Intersection of genotype and environment on the dynamics of the virome and microbiome of an estuarine cnidarian

Abstract

Estuaries host a rich diversity of microorganisms, creating opportunities for animal–microbe interactions that shape host physiology. The sea anemone Nematostella vectensis spans the eastern coast of North America from Nova Scotia to Florida, and prior work shows that anemones from different regions harbor distinct microbial communities. Although the virome of the standard laboratory population has been characterized, population-level variation in viromes remains largely unknown. To address this gap, we conducted a mesocosm experiment using six N. vectensis populations to test whether geographic origin influences the diversity and functional potential of associated viruses and bacteria. We sampled individuals before mesocosm exposure and 14 days after to sequence their viromes, microbiomes, and host transcriptomes. We also collected anemones from a natural population to compare against experimental animals. Both virome and microbiome analyses revealed increased taxonomic and functional diversity after 14 days, with the strongest increase observed in lower-latitude populations. Notably, experimental anemones did converge toward the natural population’s community composition; however, population-specific interactions with viruses and microbes persisted. Differential gene expression indicated a modest host response overall, whereas WGCNA identified a clear north–south expression pattern. Together, these findings demonstrate that N. vectensis genotypes from locations along a latitudinal gradient maintain distinct viral and microbial associations, highlighting geographically structured host–microbe–virus relationships.