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DDOC T 2019 0072 LEGEAY.Pdf AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D'autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale. Contact : [email protected] LIENS Code de la Propriété Intellectuelle. articles L 122. 4 Code de la Propriété Intellectuelle. articles L 335.2- L 335.10 http://www.cfcopies.com/V2/leg/leg_droi.php http://www.culture.gouv.fr/culture/infos-pratiques/droits/protection.htm Ecole Doctorale SIReNa (Sciences et Ingénierie des Ressources Naturelles) Thèse Présentée et soutenue publiquement pour l’obtention du titre de Docteur de l’Université de Lorraine Mention : « Biologie et écologie des forêts et des agrosystèmes » Thèse soutenue le 21/06/2019 Par Jean Legeay Ecologie des Oomycètes et champignons phytopathogènes dans les sols de forêt de Guyane Française : éclairages sur les relations entre communautés de Phytophthora et d’arbres dans les forêts tropicales Rapporteurs : Mme Cécile ROBIN, DR, UMR Biogeco, Bordeaux Mr Christian STEINBERG, DR, UMR Agroécologie, Dijon Examinateurs : Mr Renaud IOOS, DR, ANSES, Nancy Mme Lucie VINCENOT, MC, Laboratoire Ecodiv, Rouen Directeur de thèse : Marc BUEE, DR, UMR IAM, Nancy Co-directeur de thèse : Benoît MARCAIS, DR, UMR IAM, Nancy UMR INRA/Université de Lorraine Interactions Arbres-Microorganismes Ecologie des champignons pathogènes forestiers & Ecogénomique des interactions Rue d’Amance – 54280 Champenoux Remerciements Je remercie Benoît, Marc et Claude de m’avoir choisi pour cette thèse et pour leur accompagnement et patience pendant ces trois ans. Je remercie les membres du jury Cécile, Christian, Lucie et Renaud d’avoir accepté d’examiner mon travail. Ma reconnaissance à Olivier pour sa participation aux travaux de Guyane, à Anaïs pour son aide sur la paillasse, et à Emmanuelle qui a accompli tout le traitement de données de NGS ; ainsi qu’à tout les gens qui m’ont aidé et accueilli à Kourou : Jocelyn, Eliane, Heidy et Stéphane. Enfin, un grand merci à l’équipe patho toute entière qui m’a hébergé et nourri en sucreries pendant trois ans. Table des matières Introduction ........................................................................................................................... 1 Les forêts tropicales, haut lieude diversité ....................................................................... 2 L’écosystème forestier tropical .................................................................................... 2 Les forêts néo-tropicales : forêts tropicales d’Amériquedu Sud .................................. 2 Diversité microbienne desforêts tropicales .................................................................. 3 Hypothèses explicatives dela diversité ........................................................................ 3 Hypothèse Janzen-Connell et ses agents ........................................................................... 4 L’hypothèse Janzen-Connell pour expliquer le maintien de la diversité en forêts néo-tropicales .............................................................................................................. 4 Prérequis de l’hypothèse Janzen-Connell .................................................................... 7 Mécanismes de type Janzen-Connell etfeedbacks négatifs ......................................... 6 Les organismes acteurs des mécanismes detype Janzen-Connell ................................ 6 Les feedback positifs : mycorhizes et organismes suppresseursdes pathogènes ......... 8 Les Oomycètes, acteurs potentiels des mécanismes detype Janzen-Connell .................... 9 Biologie des Oomycètes .............................................................................................. 9 Etude des communautés d’Oomycètespar piégeage/isolation ..................................... 11 Etude des communautés d’Oomycètes par metabarcodingde l’ITS ............................ 12 Limites de l’ITS etmarqueurs alternatifs ..................................................................... 13 Etat des connaissances sur les communautés d’Oomycètes en milieu naturel ................... 14 Communautés des Phytophthora dans les latitudes tempéréeset boréales ................... 14 Communautés des Pythium dans les latitudes tempéréeset boréales ........................... 15 Communautés de Phytophthora et Pythium dans lesforêts tropicales ......................... 16 Spécificité à l’hôtedes Oomycètes ............................................................................... 17 Les pathogènes fongiques, autres acteurs potentiels du maintiendela diversité ................ 18 Les pathogènes fongiques dans lesforêts tropicales..................................................... 18 Difficultés de la distinction endophyte/pathogènechezles Fungi ................................. 19 Objectifs de la thèse .......................................................................................................... 20 Méthodologie .................................................................................................................... 21 Sites étudiés ................................................................................................................. 21 Echantillonnage du sol ................................................................................................. 21 Piégeage/isolement ...................................................................................................... 22 Metabarcoding .............................................................................................................. 23 Chapitre 1 .............................................................................................................................. 27 Abstract ............................................................................................................................ 30 Chapitre 2 .............................................................................................................................. 34 Abstract ............................................................................................................................ 38 Introduction ...................................................................................................................... 39 Matériel & méthode .......................................................................................................... 42 Sampling and location description ............................................................................... 42 Baiting and isolation .................................................................................................... 42 Phylogenetic analysis of isolates ................................................................................. 43 Metabarcoding and Illumina Miseq sequencing .......................................................... 43 Bioinformatics analysis ............................................................................................... 44 Data analysis ................................................................................................................ 44 Résultats ........................................................................................................................... 45 Phytophthora diversity uncovered by baiting & isolation ............................................ 45 Phylogenetic analysis of isolates .................................................................................. 46 Metabarcoding approach and comparisonwith baiting/isolation .................................. 46 Community structure analysis ...................................................................................... 47 Discussion ........................................................................................................................ 48 Chapitre 3 .............................................................................................................................. 64 Abstract ............................................................................................................................ 68 Introduction ...................................................................................................................... 69 Matériel & méthode .......................................................................................................... 72 Sites and sampling ........................................................................................................ 72 DNA extraction and PCR amplicon pyrosequencing.................................................... 73 Bioinformatics Analysis for oomycetes Miseq reads ................................................... 73 Extraction of pathogenic fungi communities data ........................................................ 75 Résultats ........................................................................................................................... 75 Communities composition ........................................................................................... 75 Factors structuring the oomycete and fungalpathogens communities .......................... 76 Discussion ......................................................................................................................... 77 Chapitre
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