Protists-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as model for studying prokaryotes-eukaryotes symbioses, so that a conspicuous amount of data is now available on this system. Nevertheless, as for most of the known microbial symbioses, acquired knowledge relies almost exclusively on laboratory cultures so that reliable data on natural populations are lacking and the ecology of these systems is completely unexplored. Here we used the well-known Euplotes symbiotic system to perform a survey on natural populations based on a single-cell microbiomic approach.Obtained results shed light, for the first time, on an unexpected variability in symbiotic communities within populations among different individual hosts. The simultaneous presence of two different essential symbionts, Polynucleobacter and “Candidatus Protistobacter”, in different individual hosts of the same population indicated an ongoing takeover, suggesting that these replacement events could be more frequent in nature than previously hypothesized. Some of the accessory symbionts showed a strong affinity for one host species, while two of them (“Candidatus Cyrtobacter” and “Candidatus Anadelfobacter”) displayed competitive exclusion between each other. Presented data represent the first insight into prevalence and patterns of these microbial associations in the natural environment.