Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

Shi, Yanmei, Tyson, Gene, Eppley, John M. and DeLong, Edward F. (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. The ISME Journal, 5 6: 999-1013. doi:10.1038/ismej.2010.189


Author Shi, Yanmei
Tyson, Gene
Eppley, John M.
DeLong, Edward F.
Title Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean
Journal name The ISME Journal   Check publisher's open access policy
ISSN 1751-7362
1751-7370
Publication date 2011-06-01
Year available 2010
Sub-type Article (original research)
DOI 10.1038/ismej.2010.189
Open Access Status Not yet assessed
Volume 5
Issue 6
Start page 999
End page 1013
Total pages 15
Place of publication New York, NY, United States
Publisher Nature Publishing Group
Language eng
Subject 2404 Microbiology
1105 Ecology, Evolution, Behavior and Systematics
Abstract As part of an ongoing survey of microbial community gene expression in the ocean, we sequenced and compared ∼38 Mbp of community transcriptomes and ∼157 Mbp of community genomes from four bacterioplankton samples, along a defined depth profile at Station ALOHA in North Pacific subtropical gyre (NPSG). Taxonomic analysis suggested that the samples were dominated by three taxa: Prochlorales, Consistiales and Cenarchaeales, which comprised 36-69% and 29-63% of the annotated sequences in the four DNA and four cDNA libraries, respectively. The relative abundance of these taxonomic groups was sometimes very different in the DNA and cDNA libraries, suggesting differential relative transcriptional activities per cell. For example, the 125 m sample genomic library was dominated by Pelagibacter (∼36% of sequence reads), which contributed fewer sequences to the community transcriptome (∼11%). Functional characterization of highly expressed genes suggested taxon-specific contributions to specific biogeochemical processes. Examples included Roseobacter relatives involved in aerobic anoxygenic phototrophy at 75 m, and an unexpected contribution of low abundance Crenarchaea to ammonia oxidation at 125 m. Read recruitment using reference microbial genomes indicated depth-specific partitioning of coexisting microbial populations, highlighted by a transcriptionally active high-light-like Prochlorococcus population in the bottom of the photic zone. Additionally, nutrient-uptake genes dominated Pelagibacter transcripts, with apparent enrichment for certain transporter types (for example, the C4-dicarboxylate transport system) over others (for example, phosphate transporters). In total, the data support the utility of coupled DNA and cDNA analyses for describing taxonomic and functional attributes of microbial communities in their natural habitats.
Keyword Metatranscriptomics
Metagenomics
Bacterioplankton
Microbial gene expression/regulation
Biogeochemical processes
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID EF0424599
Institutional Status UQ
Additional Notes Published online 9 December, 2010.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Advanced Water Management Centre Publications
 
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Created: Tue, 15 Feb 2011, 00:09:49 EST by Hong Lee on behalf of Advanced Water Management Centre