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Approches Macrocinétique, Enzymatique Et Métaprotéomique

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Approches Macrocinétique, Enzymatique Et Métaprotéomique Délivré par INSTITUT NATIONAL DES SCIENCES APPLIQUEES DE TOULOUSE (INSA de Toulouse) Adèle LAZUKA Le 28 Septembre 2018 Production de synthons par des consortia microbiens à partir de paille de blé : approches macrocinétique, enzymatique et métaprotéomique École doctorale et discipline ou spécialité ED SEVAB : Ingiénieries microbienne et enzymatique Unité de recherche Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés (LISBP) Directrice(s) ou Directeur(s) de Thèse HERNANDEZ-RAQUET Guillermina, Directrice de recherche, INRA-LISBP, Toulouse, France O’DONOHUE Michael, Directeur de recherche, INRA-LISBP, Toulouse, France Jury CARRERE Hélène, Directrice de recherche, INRA-LBE, Narbonne, France, rapporteur KURECK Bernard, Directeur de recherche, INRA-FARE, Reims, France, rapporteur GUILLON Fabienne, Directrice de recherche, INRA-BIA, Nantes, France, examinateur BERRIN Jean-Guy, Directeur de recherche, INRA-LBCF, Marseille, France, examinateur Remerciements « De la diversité nait la richesse… » Avant toute chose, il advient de mentionner que ce travail n’aurait pu être réalisé sans l’aide et le soutien de nombreuses personnes. Je remercie Guillermina et Mike de m’avoir offert la possibilité d’effectuer cette thèse et pour m’avoir encadré pendant toutes ces années…( !) Merci pour les conditions de travail assez exceptionelles, qui ont permis d’aller plus loin que ce que j’imaginais dans la compréhension des phénomènes. Merci à Lucas, binôme de thèse, pour les échanges, les coups de main et le soutien de manière général. Notre binôme, quand on y pense ce n’est pas commun ( !), aura était notre force pour aborder la compléxité du sujet, profitant de cette diversité pour décortiquer résultats, articles et autres observations. Un remerciement spécial pour ton aide lors de mon déménagement !! . Merci aussi à Emeline, presque trinôme de thèse et binôme perso-pro de mon binôme pro (# c’est beau la vie !), je vous souhaite tout le meilleur. Merci aux stagiaires, Maïder, Cécile, Camille et Gunnar. Ça a été un plaisir de travailler avec chacun de vous. J’espère vous avoir apporté un bon encadrement, en tout cas vous m’avez fait grandir et avez contribué à cette diversité de points de vue et d’expérience qui font que le Recherche en équipe est belle. (# c’est mieux en rigolant !) Comment ne pas remercier toute l’équipe SYMBIOSE (ce nom que j’adore). Et comment les remercier dignement ? D’abord une spéciale dédicace et un grand merci aux collègues et amis de bureau (Laeti et MP², sans oublier Anil), plein de fous rires, beaucoup de soutien pro mais aussi perso… (#Candy !) Ensuite les techs bien entendu (Chanta, Delphine, Mansour, Evrard et Simon). Sans vous, pas de manips, c’est aussi simple que ça, donc plus qu’un merci je veux vous dire que ce travail est le fruit du votre, tout simplement. Merci à tous les membres de l’équipe, vous m’avez tous apporté bienveillance, joie (#mots fléchés), conseil et soutien (Tata yoyo, Seb (#concert parapluie, #solidia), Xavier, Alexis, Hélène, Ana, Mathieu, Etienne...). Un remerciement spécial à Etienne, qui m’a fait mettre le pied dans la recherche en me prenant en stage avec Laeti, ça a changé ma vie ! Un autre pour Mathieu, membre de nos comités de thèse et soutien permanent, tu gères une bien belle équipe avec beaucoup d’humanité. Bien entendu je remercie ma famille qui a toujours cru en moi et m’a porté et apporté au quotidien le soutien indéfectible dont j’avais besoin. Merci Maman d’être toujours là pour et avec moi. Je remercie mes amis Cécé, Jéjé, Juju, Laurent, Erwan, Margaux, Lulu, Deixonne et tous les autres, pour m’avoir écoutée et soutenue même quand j’étais en boucle sur la thèse. Votre amitié est précieuse. Une petite phrase pour chou, qui a su s’adapter entre Toulouse et Paris, doctorat et travail, et toujours avec amour. Merci pour tout à toi et à tous tes/nos proches. Arrivant à Paris, je remercie mes collègues actuels pour leur accueil et leur soutien pour cette grande étape qu’est la fin de la thèse (#BIA). Enfin je remercie tous ceux qui ont contribué à ce travail de loin ou de près, au niveau profesionnel (Sophie, Sandrine, Julie, Nourredine, Willy, Mathias…) comme personnel (Marvin, David, Mylène, Carine…). Si je retiens bien quelque chose de tout cela c’est que de la diversité nait la richesse. Production scientifique Production scientifique Publications dans journaux à comité de lecture Efficient anaerobic transformation of raw wheat straw by a robust cow rumen-derived microbial consortium. Lazuka, A. & Auer, L., Bozonnet, S., Morgavi, D.P., O’Donohue, M., Hernandez-Raquet, G., 2015. Bioresour. Technol. 196, 241–249. CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems. Abot, A., Arnal, G., Auer, L., Lazuka, A., Labourdette, D., Lamarre, S., Trouilh, L., Laville, E., Lombard, V., Potocki-Veronese, G., Henrissat, B., O'Donohue, M., Hernandez- Raquet, G., Dumon, C., Leberre, V., 2016. BMC Genomics. 17:671. Ecofriendly lignocellulose pretreatment to enhance the carboxylate production of a rumen-derived microbial consortium. Lazuka, A., Roland, C., Barakat, A., Guillon, F., O’Donohue, M., Hernandez-Raquet, G., 2017. Bioresour. Technol. 236, 225–233 Uncovering the potential of termite gut microbiome for lignocellulose bioconversion in anaerobic batch bioreactors. Lucas Auer, Adèle Lazuka, David Sillam-Dussès, Edouard Miambi, Michael O’Donohue, Guillermina Hernandez-Raquet, 2017. Front Microbiol. 8:2623. Diversity of metabolically active bacteria associated with lignocellulose degradation by a cow rumen-derived consortium: dynamic responses to substrate pretreatment. Lazuka, A. & Auer, L., O’Donohue, M., and Hernandez-Raquet, G. In preparation. Community dynamics of an efficient lignocellulolytic bacterial consortium derived from termite-gut microbiome. Lazuka, A. & Auer, L., O’Donohue, M., and Hernandez-Raquet, G. In preparation. Dynamic profiling of efficient anaerobic consortia producing carboxylate from raw wheat straw by shotgun metaproteomics. Lazuka, A. & Flajollet, E., Jehmlich N., B. Henrissat, O’Donohue M., Hernandez-Raquet G. In preparation. I Production scientifique Conférences Impact of ecofriendly pretreatments on lignocellulose properties and its digestibility by a hydrolytic microbial consortium. Adèle Lazuka, Lucas Auer, Cécile Roland, Maïder Abadie, Michael O’Donohue, Guillermina Hernandez-Raquet. Symposium on Biotechnology for Fuels and Chemicals (San Diego, CA, USA, Feb 2015). Oral presentation Lignocellulose degradation by microbial consortia from phytophagous insect guts: microbial diversity and enzymatic activities. Maïder Abadie, Adèle Lazuka, Lucas Auer, Michael O’Donohue, Claire Dumas, Guillermina Hernandez-Raquet,. Symposium on Biotechnology for Fuels and Chemicals (San Diego, CA, USA, Feb 2015). Oral presentation Metagenomics and metaproteomics of lignocellulose transformation by enriched microbiomes from cow rumen and termite gut. Adèle Lazuka, Lucas Auer, Cécile Roland, Maïder Abadie, Michael O’Donohue, Guillermina Hernandez-Raquet, Symposium on Biotechnology for Fuels and Chemicals (San Diego, CA, USA, Feb 2015). Oral presentation Lignocellulose degradation by enriched microbial consortia from cow rumen and termite gut. Lucas Auer, Adèle Lazuka, Maïder Abadie, Gunnar Oelker, Guillermina Hernandez- Raquet,. Workshop on Control of Natural and Engineered microbial Communities (Cambridge UK, Nov 2014). Oral presentation Lignocellulose bioconversion by engineered mixed cultures from cow rumen and termite gut microbiomes. Adèle Lazuka, Cécile Roland, Lucas Auer, Abdellatif Barakat, Guillermina Hernandez-Raquet. 3rd Symposium on Biotechnology Applied to Lignocellulose (Concepcion, Chile, Oct 2014). Oral presentation Lignocellulose degradation by engineered microbial consortia from rumen and termite gut: Correlating enzymatic profiles and functional microbial diversity. Lucas Auer, Adèle Lazuka, Sandrine Païsse, Michael O’Donohue and Guillermina Hernandez-Raquet. 15th International Symposium on Microbial Ecology (Seoul, South Korea, Aug 2014). Oral presentation Exploring enzymatic behavior in xylo- and phytophagous insect’s consortia. What could be learned from Nature ? Claire Dumas, Guillermina Hernandez-Raquet, Lucile Chatellard, Amandine Gales, Adèle Lazuka, Lucas Auer, Hélène Carrère, Jean-Jacques Godon, Michael O'Donohue, Jean-Philippe Steyer. Symposium on Biotechnology for Fuels and Chemicals (Clearwater beach, FL, USA, Mai 2014). Oral presentation Valorisation de la lignocellulose : Analyse fonctionnelle de consortia microbiens enrichis. Lucas Auer, Adèle Lazuka, Maïder Abadie, Michael O’Donohue, Guillermina Hernandez- Raquet. Génomique Environnementale (Rennes, FR, Nov 2013). Poster II Production scientifique Lignocellulose bioconversion by engineered mixed cultures. Païssé S, Lazuka A, Auer L, Bozonnet S, O’Donohue M. Hernandez-Raquet G. Joint Genome Institute Users Meeting (Walnut Creek, CA, USA, March 2013). Poster. Collaborations scientifiques Production de synthons à partir de lignocelluloses par des consortia microbiens (Hi- Solids). BIA-INRA Angers-Nantes, LBE-INRA Narbonne, IATE- INRA Montpellier (2014- 2015). Financement ANR Combinaison de traitements bactériens pour fractionner la paille de blé (COMBA). FARE-INRA Reims. (2014-2015). Financement département CEPIA INRA Metaproteomic analysis of hydrolytic samples derived from natural ecosystems. UFZ Leipzig-Germany. (2014-2015). Expérience internationale dans le cadre du parcours de l'EIR- A. Financement INRA DARESE et Campus France Caractérisation
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  • Genome-Based Taxonomic Classification of Bacteroidetes
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