Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut

Abstract

In 1944, Harold Kirby described microorganisms living within nuclei of the protists Trichonympha in guts of termites; however, their taxonomic assignment remains to be accomplished. Here, we identified intranuclear symbionts of Trichonympha agilis in the gut of the termite Reticulitermes speratus. We isolated single nuclei of T. agilis, performed whole-genome amplification, and obtained bacterial 16S rRNA genes by PCR. Unexpectedly, however, all of the analyzed clones were from pseudogenes of 16S rRNA with large deletions and numerous sequence variations even within a single-nucleus sample. Authentic 16S rRNA gene sequences were finally recovered by digesting the nuclear DNA; these pseudogenes were present on the host Trichonympha genome. The authentic sequences represented two distinct bacterial species belonging to the phylum Verrucomicrobia, and the pseudogenes have originated from each of the two species. Fluorescence in situ hybridization confirmed that both species are specifically localized, and occasionally co-localized, within nuclei of T. agilis. Transmission electron microscopy revealed that they are distorted cocci with characteristic electron-dense and lucent regions, which resemble the intranuclear symbionts illustrated by Kirby. For these symbionts, we propose a novel genus and species, 'Candidatus Nucleococcus trichonymphae' and 'Candidatus Nucleococcus kirbyi'. These formed a termite-specific cluster with database sequences, other members of which were also detected within nuclei of various gut protists, including both parabasalids and oxymonads. We suggest that this group is widely distributed as intranuclear symbionts of diverse protists in termite guts and that they might have affected the evolution of the host genome through lateral gene transfer.

Rampant Host Switching Shaped the Termite Gut Microbiome

“…animal guts, are likely to have been transferred through contact with soil or through feeding. The gut microbiota of lower termites contains many bacterial lineages that are specifically associated with the surface, the cytoplasm, or the nucleus of their symbiotic flagellates (e.g., [23][24][25]). Phylogenetic analyses have documented co-speciation between flagellates and their bacterial symbionts and flagellates [8,26,27], but co-cladogenesis between bacterial symbionts and termites remains an exception [8] because of the occasional horizontal transfer of flagellates between termites of different families.…”

Comparison of Intracellular “Ca.Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA

“…Worker termites reared with cellulose powder for 3 days were subjected to the experiments. Single-cell isolation of gut protists and collection of their endosymbiotic Endomicrobium cells were performed as described previously (Hongoh et al 2008a), with an addition of 0.1% Tween 20 (Sigma-Aldrich) (Sato et al 2014). WGA was performed with the illustra GenomiPhi HY DNA Amplification Kit (GE Healthcare Life Sciences) for 8 h, as described previously (Hongoh et al 2008b).…”

The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution

“…Planctomycetes form large populations only in the posterior hindgut compartments of soil-feeding Termitinae (55), but they also occur in low abundance in other groups (92). Verrucomicrobia related to "Candidatus Nucleococcus," an intranuclear symbiont of termite gut flagellates (103), are abundant in several lower termites but found also in hosts that lack flagellates (22).…”