Limits...
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 JY, Helbig T, Lim JH, Fernando SC, Reitzel AM, Penn K, Thompson JR - Front Microbiol (2015)

Bottom Line: Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA.

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 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.

No MeSH data available.


Related in: MedlinePlus

Diversity of metatranscriptome sequences identified by BLASTX against the NCBI non-redundant protein database. Identified sequences were imported into the MEGAN software package and binned taxonomically using the least common ancestor algorithm (Bit score >40.0). Matches to bacterial phyla are presented.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4557100&req=5

Figure 6: Diversity of metatranscriptome sequences identified by BLASTX against the NCBI non-redundant protein database. Identified sequences were imported into the MEGAN software package and binned taxonomically using the least common ancestor algorithm (Bit score >40.0). Matches to bacterial phyla are presented.

Mentions: Individual sequence pair units were compared against the NCBI non-redundant protein database using BLASTX and slightly less than half of the sequences shared significant similarity with database proteins (i.e., 259,746 database matches) and were assigned to taxonomic groups using MEGAN. Consistent with assembled contigs, the majority of sequences with database matches were “Cnidarian” corresponding to the host anemone taxonomy (77.5% of assigned sequences) (Figure 6). The other top assignments were Metazoan taxa (12.6% of assigned sequences), Opisthokonta (2.2%), and Eukaryota (5.6%) suggesting that >90% of the expressed non-ribosomal sequences from the holobiont derived from the host anemone. Sequences similar to microbial eukaryotes each corresponded to < 0.15% of sequences. Of the 1746 sequences annotated as bacterial (0.67% of sequences with database matches), 1308 corresponded to Proteobacteria (75%), followed by unclassified bacteria (13%), Actinobacteria (6.4%) and Firmicutes (3.9%) (Figure 6).


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 JY, Helbig T, Lim JH, Fernando SC, Reitzel AM, Penn K, Thompson JR - Front Microbiol (2015)

Diversity of metatranscriptome sequences identified by BLASTX against the NCBI non-redundant protein database. Identified sequences were imported into the MEGAN software package and binned taxonomically using the least common ancestor algorithm (Bit score >40.0). Matches to bacterial phyla are presented.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4557100&req=5

Figure 6: Diversity of metatranscriptome sequences identified by BLASTX against the NCBI non-redundant protein database. Identified sequences were imported into the MEGAN software package and binned taxonomically using the least common ancestor algorithm (Bit score >40.0). Matches to bacterial phyla are presented.
Mentions: Individual sequence pair units were compared against the NCBI non-redundant protein database using BLASTX and slightly less than half of the sequences shared significant similarity with database proteins (i.e., 259,746 database matches) and were assigned to taxonomic groups using MEGAN. Consistent with assembled contigs, the majority of sequences with database matches were “Cnidarian” corresponding to the host anemone taxonomy (77.5% of assigned sequences) (Figure 6). The other top assignments were Metazoan taxa (12.6% of assigned sequences), Opisthokonta (2.2%), and Eukaryota (5.6%) suggesting that >90% of the expressed non-ribosomal sequences from the holobiont derived from the host anemone. Sequences similar to microbial eukaryotes each corresponded to < 0.15% of sequences. Of the 1746 sequences annotated as bacterial (0.67% of sequences with database matches), 1308 corresponded to Proteobacteria (75%), followed by unclassified bacteria (13%), Actinobacteria (6.4%) and Firmicutes (3.9%) (Figure 6).

Bottom Line: Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA.

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 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.

No MeSH data available.


Related in: MedlinePlus