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Phenotypic and Molecular Responses of Rice to Burkholderia S.L. Species Eoghan King

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Phenotypic and Molecular Responses of Rice to Burkholderia S.L. Species Eoghan King Phenotypic and molecular responses of rice to Burkholderia s.l. species Eoghan King To cite this version: Eoghan King. Phenotypic and molecular responses of rice to Burkholderia s.l. species. Vegetal Biology. Université Montpellier, 2019. English. NNT : 2019MONTG079. tel-02611007 HAL Id: tel-02611007 https://tel.archives-ouvertes.fr/tel-02611007 Submitted on 18 May 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. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Biologie des Systèmes École doctorale GAIA Unité de recherche UMR IPME Caractérisation phénotypique et moléculaire de la réponse du riz au c ours de l’ interaction avec des espèces de Burkholderia s.l. Présentée par Eoghan KING Le 11 décembre 2019 Sous la direction de Pierre CZERNIC et Lionel MOULIN RAPPORT DE GESTION Devant le jury composé de 2015 Matthieu ARLAT, Professeur des Universités, Université de Toulouse III – Paul Sabatier Rapporteur Alia DELLAGI, Professeure des Universités, AgroParisTech Rapportrice Sofie GOORMACHTIG, Professeure, VIB-UGent Examinatrice Michel LEBRUN, Professeur des Universités, Université de Montpellier Examinateur Pierre CZERNIC, Professeur des Universités, Université de Montpellier Directeur de thèse Lionel MOULIN, Directeur de Recherche, IRD Co-Directeur de thèse « Ceci est le véritable secret de la vie : Etre complètement engagé avec ce que vous faites dans l’ici et mainten ant. Et au lieu d’appeler cela travailler, réaliser que c’est jouer » Allan Watts Nous y voi là… La fameuse partie la plus lue d'une thèse, celle qui marque l’aboutissement de plusieurs années de travail, permet de se rappeler le chemin parcouru et les personnes sans qui rien de ce que j'ai accompli aux cours de ces années de thèse n'aurait été possible. On y va pour les remerciements ! Tout d'abord je me dois de remercier mes directeurs de thèse, Pierre et Lionel, pour votre confiance, vos encouragements et pour le pari que vous avez fait sur un dreadeux breton même pas padawan pour un sou il y a de cela presque 4 ans. Je remercie les membres de mon jury pour avoir accepté d'évaluer mes travaux. Mes rapporteurs, Alia Dellagi et Matthieu Arlat ainsi que mes examinateurs, Sofie Goormachtig et Michel Lebrun. Je remercie également les membres de mon comité de thèse, Jean-Benoît Morel, Florence Wisniewski- Dyé, Fabienne Cartieaux et Christophe Périn. Enfin, je remercie Valérie Verdier pour avoir accueilli mon projet au sein d'IPME Les remerciements d'usage étant fait-ce qui n'enlèvent rien à leur sincérité- je souhaite adresser à toutes les personnes qui suivent, un grand "MERCI": Aux collègues qui m'ont accueilli avec un sourire quand j'arrivais avec un service à demander, Florence, Sandrine, William, Emilie, Hervé À Gilles, pour ta vision critique et tes blagues douteuses À Agnieszka, pour nos échanges matinaux À Marine, pour avoir débroussaillé le chemin avant que je reprenne le flambeau du projet BRIO Aux chercheurs chevronnés qui se sont intéressés à mes travaux et m'ont permis de faire avancer ce projet, Stéphane, Antony, Christophe B et Sébastien À Isabelle, pour ta bienveillance et ton aide précieuse Aux étudiants et stagiaires que j'ai encadré, Harriet, Fehizoro, Patrick, Violette et Mathilde pour m’avoir fait découvrir ma capacité d’encadrement et de transfert de connaissances Aux anciens -et pas si anciens- PostDoc, Nils, Kévin, Daniel et Cindy pour vos conseils précieux À l'ancienne génération de thésards, Mathilde D, Cécile, Hélène, Rémi À mes brésiliennes préférées, Maìra et Deisy, pour votre folie À tous les stagiaires, doctorants, chercheurs du Sud croisés, Carlos, Diégane, Sondo, Kader, Hieu, Ngan, Ially pour avoir ouvert ma vision du monde étriquée d'occidental Aux "grumeaux du riz", Jérémy et Mathieu, pour vos brassages et nos discussions de couloirs À la nouvelle génération de thésards, Anne-So, Marlène, Théo PP, Leopol pour les bonnes tranches de rigolade Aux personnes qui ont partagés à un moment ou un autre mon bureau, merci de ne me pas m'avoir étranglé Aux membres du sandwich électronique, pour m'avoir sorti du monde du labo À ceux qui étaient toujours là, À mes super-nénettes, Lucile, Mathilde H, Helena et Marie, pour votre force, votre expérience, vos mots rassurants et vos encouragements À Adrian, pour trop de choses À Malo, pour tes mots, ta sagesse et nos échanges scientifiques tardifs À Thibault, pour ton amitié sans faille À ceux qui étaient plus loin, À ma métabande BZH, Elora, Ludo, Eliott, Morgane, Pilou, Pigi, Gigi À Marin, pour ce coup de téléphone dont je me souviendrai pour le restant de mes jours et l'exemple de résilience que tu incarnes dans ma vie À Théo LGLD, pour l'évidence de notre amitié À mes plus proches et fidèles soutiens, mes parents, pour votre confiance et votre amour À Maud, pour cette voie que tu as ouverte, ta compréhension de ce qu'elle implique et tes tapes occasionnelles derrière la tête. Et parce que si j'ai choisi cette voie c'est pour apporter ma pierre à l'avenir, c'est à tes enfants que je dédis ces travaux… À Louann et Romy SOMMAIRE Introduction générale .............................................................................................................. 1 Chapitre 1 Synthèse bibliographique Multicellular organisms as metaorganisms ............................................................................ 9 Animal and plant microbiome commonalities ....................................................................... 9 Plant microbiome specificities ............................................................................................. 11 Plant-associated microbial niches ........................................................................................ 13 Different types of plant-microbe interactions ...................................................................... 15 Plant-beneficial microbial interactions ................................................................................. 17 Main plant-mutualist models overview .................................................................... 17 Plant-microbe associative symbioses ....................................................................... 19 Plant-Growth promoting traits ............................................................................................. 21 The immune system of plants ............................................................................................... 27 The growth –defense trade-off in plants ............................................................................... 33 Commonalities in pathogenic and beneficial microbes interacting with plants ................... 35 Plant perception of pathogenic and beneficial microbes ...................................................... 35 Omics to unravel the complexity of plant-microbiome interactions .................................... 37 Review of transcriptomic responses of monocots to bacterial associative symbiosis .............................................................................................................................. 39 Applications of plant associative symbioses ........................................................................ 45 References ............................................................................................................................ 48 Table and figure references .................................................................................................. 61 Chapitre 2 Monitoring of rice transcriptional responses to contrasted colonizing patterns of phytobeneficial Burkholderia s.l. reveals a temporal shift in JA systemic response Introduction .......................................................................................................................... 68 Material & Methods ............................................................................................................. 70 Results .................................................................................................................................. 72 Analysis of root colonization .................................................................................... 72 Transcriptional response of rice to bacterial inoculation ......................................... 73 Validation of RNA-Seq data by qPCR ..................................................................... 87 Temporal analysis of strain-specific marker genes .................................................. 87 Discussion ............................................................................................................................ 95 References .......................................................................................................................... 101 Supplementary Material ..................................................................................................... 108 Chapitre 3 Transcriptomic response of rice to root colonization by the model endophyte Paraburkholderia phytofirmans PsJN Introduction .......................................................................................................................
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