• symbiosis
• ngs
• intracellular bacteria
• microbiome
• Holospora
• ecology
• ciliate
• bacterial endosymbionts
• "Candidatus Megaira"
• transinfection

Bacterial symbionts are common in protists, and their interactions are very diverse ranging from parasitic to mutualistic associations. Ciliates (phylum Ciliophora) represent an interesting model system to study host and bacteria relationship, but also to investigate interactions between symbionts. Ciliates in the environment play a double role, indeed they control the abundance of bacteria thanks to their phagotrophic activity, but at the same time they may become reservoirs of potentially pathogenic bacteria and other microorganisms. Indeed, ciliates with their feeding behavior may engulf bacteria present in the environment. Many cell compartments of a ciliate cell may be colonized by bacteria escaping the host digestion system, thus establishing symbiotic associations. Endosymbionts in this way exploit the host as they adapt to live inside of the cell and also they find protection from adverse environmental conditions. However, also bacteria ectosymbionts are known for ciliates, despite they are restricted to special environments or host peculiar life cycle.
In this PhD thesis, several bacterial symbionts of ciliates have been characterized applying the full- cycle rRNA and performing ultrastructural investigations. Some discovered symbionts were novel associations, while the others were findings of new strains of already described genera, well-known Paramecium symbionts, such as Holospora, Caedibacter, and the recently described “Ca. Megaira, widespread symbiont with broad host specificity.
In order to improve our knowledge on “Ca. Megaira” ways of transmission, several transinfection experiments have been carried out to investigate the transmission within the same host population by active infection or during conjugation process, between different Paramecium species, or to other unicellular hosts, such as algae or amoebae. Moreover, diversity and environmental distribution of this genus has been investigated through the screening of short amplicon databases of 16S rRNA gene in order to understand better biology of this unusual cosmopolitan symbiont.
Finally, the microbial consortia of the sessile ciliate Stentor coerules were characterized applying an innovative approach using the16S rRNA gene matabarcoding. It is the first attempt to study the microbiome of a ciliate.
The data obtained have shown that several of the newly characterized symbionts are new species, some of them representing also new genera and even one new family of Rickettsiales. Some bacteria retrieved in association with ciliates are related to pathogenic bacteria. We can conclude that ciliates host a hidden diversity of symbionts, and some of them are closely related to pathogens. Such associations are not restricted to the intracellular environment, but bacteria also may reside as part of microbial communities associated with these protists, thus suggesting that also ciliates as well as other protists can act as potential reservoirs of pathogenic bacteria in nature.