Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but do reveal the presence of giant viruses

Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4
μm) heterotrophic microbial eukaryote. The genus was named based
on the presence of endosymbiotic bacteria in its endoplasmic
reticulum, however, like most such endosymbionts neither the
identity nor functional association with its host were known. We
generated both amplification-free shotgun metagenomics and whole
genome amplification sequencing data from S. scintillans strains
RCC257 and RCC24, but were unable to detect any sequences from known
lineages of endosymbiotic bacteria. The absence of endobacteria was
further verified with FISH analyses. Instead, numerous contigs in
assemblies from both RCC24 and RCC257 were closely related to
prasinoviruses infecting the green algae Ostreococcus lucimarinus,
Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV,
respectively). Using the BpV genome as a reference, we assembled a
near-complete 190 kbp draft genome encoding all hallmark prasinovirus
genes, as well as two additional incomplete assemblies of closely related
but distinct viruses from RCC247, and three similar draft viral genomes
from RCC24, which we collectively call SsVs. A multi-gene tree showed the
three SsV genome types branched within highly supported clades with each
of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission
electron microscopy also revealed a 190 nm virus-like particle similar to
the morphology and size of the endosymbiont originally reported in S.
scintillans. Overall, we conclude that S. scintillans currently
does not harbour an endosymbiotic bacterium, but is
associated with giant viruses.