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Transcriptomics is the research of a set (or all) RNA molecules, including mRNA, rRNA, tRNA, and non-coding RNA produced in one or a population of cells (see Wikipedia for more informations). Metatranscriptomics is expanding this research to cells of multiple organisms, which are analysed in parallel, like for example in environmental samples.
My research interest lies on fungal transcripts (especially mRNAs) in soil samples. In these samples I want to detect fungal activity, i.e. the analysis of fungal mRNAs that encode for example extracellular enzymes. Hereby we apply more “classical” procedures, like screening of transcriptomic libraries using yeast mutants, either by functional complementation or the extracellular detection of enzymes using different substrates. Using this approach we avoid cost-, time- and computer-intense high-throughput (next-generation) sequencing techniques. However, the later approach will be crucial for our understanding of environmental processes in near future.
Methods
At the moment we use two approaches: i) the analyses of fungal transcripts in cDNAs by PCR with degenerate primers, hereby comparing different soil samples, and ii) the complementation of yeast mutants using metatranscriptomic libraries. The first approach is sequence based, however in limited amounts due to sequencing costs. The second approch focuses on detection and sequencing of single or few positive candidates.
Of course both approaches have limitations and need steady improvement (discussed in the publications).
Results
Currently we are able to follow the expression of more than 20 fungal genes encoding biogeochemically relevant enzymes in forest soil cDNA (Study I). Moreover, we are now generating metatranscriptomic libraries in yeast expression vectors for functional screenings (Study II). In future we will expand these studies.
Study I: Detection of transcripts encoding lignocellulolytic and chitinolytic enzymes. [link]
Study II: Detection of acid phosphatase by complemtation of a yeast pho5- mutant. [link]
Suggested literature
Bailly J, Fraissinet-Tachet L, Verner MC, Debaud JC, Lemaire M, et al. (2007) Soil eukaryotic functional diversity, a metatranscriptomic approach. ISME J 1: 632–642.
Acknowledgement
I have to thank Micheline Vandenbol, Daniel Portetelle, Sebastian Steels, Rene Martin for their help, as well as many more people involved in this particular research.
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