Microbes’ microbiomes: a single-cell approach for the characterization of associations between protist ciliates and prokaryotes.. Microbes’ microbiomes: 18S rRNA host genes.

Microbial associations represent an exceptionally common and widespread phenomenon, whose ecological significance is still to be fully understood. Symbiosis between prokaryotes and protist ciliates have been studied in a long time. Nevertheless, researches focused only on a few genera and species, mainly because characterization of the involved partners requires host cultivation. Here we present a pilot study aimed at developing a novel approach which can be easily and efficiently used for field researches on microbial associations. Single host-cell isolation followed by a simultaneous amplification of eukaryotic host and prokaryotic microbiome markers was used. The tested approach gave reliable and satisfactory results both on samples collected from different habitats (marine/freshwater) and on ciliates belonging to different taxonomic and phylogenetic groups. Obtained data show that, as already assessed for many macro-organisms like plants or metazoans, protist ciliates possess a specific, well-defined microbiome, too. The applied approach succeeded in characterizing these microbiomes and in detecting new potential symbionts and/or new candidate microbial association in many non-model host organisms. The validity and stability of such symbiotic systems, as well as their evolutionary and ecological meaning should be then further investigated by properly designed studies.