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Communautés Microbiennes De La Baie De Raisin : Incidence Des Facteurs Biotiques Et Abiotiques Guilherme Marques Martins

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Communautés Microbiennes De La Baie De Raisin : Incidence Des Facteurs Biotiques Et Abiotiques Guilherme Marques Martins Communautés microbiennes de la baie de raisin : Incidence des facteurs biotiques et abiotiques Guilherme Marques Martins To cite this version: Guilherme Marques Martins. Communautés microbiennes de la baie de raisin : Incidence des facteurs biotiques et abiotiques : Incidence des facteurs biotiques et abiotiques. Sciences du Vivant [q-bio]. Université de Bordeaux Ségalen (Bordeaux 2), 2012. Français. tel-02802218 HAL Id: tel-02802218 https://hal.inrae.fr/tel-02802218 Submitted on 5 Jun 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. Année 2012 Thèse n°1924 THÈSE pour le DOCTORAT DE L’UNIVERSITÉ BORDEAUX 2 Ecole doctorale Mention : Sciences, Technologie, Santé Option : Œnologie Présentée et soutenue publiquement Le 3 juillet 2012 Par Guilherme MARTINS Né le 7/10/81 à Coimbra, Portugal Communautés microbiennes de la baie de raisin Incidence des facteurs biotiques et abiotiques Membres du Jury Mr. P. REY, Professeur à Bordeaux Sciences Agro Président Mr. R. DURAN, Professeur à l’Université de Pau et des Pays de l'Adour Rapporteur Mme M.C. MONTEL, Directrice de recherche à l’INRA de Clermont-Ferrand Rapporteur Mr. S. COMPANT, Maître de conférences à l’Université de Toulouse Examinateur Mme A. LONVAUD-FUNEL, Professeur à l’Université Bordeaux Segalen Examinateur Mme I. MASNEUF-POMAREDE, Professeur à Bordeaux Sciences Agro Directrice de thèse Amai-vos e instruí-vos. Remerciements Ce travail a été réalisé au sein de l’Institut des Sciences de la Vigne et du Vin au sein de l’équipe Microbiologie du raisin et du Vin grâce au soutien financier du Conseil Interprofessionnel du Vin de Bordeaux, de l’Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux - Bordeaux Sciences Agro et du Conseil Régional d’Aquitaine. Cette thèse n’aurait pas pu voir le jour sans de nombreuses personnes que je souhaite remercier. En tout premier lieu, je tiens à exprimer ma profonde gratitude et ma grande reconnaissance à Mme Isabelle Masneuf-Pomarède, ma directrice de thèse, pour l’opportunité qu’elle m’a offerte, pour sa confiance ainsi que pour son soutien amical et sa disponibilité. Qu’elle veuille bien trouver ici le témoignage de toute ma gratitude pour son aide permanente. Mes remerciements vont également à Mme Aline Lonvaud-Funel pour m’avoir accueilli dans son laboratoire et pour m’avoir permis de travailler dans d’excellentes conditions. Qu’elle reçoive également toute l'expression de ma reconnaissance pour avoir accepté de participer au jury de soutenance. J’exprime ma gratitude à Mr Patrice Rey, qui m’a fait l’honneur de présider ce jury.Toute ma reconnaissance également à Mme Marie Christine Montel, Mr Robert Duran et Mr Stéphane Compant pour l’intérêt qu’ils ont bien voulu porter à ce travail en acceptant de le juger. Je remercie les châteaux Luchey Halde, Château Gombaude Guillot, Château Clinet, Château de Bellevue, Château Haut - Piquat, Château de Beauséjour et Château Soleil qui ont très cordialement accepté de me mettre à disposition du raisin pour permettre mes recherches. Je remercie Cécile Miot-Sertier, Olivier Claisse, Guy et Marie-Louise Soulas, Katharina Zott et Anne Mercier pour leur participation à ce travail, pour m'avoir formé au travail de laboratoire et pour toute l’aide technique et scientifique apportée. Je leur suis infiniment reconnaissant. Merci au personnel de la cellule de transfert Microflora (Geoffrey Bourbon, Julie Maupeu et Joana Coulon). J’ai vraiment apprécié travailler à vos côtés! Je sais tout ce que je vous dois et vous en serai éternellement reconnaissant. Je tiens à remercier à l’Equipe Environnement et Microbiologie de l’Université de Pau et des Pays de l’Adour, particulièrement à Béatrice Lauga. J’exprime tout mon respect et mes remerciements pour son accompagnement et son soutien. Je tiens à remercier l’UMR Santé et Agroécologie du vignoble INRA – Bordeaux et particulièrement à Marc Fermaud et Jean Roudet pour leur collaboration dans le dispositif expérimental. Mes sincères remercîments à Jessica Vallance, pour son soutien scientifique et technique dans la validation de la technique CE-SSCP pour l’étude de la communauté fongique de la baie de raisin. Merci pour ta gentillesse et ta bonne humeur. Une mention toute particulière pour Warren Albertin pour sa patience et disponibilité et pour ces belles figures obtenues sous "R". Merci pour tout. Merci à la cellule de transfert Amarante Process (Arnaud Massot et Fabrice Meunier) pour m’avoir accueilli dans son laboratoire et permis ainsi le dosage de cuivre. Merci pour votre bonne volonté et pour votre amitié. Merci à Emmanuel Baugier pour tout le temps qu’il m’a consacré pour le traitement des images. Je n’oublie pas ta caisse de porto. Merci également à Patrick Leger pour ses bricolages qui ont réparé plusieurs machines que j’ai cassées. A mon cher camarade de bureau, Julen Bridier, un grand merci pour tout ces cours de langue française, génétique et culture basque. À Greg Pasquier, pour le plaisir de travailler ensemble et pour sa grande aide et disponibilité. À mes chers compatriotes Maria "Laidinha" et Telma da Silva, merci pour les sourires, les coups de mains et les encouragements. Je tiens bien sur à remercier tous les stagiaires qui ont participé à ce travail parmi eux, Panagiotis Solimanoglo Stamatopoulos, Ccori Martinez et surtout Cosimo Cosini, qui même étant italien a travaillé comme un portugais. Je tiens également à remercier à mes camarades d'armes, Andrea " El Roma", Greg Schmauch, Igor Chichiuc "Генеральныйсекретарь", Kleopatra Chira, Armin Gerd Müller Schuttler et FofixTempere. Merci aux personnes que j’ai pu rencontrer au cours de cette thèse et qui grâce a leur sympathie m’ont permis de réaliser cette thèse dans les meilleures conditions: Marula, Marion, Mariette, Rémy, Fety, Patrick, Marguerite, Claire, Patricia, P. Marullo, P. Renault, Poggi, Paulo, Jean-Baptiste, Maude, Charles, Annie, Soizic, M. Claire, Laurent, Stéphanie, Davide, Julien-Michel, Cécile , Christiane, Yann, Sabine, Stéphane, …. Enfin, mes derniers remerciements je me permettrai de les faire dans ma langue maternelle : À minha grande família, do Minho a Timor, passando por Catete, Arta e Condeixa, aos meus pais e a Jiouli por todo o amor e preocupação. A minha irmã, ao meu cunhado, as minhas afilhadas e aos meus tios e primos. Aqueles que, mesmo não me apercebendo, estiveram sempre comigo, desde o principio. A todos vocês muito obrigado e bem-hajam. INTRODUCTION ...................................................................................................................... 1 CHAPITRE I - ETUDE BIBLIOGRAPHIQUE ........................................................................ 3 1. Ecologie et écosystèmes microbiens .................................................................................. 4 1.1. Définition d’un écosystème ......................................................................................... 4 1.2. Ecologie microbienne, importance et applications ..................................................... 4 1.3. Biodiversité ................................................................................................................. 6 1.4. Facteurs affectant le développement des microorganismes ........................................ 7 1.4.1 La température ....................................................................................................... 8 1.4.2 L’humidité ............................................................................................................. 9 1.4.3 L’activité de l'eau .................................................................................................. 9 1.4.4 Le pH ................................................................................................................... 10 2. Ecosystème et communautés microbiennes viticoles ....................................................... 11 2.1. La Plante et le Fruit ................................................................................................... 11 2.2 Les (différents écosystèmes) différentes communautés microbiennes viticoles ........ 13 2.2.1 Le sol et la rhizosphère viticole ........................................................................... 13 2.2.2 La partie aérienne de la vigne, la colonisation endophytes et épiphytes ............. 16 2.3 Communauté microbienne de la baie de raisin .......................................................... 18 2.3.1 Les moisissures ................................................................................................... 19 2.3.2 Les levures ........................................................................................................... 24 2.3.3 Les bactéries ........................................................................................................ 31 3. Méthodes d’analyse en écologie microbienne ................................................................. 36 3.1 Analyse des communautés microbiennes par les méthodes classiques ...................... 36 3.1.1 Milieu de culture sélectif, d’enrichissement et d’isolement
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