Work Package 2 (Rabus, Blasius, Wilkes)

"Organic matter-shaping metabolic and protein networks of Desulfobacteraceae members"

Broader background of the proposed research project

Sulfate-reducing prokaryotes (SRP) are major drivers of the carbon cycle in marine sediments. At highly active sites (e.g. Wadden Sea), terminal oxidation of organic matter (OM) is channeled to a large part through microbial sulfate reduction. This rests upon the nutritional versatility combined with complete substrate oxidation (to CO2) essentially confined to the deltaproteobacterial family of Desulfobacteraceae (Rabus et al. 2000). Indeed, its members were repeatedly demonstrated to dominate the SRP community in diverse marine sediments (e.g. Llobet-Brossa et al. 2002). Recent (proteo)genomic studies, e.g. of chemolithoautotrophic Desulfobacterium autotrophicum (Strittmatter et al. 2009) and aromatic compound-degrading Desulfobacula toluolica (Wöhlbrand et al. 2013), have revealed complex metabolic networks and thereby underpinned the necessity and benefit of comparative metabolic reconstruction of other Desulfobacteraceae members (Rabus et al. 2015). Combined proteogenomic and metabolomic studies of SRP promise to provide a valuable knowledge base on how these microbes shape the to date mostly unexplored “geo-metabolome” in marine sediments.

Outline for the proposed PhD research project

Metabolic and protein networks of Desulfobacteraceae are in the focus of this PhD project. The proposed project is based on the hypothesis that Desulfobacteraceae members by virtue of their broad metabolic capacities significantly imprint on OM composition in marine sediments. Comparative proteogenomics of metabolic networks and transporter complements will assess the strain-specific vs. cumulative metabolic potential of selected Desulfobacteraceae members with respect to (i) which organic substances can be depleted from sedimentary OM and (ii) which metabolites and cellular components are released from the cells and thereby add to OM complexity. This project will be based on (proteo)genomic data already existing in AG Rabus for D. autotrophicum, D. toluolica (both published), Desulfococcus multivorans (unpublished) and on genomes of further SRP (incl. filamentous and oil-degrading species). Thus, the main part of this project will be concerned with comparative analysis. Differential (subcellular) proteomics will be conducted for the newly genome-sequenced strains (full cycle proteomics is well established in AG Rabus). In addition, all studied SRPs will be batch-cultured with selected substrates to provide samples for targeted (WP3) and global (WP4) analysis of metabolites. To integrate the proteogenomic and metabolomic data and to unravel unnoticed causal connections, mathematical modelling will be performed by WP10. The data integration/modelling will also allow a comparison of OM dynamics between pelagic and benthic environments, generating a unique added value for EcoMol.