Intracellular prokaryotes in rumen ciliate protozoa: Detection by confocal laser scanning microscopy after in situ hybridization with fluorescent 16S rRNA probes

In situ hybridization of rumen ciliate protozoa with 16S ribosomal RNA fluorescent oligonucleotide probes specific for Archaea and Bacteria provided semi-quantitative indication of the location, type and extent of prokaryotic colonization of various protozoal species. The isotrichid holotrich ciliates generally carried a smaller load of intracellular microorganisms than did the entodiniomorphid species. Thus, the vast majority of the Dasytricha ruminantium population had neither bacterial not archaeal endosymbionts, although a very small minority of these ciliates (only 11 out of 447: 250 cells per ciliate) of intracellular Bacteria, but no Archaea. Only some Epidinium spp. had intracellular prokaryotes, whereas Entodinium spp. and Ent. simplex almost always had. Many of the larger entodiniomorphid genera were heavily colonized by both bacterial and archaeal species. Eudiplodinium maggii had no obvious bacterial associates, although the autofluorescence of ingested plant material made difficult the detection of possible endosymbionts.