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Ecologie Des Micro-Organismes Producteurs D'hydrogène Des Sources Hydrothermales Alcalines Associées À La Serpentinisation

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Ecologie Des Micro-Organismes Producteurs D'hydrogène Des Sources Hydrothermales Alcalines Associées À La Serpentinisation THESE DE DOCTORAT D’AIX-MARSEILLE UNIVERSITE Ecole Doctorale : Sciences de l’Environnement Présentée par Nan MEI En vue de l’obtention du grade de Docteur d’Aix-Marseille Université Spécialité : Océanographie Ecologie des micro-organismes producteurs d’hydrogène des sources hydrothermales alcalines associées à la serpentinisation en Baie de Prony, Nouvelle-Calédonie Date de soutenance : le 30 Septembre 2016 devant la commission d’examen Composition du jury : Mme Anne GODFROY Chercheuse Ifremer, LM2E Rapportrice M. Rémy GUYONEAUD Professeur, Université de Pau Rapporteur Mme Bénédicte MENEZ Professeur, IPGP Examinatrice M. Alain DOLLA Chercheur CNRS, DR Examinateur M. Gaël ERAUSO Professeur, AMU Directeur de thèse Mme Marianne QUEMENEUR Chercheuse IRD, MIO Co-directrice de thèse Résumé : Le système hydrothermal de la baie de Prony en Nouvelle-Calédonie est composée de plusieurs sources émettant à faible profondeur (<50 mbsl) des fluides hyperalcalins (pH ~11), mesothermiques (<40°C), et anoxiques riches en hydrogène (H2) et méthane, produits par la réaction de serpentinisation. Dans le cadre de ces travaux de thèse, la capacité potentielle des micro-organismes à produire de l’H2 dans ces écosystèmes alcalins a été évaluée par des analyses moléculaires et culturales. Nos premières analyses moléculaires basées sur le gène codant l’ARNr 16S ont permis de mettre en évidence une grande diversité de bactéries et une faible diversité d’archées dans les fluides et cheminées hydrothermales. La diversité et la distribution des populations productrices d’H2 a ensuite été spécifiquement évaluée par des analyses métagénomiques et basées sur la PCR. Les séquences de gènes hydA, codant la sous-unité catalytique des hydrogénases [Fe-Fe], utilisés comme marqueur moléculaire des bactéries productrices d’H2, étaient principalement associées à celles du phylum des Firmicutes (ordre des Clostridiales). Deux groupes de séquences hydA se sont distinguées en fonction de l’origine « sous-marine/anoxique » ou « intertidale/oxique » des échantillons. De plus, plusieurs nouvelles bactéries alcalophiles ont été isolées des cheminées hydrothermales de différents sites intertidaux ou sous-marins de la baie de Prony. Parmi elles, la souche alcalophile et anaérobie, PROH2 (appartenant au genre Clostridium) a été isolée de l’Aiguille de Prony et est capable de produire efficacement de l’H2 par voie fermentaire (2,71 moles d’H2/mole de glucose) en condition alcaline (pH 9,5), de façon comparable aux espèces de Clostridium neutrophiles. Ces travaux présentent également la caractérisation d’une nouvelle espèce bactérienne anaérobie, mésophile et alcalophile (pH optimum de 9,5) d’un nouveau genre, nommée Serpentinicella alkaliphila, isolée d’un site intertidal de la baie de Prony. Contrairement à la souche PROH2, la souche 3bT, produit peu d’H2 et les principaux produits de fermentation du lactate sont l’acétate et le propionate, tandis que le crotonate est dismuté en acétate et butyrate. L’ensemble des données moléculaires et issues de la culture démontre la capacité des Firmicutes des environnements associés à la serpentinisation à produire de l’H2 par voie fermentaire. Mots clefs : Serpentinisation, Hydrogène, Séquençage à haut-débit, Diversité microbienne, Hydrothermalisme, Firmicutes. Abstract: The Prony hydrothermal field (PHF, New Caledonia) is composed of several shallow-submarine springs (<50 mbsl) discharging into the lagoon seawater high pH (~11), moderate temperature (<40°C), low-salinity fluids, enriched in hydrogen (H2) and methane produced by serpentinization. In this work, we evaluated the potential ability of microorganisms to produce H2 in this alkaline ecosystem by using both molecular and cultural approaches. Our first molecular analyses based on 16S rRNA genes provided evidence of high bacterial abundance and diversity contrasting with low archaeal diversity in the PHF chimneys. The diversity and distribution of potential H2- producing bacteria were specifically investigated by using metagenomic analyses and different PCR-sequencing methods. The sequences of hydA genes encoding the catalytic subunit of [FeFe]-hydrogenases, used as molecular marker of H2-producing bacteria, were mainly related to those of Firmicutes (order Clostridiales). Two groups of hydA sequences were distinguished according to the "submarine/anoxic" or "intertidal/oxic" origin of the samples. Moreover, novel alkaliphilic H2-producing Firmicutes were successfully cultivated from both intertidal and submarine PHF chimneys. Among them, an alkaliphilic and anaerobic strain, Clostridium sp. PROH2, belonging to the genus Clostridium, was isolated from the Prony Needle and demonstrated efficient H2 production (2.71 mol H2/mol glucose) at a high pH (9.5), which is comparable to neutrophilic clostridial species. This manuscript also present the characterization of a novel anaerobic, mesophilic and alkaliphilic species belonging to a new genus, named Serpentiniticella alkaliphila 3bT, isolated from an intertidal PHF site. Contrary to the strain PROH2, the strain T 3b produces few H2 and the main lactate fermentation products are acetate and propionate, while crotonate is disproportionated into acetate and butyrate. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce H2 by fermentation. Keywords: Serpentinization, Hydrogen, High-throughput sequencing, Microbial diversity, Hydrothermalism, Firmicutes. Remerciements Une belle aventure touche à sa fin, une aventure Marseillaise et Luminyenne de 3 ans, sous le pied de Mont Puget près des belles calanques, avec de magnifiques collègues du MIO, qui m’ont appris le français, fait découvrir la science, et m’ont changé la vie. Je remercie Richard Sempéré, directeur de l’unité, pour m’avoir accueillie au sein de l’institut, sans qui je n’aurais pas eu la chance de commencer cette aventure, ainsi que Chinese Scholarship Council (CSC) pour le soutien financier de ma thèse. Je tiens à remercier les membres du jury qui ont accepté de juger ce travail de thèse et de participer à ma soutenance : Anne Godfroy, Rémy Guyoneaud, Bénédicte Ménez et Alain Dolla. Je remercie Bernard Ollivier, directeur de recherche à l’IRD, pour m’avoir accueillie dans son laboratoire, pour son humour et ses connaissances scientifiques ; mon directeur de thèse Gaël Erauso, pour m’avoir permis de travailler sur ce projet passionnant, et pour la confiance qu’il m’a apportée ; Anne Postec ainsi que tout l’équipe Prony pour leur soutien tout au long de la thèse. Je voudrais exprimer particulièrement mon immense reconnaissance envers Marianne Quéméneur, ma chère encadrante et co-directrice de thèse, pour son encadrement, ses conseils, son soutien, sa patience (surtout pour les nombreuses corrections de mon manuscrit), son écoute, et toutes les connaissances qu’elle a pu m’apporter au cours des 3 ans. MERCI ! Un grand merci à : - Marie-Laure Fardeau, Manon Bartoli et Wajdi Ben Hania pour m’avoir enseigné la culture en anaérobiose, et Sophie Guasco pour partager ses astuces de qPCR, -Fabrice Armougom de m’avoir formée à Linux et à la bioinformatique, et Eléonore, toujours prête à m’expliquer et donner un coup de main quand je rencontre des problèmes sur QIIME, - Bernard Ollivier, Anne Postec, Christophe Monnin, Bénédicte Ménez et Gaël Erauso pour leurs corrections d’articles, - Patricia Bonin et Valérie Michotey pour les pilotages de thèse et leurs conseils précieux, - L’organisation Deep Carbon Observatory (DCO) pour m’avoir donné l’opportunité de participer en 2015 au « Deep Life Meeting » à Lisbonne, qui m’a permis de rencontrer les chercheurs les plus connus du monde dans le domaine, ainsi que l’Association Francophone d’Ecologie Microbienne (AFEM) et la fondation Gordon and Betty Moorede m’avoir attribué une bourse pour participer au « Ramon Margalef Summer Colloquia 2016» à Barcelone. Je tiens aussi à remercier mes camarades Eléonore, Fatma, Amira, Méline, Fernanda, Manel, Maxime, Axel, Guillaume et Yannick pour leur soutien moral et les nombreuses discussions intéressantes. Et merci à Clara, de m’avoir motivé plusieurs fois à courir aux calanques, qui m’a donné la pêche pour faire face aux difficultés. Je voudrais aussi remercier Agnès, Manon, Wajdi, Jean-Luc, Jean, Sylvain, Pierre- Pol, Nathalie, Grégoire, Philippe, Laurie, Corinne et tous ceux qui ont partagé leur bonne humeur avec moi, pour leur sympathie et leur bienveillance. Je n’oublie pas de remercier mes chers amis Chinois à Marseille pour les merveilleux moments partagés, et Cappuccino, mon petit félin malin qui me fait rigoler et me donne de la douceur chaque jour. Enfin, j’adresse toute mon affection à ma famille : leur confiance, leur tendresse, et leur amour me portent tous les jours, et à ma moitié qui est toujours à mes cotés pour m’écouter et me soutenir, m’amène à voyager à chaque fois j’ai besoin de me vider la tête, en Europe, en Afrique du nord, en arctique, merci de me montrer que le monde est si beau. Merci à tous pour cette belle aventure ! Que tous ceux qui ont contribué à faciliter cette thèse trouvent ici le témoignage de ma sincère gratitude ! Sommaire LISTE DES COMMUNICATIONS .................................................................................................................... 1 LISTE DES FIGURES ......................................................................................................................................... 3 LISTE DES TABLEAUX ....................................................................................................................................
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