AUTHOR=Har Jia Y., Helbig Tim , Lim Ju H., Fernando Samodha C., Penn Kevin , Reitzel Adam M., Thompson Janelle R.

TITLE=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

JOURNAL=Frontiers in Microbiology

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.00818

DOI=10.3389/fmicb.2015.00818

ISSN=1664-302X

ABSTRACT=<p>We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone <italic>Nematostella vectensis</italic>, 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 <italic>N. vectensis</italic> at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing &lt;85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing &gt;99% 16S rRNA identity with <italic>Endozoicomonas elysicola</italic> and <italic>Pseudomonas oleovorans</italic>, respectively. Species-specific PCR revealed that these populations persisted in <italic>N. vectensis</italic> asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and <italic>Endozoicomonas</italic> 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised <italic>N. vectensis</italic> was dominated by isolates from <italic>P. oleovorans</italic> and <italic>Rhizobium radiobacter</italic>. Isolates from field-collected anemones revealed an association with <italic>Limnobacter</italic> and <italic>Stappia</italic> isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., <italic>Limnobacter</italic> spp., <italic>Stappia</italic> spp., <italic>P. oleovorans</italic> and <italic>R. radiobacter</italic>. Genomes contained multiple genes identified as virulence (host-association) factors while <italic>S. stellulata</italic> and <italic>L. thiooxidans</italic> genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised <italic>N. vectensis</italic> was compared to the isolate genomes and indicated expression of ORFs from <italic>L. thiooxidans</italic> 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 <italic>N. vectensis</italic> holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.</p>