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<p>Abstract</p> <p>Background</p> <p><it>Geobacter </it>species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. <it>Geobacter bemidjiensis</it>, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to <it>Geobacter </it>species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of <it>G. bemidjiensis </it>compared to non-subsurface <it>Geobacter </it>species.</p> <p>Results</p> <p>Annotation of the genome sequence of <it>G. bemidjiensis </it>indicates several differences in metabolism compared to previously sequenced non-subsurface <it>Geobacteraceae</it>, which will be useful for <it>in silico </it>metabolic modeling of subsurface bioremediation processes involving <it>Geobacter </it>species. Pathways can now be predicted for the use of various carbon sources such as propionate by <it>G. bemidjiensis</it>. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in <it>G. bemidjiensis </it>may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that <it>G. bemidjiensis </it>is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, <it>G. bemidjiensis </it>is auxotrophic for 4-aminobenzoate, which makes it the first <it>Geobacter </it>species identified as having a vitamin requirement. Several features of the genome indicated that <it>G. bemidjiensis </it>has enhanced abilities to respire, detoxify and avoid oxygen.</p> <p>Conclusion</p> <p>Overall, the genome sequence of <it>G. bemidjiensis </it>offers surprising insights into the metabolism and physiology of <it>Geobacteraceae </it>in subsurface environments, compared to non-subsurface <it>Geobacter </it>species, such as the ability to disproportionate fumarate, more efficient oxidation of propionate, enhanced responses to oxygen stress, and dependence on the environment for a vitamin requirement. Therefore, an understanding of the activity of <it>Geobacter </it>species in the subsurface is more likely to benefit from studies of subsurface isolates such as <it>G. bemidjiensis </it>than from the non-subsurface model species studied so far.</p>