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Background  Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world’s oceans. Habitat relevant SRBs are often members of the  Desulfosarcina - Desulfococcus  clade belonging to the deltaproteobacterial family of  Desulfobacteraceae . Despite this environmental recognition, their molecular (genome-based) physiology and their potential to contribute to organic carbon mineralization as well as to adapt to changing environmental conditions have been scarcely investigated. A metabolically versatile representative of this family is  Desulfococcus multivorans  that is able to completely oxidize (to CO 2 ) a variety of organic acids, including fatty acids up to C 14,  as well as aromatic compounds.    Results  In this study the complete 4.46 Mbp and manually annotated genome of metabolically versatile  Desulfococcus multivorans  DSM 2059 is presented with particular emphasis on a proteomics-driven metabolic reconstruction. Proteomic profiling covered 17 substrate adaptation conditions (6 aromatic and 11 aliphatic compounds) and comprised 2D DIGE, shotgun proteomics and analysis of the membrane protein-enriched fractions. This comprehensive proteogenomic dataset allowed for reconstructing a metabolic network of degradation pathways and energy metabolism that consists of 170 proteins (154 detected; ~91 % coverage). Peripheral degradation routes feed via central benzoyl-CoA, (modified) β-oxidation or methylmalonyl-CoA pathways into the Wood-Ljungdahl pathway for complete oxidation of acetyl-CoA to CO 2 . Dissimilatory sulfate reduction is fueled by a complex electron transfer network composed of cytoplasmic components (e.g., electron transfer flavoproteins) and diverse membrane redox complexes (Dsr, Qmo, Hmc, Tmc, Qrc, Nuo and Rnf). Overall, a high degree of substrate-specific formation of catabolic enzymes was observed, while most complexes involved in electron transfer appeared to be constitutively formed.    Conclusions  A highly dynamic genome structure in combination with substrate-specifically formed catabolic subproteomes and a constitutive subproteome for energy metabolism and electron transfer appears to be a common trait of  Desulfobacteraceae  members.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3236-7) contains supplementary material, which is available to authorized users.

Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium Desulfococcus multivorans DSM 2059