ETD

• Metagenomics

The ciliate Euplotes constitutes a well-established model of protist symbiosis, but most current knowledge of this system derives exclusively from laboratory cultures. This thesis applied single-cell metagenomic approaches to obtain a genome-resolved characterization of bacterial symbionts associated with natural populations of Clade B Euplotes. Individual cells were isolated, screened and sequenced; multiple bioinformatic workflows were employed and combined to retrieve metagenome-assembled genomes (MAGs), which were analyzed through comparative genomics and phylogenomics. Novel lineages were identified within established symbiont groups, as well as putative endosymbionts from other taxa. Patterns of genome erosion in the predominant Polynucleobacter symbiont were highly distinct between host populations and independent of other harbored symbionts. The study also provided genome-resolved evidence supporting the essential nature of 'Candidatus Bandiella' in Euplotes woodruffi and investigated complex patterns involving multiple stable symbionts, including a putative case of co-occurrence consistent with an ongoing replacement of a Polynucleobacter lineage. These findings support the importance of studying natural populations to detect patterns which remain hidden from laboratory cultures.