Abstract
Microbiome refers to the ecological communities of microorganisms hosted by a host. Microbiomes are now perceived as true accessory genomes that determine the extended phenotype of their hosts. They are, like theirs hosts, extremely diverse and structured by a wide range of biotic, abiotic and stochastic drivers. These factors vary according to the resolution scale: the structure of microbiomes will not be impacted by the same factors at an individual scale or an interspecific scale. In this fundamental context of community ecology, my thesis tried to determine what the microbiome drivers at different resolution scales are. To answer this question, we studied the microbial community sheltered by ticks in French Guiana. This model is particularly relevant for two reasons: 1/ It is recognized that ticks harbour complex microbial communities that appear to be subject to a diversity of potential drivers. 2/ There are no recent data on the diversity, biology or infectious risks associated with ticks in French Guiana. As a result, in this thesis we described tick species which were never observed in French Guiana and characterized unknown strains of potentially pathogenic bacteria, including a new borrelia related to Lyme disease and to relapsing fever ones. Then, we demonstrated the ubiquity of biases in tick microbiome studies and their impact on the interpretation of microbiome data by confusing cuticular and internal microbes. Tick microbiomes actually appear mainly structured by the identity, the presence/absence and the interactions between mutualistic intracellular bacteria of ticks, whether on an intra- or interspecific scale. Finally, we have shown that the association between ticks and their microbiome is also subject to co-evolutionary patterns, typical of intracellular symbionts of arthropods, as well as phylogeographic and bio-ecological factors depending of the tick hosts. However, the microbiome structure in ticks, is still far from being fully understood and future studies are necessary to resolve the various controversies on the biological reality of microbiomes hosted by ticks.