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Diversité Des Espèces De Levures Dans Des Levains Naturels Français Diversité des espèces de levures dans des levains naturels français produits à partir de farine issue de l’Agriculture Biologique : une étude pilote pour analyser les pratiques boulangères et les patterns des communautés microbiennes Charlotte Urien To cite this version: Charlotte Urien. Diversité des espèces de levures dans des levains naturels français produits à partir de farine issue de l’Agriculture Biologique : une étude pilote pour analyser les pratiques boulangères et les patterns des communautés microbiennes. Ecologie, Environnement. Université Paris Sud - Paris XI, 2015. Français. NNT : 2015PA112007. tel-01249573 HAL Id: tel-01249573 https://tel.archives-ouvertes.fr/tel-01249573 Submitted on 4 Jan 2016 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. UNIVERSITÉ PARIS-SUD ÉCOLE DOCTORALE : Structure et Dynamique des Systèmes Vivants (anciennement ED 426 : Gènes, Génomes, Cellules) Laboratoire : UMR de Génétique Quantitative et Evolution – Le Moulon THÈSE DE DOCTORAT SCIENCES DE LA VIE ET DE LA SANTÉ par Charlotte URIEN Diversité des espèces de levures dans des levains naturels français produits à partir de farine issue de l'Agriculture Biologique : une étude pilote pour analyser les pratiques boulangères et les patterns des communautés microbiennes Date de soutenance : 23/01/2015 Composition du jury : Directrice de thèse : Delphine SICARD Directrice de Recherche (INRA, Montpellier) Co-encadrante de thèse : Judith LEGRAND Maître de Conférences (Université Paris-Sud, Orsay) Rapporteurs : Teun BOEKHOUT Senior researcher (Fungal Biodiversity Centre, Pays-Bas) Joëlle DUPONT Professeur (Muséum National d’Histoire Naturelle, Paris) Président du jury : Olivier LESPINET Professeur (Université Paris-Sud, Orsay) Examinateur : Hubert CHIRON Ingénieur d'Etudes (INRA, Nantes) Remerciements Je tiens à remercier chaleureusement les membres de mon jury de thèse : merci aux rapporteurs Joëlle Dupont et Teun Boekhout d'avoir pris le temps de lire, d’évaluer et de commenter mon travail ; merci à Olivier Lespinet d'avoir accepté de faire partie de ce jury ; merci Hubert Chiron pour ta présence et les opportunités que tu m'as offertes au cours de cette thèse afin de valoriser mon travail ; enfin, je tiens à remercier Judith Legrand et Delphine Sicard qui ont co-encadré ce travail. Delphine, merci de m’avoir offert l’opportunité de faire un stage de Master 2 et découvrir le monde de la boulange ainsi que l’univers des levures, merci de m'avoir suffisamment fait confiance pour m'envoyer en mission à Stanford : ça a été une expérience professionnelle unique, et très enrichissante d'un point de vue personnel, merci de m’avoir encouragée à faire cette thèse, d’avoir eu confiance en moi, de m’avoir permis de faire un peu d’enseignement, merci également pour ton enthousiasme. Judith, merci d’avoir accepté de co-encadrer ce travail et d’y avoir apporté ton expertise de statisticienne. Merci à toutes les deux pour l'autonomie que vous m'avez permis d'acquérir durant ces années. Merci à Dominique de Vienne de m'avoir accueilli au sein de l'ancienne UMR de Génétique Végétale du Moulon (rebaptisée aujourd’hui UMR Génétique Quantitative et Evolution – Le Moulon), et merci d'avoir permis au club gym de se réunir plusieurs fois par semaine au labo. Merci à la région Ile-de- France qui a financé cette thèse via un financement du DIM-Astréa. Un grand MERCI aux boulangers et paysans-boulangers pour nous avoir ouvert leurs portes à Emilie et moi, pour nous avoir fait partager leur savoir et leur savoir-faire, pour nous avoir permis de mettre la main à la pâte (au sens propre comme au figuré)! Merci à Emilie Lhomme, ma camarade, mon "pendant bactéries lactiques": merci pour nos échanges, pour notre entre-aide, pour nos longues réunions téléphoniques. Merci aux stagiaires que j'ai pu encadrer et particulièrement à Candice Aulard pour tout le travail que tu as mené pendant tes 6 mois parmi nous. Merci aux membres de mon comité de thèse: Aymé Spor, Purification Lopez-Garcia, Pierre Capy, Emmanuelle Porcher, Philippe Roussel, Cécile Neuveglise et Laurence Bérard: pour votre écoute et vos remarques qui m'ont permis d'orienter mon projet vers son résultat final. Merci Mathieu Falque pour tes conseils notamment sur les PCR. Merci Aymé pour ton expertise et ton aide pour les analyses bioinfo. Merci Pierre Montalent pour le temps passé aux analyses NGS. Merci à Bernard Onno et Xavier Dousset pour notre collaboration dans le projet "dynamique des communautés microbiennes"! Merci à Serge Casaregola et Noémie Jacques du CIRM-levures pour votre expertise sur les marqueurs moléculaires et le travail en cours sur les souches de Kazachstania : le projet continue... Ces années au Moulon ont été très riches. J'ai appris tout ce que je sais à la paillasse grâce à Xavier Raffoux, Carine Remoué, Aurélie Bourgais et Delphine : un grand merci pour cela! Xavier, merci de m'avoir présentée à tous au départ, merci pour ton soutien ces derniers mois. Carine, merci pour ton sourire permanent: tu es un rayon de soleil au labo! Merci aux autres personnes qui arpentent le labo (où il y a les paillasses) et notamment à Valérie : merci pour tes compliments sur mes tenues vestimentaires et tes attentions: ça m'a toujours fait chaud au cœur. Merci à l'ensemble de l'équipe GQF d'hier et BASE d'aujourd'hui. Merci Marie Ragon (ESE) de m'avoir initiée aux techniques de clonage. Merci Marion Richard pour l'accès à la centrifugeuse de l'IPB lorsque nous avions une panne au Moulon. Merci au Centre de Vulgarisation de la Connaissance de m’avoir intégrée pour 17 mois dans leurs projets et de m’avoir permis de me frotter aux hautes instances de l'administration française! Merci à Bruno Bost et l’Université Paris-sud pour m’avoir aidé dans ce long périple. Enfin, merci Maud Tenaillon d’avoir pris du temps pour lire mon travail et me rassurer à un moment critique. Ces années au Moulon m'ont aussi permis de rencontrer des potes et des amis, plus chers à mon cœur qu'ils ne l'imaginent... Merci à ceux qui ont été particulièrement présents ces derniers mois, ceux qui ont été à la fois ou séparément mes piliers, mes refuges, mes soutiens sans faille, mes nourriciers, mes conseillers, mes épaules, mes éclaircis, mes distributeurs de rire et de bonne humeur, mes oasis dans le désert, mes relecteurs, … : Yannick (merci pour les dizaines de fois où tu m’as laissé piloter ta clio d’homme sans enfant), Pierrot (merci de m’avoir encouragé dès le départ, merci pour tous tes conseils et nos longues journées à bosser sur les analyses de "Pierrot- séquençage", merci pour les ZC et pour tout ce que tu sais), Bub (merci de raser ta barbe !!!!!!!), Xavier (merci pour ta présence et ton investissement dans le travail d’équipe), Chris (merci d’avoir supporté mon visage et mes remarques « en tant que tel - en tant que tel - en tant que tel - en tant que tel !!!», merci pour ce fou-rire magistral à propos du « Boulon », merci pour la migration à l'IE, merci pour ton écoute, merci d'avoir adouci mon humeur et merci de m'avoir supportée (dans tous les sens du terme!)), Margaux-Alison (merci ma belle pour notre projet d'escargots, merci d’avoir organisé la béqué, merci pour tes commentaires avisés, tes critiques toujours constructives et ton soutien de façon générale), Héloïse (merci pour le week-end au soleil qu’on va pouvoir se faire et pour m’avoir aidé à boucler les résumés), Yasmine (merci pour les révisions d'allemand et ton assiduité à la gym), JT & Fabien (merci pour cette image que je ne décrirai pas ici mais qui restera a jamais gravée dans ma mémoire !!!, merci pour votre disponibilité), Cyril (merci pour cet instant magique à la cafèt'… oui, celui qui faisait appel à un torchon !), Steph (merci pour les cakes pas au chèvre et pour tout ce que je ne listerai pas ici...), Paulina (merci d’aimer les bretonnes!!!), Sara (merci pour le pied à terre milanais). Mes "colocs de jour", ce fût un plaisir de partager le bureau avec vous : Pierre (merci pour nos délires M&M's et pour Junior), Marie (merci pour ton rire omniprésent et les débogages de code), Hélo et Chris (ah, mais vous êtes encore là??!!!). Merci à la team originelle pour l'intégration durant mon stage (et après), merci également aux gymnastes pour ces moments de défoulement: je peux le dire maintenant : "et on relâche COMPLETEMENT!". Merci à mes potes hors-moulon qui ont également été présents durant ma thèse : Merci notamment à Hélène (pour nos papotages et tes conseils) et à Mathieu (pour les promenades-ciné-guitare et l'excursion à London qui tombait juste à point). Merci à mes "colocs de nuit" d'avoir partagé leur quotidien avec moi : Sophie, et maintenant Jojo (dernière ligne droite!!) et Robin. Merci à mes zouaves d'adoucir mon quotidien. Thank's Barbara Dunn to be so close even so far. Merci à ma famille et particulièrement à mes sœurs et mes parents. Merci à Aïda, Math et Gwen pour leurs relectures/remarques/corrections de langue même à la dernière minute! Ce manuscrit de thèse clôt une période fructueuse professionnellement et personnellement, je remercie tous les protagonistes qui ont aidé à ce que ce travail voit le jour.
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