@article {502,
	title = {Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.},
	journal = {BMC Genomics},
	volume = {8},
	year = {2007},
	month = {2007},
	pages = {180},
	abstract = {BACKGROUND: Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known.

RESULTS: The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold induced during benzoate oxidation.

CONCLUSION: G. metallireducens appears to convert aromatic compounds to benzoyl-CoA, then to acetyl-CoA via fatty acid oxidation, and then to carbon dioxide via the TCA cycle. The enzyme responsible for dearomatizing the aromatic ring may be novel, and energetic investments at this step may be offset by a change in succinate metabolism. Analysis of a field isolate suggests that the pathways inferred for G. metallireducens may be applicable to modeling in situ bioremediation.},
	keywords = {Biodegradation, Environmental, Citric Acid Cycle, Gene Expression Regulation, Bacterial, Genomics, Geobacter, Hydrocarbons, Aromatic, Microarray Analysis, Models, Chemical, Models, Genetic, Multigene Family, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Phylogeny, Soil Pollutants, Water Pollutants, Chemical},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-8-180},
	author = {Butler, Jessica E and He, Qiang and Nevin, Kelly P and He, Zhili and Zhou, Jizhong and Lovley, Derek R}
}
@article {493,
	title = {Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments.},
	journal = {ISME J},
	volume = {1},
	year = {2007},
	month = {2007 Dec},
	pages = {663-77},
	abstract = {There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.},
	keywords = {Biodegradation, Environmental, Ecosystem, Ferric Compounds, Geobacter, Hydrocarbons, Aromatic, Molecular Sequence Data, Oxidation-Reduction, Petroleum, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Uranium},
	issn = {1751-7362},
	doi = {10.1038/ismej.2007.85},
	author = {Holmes, Dawn E and O{\textquoteright}Neil, Regina A and Vrionis, Helen A and N{\textquoteright}guessan, Lucie A and Ortiz-Bernad, Irene and Larrahondo, Maria J and Adams, Lorrie A and Ward, Joy A and Nicoll, Julie S and Nevin, Kelly P and Chavan, Milind A and Johnson, Jessica P and Long, Philip E and Lovley, Derek R}
}
@article {598,
	title = {Anaerobic degradation of aromatic compounds coupled to Fe(III) reduction by Ferroglobus placidus.},
	journal = {Environ Microbiol},
	volume = {3},
	year = {2001},
	month = {2001 Apr},
	pages = {281-7},
	abstract = {Aromatic compounds are an important component of the organic matter in some of the anaerobic environments that hyperthermophilic microorganisms inhabit, but the potential for hyperthermophilic microorganisms to metabolize aromatic compounds has not been described previously. In this study, aromatic metabolism was investigated in the hyperthermophile Ferroglobus placidus. F. placidus grew at 85 degrees C in anaerobic medium with a variety of aromatic compounds as the sole electron donor and poorly crystalline Fe(III) oxide as the electron acceptor. Growth coincided with Fe(III) reduction. Aromatic compounds supporting growth included benzoate, phenol, 4-hydroxybenzoate, benzaldehyde, p-hydroxybenzaldehyde and t-cinnamic acid (3-phenyl-2-propenoic acid). These aromatic compounds did not support growth when nitrate was provided as the electron acceptor, even though nitrate supports the growth of this organism with Fe(II) or H2 as the electron donor. The stoichiometry of benzoate and phenol uptake and Fe(III) reduction indicated that F. placidus completely oxidized these aromatic compounds to carbon dioxide, with Fe(III) serving as the sole electron acceptor. This is the first example of an Archaea that can anaerobically oxidize an aromatic compound. These results also demonstrate for the first time that hyperthermophilic microorganisms can anaerobically oxidize aromatic compounds and suggest that hyperthermophiles may metabolize aromatic compounds in hot environments such as the deep hot subsurface and in marine and terrestrial hydrothermal zones in which Fe(III) is available as an electron acceptor.},
	keywords = {Anaerobiosis, Archaea, Electron Transport, Ferric Compounds, Hot Temperature, Hydrocarbons, Aromatic, Oxidation-Reduction},
	issn = {1462-2912},
	author = {Tor, J M and Lovley, D R}
}
@article {591,
	title = {Bioremediation. Anaerobes to the rescue.},
	journal = {Science},
	volume = {293},
	year = {2001},
	month = {2001 Aug 24},
	pages = {1444-6},
	keywords = {Bacteria, Aerobic, Bacteria, Anaerobic, Biodegradation, Environmental, Euryarchaeota, Ferric Compounds, Genome, Archaeal, Genome, Bacterial, Hydrocarbons, Aromatic, Hydrocarbons, Chlorinated, Metals, Methane, Nitrates, Oxidation-Reduction, Oxygen, Soil Microbiology, Sulfates, Sulfur-Reducing Bacteria, Water Pollutants, Chemical},
	issn = {0036-8075},
	doi = {10.1126/science.1063294},
	author = {Lovley, D R}
}
