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

ISME J. 2011 Jun;5(6):999-1013. doi: 10.1038/ismej.2010.189. Epub 2010 Dec 9.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alphaproteobacteria / genetics
  • Alphaproteobacteria / isolation & purification
  • Crenarchaeota / genetics
  • Crenarchaeota / isolation & purification
  • DNA, Complementary / genetics
  • Ecosystem
  • Gene Expression Profiling*
  • Gene Library
  • Metabolic Networks and Pathways
  • Metagenomics / methods*
  • Oceans and Seas
  • Prochlorococcus / genetics
  • Prochlorococcus / isolation & purification
  • Prochlorococcus / metabolism
  • RNA, Bacterial / genetics
  • Roseobacter / genetics
  • Roseobacter / isolation & purification
  • Seawater / microbiology*


  • DNA, Complementary
  • RNA, Bacterial