The diversity and genomic composition of marine microorganisms in surface waters of the ocean has been the focus of several recent studies. Their assemblages are astonishingly diverse and communities are variable spatially concomitant with variability in physicochemical habitat. Metagenomic (i.e. DNA-based) studies elucidate the genomic potential for particular physiological and biosynthetic functions within assemblages. However, there is little information on the utilization of genes (i.e. gene expression) within assemblages, and how their transcription varies between habitats.
Metatranscriptomics (random sequencing of gene transcripts) holds promise to elucidate active transcriptional processes in complex microbial assemblages. This approach recently demonstrated a large proportion of novel transcript sequences at station ALOHA (Frias-Lopez et al., 2008) and in a Norwegian fjord (Gilbert et al., 2008). Because there can be differential expression of genes between taxa and even between cells of the same taxon, metatranscriptomics does not elucidate the diversity of microorganisms, but rather provides snapshots of dominant gene transcripts. Because > 99 % of total RNA is rRNA, the efficiency of sequencing is improved by protocols to enrich mRNAs relative to rRNAs. Thus, unlike metagenomics, quantitative analysis of rRNAs recovered from metatranscriptomes is not possible where attempts to remove rRNAs have been made.
In our study, surface water microorganisms were collected on two research cruises in the equatorial North Atlantic ocean and South Pacific Subtropical gyre to understand variability in gene expression and gene complement in the oligotrophic ocean. Because sunlight exerts profound influence upon biogeochemical processes in the upper ocean (e.g. photosynthesis and nitrogen fixation), samples for RNA were collected in both light and dark phases to compare diel gene expression patterns. These samples complement samples collected for investigation of important biogeochemical processes related to N (N2-Fixation) and C (CO2 fixation) cycles.
