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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 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 U.F.R. Sciences & Technologies IFR 110 Génomique, Ecophysiologie et Ecologie E.D. Ressources, Procédés, Produits et Fonctionnelle Environnement Unité Mixte de Recherche INRA/UL-1136 Biologie Végétale et Forestière Interactions Arbres-Microorganismes Thèse Présentée pour l'obtention du titre de Docteur de l'Université de Lorraine en Biologie Végétale et Forestière par MATHIEU Yann Diversité écologique et fonctionnelle des champignons décomposeurs du bois : l’influence du substrat de la communauté à l’enzyme. Soutenance publique prévue le 11 Décembre 2012 Membres du jury : Rapporteurs : Eric RECORD, Directeur de Recherche, INRA Jean-François COLLET, Professeur, Université Catholique de Louvain Examinateurs : Gaétan LE FLOCH, Maître de Conférences, Université de Bretagne Occidentale Pierre-Emmanuel COURTY, Research Associate, Université de Bâle Philippe GERARDIN, Professeur, Université de Lorraine Eric GELHAYE, Professeur, Université de Lorraine, Directeur de Thèse Invités : Marc BUEE, Chargé de Recherche, INRA, Co-directeur de Thèse Luc HARVENGT, Responsable Scientifique Biotech, FCBA, Co-directeur de Thèse Mélanie Morel, Maître de Conférences, Université de Lorraine Claude DIDIERJEAN, Maître de Conférences, Université de Lorraine La Science est fille de l’étonnement. REMERCIEMENTS Je tiens d’abord à remercier les membres du jury, Eric Record, Jean-François Collet, Gaétan Le-Floch, Pierre Emmanuel Courty et Philippe Gérardin pour avoir accepté de lire ce manuscrit et d’évaluer mes travaux de thèse. Je voudrais également remercier les personnes qui ont collaboré avec moi sur ces travaux, Mélanie Morel et Claude Didierjean, notamment pour les conseils de rédaction des différents articles ainsi que pour leur disponibilité. Je remercie ensuite mes « nombreux » directeurs de thèse Eric, Marc et Luc pour la confiance et la grande autonomie qu’ils m’ont accordées durant ces trois années de doctorat et surtout pour leur disponibilité au jour le jour que ce soit pour des questions pratiques et surtout scientifiques, mais également pour leur patience, leurs encourgaments et leur bonne humeur qui sont des qualités rares. Je remercie particulièrement Nico qui malgré mon arrivée en retard systématique à ses cours (surtout à 8h00) m’a quand même orienté vers cette bourse de thèse. Enfin une dédicace spéciale à Jean Pierre qui a marqué à jamais ma vision de l’enseignement supérieur ! Je voudrais ensuite remercier les personnes avec qui j’ai partagé un de mes multiples bureaux : Edgar pour ta gay attitude, ta curiosité musicale et ton gardiennage de chat, Benjy pour tes blagues douteuses sur les curés et les petits enfants, Anne pour la touche de féminité apportée au bureau, PA pour ta gentillesse et tes remarques souvent à coté de la plaque, Stéphane pour ta culture métal et le petit Grégory, Vincent (le bucheron) pour ton humour douteux et les bières partagées, Nicolas pour ton régime alimentaire digne d’un extra terrestre et Cendrella pour ta culture geek et cinématographique. J’aimerai aussi remercier les personnes avec qui j’ai pu échanger sur tout et n’importe quoi durant ces années : Arnaud, Kamel, Jérémy, Tiphaine, Antoine, Henri (à toi d’assurer la relève !), Andrew, Seb, Ben, Béatrice, JB, Emeline, PJ, Christine, Jean-Louis, Cyrille, Manue, Annegret, Francis, Yohann, Aude, Adeline, Alice, Sara, Juliette, Jaime, Pete, Bruno (aka vomito), Patrice, Emilie, Angela, Claude, Aurore, Stéphane, Claire, Valérie, Aurélie, Agnès, et les nombreux stagiaires. Au cas où j’oublierai quelqu’un je remercie tout simplement toutes les personnes avec lesquelles j’ai interagi durant ces trois dernières années. Pour finir j’adresse un énorme merci à mes parents et ma soeur qui grâce à leur patience, leur soutien moral et surtout financier, m’ont permis de mener à bout mes études dans d’excellentes conditions pour un domaine qui me passionne. Enfin, j’adresse également un énorme merci à celle qui partage ma vie depuis bientôt cinq ans : Caroline. Merci d’avoir supporté cette période délicate de fin de thèse où j’ai passé plus de temps collé à mon écran qu’à toi, merci pour tes encouragements quand le moral n’était pas présent, et je te remercie d’avance pour la patience dont tu feras preuve lors de mes multiples répétitions de l’oral à venir… Merci également pour tout ce que tu m’apportes quotidiennement. Pour toutes ces raisons, je te dédicace ce travail. Abréviations 2,5-DMHQ : 2,5-diméthoxyhydroquinone H : p-hydroxyphényl AAO : aryl-alcool oxydase HAP : hydrocarbure aromatique ABTS : 2,2’-azinobis-(3-ethylbenzthiazoline- polycyclique 6-sulfonate) HBT : 1-hydroxybenzotriazole ADN : acide désoxyribonucléique HCCA : 2-hydroxychromène-2-carboxylate ANS : 8-anilino-1-napthalenesulfonic acid ITS : Internal Transcribed Spacer ARN : acide ribonucléique kDA : kilodalton ARNm : ARN messaGer LiP : pour lignin peroxydase ARNr : ARN ribosomique MnP : pour manGanese peroxydase ATP : adénosine triphosphate MID : Multiplex IDentifier CAZy : pour Carbohydrate Active enZyme ML : Lamelle moyenne CBH : cellobiohydrolase MOTU : pour molecular operational CBM : pour cellulose bindinG domain taxonomic units CDH : cellobiose déshydroGénase MUA : 4-Methylumbelliferyl acétate CE : pour carbohydrate esterase NADP(H) : nicotinamide adénine CLIC : pour chloride intracellular channel dinucléotide phosphate COA : analyse de correspondance PMO : monooxyGénase de polysaccharides DGGE : Electrophorèse sur gel en gradient POD : pyranose-2-oxydase dénaturant (T)RFLP : Polymorphisme de lonGueur des DHAR : pour dehydroascorbate reductase fraGments de restriction (terminaux) Dsb : pour disulfide bond protein S : syrinGyle ECM : ectomycorhizien TGGE : Electrophorèse sur gel en gradient EG : endoGlucanase de température FAD : flavine adénine dinucléotide TRX : thiorédoxine G : guaiacyle VP : pour versatile peroxydase GH : pour glycoside hydrolase GOx : glyoxal oxydase GRX : glutarédoxine GST : glutathion S-transférase GSH : glutathion GTE : pour glutathione transferase etherase like GTO : glutathion transférase OméGa Table des matières 2 Table des matières TABLE DES MATIERES 1 INTRODUCTION 7 ANALYSE BIBLIOGRAPHIQUE 11 1) DIVERSITE DE LA COMPOSITION STRUCTURALE ET CHIMIQUE DU BOIS 13 1.A) FORMATION ET COMPOSITION DU BOIS .............................................................................................. 13 1.A.I) ANATOMIE ET ORGANISATION CELLULAIRE DU BOIS ...................................................................................... 13 1.A.II) COMPOSITION CHIMIQUE DU BOIS .................................................................................................................... 16 1.B) SUBSTANCES MACROMOLECULAIRES ................................................................................................... 16 1.B.I) LA CELLULOSE ........................................................................................................................................................ 16 1.B.II) LES HEMICELLULOSES ......................................................................................................................................... 18 1.B.III) LA LIGNINE .......................................................................................................................................................... 20 1.C) SUBSTANCES DE FAIBLE POIDS MOLECULAIRE .................................................................................... 22 1.C.I) LES EXTRACTIBLES ................................................................................................................................................ 22 1.C.II) TERPENES ET TERPENOÏDES .............................................................................................................................. 22 1.C.III) COMPOSES PHENOLIQUES ................................................................................................................................. 23 1.C.IV) LES INERTES ........................................................................................................................................................ 25 2) DIVERSITE DES MICROORGANISMES SAPROPHYTES 26 2.A) MOISISSURES (« MOULDS ») ET AGENTS DE BLEUISSEMENT (« BLUE STAIN ») .............................. 29 2.B) LES AGENTS DE POURRITURE MOLLE (« SOFT ROT ») ....................................................................... 29 2.C) LES AGENTS DE POURRITURE BRUNE (« BROWN ROT ») ................................................................... 30 2.D) LES AGENTS DE POURRITURE BLANCHE (« WHITE ROT ») ............................................................... 31 3) DIVERSITE DES SYSTEMES ENZYMATIQUES IMPLIQUES DANS LA DECOMPOSITION DU BOIS : 34 3.A) DEGRADATION DE LA CELLULOSE ........................................................................................................ 36 3.A.I) DEGRADATION
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