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We studied the microbial communities associated with the Baikal ostracods,
Candona
sp. (Candonidae). Bacterial biofilms were identified on the shell valves of the ostracods localized near epibiotic ciliates of the genus
Lagenophrys
(Ciliophora: Lagenoprydae). In situ hybridization confirmed the presence of eubacterial cells in different parts of the ostracod’s body. Bacteria of two morphotypes were detected in bacterial biofilms, including filamentous bacteria
.
Next-generation sequencing of 16S rRNA bacterial gene fragment allowed us to identify representatives of five bacterial phyla. Members of the phyla
Proteobacteria
and
Bacteroidetes
typical of non-marine epibiotic associations of ostracods were dominant taxa in the ostracod microbiomes. Members of other taxa (
Actinobacteria, Gracilibacteria
and
Cyanobacteria
) are likely facultative and consumed by ostracods together with detritus. In the ostracod microbiome, a significant proportion (20% of all reads) belonged to the sequences of the genus
Rickettsia
related to intracellular parasites
.