Department of Genetics In Ecology

Meta-transcriptomics to study the function and structure of complex microbial communities

FUNDING

PARTICIPANTS

We are interested in the characterisation of complex microbial communities with cultivation-independent molecular genomic approaches to disclose the ecological function of uncultured archaea and bacteria. Meta-genomic technologies have been used for many years for this purpose and as a logical next step we have recently established meta-transcriptomic approaches in our laboratory.
Meta-transcriptomics offers the opportunity to reach beyond the community’s genomic potential as assessed in DNA-based methods, towards its in situ activity. In addition, the analysis of the RNA pool of a community links its taxonomic structure and function, as it is naturally enriched not only in functionally but also taxonomically relevant molecules, i.e. mRNA and rRNA, respectively. In addition rRNA can be used for PCR-independent community profiling of all three domains of life.
We have established appropriate experimental and analytical procedures (the “double-RNA” approach) for in-depth characterization of microbial communities by studying mRNA and rRNA molecules simultaneously from the same sample.

We are especially interested in soil ecosystems as they cover almost all of the terrestrial area on Earth and have an indispensable ecological function in the global cycles of carbon, nitrogen and sulfur. Due to their physico-chemical complexity with many micro-niches, they teem with bio-diversity, both phylogenetically and functionally.
In addition, meta-transcriptomics is applied and further developed on different biological systems, such as sponges (host-symbiont) and hydrothermal vents.

Abundance-dependent plot of presumably archaeal mRNA-tags onto the crenarchaeal fosmid clone 54d9. The x-axis represents the annotated open reading frames (orfs).

http://genetics-ecology.univie.ac.at/metatranscriptomics-gbarretti