The transcriptome is the set of all the mRNA within the cell. Unlike the genome, which is the all DNA present within the cell, the transcriptome only reveals those genes which are being turned into proteins. This therefore acts as an indication of the changes in protein production within the cell.
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For large bacterial colonies however, individual transcriptomic studies aren't much use for finding out the state of the whole colony. Each bacteria within the colony will not only be reacting slightly differently, but will also be experiencing different conditions within the colony depending on where it is within the colony. It's often best, therefore to treat the entire colony as one 'cell' and carry out transcriptome studies on the whole lot. This is metatranscriptomics.
Nowadays one of the easiest ways to carry this out is by isolating the RNA and getting it all directly sequenced by Pyrosequencing (which saves the trouble of making microarrays). As well as giving information about the changes within a colony due to environmental factors, it can also show the changes in protein production at different stages in the colony lifecycle such as at the beginning and end of an algal bloom. The integration of new third-generation sequencing methods into this process will make it faster and hopefully allow isolation of the rarer, less abundant transcripts to find more subtle changes in gene expression.
This has important implications for things like oceanic cyanobacteria which are involved in carbon sequestration in the oceans. Understanding how changes such as increases in ocean acidity (or decreases in salinity) affects their growth and ability to remove carbon from the atmosphere could have important implications for global warming, and how it can be dealt with.
Gilbert JA, Field D, Huang Y, Edwards R, Li W, Gilna P, & Joint I (2008). Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PloS one, 3 (8) PMID: 18725995