Work package 3 (Wilkes, Rabus, Christoffers)
"Targeted metabolome analysis of Desulfobacteraceae members"
Broader background of the proposed research project
Key to the central role of sulfate-reducing prokaryotes (SRP) in the mineralization of organic matter in marine sediments is not only their capacity for complete oxidation but also their broad nutritional versatility. The latter comprises simple fermentation end products, long-chain fatty acids and even recalcitrant aromatic compounds and hydrocarbons (incl. crude oil) (e.g. Rueter et al. 1994, Rabus et al. 1996, Wilkes et al. 2000, Wöhlbrand et al. 2013). Therefore, SRP can be expected to significantly contribute to the compositional shaping of organic matter in marine sediments. However, systematic studies investigating comparatively the intracellular metabolites and the exometabolome of marine SRP are lacking. With respect to the overall goals of EcoMol, we envisage that the integrated evaluation and interpretation of results from targeted metabolome analysis and FT-ICR-MS to be performed will contribute to the development of new conceptual approaches with respect to the use of unique molecular formula patterns in a comprehensive assessment of the “geo-metabolome”.
Outline for the proposed PhD research project
Exometabolomes of Desulfobacteraceae is in the focus of this PhD project. Using targeted and non-targeted metabolite analysis we will test the hypothesis that metabolism of Desulfobacteraceae exerts a key control on organic matter composition in marine sediments. The comparative analysis of intracellular and excreted metabolite patterns will enable distinguishing those parts of the organism-specific metabolic network established by proteogenomic reconstruction (WP2) that are most crucial with respect to shaping the “geo-metabolome” from those which predominantly play a role in intracellular metabolism. Comparison of targeted metabolomes assessed upon cultivation with different substrates will provide detailed insights into the influence of an important environmental parameter, i.e. the availability of a specific substrate. This conceptual approach may be extended to cultivation experiments with mixed or complex substrates (WP1) and / or mixed cultures which will more realistically represent the living conditions in a natural ecosystem. Structural analysis and quantification of metabolites will be mainly conducted with LC-MS (incl. a new Orbitrap system expected to be operational in 2016). These analyses will be complemented by FT-ICR-MS measurements (WP4) to achieve highest resolution of the dissolved organic matter. A beneficial spin-off will be structure assignments to molecular formulas usually generated by FT-ICR-MS analysis.