Abstract
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.