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Richesse Et Diversité Des Assemblages De Champignons Et D Richesse et diversité des assemblages de champignons et d’oomycètes de hêtraies, en relation avec des facteurs climatiques et édaphiques : de la parcelle au continent Aurore Coince To cite this version: Aurore Coince. Richesse et diversité des assemblages de champignons et d’oomycètes de hêtraies, en relation avec des facteurs climatiques et édaphiques : de la parcelle au continent. Sylviculture, foresterie. Université de Lorraine, 2013. Français. NNT : 2013LORR0177. tel-02809009v2 HAL Id: tel-02809009 https://hal.univ-lorraine.fr/tel-02809009v2 Submitted on 29 Mar 2018 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. 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 Collegium Sciences et Technologies Institut National de la Recherche Agronomique Ecole Doctorale Ressources Procédés Produits Environnement Thèse présentée pour l’obtention du titre de Docteur de l’Université de Lorraine en Biologie Végétale et Forestière par Aurore Coince RICHESSE ET DIVERSITé DES ASSEMBLAGES DE CHAMPIGNONS ET D'OOMYCèTES DE HêTRAIES, EN RELATION AVEC DES FACTEURS CLIMATIQUES ET éDAPHIQUES : DE LA PARCELLE AU CONTINENT Soutenance publique le 3 octobre 2013 Membres du jury : Pr. Monique Gardes Professeur, Université Paul Sabatier, Toulouse Rapporteur Dr. Roberto Geremia Directeur de Recherches, CNRS, Grenoble Rapporteur Dr. Lionel Ranjard Directeur de Recherches, INRA, Dijon Examinateur Pr. Eric Gelhaye Professeur, Université de Lorraine, Nancy Examinateur Dr. Benoît Marçais Directeur de Recherche, INRA, Nancy Directeur de thèse Dr. Marc Buée Chargé de Recherche, INRA, Nancy Co-directeur de thèse UMR INRA/Université de Lorraine Interactions Arbres-Microorganismes Ecologie des champignons pathogènes forestiers & Ecogénomique des interactions Centre INRA de Champenoux – 54280 Champenoux … « De sorte que toute la suite des hommes, pendant le cours de tant de siècles, doit être considérée comme un m ême homme qui subsiste toujours et qui apprend continuellement … » Pascal, Préface au Traité du Vide … Je, soussignée Aurore Coince, déclare avoir écrit ce manuscrit et porter l’entière responsabilité des erreurs ou oublis qui pourraient subsister malgré les relectures. Aurore Coince 2 TABLES DES MATIERES PROBLEMATIQUE ET OBJECTIFS ..................................................................................... 6 INTRODUCTION ..................................................................................................................... 9 1. Les communautés microbiennes eucaryotes telluriques forestières .................................... 9 1.1. Définitions et concepts ......................................................................................................... 9 1.2. Fonctions écosystémiques et rôle structurant .................................................................. 10 1.2.1. Participation aux cycles biogéochimiques ................................................................... 10 1.2.2. Structuration des communautés végétales .................................................................. 11 1.3. Caractéristiques générales ................................................................................................ 13 1.3.1. Les différentes formes morphologiques et mode de vie .............................................. 13 1.3.2. Les différents groupes taxonomiques ........................................................................... 15 1.4. Diversité .............................................................................................................................. 16 1.4.1. Concepts ......................................................................................................................... 16 1.4.2. La diversité en chiffres .................................................................................................. 17 1.4.3. Maintien de la diversité ................................................................................................. 17 2. Méthodes et outils de description des communautés microbiennes ................................... 19 2.1. Problématique de l’échantillonnage ................................................................................. 19 2.1.1. Le grain ........................................................................................................................... 19 2.1.2. L’intervalle et l’étendue ................................................................................................ 20 2.2. Méthodes de détection et de caractérisation .................................................................... 21 2.2.1. Les méthodes non-moléculaires .................................................................................... 21 2.2.2. Les bases des méthodes moléculaires ........................................................................... 23 2.2.3. Les méthodes d’analyse moléculaire ............................................................................ 25 2.3. Atouts et défis de l’analyse haut-débit d’amplicons ........................................................ 27 2.3.1. Les atouts ........................................................................................................................ 27 2.3.2. Les limitations ................................................................................................................ 28 3. Distribution et facteurs de structuration des communautés eucaryotes telluriques forestières ......................................................................................................................................... 31 3.1. Hétérogénéité spatiale et temporelle ................................................................................ 32 3.1.1. Structure verticale ......................................................................................................... 32 3.1.2. Structure horizontale .................................................................................................... 33 3.1.3. Structure le long de gradients environnementaux ...................................................... 33 3.2. Structuration par les facteurs biotiques ........................................................................... 36 3.3. Structuration par les facteurs édaphiques ....................................................................... 38 3.4. Structuration par les facteurs climatiques ....................................................................... 40 DEMARCHE EXPERIMENTALE ........................................................................................ 42 3 CHAPITRE I. ETUDE PILOTE A L’ECHELLE LOCALE D’UNE PARCELLE ............. 47 1. Problématique ......................................................................................................................... 47 2. Méthodologie ........................................................................................................................... 47 3. Résultats .................................................................................................................................. 49 CHAPITRE II. DIVERSITE ET STRUCTURE DES COMMUNAUTES FONGIQUES LE LONG DE GRADIENTS D’ALTITUDE ............................................................................... 50 1. Problématique ......................................................................................................................... 50 2. Méthodologie ........................................................................................................................... 50 3. Résultats .................................................................................................................................. 52 CHAPITRE III. DIVERSITE ET STRUCTURE DES COMMUNAUTES FONGIQUES ET OOMYCETES LE LONG D’UN GRADIENT LATITUDINAL EUROPEEN .............. 54 1. Problématique ......................................................................................................................... 54 2. Méthodologie ........................................................................................................................... 54 3. Résultats .................................................................................................................................. 55 DISCUSSION .......................................................................................................................... 74 1. Stratégie d’échantillonnage
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