Recent works has highlighted the contribution of microbes to animal function. In this regard, the microbial community associated with corals has become a growing field of research in order to understand how microbes contribute to the host organisms’ response to environmental changes. It has been shown that microbes associated with corals have important functions in the coral holobiont such as immunity and nutrient assimilation. However, corals are notoriously difficult to work with. To this end, the sea anemone Aiptasia is becoming a model organism for coral symbiosis. Given the importance of host-­microbiome interactions, the topic of this thesis is to assess microbial structure of Aiptasia, culture prominent bacterial members, and compare bacterial community structure to corals. Different molecular methods have been applied using 16S rRNA bacterial gene fragments to characterize the microbial composition of Aiptasia. 16S rRNA gene sequence derived from cultured bacteria was compared to 16S rRNA gene sequences retrieved from native Red Sea Aiptasia. Inter-­individual as well as methodological differences were found to account for variance in microbiome composition. However, all approaches showed a highly abundant microbial taxon belonging to the genus Alteromonas in all samples. The Alteromonas species was successfully isolated for further research targeting microbiome selection mechanisms in Aiptasia. Future investigations by using different molecular tools will help to define the functions and relationship between the Aiptasia and its complex microbiome.

Viruses constitute the vast majority of all biological entities in the biosphere and represent one of the biggest reservoirs of undetected genetic diversity on Earth. Of all the viral particles inhabiting the ocean, phages are the most abundant and can affect the overall microbial composition of marine ecosystems and the dynamics of global biogeochemical cycles. The interaction between prokaryotic cells and their phages is among the oldest and most intertwined host-parasite relationships on the planet. It has been extensively studied by culture, molecular biology, and experimental evolution. However, due to the difficulties of culture with environmental samples, only a few studies have analyzed the mechanisms of phage-host interaction in the marine environment. Here, we have studied the genes involved in viral host recognition and their evolutionary dynamics by focusing on two species of the marine copiotrophic bacterium Alteromonas and several phages infecting them. We described the genomic and morphological characterization of the first Alteromonas phage belonging to the Myoviridae family (Alteromonas myovirus V22) that was isolated in coastal waters of the Mediterranean Sea, and we identified its receptor-binding protein (RBP) used for host recognition by combining fluorescence microscopy and spectrometry. In addition, using size-exclusion chromatography, we showed how this protein required co-expression with a downstream protein to be functional, which later was identified as a new type of intermolecular chaperone crucial for RBP maturation. We also identified a conserved host recognition module in V22 and other unrelated alterophages belonging to different viral families and with completely different morphologies, suggesting horizontal gene transfer between the ancestors of these phages. Furthermore, we described the first coevolution study of a host-parasite system performed with Alteromonas using a metagenomics-like approach. Finally, we analyzed the micro- and macrodiversity of an alterophage population that was able to survive over a long period of time and showed remarkable genomic stability, indicating stable interactions over time between phage-host recognition structures. Overall, this study has contributed to extend the knowledge of known phage-host recognition mechanisms present in the marine ecosystem and has provided a first glimpse of the evolutionary dynamics in phages infecting Alteromonas.