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The role of bacterial endosymbionts harbored by heterotrophic  Paramecium  species is complex. Obligate intracellular bacteria supposedly always inflict costs as the host is the only possible provider of resources. However, several experimental studies have shown that paramecia carrying bacterial endosymbionts can benefit from their infection. Here, we address the question which endosymbionts occur in natural paramecia populations isolated from a small lake over a period of 5 years and which factors might explain observed shifts and persistence in the symbionts occurrence. One hundred and nineteen monoclonal strains were investigated and approximately two-third harbored intracellular bacteria. The majority of infected paramecia carried the obligate endosymbiotic “ Candidatus  Megaira polyxenophila”, followed by  Caedimonas varicaedens , and  Holospora undulata . The latter was only detected in a single strain. While “ Ca . M. polyxenophila” was observed in seven out of 13 samplings,  C. varicaedens  presence was limited to a single sampling occasion. After the appearance of  C. varicaedens , “ Ca . M. polyxenophila” prevalence dramatically dropped with some delay but recovered to original levels at the end of our study. Potential mechanisms explaining these observations include differences in infectivity, host range, and impact on host fitness as well as host competitive capacities. Growth experiments revealed fitness advantages for infected paramecia harboring “ Ca . M. polyxenophila” as well as  C. varicaedens . Furthermore, we showed that cells carrying  C. varicaedens  gain a competitive advantage from the symbiosis-derived killer trait. Other characteristics like infectivity and overlapping host range were taken into consideration, but the observed temporal persistence of “ Ca . M. polyxenophila” is most likely explained by the positive effect this symbiont provides to its host.

Natural Shifts in Endosymbionts' Occurrence and Relative Frequency in Their Ciliate Host Population