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I. Freezing Lactic Acid Bacteria Study of the cryopreservation-related stresses in the lactic acid bacterium Lactobacillus delbrueckii subsp. bulgaricus through a global and multi-scale approach Julie Meneghel To cite this version: Julie Meneghel. Study of the cryopreservation-related stresses in the lactic acid bacterium Lacto- bacillus delbrueckii subsp. bulgaricus through a global and multi-scale approach. Biotechnology. Université Paris Saclay (COmUE), 2017. English. NNT : 2017SACLA030. tel-02965060 HAL Id: tel-02965060 https://tel.archives-ouvertes.fr/tel-02965060 Submitted on 13 Oct 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. Study of the cryopreservation- related stresses in the lactic acid bacterium Lactobacillus delbrueckii 2017SACLA030 : subsp. bulgaricus through a global NNT and multi-scale approach Thèse de doctorat de l'Université Paris-Saclay préparée à l’Institut des sciences et industries du vivant et de l'environnement (AgroParisTech) École doctorale n°581 Agriculture, alimentation, biologie, environnement et santé (ABIES) Spécialité de doctorat: Sciences de la vie et de la santé Thèse présentée et soutenue à Paris, le 12 octobre 2017, par Julie Meneghel Composition du Jury : Pascale Serror Directeur de recherches, INRA Jouy-en-Josas – Institut MICALIS Président Laurent Beney Professeur, AgroSupDijon – UMR PAM Rapporteur Andrea Gomez-Zavaglia Directeur de recherches, CONICET– CIDCA Rapporteur George John Morris Président Directeur Général, Asymptote Rapporteur Muriel Mercier-Bonin Chargé de recherches, HDR, INRA Toulouse – UMR TOXALIM Examinateur Fernanda Fonseca Directeur de recherches, INRA Grignon – UMR GMPA Directeur de thèse Paul Dumas Directeur de recherches émérite, CNRS – Synchrotron SOLEIL Co-Directeur de thèse INRA Grignon, UMR 0782 GMPA, Avenue Lucien Brétignières, 78850 Thiverval-Grignon Synchrotron SOLEIL, lignes de lumière SMIS et DISCO, 91190 Gif-sur-Yvette PARTAGER « À trop se soucier de l’achèvement des choses, On n’entreprend jamais rien » François Ier, à propos de la construction du Château de Chambord This statement, pronounced by François Ier during the building of the Château de Chambord, could probably be translated to: Worrying too much about the completion of things, One never engages in anything. REMERCIEMENTS (ACKNOWLEDGEMENTS) Tout d’abord, je souhaiterais remercier chaleureusement Andrea Gomez-Zavaglia, Directrice de Recherches du CIDCA CONICET argentin ainsi que Laurent Beney, Professor à AgroSup Dijon, d’avoir accepté la tâche de rapporteur de ces travaux. Merci également à Muriel Mercier-Bonin, Chargée de Recherches à l’INRA de Toulouse, à Pascale Serror, Directrice de Recherches à l’INRA de Jouy-en-Josas, ainsi qu’à John Morris de faire partie de ce jury de thèse et d’examiner mes travaux. Je voudrais ensuite remercier le laboratoire GMPA de l’INRA de Grignon, dirigé par François Boué puis Pascal Bonnarme, pour m’avoir accueillie et offert des conditions de travail optimales. Merci également au Synchrotron SOLEIL de m’avoir offert un accès permanent à son site ainsi qu’un bureau lors de mes séjours ponctuels. Parlant de conditions de travail optimales, je remercie vivement le département CEPIA de l’INRA (Caractérisation et Elaboration de Produits Issus de l’Agriculture), ainsi que l’Université Paris- Saclay via le programme interdisciplinaire IDI, pour avoir chacun co-financé ce projet doctoral. Enfin, j’adresse de sincères remerciements à l’école doctorale ABIES, au travers de Cyril Kao puis d’Alexandre Pery qui l’ont dirigée, une école doctorale humaine et souciante de chacun de ses doctorants. Je la remercie surtout au travers d’Irina Vassileva, pour son écoute bienveillante et son soutien qui ont énormément compté pour moi. Maintenant, j’adresse un immense et sincère remerciement à Fernanda Fonseca et Stéphanie Passot, respectivement directrice et chargée de recherches au GMPA et co-directrice et co-encadrante de ma thèse. Merci pour tous vos précieux enseignements, conseils et encouragements ! Merci aussi à Paul Dumas et Frédéric Jamme, scientifiques au Synchrotron SOLEIL et respectivement co- directeur et co-encadrant de ma thèse. J’ai énormément appris à vos côtés, tant sur un plan scientifique que personnel et humain ! Merci à vous quatre de m’avoir laissé une grande autonomie au quotidien, mais aussi le choix parmi les vastes possibilités d’investigation permises par ce projet ainsi que les moyens adéquats pour leur réalisation. Merci enfin pour votre disponibilité, votre patience, et d’avoir mis la main à la pâte côté manipes et de ne jamais avoir compté vos heures à SOLEIL, fussent-elles diurnes ou nocturnes ! Un grand merci également à Séverine Layec, Enseignant-chercheur AgroParisTech, Maarten van de Guchte, Directeur de Recherches à l’INRA de Jouy-en-Josas, et Ganesh Sockalingum, Professeur à l’Université de Reims Champagne-Ardenne, pour m’avoir conseillée et accompagnée tout au long de cette thèse en tant que membres de comité de cette thèse. Merci en particulier à Maarten pour m’avoir confié la souche L. bulgaricus ATCC 11842 qui m’aura finalement considérablement servi ! ainsi qu’à Ganesh pour avoir aimablement proposé d’effectuer (puis effectué !) quelques tests Raman. Côté SOLEIL, je remercie toute l’équipe SMIS et toute l’équipe DISCO pour m’avoir chaleureusement accueillie à chacun de mes séjours au Synchrotron et pour m’avoir fait découvrir la physique de pointe. Ça a toujours été un réel plaisir pour moi d’échanger avec vous et de travailler à vos côtés. Un grand merci donc, et ce tout particulièrement à Christophe Sandt, Stéphane Lefrançois et Wiliam André côté SMIS, et à Matthieu Réfrégiers côté DISCO. D’un point de vue un peu plus spécifique des travaux qui ont été effectués, j’adresse un chaleureux remerciement à Stéphanie Cénard, technicienne au GMPA jusqu’à la réussite de son concours et son envol dans le Sud (qui sont arrivés trop tôt !). Merci pour m’avoir d’abord formée à la microbio du GMPA, puis pour avoir partagé la paillasse avec moi et m’avoir soutenue dans les nombreuses récoltes, lavages cellulaires et CinAc ! Merci également d’avoir toujours accepté de me filer un coup de main dans les coups de bourre ! Ta bonne humeur au quotidien a été communicante et précieuse, pareil pour ta fermentite aigue (surtout pour le brassage) que tu as su me transmettre ! Pour son importante contribution à mon projet de thèse, son travail impeccable, sa douceur et sa gentillesse, je souhaite remercier vivement Jiawei Xu d’avoir choisi d’effectuer son stage UTC à mes côtés. J’ai beaucoup apprécié cette expérience d’encadrement et te souhaite bonheur et réussite ! Côté formation, je tiens à remercier toutes les personnes qui ont donné de leur temps pour me transmettre leur savoir-faire : Pascale Lieben pour la spectro infrarouge, Sébastien Dupont pour la spectrofluorimetrie à Dijon, Caroline Pénicaud pour l’ASE et la GC-MS ainsi qu’Armelle Delile et Brigitte Pollet lors d’éventuels soucis sur ces appareils, Marielle Bouix et Sarah Ghorbal pour la cytométrie en flux, Eric Dugat-Bony pour la transcripto, Christophe Monnet et Séverine Layec pour la génomique comparative, Jérôme Delettre pour la protéo… Merci aussi Jérôme pour les toutes dernières manipes in extremis et le gardiennage ponctuel de la bête ! Merci à nouveau à Stéphane Lefrançois de s’être autant impliqué dans les travaux de conception du microscope inversé et des multiples petits équipements qui ont été d’une utilité cruciale. Merci aussi encore une fois à Christophe Sandt pour avoir toujours eu une oreille attentive, un conseil ou une solution pertinente en cas de besoin ! Merci à vous deux pour votre générosité. Pour leur travail administratif indispensable, mais aussi pour leur disponibilité, leur grande amabilité et l’approvisionnement en chocolats et pâte à tartiner, je remercie également Laurence Fruchart, Thierry Feugnet et Evelyne Philippe, gestionnaires au GMPA. Merci aussi à Michel Savy pour les dépannages informatiques, à Bruno Perret pour avoir fait des adaptations logicielles sur- mesure, et aux gars de l’atelier pour le soutien logistique (Jérôme Bussière, David Lévêque et Frédéric Lecornué) ! Pour en finir avec le GMPA, je souhaite remercier l’ensemble de son personnel que j’ai pu côtoyer, des personnes avec chacune desquelles j’ai pu entretenir des liens souvent amicaux. Je pense en premier lieu à mes compatriotes de bureau : Hélène et Greg (Grogware), puis Sichao, Michele, Marine, Florence et Phuong. Ç’a vraiment été chouette d’avoir passé bout de temps plus ou moins (mais jamais assez !) long à vos côtés ! Les voisins tout proches de la plateforme et autres thésards ont également largement contribué à rendre le travail quotidien au GMPA plus qu’agréable : Solenne (Mich’Miche), Vincent (Chaton), Vincent (Bibiche), Nadège (Nadou), David (Dave), Salma (Princesse au petit pois), Hélène (Bidochette), Florian, Gilles, Mathieu (Batman), Daniela, Phuong et les expatriés de Malices au 2ème étage : Thuy Minh, Julien, Benoît, Thomas, Marc et Bernadette. Également les stagiaires, avec la fournée « Batman contre Joker »
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