A Metatranscriptome. Better than a Metagenome?

The Eastern Tropical South Pacific Oxygen Minimum Zone (ETSP-OMZ) off the coast of northern Chile is one of the world's permanent naturally occurring OMZs. The microbial communities which dominate OMZs and the processes carried out by them have been studied in great detail in recent years. This has been undertaken by assessing the presence and abundance of functional genes, presence of taxonomic groups and pathways to name a few. But much work remains to determine which genes relating to specific metabolic processes from different taxa are important in the overall context of the community. This calls for the use of metatranscriptomics, which investigates the expression of genes by detecting RNA rather than examining just the presence of a gene (via metagenomics), so can tell us which genes are being most actively used.

Stewart et al. (2012), produced a metatranscriptome and metagenome using pyrosequencing on samples from four depth sites in the ETSP-OMZ, spanning the aerobic photic zone (50m) the oxic-anoxic transition zone (85, 110m) and the anoxic OMZ core (200m). They then characterised the main patterns of the metatranscriptomes for protein coding genes using BLAST and used the metagenomics data to provide a comparison to each transcriptome. Interestingly the authors created a phylogeny using the transcriptome of protein coding genes. This allowed which transcripts belonged to which taxanomic groups to be determined, so indicating how active each group was. For example, metabolic activity along the oxic-suboxic transition was dominated by the Crenarchaeota, with a third of all identifiable protein-coding transcripts from upper waters being produced by them. This was much higher than the most abundant organism at all depths in terms of DNA Pelagibacter. So indicating that metatanscriptomics can reveal functionally important organisms which might be thought to play only a minor role from metagenomics or be poorly represented in 16S rRNA phylogenies.

In terms of expression of functional genes, one of the most highly expressed genes in the upper three samples was the ammonia oxidation gene, amo. Produced almost exclusively by the Crenarchaeota, which dominated ammonia oxidation along the oxycline and into the OMZ. This was in contrast to previous results and the metagenomes which suggested the presence of nitrifying bacteria. Although at this point it is important to point out that this emerging technology can at times be biased, as a few highly transcribed genes can mask less transcribed genes. Therefore the bacteria could still be active at low levels. The transcriptomes also showed a shift to anaerobic nitrogen metabolism with depth in the OMZ and an increase in transcripts encoding enzymes used by Planctomycetes, common and active in the OMZ core, in ANOMOX processes. In contrast genes involved in sulphur-based energy metabolism were expressed throughout the OMZ with an indication of the coupling of sulphur oxidation and denitrification. Sulphur-oxidising microbes were also detected in the phylogeny which further supports other studies suggesting an active sulphur cycle.    

Overall I feel that this study shows how powerful these methods can for determining which organisms are most active in ocean processes, despite some problems with method. It would be particularly interesting to extend this study by repeatedly sampling over a few days to build a time series of gene expression at the community level to see how this varies over time. Personally I think these studies lend us an extra level of detail in determining how our oceans function and it would be interesting to look at other systems where metatranscriptomics has been used.

Ref: Stewart, F.J., Ulloa, O. and DeLong, E.F. (2012). Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environmental Microbiology, 14(1), 23-40.