@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 {469,
	title = {Polar lipid fatty acids, LPS-hydroxy fatty acids, and respiratory quinones of three Geobacter strains, and variation with electron acceptor.},
	journal = {J Ind Microbiol Biotechnol},
	volume = {36},
	year = {2009},
	month = {2009 Feb},
	pages = {205-9},
	abstract = {The polar lipid fatty acids, lipopolysaccharide hydroxy-fatty acids, and respiratory quinones of Geobacter metallireducens str. GS-15, Geobacter sulfurreducens str. PCA, and Geobacter bemidjiensis str. Bem are reported. Also, the lipids of G. metallireducens were compared when grown with Fe(3+) or nitrate as electron acceptors and G. sulfurreducens with Fe(3+) or fumarate. In all experiments, the most abundant polar lipid fatty acids were 14:0, i15:0, 16:1 omega 7c, 16:1 omega 5c, and 16:0; lipopolysaccharide hydroxy-fatty acids were dominated by 3oh16:0, 3oh14:0, 9oh16:0, and 10oh16:0; and menaquinone-8 was the most abundant respiratory quinone. Some variation in lipid profiles with strain were observed, but not with electron acceptor.},
	keywords = {Culture Media, Electrons, Environmental Microbiology, Fatty Acids, Ferrous Compounds, Geobacter, Lipids, Lipopolysaccharides, Nitrates, Quinones, Vitamin K 2},
	issn = {1476-5535},
	doi = {10.1007/s10295-008-0486-7},
	author = {Hedrick, D B and Peacock, A D and Lovley, D R and Woodard, T L and Nevin, K P and Long, P E and White, D C}
}
@article {563,
	title = {Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer.},
	journal = {Appl Environ Microbiol},
	volume = {69},
	year = {2003},
	month = {2003 Oct},
	pages = {5884-91},
	abstract = {The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 micro M in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.},
	keywords = {Acetates, DNA, Ribosomal, Ecosystem, Fatty Acids, Ferric Compounds, Fresh Water, Geobacter, Mining, Oxidation-Reduction, Phospholipids, RNA, Ribosomal, 16S, Sulfates, Uranium, Water Pollution, Chemical},
	issn = {0099-2240},
	author = {Anderson, Robert T and Vrionis, Helen A and Ortiz-Bernad, Irene and Resch, Charles T and Long, Philip E and Dayvault, Richard and Karp, Ken and Marutzky, Sam and Metzler, Donald R and Peacock, Aaron and White, David C and Lowe, Mary and Lovley, Derek R}
}
@article {581,
	title = {Geoglobus ahangari gen. nov., sp. nov., a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor.},
	journal = {Int J Syst Evol Microbiol},
	volume = {52},
	year = {2002},
	month = {2002 May},
	pages = {719-28},
	abstract = {A novel, regular to irregular, coccoid-shaped, anaerobic, Fe(III)-reducing microorganism was isolated from the Guaymas Basin hydrothermal system at a depth of 2000 m. Isolation was carried out with a new technique using Fe(III) oxide as the electron acceptor for the recovery of colonies on solid medium. The isolate, designated strain 234T, was strictly anaerobic and exhibited a tumbling motility. The cells had a single flagellum. Strain 234T grew at temperatures between 65 and 90 degrees C, with an optimum at about 88 degrees C. The optimal salt concentration for growth was around 19 g l(-1). The isolate was capable of growth with H2 as the sole electron donor coupled to the reduction of Fe(III) without the need for an organic carbon source. This is the first example of a dissimilatory Fe(III)-reducing micro-organism capable of growing autotrophically on hydrogen. In addition to molecular hydrogen, strain 234T oxidizes pyruvate, acetate, malate, succinate, peptone, formate, fumarate, yeast extract, glycerol, isoleucine, arginine, serine, glutamine, asparagine, stearate, palmitate, valerate, butyrate and propionate with the reduction of Fe(III). This isolate is the first example of a hyperthermophile capable of oxidizing long-chain fatty acids anaerobically. Isolate 234T grew exclusively with Fe(III) as the sole electron acceptor. The G+C content was 58.7 mol\%. Based on detailed analysis of its 16S rDNA sequence, G+C content, distinguishing physiological features and metabolism, strain 234T is proposed to represent a novel genus within the Archaeoglobales. The name proposed for strain 234T is Geoglobus ahangari gen. nov., sp. nov..},
	keywords = {Anaerobiosis, Archaea, Bacterial Typing Techniques, DNA, Ribosomal, Electron Transport, Fatty Acids, Ferric Compounds, Hot Temperature, Hydrogen, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Water Microbiology},
	issn = {1466-5026},
	author = {Kashefi, Kazem and Tor, Jason M and Holmes, Dawn E and Gaw Van Praagh, Catherine V and Reysenbach, Anna-Louise and Lovley, Derek R}
}
@article {637,
	title = {Desulfuromonas palmitatis sp. nov., a marine dissimilatory Fe(III) reducer that can oxidize long-chain fatty acids.},
	journal = {Arch Microbiol},
	volume = {164},
	year = {1995},
	month = {1995 Dec},
	pages = {406-13},
	abstract = {Studies on the microorganisms living in hydrocarbon-contaminated sediments in San Diego Bay, California led to the isolation of a novel Fe(III)-reducing microorganism. This organism, designated strain SDBY1, was an obligately anaerobic, non-motile, non-flagellated, gram-negative rod. Strain SDBY1 conserves energy to support growth from the oxidation of acetate, lactate, succinate, fumarate, laurate, palmitate, or stearate. H2 was also oxidized with the reduction of Fe(III), but growth with H2 as the sole electron donor was not observed. In addition to various forms of soluble and insoluble Fe(III), strain SDBY1 also coupled growth to the reduction of fumarate, Mn(IV), or S0. Air-oxidized minus dithionite-reduced difference spectra exhibited peaks at 552.8, 523.6, and 422.8 nm, indicative of c-type cytochrome(s). Strain SDBY1 shares physiological characteristics with organisms in the genera Geobacter, Pelobacter, and Desulfuromonas. Detailed analysis of the 16S rRNA sequence indicated that strain SDBY1 should be placed in the genus Desulfuromonas. The new species name Desulfuromonas palmitatis is proposed. D. palmitatis is only the second marine organism found (after D. acetoxidans) to oxidize multicarbon organic compounds completely to carbon dioxide with Fe(III) as an electron acceptor and provides the first pure culture model for the oxidation of long-chain fatty acids coupled to Fe(III) reduction.},
	keywords = {Electron Transport, Fatty Acids, Gram-Negative Anaerobic Bacteria, Iron, Microscopy, Electron, Scanning, Oxidation-Reduction, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Water Microbiology},
	issn = {0302-8933},
	author = {Coates, J D and Lonergan, D J and Philips, E J and Jenter, H and Lovley, D R}
}
@article {651,
	title = {Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals.},
	journal = {Arch Microbiol},
	volume = {159},
	year = {1993},
	month = {1993},
	pages = {336-44},
	abstract = {The gram-negative metal-reducing microorganism, previously known as strain GS-15, was further characterized. This strict anaerobe oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. Furthermore, acetate is also oxidized with the reduction of Mn(IV), U(VI), and nitrate. In whole cell suspensions, the c-type cytochrome(s) of this organism was oxidized by physiological electron acceptors and also by gold, silver, mercury, and chromate. Menaquinone was recovered in concentrations comparable to those previously found in gram-negative sulfate reducers. Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative. The organism contained three lipopolysaccharide hydroxy fatty acids which have not been previously reported in microorganisms, but have been observed in anaerobic freshwater sediments. The 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria. Its closest known relative is Desulfuromonas acetoxidans. The name Geobacter metallireducens is proposed.},
	keywords = {Cytochrome c Group, Fatty Acids, Gram-Negative Anaerobic Bacteria, Iron, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S},
	issn = {0302-8933},
	author = {Lovley, D R and Giovannoni, S J and White, D C and Champine, J E and Phillips, E J and Gorby, Y A and Goodwin, S}
}
