Microbe's microbiomes: 18S rRNA gene sequences.. Microbe's microbiomes: 18S rRNA gene sequences.

Microbial associations are among the most common and important phenomena in ecology and evolution. Symbiosis between prokaryotes and microbial eukaryotes, particularly protist ciliates, have been studied for a long time. Nevertheless, researches focused only on a few host genera and species, mainly because characterization of the involved partners requires host cultivation, and usually considering a single symbiont at a time. Here we present a pilot study describing a novel approach which can be efficiently used for cultivation-independent researches on microbial associations. Single host-cell isolation followed by simultaneous amplification of eukaryotic host and prokaryotic markers was used. The tested approach gave reliable and satisfactory results both on samples collected from different habitats (marine and freshwater) and on ciliates belonging to different taxonomic groups. Obtained data show that, as already assessed for many macro-organisms like plants and metazoans, protist ciliates do possess a specific, well-defined microbiome. The applied approach succeeded in characterizing these microbiomes and in detecting new potential symbionts as well as new hosts for previously known ones, with relatively low time and cost effort. Single-cell microbiomics for protists can be flexibly applied to a large number of studies aiming to unravel the evolutionary and ecological meaning of these symbiotic systems.