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Origins of the Blemishes of Potato Tubers: from the Soil Microbiology to the Pedoclimatic Environment Doctorate

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Origins of the Blemishes of Potato Tubers: from the Soil Microbiology to the Pedoclimatic Environment Doctorate Origins of the blemishes of potato tubers : from the soil microbiology to the pedoclimatic environment Marie Fiers To cite this version: Marie Fiers. Origins of the blemishes of potato tubers : from the soil microbiology to the pedoclimatic environment. Food and Nutrition. Université de Bourgogne, 2010. English. NNT : 2010DIJOS015. tel-00572491 HAL Id: tel-00572491 https://tel.archives-ouvertes.fr/tel-00572491 Submitted on 1 Mar 2011 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. UNIVERSITE DE BOURGOGNE Unité Mixte de Recherche Microbiologie du Sol et de l'Environnement THESE Pour obtenir le grade de Docteur Discipline: Ecologie microbienne par Marie FIERS le 21 Juin 2010 Origine des altérations superficielles du tubercule de pomme de terre:e De la microbiologie du sol à l'environnement pédo-climatique Co-directeurs: Christian STEINBERG, Catherine CHATOT, Véronique EDEL- HERMANN et Yves LE HINGRAT Membres du jury Prof. Monica HÖFTE Université de Gand, Belgique Rapporteur Prof. Jean-Loup NOTTEGHEM SupAgro, Montpellier, France Rapporteur Prof. Andreas KEISER Haute école suisse d'agronomie, Zollikofen, Suisse Examinateur Prof. Daniel WIPF INRA / Université de Bourgogne, Dijon, France Examinateur Dr. Véronique EDEL-HERMANN INRA, Dijon, France Co-directrice Dr. Catherine CHATOT Germicopa, Quimper, France Co-directrice Dr. Christian STEINBERG INRA, Dijon, France Directeur UNIVERSITE DE BOURGOGNE Unité Mixte de Recherche Microbiologie du Sol et de l'Environnement DOCTORATE For the degree of Doctor Discipline: Microbial ecology Presented by Marie FIERS on 21 st June 2010 Origins of the blemishes of potato tubers:s From the soil microbiology to the pedoclimatic environment Supervisors: Christian STEINBERG, Catherine CHATOT, Véronique EDEL- HERMANN and Yves LE HINGRAT Members of the jury Prof. Monica HÖFTE University of Gent, Belgium Reviewer Prof. Jean-Loup NOTTEGHEM SupAgro, Montpellier, France Reviewer Prof. Andreas KEISER Haute école suisse d'agronomie, Zollikofen, Suisse Examiner Prof. Daniel WIPF INRA / Université de Bourgogne, Dijon, France Examiner Dr. Véronique EDEL-HERMANN INRA, Dijon, France Supervisor Dr. Catherine CHATOT Germicopa, Quimper, France Supervisor Dr. Christian STEINBERG INRA, Dijon, France Supervisor 3 La science ouvre à l'esprit humain une voie infinie, et le lance, par une série d'étapes sans nombre, sur l'Asymptote de la Vérité. Paul Bert (1933 – 1986) 5 Remerciements Voila 3 ans et demi que ce travail a commencé; 3 ans et demi de recherche, de tâtonnements et de découvertes. Je tiens à remercier toutes celles et ceux qui ont pris part à cette aventure. Je veux remercier tout d'abord Germicopa - Eric Bargy, son président directeur général et Eric Bonnel, directeur de la recherche -, Bretagne Plants, particulièrement Emmanuel Guillery, son directeur, la Région Bretagne et l'ANRT pour avoir accepté de financer ce projet. Je remercie Philippe Lemanceau, directeur de l'UMR MSE de l'INRA de Dijon pour m'y avoir accueillie. Je tiens à remercier les membres du jury. Monica Höfte, Jean-Loup Notteghem et Andreas Keiser qui ont accepté d'être les rapporteurs de ce travail, je leur en suis très reconnaissante. Merci également à Daniel Wipf pour sa participation en tant qu'examinateur. Ma reconnaissance va également aux membres du comité de pilotage de cette thèse qui ont accepté de passer de longues heures à réfléchir, discuter et débattre sur les travaux effectués et à venir. Safya Menasseri, Claire Campion et Emile Benizri ont apporté leurs points de vue variés et ont participé à la richesse de ce travail. Merci Un immense merci à Catherine Chatot, pour l'énergie dépensée sans compter à la mise en place et à l'exécution de ce projet et pour sa disponibilité malgré l'éloignement (Dijon – Châteauneuf du Faou, 800 km, c'était pas gagné). Merci de m'avoir fait découvrir "le monde de la patate" depuis le processus de création de nouvelles variétés jusqu'au tri des pommes de terre par laser (impressionnant!), et de m'avoir permis de participer à de nombreux congrès en France et à l'étranger dans lesquels j'ai pu partager mon expérience de recherche. Merci à Yves Le Hingrat, pour le temps qu'il à consacré à ce projet, ses conseils et les informations précieuses que avons échangées. Je suis également reconnaissante à toutes les personnes de Germicopa et Bretagne Plants qui ont participé de près ou de loin à ce travail: Jean-Yves Abgrall, Gisèle Hemery, Jean Marhic, Robert Roudaut et Yvon Pouliquen et les producteurs de pommes de terre qui m'ont fourni des échantillons, en particulier Jean Marc Guillermic qui a mis une de ses parcelles à ma disposition pour effectuer des prélèvements. Je voudrais aussi dire un grand merci à Karima Bouchek-Mechiche qui a toujours été présente lorsque je lui demandais un conseil ou un service. Je me souviens de l'épisode "recette de cuisine" lorsqu'elle m'a montré comment isoler des 7 Remerciements Streptomyces. Merci aussi pour les bons moments passés en congrès avec toute la clique de l'INRA du Rheu. Je n'oublie pas non plus Sonia Hallier et Katie Craddock de BBV, qui travaillent sur la même problématique que moi et avec qui les échanges ont été fructueux. Ce n'est pas sans un peu d'émotion que je remercie les personnes de l'INRA de Dijon avec qui j'ai travaillé au quotidien. Christian Steinberg qui, malgré un emploi du temps impressionnant, a toujours été là quand j'avais besoin. Merci pour les discussions mensuelles où les cerveaux fumaient, pour les idées qui fusent dans ta tête et pour ta générosité. Merci aussi pour les petits moments de détente au détour d'un couloir où tu me racontais tes exploits sportifs… Véronique Edel-Hermann, Véro. Elle aussi a été un pilier de ce travail. Toujours partante pour se triturer les méninges et trouver de nouvelles idées pour faire avancer le schmilblick, elle a fait preuve d'une incroyable méticulosité quand il s'agissait d'analyser des données ou de corriger les articles. Je veux te dire toute ma reconnaissance. Merci d'avoir repris toutes mes séquences d'ITS et merci pour ton acharnement à faire "parler" les données d'AFLP. La science est parfois coriace, mais travailler avec toi a été un plaisir. Claude Alabouvette a été à l'origine de la venue de ce projet à Dijon et je l'en remercie. Claude appartient à une espèce de chercheur en voie de disparition, phytopathologiste véritable à l'œil critique développé, d'une grande ouverture d'esprit et un brin rebelle. Tous les labos devraient avoir un Claude! Nadine Gautheron a été mon guide, dès le début quand j'ai débarqué un peu perdue au milieu du laboratoire. Elle m'a appris toutes les techniques et les habitudes du labo. Merci pour le travail que tu as fait sur la T-RFLP. Je te dois une grosse partie du chapitre 4 de cette thèse. Merci aussi, Nad, pour les apéros, les week-ends au ski, tes conseils spectacle et ciné et les discussions à la pause café. Cécile Héraud a également beaucoup donné pour ce travail. Elle a chouchouté et mis en collection les centaines de souches de champignons et de bactéries que j'ai isolées et elle s'est cassé les dents sur la mise au point des PCR de facteur d'élongation Rhizo, toujours avec grand professionnalisme et beaucoup (trop?) de discrétion. Merci beaucoup Cécile. Abel Yanougo Konate a été mon stagiaire pendant une année. Le climat français n'a pas été tendre avec lui et le soleil burkinabé lui a sûrement manqué plus d'une fois, et je le remercie pour le travail qu'il a fourni pendant son passage au labo. Ce travail doit également beaucoup à Barbara Burakowski pour la préparation des milieux, les autoclaves et pour le matériel, toujours propre et à sa place, à Bernard Le Bihan, responsable informatique râleur mais efficace, à Delphine Ramillon et Sébastien Brenot qui veillent sur les essais en serre et à Arnaud Bartet qui m'a appris le maniement de la perceuse à cloche! Merci également à toutes les 8 Remerciements secrétaires, Catherine, Fabienne, Sylvie et Stéphanie pour leur efficacité et leur bonne humeur. Je voudrais remercier aussi l'équipe 3, Sébastien Aimé pour ses petites blagues au café, Fabiola Bastian, gracias Mamita pour ton grain de folie, bisoutitos ti!, Elodie Gautheron, pour les petites pauses quand mon bureau se trouvait sur son chemin, Johann Leplat, Julie Laurent et Marion Bégin; Grégory Girardot qui a partagé mon bureau pendant son stage. Un merci particulier à Chantal Olivain pour m'avoir fait confiance pour donner des TP à l'IUT de Génie Biologique. Ce fut une expérience très enrichissante. La vie au labo aurait été moins drôle sans Céline Janvier, ma "maîtresse" de stage du tout début qui m'a appris beaucoup et avec qui on a vraiment bien rigolé. Merci à tous les stagiaires, thésards et permanents, Abdel, Amandine, Noémie, Mélanie, Sam, Fafa, Thérèse, Francky, Florence, pour les déjeuners à la cantine et les sorties le week-end. Enfin merci à tous ceux qui comptent pour moi, tous mes amis, en particulier les Boubous dont j'ai fait la connaissance au milieu de ma thèse et avec qui les mardi soirs et les week-ends n'ont plus jamais été comme avant. Merci à ma famille, mes parents et ma sœur que j'aime.
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