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Les Differents Microbiotes De L'holobionte Grand

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Les Differents Microbiotes De L'holobionte Grand LES DIFFERENTS MICROBIOTES DE L’HOLOBIONTE GRAND COREGONE (COREGONUS CLUPEAFORMIS) DANS UN CONTEXTE DE SPECIATION Thèse Maelle Sevellec Doctorat en biologie Philosophiae doctor (Ph. D.) Québec, Canada © Maelle Sevellec, 2018 LES DIFFERENTS MICROBIOTES DE L’HOLOBIONTE GRAND COREGONE (COREGONUS CLUPEAFORMIS) DANS UN CONTEXTE DE SPECIATION Thèse Maelle Sevellec Sous la direction de : Louis Bernatchez directeur de recherche Nicolas Derome, codirecteur de recherche Résumé Les animaux ont toujours évolué avec leur microbiote. Toutefois, peu d’études ont analysé le rôle des bactéries sur la spéciation. Il a été démontré que le microbiote oriente la spéciation de son hôte. L’objectif principal de cette thèse est d’évaluer l’influence des bactéries sur la spéciation du grand corégone (Coregonus clupeaformis). Sous certaines conditions, il existe deux espèces de corégone qui ont évolué de façon parallèle ; l’espèce naine et l’espèce normale qui sont caractérisées par des niches trophique et écologique différentes. Plusieurs types d’interaction hôte-bactéries ont été analysés au niveau de populations de corégones sauvages et de corégones captifs, qui ont été élevés dans des conditions identiques. Chez les corégones sauvages, les résultats supportent un effet de parallélisme au niveau de la diversité bactérienne, mais cet effet n’a pas été observé au niveau de la structure des communautés bactériennes entre l’espèce naine et normale. La présence d’un noyau bactérien très conservé au niveau du microbiote intestinal démontre une influence marquée de l'hôte sur ses communautés bactériennes. L’ensemble de ces résultats soulignent la complexité de l'holobionte (hôte + bactéries) en démontrant que la direction de sélection peut différer entre l'hôte et son microbiote. Chez les corégones captifs, la différence de la structure bactérienne chez les nains, les normaux et les hybrides F1 réciproques met en évidence l’influence de l’hôte sur le microbiote. Finalement, cette étude pionnière des communautés bactériennes du grand corégone ouvre la voie à des nouvelles directions de recherche liées à l’évolution de l’holobionte. iii Abstract Animals have evolved with their microbiota. However, little is known about the role of bacteria over the course of this evolution. These last few years, it has been shown that the microbiota influences speciation by controlling the pre-zygotic and post-zygotic reproductive isolation. The main goal of the thesis is to analysis for the first time the influence of the microbiota on the Lake Whitefish (Coregonus clupeaformis) which represents a continuum in the early stage of ecological speciation. Some species pairs of dwarf (limnetic niche specialist) and normal (benthic niche specialist) evolved in parallel inside several lakes in northeastern North America. Bacterial communities have been compared among five wild sympatric species pairs of whitefish as well as captive dwarf, normal and hybrids whitefish reared in identical controlled conditions. For the wild fish, difference of the bacterial community structure was highlighted in the three studied interactions between the bacterial community and the host: host-pathogen, host-symbiont and host-transient bacteria. Although no parallelism was detected for the bacterial community structure for these interactions, it was highlighted at the bacterial diversity level. Moreover, parallelism was not observed within the bacteria community structure, likely because the water bacterial communities, studied in this thesis, and the biotic and abiotic factors were characterized by important variation between the lake populations of whitefish. Furthermore, results revealed a strong influence of the host (dwarf or normal) on the bacterial communities with pronounced conservation of the core intestinal microbiota. Finally, our result highlighted the complexity of the holobiont (host + bacteria), suggesting that the direction of selection could differ between the host and its microbiota. In fact, three evolutionary directions have been highlighted between the fish and its bacterial communities. For the captive whitefish, an influence of host (normal, dwarf and hybrids) was also detected on bacterial taxonomic composition. Hybrid microbiota was not intermediate and its composition fell outside of that observed in the parental forms. This pioneer study on the bacterial communities of the Lake whitefish opens new research fields related to the evolution of the holobiont. iv Table des matières Résumé ............................................................................................................................. iii Abstract ............................................................................................................................ iiv Table des matières ............................................................................................................ v Liste des tableaux ………………………………………………………………………………...vii Liste des figures ............................................................................................................... viii Liste des abréviations ....................................................................................................... iix Remerciements .................................................................................................................. xi Chapitre 1 : Introduction ..................................................................................................... 1 1.1 Le surprenant potentiel des microorganisms ........................................................ 2 1.1.1 Chez les animaux et les plantes .................................................................... 2 1.1.2 Dans les cycles biogéochimiques .................................................................. 2 1.1.3 Découverte des bactéries par l’Homme ......................................................... 3 1.2 Les différents types d’interaction hôte-bactéries ................................................... 3 1.3 Le concept de l’hologénome et l’évolution ............................................................ 5 1.3.1 Le concept de l’hologénome ......................................................................... 5 1.3.2 Diversité et abondance du microbiote ........................................................... 5 1.3.3 La transmission de génération en génération du microbiote .......................... 7 1.3.4 Les propriétés du microbiote sur la valeur sélective ...................................... 7 1.4 Evolution de l’holobionte : cas de la spéciation..................................................... 8 1.5 Le Grand corégone ............................................................................................ 10 1.6 Objectifs de la thèse ........................................................................................... 12 Chapitre 2 : Microbiome investigation in the ecological speciation context of Lake Whitefish (Coregonus clupeaformis) using next generation sequencing .............................. 15 2.1 Résumé.............................................................................................................. 16 2.2 Abstract .............................................................................................................. 17 2.3 Introduction ........................................................................................................ 18 2.4 Material and methods ......................................................................................... 21 2.5 Results ............................................................................................................... 25 2.6 Discussion .......................................................................................................... 29 2.7 Conclusion ......................................................................................................... 38 2.8 Acknowledgments .............................................................................................. 39 2.9 Data Accessibility ............................................................................................... 40 2.10 Tables ................................................................................................................ 41 2.11 Figures ............................................................................................................... 46 Chapitre 3 : Holobionts and ecological speciation: the intestinal microbiota of Lake Whitefish species pairs. ....................................................................................................... 51 3.1 Résumé.............................................................................................................. 52 3.2 Abstract .............................................................................................................. 53 3.3 Introduction ........................................................................................................ 54 3.4 Methods ............................................................................................................. 57 3.5 Results ............................................................................................................... 61 3.6 Discussion .......................................................................................................... 66 3.7 Conclusion ......................................................................................................... 73 3.8 Availability of data and material .........................................................................
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