Genomic and Applied Microbiology

Research project:

Ecology, Physiology and Molecular Biology of the Roseobacter clade: Towards a Systems Biology Understanding of a Globally Important Clade of Marine Bacteria

Transregio Sonderforschungsbereich (TRR51), supported by the Deutsche Forschungsgemeinschaft (DFG)

Subproject: Assessment and exploitation of the metabolic potential and molecular characterization of uncultivated members of the Roseobacter clade

In this subproject, the genomic potential and important functions of Roseobacter populations will be analyzed by culture-independent metagenomic and metatranscriptomic approaches. To identify indigenous gene- and taxon-specific patterns and key metabolic functions comparative metabolic and functional profiling of representative samples from the North Sea, the Southern Ocean, biofilms, and mesocosms will be performed by employing large-scale pyrosequencing. The mesocosm experiments will be focused on the effect of addition of organic sulfur compounds, defined phytoplankton algae, or organic compounds on the functional and phylogenetic structure of the community. The influence of incubation at light and dark as well as different salinities and pH values will be also evaluated. For metagenomic sequence analysis and for metatranscriptomic analyses, DNA and RNA, respectively, will be isolated from all samples, simultaneously. In addition, metagenomic libraries are constructed and screened for important functions such as genes involved in quorum sensing, energy metabolism, production of secondary metabolites and the corresponding regulatory networks. The large-insert libraries are also screened for phylogenetic anchors such as 16S rRNA genes. Recombinant fosmids harbouring 16S rRNA genes are sequenced. In this way, a phylogenetic marker is linked to other genes of the same organisms. This approach will be extended to other marker genes and gene clusters. These studies in close cooperation with the results of the systems biology approaches to model organism allow a partial genome characterization of uncultivated roseobacters via comparison to the data obtained for the cultivated Roseobacter strains. The distribution and variability of certain genes and pathways in environmentally abundant members of the Roseobacter group are mirrored. In this way, generated systems biology models from other subprojects can be extended to uncultivated Roseobacter clade bacteria.

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