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Discrimination Des Procédés De Transformation Post-Récolte Du Cacao Et Du Café Par Analyse Globale De L’Écologie Microbienne Yasmine Hamdouche

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Discrimination Des Procédés De Transformation Post-Récolte Du Cacao Et Du Café Par Analyse Globale De L’Écologie Microbienne Yasmine Hamdouche Discrimination des procédés de transformation post-récolte du Cacao et du Café par analyse globale de l’écologie microbienne Yasmine Hamdouche To cite this version: Yasmine Hamdouche. Discrimination des procédés de transformation post-récolte du Cacao et du Café par analyse globale de l’écologie microbienne. Sciences agricoles. Montpellier SupAgro, 2015. Français. NNT : 2015NSAM0014. tel-01404879 HAL Id: tel-01404879 https://tel.archives-ouvertes.fr/tel-01404879 Submitted on 29 Nov 2016 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. Délivré par le &HQWUH,QWHUQDWLRQDOG¶eWXGHV6XSpULHXUHV en Sciences Agronomiques Montpellier 3UpSDUpHDXVHLQGHO¶pFROHGRFWRUDOH Sciences des Procédés - Sciences des Aliments (WGHO¶8 nité Mixte de Recherche Qualisud Spécialité : Biotechnologie, Microbiologie Présentée par Yasmine HAMDOUCHE Discrimination des procédés de transformation post-récolte du Cacao et du Café SDUDQDO\VHJOREDOHGHO¶pFRORJLHPLFURELHQQH Soutenue le 22 Septembre 2015 devant le jury composé de : M. Didier MONTET, Dr, Cirad, Montpellier Directeur de thèse M. Jean-Christophe MEILE, Dr, Cirad, Montpellier Encadrant M. Rémy CACHON, Pr, AgroSup, Univ. de Président et Rapporteur Bourgogne, Dijon M. Pascal BONNARME, Dr, AgroParisTech Rapporteur INRA, Grignon Mme. Corinne TEYSSIER, Dr, Cirad, Univ. de Examinateur Montpellier M. Sévastianos ROUSSOS, DU ,5' 8QLY G¶$L[ Examinateur Marseille. Remerciements Je désire remercier grandement tous ceux qui m ¶RQW de près ou de loin, aidé à réaliser ce travail: Je voudrais tout G¶DERUG remercier la société HUBBARD en particulier M. Jean François HAMON pour le financement accordé durant ces trois ans de thèse. Je voudrais également UHPHUFLHUO¶8054XDOLVXGDX&,5$'GH0RQWSHOOLHUSRXUP¶DYRLUUHoXGDQVVHVODERUDWRLUHV Je remercie vivement mon directeur de thèse, Dr Didier MONTET, pour m'avoir accueillie au sein de son équipe et pour la confiance TX¶LO m ¶D témoignée en acceptant la direction scientifique de mes travaux. Je lui suis également reconnaissante pour le temps conséquent TX¶LO m¶D accordé, ses qualités pédagogiques et scientifiques, sa franchise, sa sympathie et son efficacité certaine que je Q¶RXEOLHUDLMD mais. -¶DL beaucoup appris à ses côtés et je lui adresse ma gratitude pour tout cela. -¶DGUHVVH de chaleureux remerciements à mon encadrant de thèse, Dr Jean Christophe MEILE pour son attention sur mes travaux, pour ses conseils avisés et son écoute qui ont été prépondérants pour la bonne réussite de cette thèse. Sa confiance a été un élément moteur pour moi. -¶DL pris un grand plaisir à travailler avec lui. Un grand merci à Mme Corinne TEYSSIER, maitre de conférence à O¶8QLYHUVLWp GH Montpellier de Q¶DYRLU jamais cessé de m ¶apporter son soutien moral. Je la remercie également G¶DYRLU FRQWULEXp grandement à la réalisation de ce travail et G¶DYRLU DFFHSWp G¶rWUH examinatrice. Je tiens à O¶DVVXUHU de ma profonde reconnaissance pour O¶LQWpUrW TX¶HOOH porte à ce travail. Je suis très honorée de la présence de mon jury de thèse et je tiens à remercier : M. Rémy CACHON, Professeur à Université de Bourgogne à Dijon pour O¶KRQQHXU TX¶LO P¶D fait pour sa participation à mon jury de thèse en tant que président et rapporteur. Je lui exprime ma profonde gratitude. M. Pascal BONNARME, directeur de recherche à INRA à Grignon pour sa participation en qualité de rapporteur de mon travail, pour le temps consacré à la lecture de cette thèse, pour ces remarques et suggestions à améliorer la qualité de ce mémoire, et je lui en suis très reconnaissante. M. Sevastianos ROUSSOS, Directeur de Recherche à O¶, RD à Marseille de O¶KRQQHXU TX¶LO m¶D fait en acceptant G¶H[D miner ce travail. Je lui exprime ma profonde gratitude. J'associe à ces remerciements M. Marc LEBRUN, M. Renaud BOULANGER et M. Noël DURAND pour leur implication dans mes travaux et leur sympathie. -¶DL eu beaucoup de plaisir à travailler avec eux. -¶DGUHVVH de sincères remerciements à Mme Marie-Pierre OBEDE pour sa sympathie, la relecture et la mise en forme de ce mémoire. Je tiens également à exprimer ma reconnaissance à Mme Isabelle PIRO-METAYER et M. Laurent BERTHIOT pour leur bonne humeur et leur aide indispensable. Je voudrais remercier à Mesdames Nathalie PAILLUSSON et Chantal CANALES pour leur aide et leur disponibilité. A titre plus personnel, Je remercie chaleureusement mon amie Adiara, pour O¶HQFR uragement et O¶DLGH précieuse. Je tiens à la remercier surtout pour son soutien moral ininterrompu. Je tiens à remercier Amine BELBAHI et Gabrielle DEUNEUX pour leurs coups de main indispensables et sans oublier tous mes amis de Montpellier Ali, Thiziri, Magali, Adeline. -HWLHQVjUHPHUFLHUGXIRQGGXF°XU&pOLQHDYHFTXLM¶DLSDUWDJpOHPrPHEXUHDXSHQGDQWFHV WURLVDQQpHVGHWKqVH0HUFLSRXUOHVPRPHQWVLQRXEOLDEOHVTX¶RQDSDVVpHQVHPEOH ! Je tiens à remercier Mme Catherine BRABET, Mme Angélique FONTANA, Mme Pascaline ALTER, Mme Nelly FORESTIER-CHIRON, M. Eric TARDAN, M Gille Morel «« .et tous ceux TXHM¶RXEOLH Enfin, je remercie mes parents pour leur soutien au cours de ces trois années et sans lesquels je n'en serai pas là aujourd'hui. A mes chers parents A mes frères A El-Hadj El-Rabi A toute la famille HAMDOUCHE Liste des abréviations AAB Bactéries acétiques AC Café coque Arabica ACC Analyse Canonique des Correspondances ACP Analyse en Composantes Principales ADN Acide désoxyribonucléique ADNr 16S ADN codant pour la VRXVXQLWp6GHO¶$51ULERVRPDO $'1U6$'1FRGDQWSRXUODVRXVXQLWp6GHO¶$51ULERVRPDO $'1U6$'1FRGDQWSRXUODVRXVXQLWp6GHO¶$51ULERVRPDO ADNr Acide désoxyribonucléique ribosomique ANOVA Analyse de la variance ANV Café vert Arabica obtenu par voie sèche AP Café parche Arabica $363HUVXOIDWHG¶DPPRQLXP ARDRA amplified ribosomal DNA restriction analysis ARNr ARN ribosomal AV Café vert Arabica obtenu par voie humide Aw Activité de l'eau B1, B2 et B3 fermes à Bafoussam CAH Classification Ascendante Hiérarchique CIRAD Centre International de Recherche Agronomique pour le Développement D1, D2 et D3 fermes à Dschang DGGE Denaturing Gradient Gel Electrophoresis DO Densité Optique EDTA Ethylenediaminetetraacetic acid ESB Encéphalopathie spongiforme bovine F1, F2 et F3 fermes à Bafia GPC Chromatographie en phase gazeuse HPLC Chromatographie Liquide Haute Performance ICO International coffee organization ICCO International cocoa organization IK Indice de Kovats ITS Internal transcribed spacer LAB Bactéries lactiques M Molarité MATAB Mixed Alkyl Trimethyl Ammonium Bromide MS Spectrométrie de masse MS% Pourcentage en matière sèche NCBI National Center for Biotechnology Information NIRS Spectroscopie proche infrarouge OCDE Atlas régional de l'Afrique de l'Ouest OGM Organismes génétiquement modifiés OTA Ochratoxine A pb Paires de bases PCR Polymerase Chain Reaction pH Potentiel hydrogène PSM Pulp Simulation Media RADP randomly amplified polymorphic DNA RC Café coque Robusta RFLP restriction fragment length polymorphism rpm Rotation par minute RV Café vert Robusta obtenu par voie humide SDS Sodium dodecyl sulphate SPME Micro-extraction en phase solide SSCP Single-Stranded Conformation Polymorphism T1, T2 et T3 fermes à Batouri TAE Tris/ Ammonium/ EDTA (tampon) TE Tris/ EDTA (tampon) 7(0('111¶1¶7pWUDPpWK\OpWK\OqQHGLDPLQH TGGE Temperature Gradient Gel Electrophoresis TRFLP terminal RFLP UFC Unités formant colonies UV Ultraviolet VH Café vert obtenu par voie humide VN Café vert obtenu par voie naturelle par Luwak VS Café vert obtenu par voie sèche VSH Café vert obtenu par voie semi-humide Listes des figures Première partie : Synthèse bibliographique Figure 1 : Répartition géographique de la culture du café. Figure 2 : Cerises du café. Figure 3 : Représentation schématique des tissus présents dans le fruit de Coffea sp. Figure 4 : Schéma montrant les différents types de traitements du café. Figure 5 : Traitement du café par voie sèche. Figure 6 : Lavage du café par voie humide. Figure 7 : Fruit du cacaoyer ou cabosse Figure 8 : Graines de cacao avec et sans pulpe. Figure 9: Structure chimique de la théobromine (a) et de la caféine (b). Figure 10 : Principaux pays producteurs de cacao. Figure 11 : Écabossage du cacao. Figure 12 : Fermentation en tas du cacao. Figure 13 : Fermentation en caisse du cacao. Figure 14 : Techniques de brassage au cours de la fermentation du cacao. Figure 15 6WUXFWXUHFKLPLTXHGHTXHOTXHVFRPSRVpVG¶DU{PHGXFDFDR Figure 16 : 'LDJUDPPHGHVGLIIpUHQWHVpWDSHVGHO¶DQDO\VH3&5 -'**($SSOLFDWLRQjO¶DQDO\VH GHVpFKDQWLOORQVHQYLURQQHPHQWDX[RXG¶pFKDQWLOORQVDOLPHQWDLUHV Deuxième partie : Matériels et Méthodes Figure 17 : Carte du Cameroun indiquant les régions de prélèvement. Figure 18 : Étapes de traitement des cerises fraîches aux grains de café au Cameroun. Figure 19 : Représentation des trois voies de traitement de café en Indonésie. Figure 20 : Echantillonnage au cours du procédé post-récolte du cacao. Figure 21 : Représentation schématique de l'ITS (ITS1 et ITS4) de l'unité répétée de l'ADN ribosomique chez les eucaryotes. Les flèches représentent les sites de fixation des amorces. Figure 22 &DOFXO GH OD SRVLWLRQ UHODWLYH 35 GH FKDTXH EDQGH SDU H[SORLWDWLRQ G¶XQ JHO DGGE. Figure 23 : Photo des tubes
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