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We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone  Nematostella vectensis , a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with  N. vectensis  at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with  Endozoicomonas elysicola  and  Pseudomonas oleovorans , respectively. Species-specific PCR revealed that these populations persisted in  N. vectensis  asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and  Endozoicomonas  16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised  N. vectensis  was dominated by isolates from  P. oleovorans  and  Rhizobium radiobacter . Isolates from field-collected anemones revealed an association with  Limnobacter  and  Stappia  isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e.,  Limnobacter  spp.,  Stappia  spp.,  P. oleovorans  and  R. radiobacter . Genomes contained multiple genes identified as virulence (host-association) factors while  S. stellulata  and  L. thiooxidans  genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised  N. vectensis  was compared to the isolate genomes and indicated expression of ORFs from  L. thiooxidans  with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a  N. vectensis  holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.

frontiers in microbiology

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression