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 as well as facilitate identification of core microbial symbionts that would have otherwise been overlooked by bulk sampling methods. In this study, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct body regions: the capitulum, mesenteries, and physa. This sampling design allowed us to uncover distinct bacterial community compositions between compartments, including the 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. Spirochetes are known to play significant roles in nitrogen and carbon cycling as symbionts of other invertebrates. The capitulum community also exhibited significantly lower Alpha-diversity compared to the other two compartments, however Beta-diversity metrics between the compartments were inconclusive as to their distinctness. A phylogenetic analysis of the predominate Spirochete sequence recovered from N. vectensis showed higher similarity to Spirochaeta spp. recovered from the Pacific Oyster, Crassostrea gigas, the cold water coral, Lophelia pertusa, and the soft coral, Millepora sp., but not to a Spirochete previously recovered from N. vectensis. This suggests a flexible capitulum niche in N. vectensis open to different groups of Spirochaetales depending on the environmental circumstances of the association.