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Phytostimulation Du Maïs Par La Bactérie Azospirillum Lipoferum CRT1 : Impact Sur Des Communautés Fonctionnelles Du Microbiote Racinaire Sebastien Renoud

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Phytostimulation Du Maïs Par La Bactérie Azospirillum Lipoferum CRT1 : Impact Sur Des Communautés Fonctionnelles Du Microbiote Racinaire Sebastien Renoud Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : impact sur des communautés fonctionnelles du microbiote racinaire Sebastien Renoud To cite this version: Sebastien Renoud. Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : impact sur des communautés fonctionnelles du microbiote racinaire. Ecologie, Environnement. Université de Lyon, 2016. Français. NNT : 2016LYSE1143. tel-01433755 HAL Id: tel-01433755 https://tel.archives-ouvertes.fr/tel-01433755 Submitted on 13 Jan 2017 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. THESE DE DOCTORAT DE L’UNIVERSITE DE LYON opérée au sein de l’Université Claude Bernard Lyon 1 Ecole Doctorale N° 341 Evolution Ecosystèmes Microbiologie Modélisation Spécialité de doctorat : Ecologie Microbienne Discipline : Biologie N° d’ordre NNT : 2016LYSE1143 Soutenue publiquement le 12 Septembre 2016 par : Sébastien RENOUD Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : Impact sur des communautés fonctionnelles du microbiote racinaire. Devant le jury composé de : ARSENE-PLOETZE Florence, Maître de conférences, Université de Strasbourg Rapporteur SPAEPEN Stijn, Chercheur, Institut Max Planck de Cologne Rapporteur VANDENKOORNHUYSE Philippe, Professeur, Université Rennes 1 Rapporteur RICHAUME-JOLION Agnès, Professeur, Université Lyon 1 Examinatrice MOËNNE-LOCCOZ Yvan, Professeur, Université Lyon 1 Co-directeur de thèse MULLER Daniel, Maître de conférences, Université Lyon 1 Directeur de thèse UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M. le Professeur Frédéric FLEURY Président du Conseil Académique M. le Professeur Hamda BEN HADID Vice-président du Conseil d’Administration M. le Professeur Didier REVEL Vice-président du Conseil Formation et Vie Universitaire M. le Professeur Philippe CHEVALIER Vice-président de la Commission Recherche M. Fabrice VALLÉE Directeur Général des Services M. Alain HELLEU COMPOSANTES SANTE Faculté de Médecine Lyon Est – Claude Bernard Directeur : M. le Professeur J. ETIENNE Faculté de Médecine et de Maïeutique Lyon Sud – Charles Directeur : Mme la Professeure C. BURILLON Mérieux Directeur : M. le Professeur D. BOURGEOIS Faculté d’Odontologie Directeur : Mme la Professeure C. Institut des Sciences Pharmaceutiques et Biologiques VINCIGUERRA Institut des Sciences et Techniques de la Réadaptation Directeur : M. le Professeur Y. MATILLON Département de formation et Centre de Recherche en Directeur : Mme la Professeure A-M. SCHOTT Biologie Humaine COMPOSANTES ET DEPARTEMENTS DE SCIENCES ET TECHNOLOGIE Faculté des Sciences et Technologies Directeur : M. F. DE MARCHI Département Biologie Directeur : M. le Professeur F. THEVENARD Département Chimie Biochimie Directeur : Mme C. FELIX Département GEP Directeur : M. Hassan HAMMOURI Département Informatique Directeur : M. le Professeur S. AKKOUCHE Département Mathématiques Directeur : M. le Professeur G. TOMANOV Département Mécanique Directeur : M. le Professeur H. BEN HADID Département Physique Directeur : M. le Professeur J-C PLENET UFR Sciences et Techniques des Activités Physiques et Directeur : M. Y.VANPOULLE Sportives Directeur : M. B. GUIDERDONI Observatoire des Sciences de l’Univers de Lyon Directeur : M. le Professeur E.PERRIN Polytech Lyon Directeur : M. G. PIGNAULT Ecole Supérieure de Chimie Physique Electronique Directeur : M. le Professeur C. VITON Institut Universitaire de Technologie de Lyon 1 Directeur : M. le Professeur A. MOUGNIOTTE Ecole Supérieure du Professorat et de l’Education Directeur : M. N. LEBOISNE Institut de Science Financière et d'Assurances Phytostimulation du maïs par la bactérie Azospirillum lipoferum CRT1 : Impact sur des communautés fonctionnelles du microbiote racinaire Résumé Le développement des plantes est conditionné par leurs interactions avec le microbiote racinaire, dont le fonctionnement repose sur des fonctions élémentaires partagées par plusieurs taxons, au sein de groupes fonctionnels. Certains de ces groupes incluent des PGPR (Plant Growth-Promoting Rhizobacteria), qui stimulent la croissance des plantes grâce à différentes fonctions phytobénéfiques. L’inoculation d’une PGPR peut avoir un impact sur la physiologie de la plante et sur les autres partenaires microbiens de la racine. D’ailleurs, une PGPR inoculée peut modifier la structure génétique du microbiote racinaire global, sans que l’on sache comment cet impact se concrétise au niveau de groupes fonctionnels particuliers. L’hypothèse de cette thèse est que les PGPR inoculées peuvent modifier la structure de communautés microbiennes fonctionnelles importantes pour le développement de la plante. Ces travaux ont évalué l’impact de l’inoculation de la PGPR Azospirillum lipoferum CRT1 sur la taille et/ou la diversité des diazotrophes, des producteurs d’1-aminocyclopropane-1-carboxylate (ACC) désaminase et des producteurs de 2,4-diacétylphloroglucinol (ainsi que de la communauté bactérienne totale) dans la rhizosphère du maïs cultivé en champ sous différents intrants azotés. Nos travaux ont montré que diazotrophes et producteurs d’ACC désaminase pouvaient être co- sélectionnés dans la rhizosphère du maïs, et que l’inoculation modifiait la composition taxonomique de ces groupes fonctionnels. En conclusion, l’inoculation de PGPR module la sélection rhizosphérique de taxons telluriques portant des fonctions phytobénéfiques, ce qui pourrait contribuer aux effets phytobénéfiques observés. Phytostimulation of maize by the bacterium Azospirillum lipoferum CRT1: Impact on functional communities in the root microbiota Summary Plant development is influenced by interactions established with root microbiota. Microbiota functioning relies on individual functions carried out by functional groups, which often contain multiple microbial taxa. Some of these groups include plant growth-promoting rhizobacteria (PGPR), which stimulate plant growth thanks to several plant-beneficial functions. PGPR inoculation may impact plant physiology and microbial partners of roots, and inoculated PGPR can modify the genetic structure of the root microbiota. However, it is not known how this impact materializes at the level of particular microbial functional groups. The hypothesis of this thesis is that inoculated PGPR will also modify the structure/composition of microbial functional groups important for plant development. This work assessed the impact of inoculation with the PGPR Azospirillum lipoferum CRT1 on the size and/or diversity of diazotrophs, 1-aminocyclopropane-1-carboxylate (ACC) deaminase producers and 2,4- diacetylphloroglucinol producers (as well as the total bacterial community) colonizing the maize rhizosphere in three fields and under different nitrogen fertilization regimes. Our work showed that diazotrophs and ACC deaminase producers could be co-selected in maize rhizosphere and that PGPR inoculation modified the taxonomic composition of functional groups. To conclude, PGPR inoculation modulates rhizospheric selection of microbial members of functional groups important for plant growth, which may mediate some of the plant- beneficial effects of PGPR inoculants. Remerciements Tout d’abord, je tiens à remercier Florence ARSENE-PLOETZE, Stijn SPAEPEN et Philippe VANDENKOORNHUYSE d’avoir accepté d’évaluer ces travaux de these, ainsi qu’Agnès RICHAUME-JOLION de s’être joint à eux pour constistuer mon jury de these. Mes premiers remerciements s’adressent bien sûr à mes directeurs de thèse Daniel MULLER et Yvan Moënne-Loccoz sans qui ces travaux n’auraient pas pu avoir lieu. Yvan, même si nous ne sommes pas toujours d’accord sur la façon d’aborder les choses, j’ai énormément de respect pour toi et tes qualités scientifiques mais aussi pour le bourreau de travail que tu es. Daniel, merci pour ton soutien tout au long de ces 3 années difficiles, pour ces discussions sur tout et parfois n’importe quoi, il faut bien dire que l’on a pas toujours parlé de science! Merci pour tes anecdotes historiques que seul toi peux nous sortir inopinément au milieu d’une conversation, preuve de ta grande culture générale. Dois-je te remercier pour tes jeux de mots et blagues douteuses? Sans doute, mais je trouve que tu as eu une mauvaise influence sur l’humour de mon cher collègue Vacheron!! Bref, à votre contact à tous les deux je suis sans nul doute devenu un scientifique plus complet et je vous en remercie. J’èspère avoir répondu à vos attentes lors de ces travaux. D’ailleurs ne croyez pas que c’est fini, il faut publier ces travaux maintenant! Je n’oublie pas ma chef d’équipe et co-encadrante Claire PRIGENT-COMBARET pour son soutien pendant ces 3 années, pour son implication dans la vie et l’ambiance de l’équipe afin de favoriser un travail collaboratif. J’espère que tu arriveras à democratiser l’OwnCloud, le partage des protocoles et la gestion des stocks, ça ne sera pas facile! Merci de m’avoir fait participer à SymbioMaize et de souvent être à l’écoute des étudiants de ton équipe. Par contre il faut arrêter de prendre des Jordan dans l’équipe parce que sinon faudra en changer le numéro et devenir l’équipe
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