@article {434,
	title = {The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.},
	journal = {BMC Genomics},
	volume = {11},
	year = {2010},
	month = {2010},
	pages = {490},
	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.},
	keywords = {Aldehyde Oxidoreductases, Biodegradation, Environmental, Carbohydrate Metabolism, Carbon Dioxide, Cell Wall, Electrons, Environmental Microbiology, Fatty Acids, Frameshift Mutation, Fumarates, Genes, Bacterial, Genome, Bacterial, Geobacter, Glucose, Iron, Metabolic Networks and Pathways, Multienzyme Complexes, Multigene Family, Osmosis, Oxidation-Reduction, Oxo-Acid-Lyases, Propionic Acids, Pyruvic Acid, Species Specificity, Surface Properties},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-11-490},
	author = {Aklujkar, Muktak and Young, Nelson D and Holmes, Dawn and Chavan, Milind and Risso, Carla and Kiss, Hajnalka E and Han, Cliff S and Land, Miriam L and Lovley, Derek R}
}
@article {463,
	title = {Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species.},
	journal = {BMC Genomics},
	volume = {10},
	year = {2009},
	month = {2009},
	pages = {103},
	abstract = {BACKGROUND: The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration.

RESULTS: In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern Geobacter and Desulfuromonas species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in Pelobacter carbinolicus and Pelobacter propionicus. Furthermore, P. carbinolicus gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the Pelobacter species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the c-type cytochromes required for extracellular electron transfer.

CONCLUSION: The results suggest that Pelobacter species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.},
	keywords = {Anaerobiosis, Bacteria, Anaerobic, Biological Evolution, Cluster Analysis, Deltaproteobacteria, DNA, Bacterial, Fermentation, Gene Transfer, Horizontal, Genome, Bacterial, Genomics, Multigene Family, Phylogeny, Sequence Analysis, DNA},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-10-103},
	author = {Butler, Jessica E and Young, Nelson D and Lovley, Derek R}
}
