Is the trophosome of Ridgeia piscesae monoclonal?

Abstract

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 (insertions, 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 diversity 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.