Microniche sampling of the microbiome in the Starlet Sea Anemone, Nematostella vectensis, reveals a compartment-specific dominance of Spirochetes

Microniche sampling can reveal highly specialized bacterial associations within the holobiont and also facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. We characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct body regions. This sampling design allowed us to uncover a compartment-specific dominance of spirochetes within the capitulum of N. vectensis. Bacteria from the Spirochaetaceae family made up 65.8% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. The capitulum community also exhibited significantly lower alpha-diversity compared to the other two compartments. A phylogenetic analysis of the predominate spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this genus. This suggests a consistent and potentially important association between N. vectensis and spirochetes from the Spirochaetales family.