon: Mia, Concepcion, Rose, Benoît, Arthur and Adrien (all PhD students) as well as Christoph, Cécile, Graeme, Christina, Laure and Pascal. It was so nice to work with you and I would like to keep you all and bring you with me to my next lab. To PhD students: it was really nice to share this PhD experience with you, you were a real every day motivation and by far an important element that made my PhD succeed. I would like to thank particularly Mia: we spent so much time together in the lab during these three years, your presence was so motivating and reassuring, you helped me a lot. It was really nice to meet Nora from Innsbruck and Frederik from Copenhagen, both PhD students invited in our lab. We also spent good times in conferences. I thank Laurent Pouilloux, a competent and nice computer scientist from the ECL, for helping me on some of my scripts and for always answering me rapidly when I got computing problems. I will finish by thanking my family as well as my life partner Robin who made big concessions to be at my sides in Lyon and gave me endless support. 2 3 “All models are wrong, but some are useful.” George Box, statistician at the University of Wisconsin 4 5 Résumé (French) La couche limite planétaire est la couche atmosphérique la plus basse qui est en interaction directe et constante avec les surfaces terrestres et marines sur lesquelles se concentrent les activités humaines, les cultures et divers écosystèmes. Comprendre l’origine de sa composition à la fois chimique et microbiologique est fondamental dans notre étude approfondie de la biosphère. Alors que les microorganismes de la couche limite planétaire – retrouvés jusqu’à 106 cellules par mètre cube d’air – semblent varier significativement à l’échelle spatiale et temporelle en termes de concentration et de diversité, ils restent largement méconnus. L’objectif principal de cette thèse est de comprendre comment se structurent les communautés microbiennes dans la troposphère, et en particulier dans la couche limite planétaire, ainsi que d’identifier les facteurs de contrôle majeurs. En travaillant sur des échantillons collectés pendant plusieurs semaines sur neuf sites répartis sur la planète, et en utilisant les technologies de séquençage ADN haut-débit, nous avons étudié la composition taxonomique et fonctionnelle des communautés microbiennes de la phase gazeuse et solide de l’atmosphère (c’est-à-dire non associés aux nuages). Nos premiers résultats sur la taxonomie des communautés microbiennes révèlent que les surfaces proches des sites sont les contributeurs principaux de distribution des communautés microbiennes atmosphériques, malgré l’occurrence potentielle du transport longue-distance des microorganismes atmosphériques. Egalement, les conditions météorologiques combinées à la diversité des surfaces locales terrestres ou océaniques jouent un rôle important dans la variation temporelle de la structure des communautés microbiennes de la couche limite planétaire. Une deuxième étude nous a permis d’étudier davantage la variation temporelle des communautés microbiennes atmosphériques sur un site continental montagneux en France (1465 m d’altitude) sur une année complète. Cette étude révèle l’importance des conditions de surface des paysages aux alentours dans la composition taxonomique des communautés atmosphériques. L’évolution au cours de l’année des terres agricoles et de la
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