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Etude De La Diversité Des Souches D'oenococcus Oeni Responsables

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Etude De La Diversité Des Souches D'oenococcus Oeni Responsables Etude de la diversit´edes souches d'Oenococcus oeni responsables de la fermentation malolactique des vins dans diff´erentes r´egionsvitivinicoles Mariette El Khoury To cite this version: Mariette El Khoury. Etude de la diversit´edes souches d'Oenococcus oeni responsables de la fermentation malolactique des vins dans diff´erentes r´egionsvitivinicoles. Sciences agricoles. Universit´ede Bordeaux, 2014. Fran¸cais. <NNT : 2014BORD0357>. <tel-01309805> HAL Id: tel-01309805 https://tel.archives-ouvertes.fr/tel-01309805 Submitted on 1 May 2016 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. THÈSE PRÉSENTÉE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE BORDEAUX École doctorale des Sciences de la Vie et de la Santé Spécialité : Œnologie Par Mariette EL KHOURY Etude de la diversité des souches d’Oenococcus oeni responsables de la fermentation malolactique des vins dans différentes régions vitivinicoles Sous la direction de M. Patrick LUCAS Soutenue le 16 décembre 2014 Membres du jury : M. E. COTON Professeur à l’Université de Bretagne Occidentale Président M. A. BORDONS Professeur à l’Université Rovira i Virgili de Tarragone Rapporteur Mme. R. TOURDOT-MARECHAL Maître de Conférence à l’Université de Bourgogne Examinateur M. P. LUCAS Professeur à l’Université de Bordeaux Directeur de thèse Etude de la diversité des souches d’Oenococcus oeni responsables de la fermentation malolactique des vins dans différentes régions vitivinicoles Oenococcus oeni est la principale espèce de bactérie lactique d’intérêt œnologique, elle réalise la plupart des fermentations malolactiques. Les souches d’O. oeni ont souvent été étudiées dans le but de sélectionner des levains malolactiques. Ces souches possèdent des caractéristiques génétiques, et phénotypiques variées. Néanmoins, l’utilisation de différentes méthodes de typage n’a pas permis à ce jour d’obtenir une image exhaustive de la diversité œnologique de cette espèce. L’intérêt grandissant des viticulteurs pour mieux maitriser les FML spontanées nécessite de mieux connaitre cette diversité. La population de souches indigènes d’O. oeni présentes dans les FML de différentes régions a été étudiée, pour tenter d’obtenir une image plus complète de la diversité de cette espèce et savoir s’il serait pertinent de sélectionner des souches de régions ou d’exploitations. L’analyse d’un très grand nombre de vins a mis en évidence la présence de souches spécifiques aux régions, appellations, produits et exploitations étudiées. Un génotypage à l’aide de SNP a permis de les classer dans les groupes génétiques déjà connu et a confirmé l’existence de groupes spécifiques à un type de produit. Certaines de ces groupes rassemblent des souches présentant des comportements phénotypiques et des capacités fermentaires similaires. En complément de l’analyse de diversité, des essais ont été menés pour proposer des protocoles de production de souches et d’utilisation de lies pour améliorer la réalisation des FML spontanées. L’ensemble de ces travaux soulignent la grande diversité génétique de l’espèce O. oeni, l’étude des souches spécifiques de type de vin pourrait aider à comprendre son adaptation à cet environnement. Mots clés : Oenococcus oeni, diversité, indigène, fermentation malolactique, SNP Study of the diversity of Oenococcus oeni strains responsible for malolactic fermentation of wine in different winemaking regions Oenococcus oeni is the main species of lactic acid bacteria of oenological interest, it performs most of malolactic fermentation. O. oeni strains have often been studied to select malolactic starters. These strains have various genetic and phenotypic characteristics. However, the use of different typing methods failed so far to obtain a complete picture of the enological diversity of this species. The growing interest of winegrowers to better control the spontaneous requires a better knowledge of this diversity. The population of indigenous O. oeni strains present during MLF in different regions has been studied in an attempt to obtain a more complete picture of the diversity of the species and to know whether it would be appropriate to select strains of regions or wineries. The analysis of a large number of wines showed the presence of strains specific to wineproducing areas, different kind of wines, and wineries. SNP Genotyping allowed us to classify these strains in the already known genetic groups and confirmed the existence of specific groups to a specific kind of product. Some of these strains belonging to the same specific genetic groups showed similar behavior and technological properties. In addition to the diversity analysis, trials of production of strains and use of lees to ameliorate the MLF have been done to improve the achievement of spontaneous MLF. Taken together, these studies emphasize the high genetic diversity of the species O. oeni, the study of specific strains of type of wine could help understand the adaptation of this species to this environment. Keywords : Oenococcus oeni, diversity, indigenous, malolactic fermentation, SNP Unité de recherche Œnologie, EA 4577, USC 1366 INRA Institut des Sciences de la Vigne et du Vin, 210 Chemin de Leysotte, 33882 Villenave d’Ornon À mes parents, À mon parrain Remerciements Je tiens tout d’abord à adresser mes sincères remerciements aux membres du jury M. Emmanuel COTTON, M. Albert BORDONS et Mme. Raphaëlle TOURDOT-MARECHAL qui ont accepté de juger mon travail de thèse et qui ont fait le déplacement depuis Nantes, Tarragone et Dijon. Merci pour tous vos conseils et vos remarques pertinentes qui m’ont été précieuses. J’adresse également mes chaleureux remerciements à mon directeur de thèse M. Patrick Lucas pour m’avoir accueilli au sein de l’équipe de microbiologie du raisin et du vin. Merci pour tes conseils avisés, ta disponibilité malgré ton emploie du temps serré, ta confiance et la grande part d’autonomie que tu m’as accordé sur ce sujet passionnant. Merci de m’avoir permis de voyager autant grâce aux projets et de réaliser du monitorat, c’était une très belle expérience. Je suis très contente d’avoir pu travailler en ta compagnie. Je remercie de même tous les partenaires des projets LevainsBio et WildWine, les centres IFV, l’IFPC, le SVBA et plus particulièrement Stéphane Becquet et les châteaux partenaires, qui m’ont fourni des centaines d’échantillons, sans qui ce projet n’aurait pas été réalisable. Au cours de cette période l’aide de certaines personnes a été indispensable pour mener à bien ce travail. Un grand merci à Olivier Claisse et Marion Favier pour m’avoir formée et soutenue depuis le master et jusqu’au bout de la thèse. Merci pour toutes vos explications, votre patience à toute épreuve et vos encouragements. Olivier merci de m’avoir prêté si souvent ton ordi et bureau même quand tu en avais besoin. Merci à Julie Maupeu et Cécile Miot-Sertier (Tatie) pour votre gentillesse, votre bonne humeur et tous vos conseils pratiques et techniques. Un grand merci à tous les membres de l’équipe microbio; Geoffrey (le roi des µFML), Marie, Aurélie, Hugo (notre bioinformaticien), Claire, Isabelle, Mme. Aline Lonvaud, Marguerite, Marina, Patricia, Guilherme, Marine B., Marion B., et à mes compagnons de bureau ; Margaux, Maxime et Cécile; pour vos encouragements et tous les bons moments passés en votre compagnie. Je me suis sentie tellement bien parmi vous que ces trois années sont passées en un clin d’œil, j’ai eu beaucoup de chance de vous rencontrer et de partager les apéros/carnavals du labo avec vous. Merci aussi à tous les stagiaires qui m’ont bien aidé, Guillaume, Cécile G., Charly, Camille, Marine et Florian. Une pensée particulière va à mes collègues et maintenant amis, Fety Jaomanjaka (mon partenaire de rock) et Maroula Dimopoulou (ma grec préférée). Je n’aurais pu imaginer ces dernières années sans votre présence joyeuse à mes côtés dans tous les bons moments mais aussi les mauvais, merci pour tout. Un grand merci à Nathalie Alvarez, Caroline Baz et Soizic Lacampagne pour votre gentillesse vos encouragements et d’avoir toujours été à mon écoute. Et merci à l’équipe du Hall Techno, à Julien et Isa pour vos petites blagues et votre bonne humeur communicative. Merci à Marine Gammacurta, Adrien et Charline Zimmer, et à mes amis Alsaciens Lucile, Neila, Nicolas et David pour votre soutient et tous les bons moments ponctués de déco de bureau, brunchs, soirées et weekend inoubliables et surtout merci Rany qui a assuré l’intendance pendant les derniers mois difficile de la rédaction. Pour finir je souhaite remercier mes parents, mes grands frères, ma belle-sœur pour leur soutien inconditionnel. J’ai de la chance d’avoir une famille qui comprend mon travail et qui a su m’accompagner et me conseiller tout au long de cette aventure. Un Merci tout particulier à Etienne et Nath, vous m’avez poussé à me lancer dans cette voie (la bio la recherche tout ça…) et vous avez eu bien raison. Et puis merci à mon petit neveu Lucas parce que c’est le plus mignon et qu’il était presque sage pendant ma soutenance. TABLE DES MATIERES INTRODUCTION.................................................................................................. 1 ETUDE BIBLIOGRAPHIQUE ................................................................................. 3 1. Les bactéries lactiques du vin et la fermentation malolactique ................... 3 1.1. Découverte et diversité des bactéries lactiques du vin .......................................................... 3 1.2. Evolution de la population des bactéries lactiques au cours de la vinification ...................... 4 1.3. Les facteurs influençant la croissance des bactéries dans le vin ...........................................
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