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

Jia Yi Har, Tim Helbig, Ju Hyoung Lim, Samodha C. Fernando, Adam M. Reitzel, Kevin Penn, Janelle R. Thompson

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

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 e-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.

Original languageEnglish (US)
Article number818
JournalFrontiers in Microbiology
Volume6
Issue numberJUL
DOIs
StatePublished - Jan 1 2015

Fingerprint

Pseudomonas oleovorans
rRNA Genes
Anemone
Genome
Ribotyping
Gene Expression
Agrobacterium tumefaciens
Wetlands
Polyhydroxyalkanoates
Sea Anemones
Cnidaria
Bacteria
Food
Developmental Biology
Porins
Spirochaetales
Acclimatization
Microbiota
Gene Library
DNA Sequence Analysis

Keywords

  • Cnidaria
  • Holobiont
  • Microbiota
  • Mixotrophy
  • Nematostella vectensis
  • Phasins

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

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. / Har, Jia Yi; Helbig, Tim; Lim, Ju Hyoung; Fernando, Samodha C.; Reitzel, Adam M.; Penn, Kevin; Thompson, Janelle R.

In: Frontiers in Microbiology, Vol. 6, No. JUL, 818, 01.01.2015.

Research output: Contribution to journalArticle

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abstract = "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 e-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.",
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