Project TP1: (Meta)proteomic of marine model bacteria and model habitats

Responsible: Thomas Schweder, EMAU Greifswald


In order to get deeper insights into the interaction of marine bacteria and their environment, in situ expression analyses are indispensible. A primary goal of this project is the development of suitable techniques for metaproteome analyses of complex microbial assemblages in marine ecosystems. Gene expression analysis tools would facilitate the enhanced determination of key organisms and their role in global energy- and nutrient cycles in natural marine habitats. Hitherto, in situ proteomic techniques have been used only sporadically for the analysis of metaproteomes of microbial communities from environmental samples. One reason is that established proteomic techniques are geared to the analysis of cellular proteomes of one defined sequenced organism but not adapted to the special requirements of the monitoring of complex microbial assemblages with low genome sequence background. Thus, a prerequisite for successful mass spectrometry (ms) -based protein identifications of complex environmental samples is the availability of a sufficient metagenome sequence background. But also new software tools are required, which allow for an improved de novo sequencing of identified peptides.


tl_files/images/tp1_1.jpgIn the frame of this project strategies for a reproducible metaproteome analysis of complex marine microbial communities will be established and verified. Cell density gradient centrifugation approaches will be used to decrease the microbial complexity in the water samples and to fractionate related bacterial cell populations. Furthermore, different protein- and peptide-separation techniques will be tested for an improved sensitivity of the mass-spectrometrical identification of complex protein samples. The sequencing activities (TP 5) of the metagenome libraries (TP 3 und TP4) and the ESTs (TP 2) provide an essential basis for the comprehensive analysis of the ms data. Developed metaproteomic strategies will be exemplarily verified on two model locations (Helgoland and Gotland Deep), which are of central importance for the German marine ecosystem research.


Furthermore, in depth proteome analyses of marine model bacteria, which are supposed to be representative of abundant taxonomical groups at the two model habitats, will be undertaken. The proteomes of the planctomycete Rhodopirellula baltica SH 1T, of the gammaproteobacterium Congregibacter litoralis KT71, and of the chemolithoautotrophic epsilonproteobacterium Sulfurimonas strain „GD1“ will be analyzed under growth conditions, which are as close to the in situ conditions as possible. Proteomic signatures under defined stress- and nutrient starvation conditions will be determined. By these analyses environmentally relevant marker proteins can be identified and genes with so far unknown functions can be functionally classified. Finally, in situ metaproteome samples of the corresponding model habitat will be searched for in vitro identified marker proteins of these key bacteria.