The hydrothermal vent tubeworm Ridgeia piscesae
relies on intracellular chemolithoautotrophic symbionts for its
nutrition. Yet, little is known about symbiont diversity within
and between individual worms. We report several lines of
molecular evidence for multiple genotypes of very closely
related symbionts within the trophosome of the R. piscesae.
We examined the distribution of genotypic variants (inser-
tions, deletions, and substitutions) in whole genome shotgun
sequences of symbionts from the trophosome of a unique
individual R. piscesae and the pooled sequences of five other
tubeworms of the same species. Observed heterogeneity is
unlikely to be the result of recent point or structural mutations
of a monoclonal symbiont lineage. To assess inter-host diver-
sity we examined single nucleotide polymorphisms (SNPs) in
pyrosequences of the highly variable regions V1 to V3 of the
symbiont 16S rRNA gene across 53 individual hosts from two
vent sites. Most of the identified SNPs were found in more
than one individual, and one seemed to be region specific.
Two of the identified SNPs were also present in metagenomic
data generated from high-throughput sequencing of
trophosome material from an individual R. piscesae. Finally,
we observed compositional and structural variations of
CRISPR spacers within a CRISPR array.

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• Is the trophosome of Ridgeia piscesae monoclonal?