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Background   Geobacter  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.  Geobacter bemidjiensis , a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to  Geobacter  species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of  G. bemidjiensis  compared to non-subsurface  Geobacter  species.    Results  Annotation of the genome sequence of  G. bemidjiensis  indicates several differences in metabolism compared to previously sequenced non-subsurface  Geobacteraceae , which will be useful for  in silico  metabolic modeling of subsurface bioremediation processes involving  Geobacter  species. Pathways can now be predicted for the use of various carbon sources such as propionate by  G. bemidjiensis . 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  G. bemidjiensis  may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that  G. bemidjiensis  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,  G. bemidjiensis  is auxotrophic for 4-aminobenzoate, which makes it the first  Geobacter  species identified as having a vitamin requirement. Several features of the genome indicated that  G. bemidjiensis  has enhanced abilities to respire, detoxify and avoid oxygen.    Conclusion  Overall, the genome sequence of  G. bemidjiensis  offers surprising insights into the metabolism and physiology of  Geobacteraceae  in subsurface environments, compared to non-subsurface  Geobacter  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  Geobacter  species in the subsurface is more likely to benefit from studies of subsurface isolates such as  G. bemidjiensis  than from the non-subsurface model species studied so far.

bmc genomics

The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.