@article {419,
	title = {Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus.},
	journal = {ISME J},
	volume = {6},
	year = {2012},
	month = {2012 Jan},
	pages = {146-57},
	abstract = {Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (>80{\textdegree} C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA (coenzyme A) reductase (BCR) found in all strictly anaerobic bacteria, but has instead genes coding for a bzd-type ATP-consuming class I BCR, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for phenol carboxylation proceeding through a phenylphosphate intermediate were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative reverse transcriptase polymerase chain reaction demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates vs growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism are highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.},
	keywords = {Acetates, Archaea, Bacteria, Anaerobic, Benzoates, Metabolic Networks and Pathways, Phenol, Rhodopseudomonas},
	issn = {1751-7370},
	doi = {10.1038/ismej.2011.88},
	author = {Holmes, Dawn E and Risso, Carla and Smith, Jessica A 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}
}
@article {566,
	title = {Metabolism of organic compounds in anaerobic, hydrothermal sulphate-reducing marine sediments.},
	journal = {Environ Microbiol},
	volume = {5},
	year = {2003},
	month = {2003 Jul},
	pages = {583-91},
	abstract = {Previous studies of hot (>80 degrees C) microbial ecosystems have primarily relied on the study of pure cultures or analysis of 16S rDNA sequences. In order to gain more information on anaerobic metabolism by natural communities in hot environments, sediments were collected from a shallow marine hydrothermal vent system in Baia di Levante, Vulcano, Italy and incubated under strict anaerobic conditions at 90 degrees C. Sulphate reduction was the predominant terminal electron-accepting process in the sediments. The addition of molybdate inhibited sulphate reduction in the sediments and resulted in a linear accumulation of acetate and hydrogen over time. [U-14C]- acetate was completely oxidized to 14CO2, and the addition of molybdate inhibited 14CO2 production by 60\%. [U-14C]-glucose was oxidized to 14CO2, and this was inhibited when molybdate was added. When the pool sizes of short-chain fatty acids were artificially increased, radiolabel from [U-14C]-glucose accumulated in the acetate pool. L-[U-14C]-glutamate, [ring-14C]-benzoate and [U-14C]-palmitate were also anaerobically oxidized to 14CO2 in the sediments, but molybdate had little effect on the oxidation of these compounds. These results demonstrate that natural microbial communities living in a hot, microbial ecosystem can oxidize acetate and a range of other organic electron donors under sulphate-reducing conditions and suggest that acetate is an important extracellular intermediate in the anaerobic degradation of organic matter in hot microbial ecosystems.},
	keywords = {Acetates, Anaerobiosis, Bacteria, Anaerobic, Benzoates, Carbon Dioxide, Ecosystem, Geologic Sediments, Glucose, Glutamic Acid, Hot Temperature, Hydrogen, Italy, Molybdenum, Organic Chemicals, Oxidation-Reduction, Palmitates, Seawater, Sulfates, Water Microbiology},
	issn = {1462-2912},
	author = {Tor, Jason M and Amend, Jan P and Lovley, Derek R}
}
@article {575,
	title = {Anaerobic, sulfate-dependent degradation of polycyclic aromatic hydrocarbons in petroleum-contaminated harbor sediment.},
	journal = {Environ Sci Technol},
	volume = {36},
	year = {2002},
	month = {2002 Nov 15},
	pages = {4811-7},
	abstract = {It has previously been demonstrated that [14C]-labeled polycyclic aromatic hydrocarbons (PAHs) can be oxidized to 14CO2 in anoxic, PAH-contaminated, marine harbor sediments in which sulfate reduction is the terminal electron-accepting process. However, it has not previously been determined whether this degradation of [14C]-PAHs accurately reflects the degradation of the in situ pools of contaminant PAHs. In coal tar-contaminated sediments from Boston Harbor, [14C]-naphthalene was readily oxidized to 14CO2, but, after 95 d of incubation under anaerobic conditions, there was no significant decrease in the detectable pool of in situ naphthalene in these sediments. Therefore, to better evaluate the anaerobic biodegradation of the in situ PAH pools, the concentrations of these contaminants were monitored for ca. 1 year during which the sediments were incubated under conditions that mimicked those found in situ. There was loss of all of the PAHs that were monitored (2-5 ring congeners), including high molecular weight PAHs, such as benzo[a]pyrene, that have not previously been shown to be degraded under anaerobic conditions. There was no significant change in the PAH levels in the sediments amended with molybdate to inhibit sulfate-reducing bacteria or in sediments in which all microorganisms had been killed with glutaraldehyde. In some instances, over half of the detectable pools of in situ 2-3 ring PAHs were degraded. In general, the smaller PAHs were degraded more rapidly than the larger PAHs. A distinct exception in the Boston Harbor sediment was naphthalene which was degraded very slowly at a rate comparable to the larger PAHs. In a similar in situ-like study of fuel-contaminated sediments from Liepaja Harbor, Latvia, there was no decline in PAH levels in samples that were sulfate-depleted. However, when the Latvia sediments were supplemented with sufficient sodium sulfate or gypsum to elevate pore water levels of sulfate to approximately 14-25 mM there was a 90\% decline in the naphthalene and a 60\% decline in the 2-methylnaphthalene pool within 90 days. These studies demonstrate for the first time that degradation by anaerobic microorganisms can significantly impact the in situ pools of PAHs in petroleum-contaminated, anoxic, sulfate-reducing harbor sediments and suggest that the self-purification capacity of contaminated harbor sediments is greater than previously considered.},
	keywords = {Bacteria, Anaerobic, Biodegradation, Environmental, Environmental Monitoring, Geologic Sediments, Molecular Weight, Petroleum, Polycyclic Hydrocarbons, Aromatic, Ships, Sulfur-Reducing Bacteria, Transportation, Water Pollutants, Chemical},
	issn = {0013-936X},
	author = {Rothermich, Mary M and Hayes, Lory A and Lovley, Derek 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}
}
@article {593,
	title = {Anaerobic benzene degradation.},
	journal = {Biodegradation},
	volume = {11},
	year = {2000},
	month = {2000},
	pages = {107-16},
	abstract = {Although many studies have indicated that benzene persists under anaerobic conditions in petroleum-contaminated environments, it has recently been documented that benzene can be anaerobically oxidized with most commonly considered electron acceptors for anaerobic respiration. These include: Fe(III), sulfate, nitrate, and possibly humic substances. Benzene can also be converted to methane and carbon dioxide under methanogenic conditions. There is evidence that benzene can be degraded under in situ conditions in petroleum-contaminated aquifers in which either Fe(III) reduction or methane production is the predominant terminal electron-accepting process. Furthermore, evidence from laboratory studies suggests that benzene may be anaerobically degraded in petroleum-contaminated marine sediments under sulfate-reducing conditions. Laboratory studies have suggested that within the Fe(III) reduction zone of petroleum-contaminated aquifers, benzene degradation can be stimulated with the addition of synthetic chelators which make Fe(III) more available for microbial reduction. The addition of humic substances and other compounds that contain quinone moieties can also stimulate anaerobic benzene degradation in laboratory incubations of Fe(III)-reducing aquifer sediments by providing an electron shuttle between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides. Anaerobic benzene degradation in aquifer sediments can be stimulated with the addition of sulfate, but in some instances an inoculum of benzene-oxidizing, sulfate-reducing microorganisms must also be added. In a field trial, sulfate addition to the methanogenic zone of a petroleum-contaminated aquifer stimulated the growth and activity of sulfate-reducing microorganisms and enhanced benzene removal. Molecular phylogenetic studies have provided indications of what microorganisms might be involved in anaerobic benzene degradation in aquifers. The major factor limiting further understanding of anaerobic benzene degradation is the lack of a pure culture of an organism capable of anaerobic benzene degradation.},
	keywords = {Bacteria, Anaerobic, Benzene, Biodegradation, Environmental, Oxidation-Reduction},
	issn = {0923-9820},
	author = {Lovley, D R}
}
@article {608,
	title = {Novel forms of anaerobic respiration of environmental relevance.},
	journal = {Curr Opin Microbiol},
	volume = {3},
	year = {2000},
	month = {2000 Jun},
	pages = {252-6},
	abstract = {Novel forms of anaerobic respiration continue to be discovered. Many of these are environmentally significant as they have important impacts on the fate of organic carbon and the cycling of many inorganic compounds. Furthermore, anaerobic respiration is becoming increasing recognized as a strategy for the remediation of organic and metal contaminants in the subsurface.},
	keywords = {Anaerobiosis, Bacteria, Anaerobic, Environment, Industrial Microbiology, Industrial Waste},
	issn = {1369-5274},
	author = {Lovley, D R and Coates, J D}
}
@article {627,
	title = {Dissimilatory arsenate and sulfate reduction in Desulfotomaculum auripigmentum sp. nov.},
	journal = {Arch Microbiol},
	volume = {168},
	year = {1997},
	month = {1997 Nov},
	pages = {380-8},
	abstract = {A newly discovered arsenate-reducing bacterium, strain OREX-4, differed significantly from strains MIT-13 and SES-3, the previously described arsenate-reducing isolates, which grew on nitrate but not on sulfate. In contrast, strain OREX-4 did not respire nitrate but grew on lactate, with either arsenate or sulfate serving as the electron acceptor, and even preferred arsenate. Both arsenate and sulfate reduction were inhibited by molybdate. Strain OREX-4, a gram-positive bacterium with a hexagonal S-layer on its cell wall, metabolized compounds commonly used by sulfate reducers. Scorodite (FeAsO42. H2O) an arsenate-containing mineral, provided micromolar concentrations of arsenate that supported cell growth. Physiologically and phylogenetically, strain OREX-4 was far-removed from strains MIT-13 and SES-3: strain OREX-4 grew on different electron donors and electron acceptors, and fell within the gram-positive group of the Bacteria, whereas MIT-13 and SES-3 fell together in the epsilon-subdivision of the Proteobacteria. Together, these results suggest that organisms spread among diverse bacterial phyla can use arsenate as a terminal electron acceptor, and that dissimilatory arsenate reduction might occur in the sulfidogenic zone at arsenate concentrations of environmental interest. 16S rRNA sequence analysis indicated that strain OREX-4 is a new species of the genus Desulfotomaculum, and accordingly, the name Desulfotomaculum auripigmentum is proposed.},
	keywords = {Arsenates, Bacteria, Anaerobic, Biotransformation, Geologic Sediments, Gram-Positive Endospore-Forming Rods, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Substrate Specificity, Sulfates, Sulfides, Sulfur-Reducing Bacteria, Water Microbiology},
	issn = {0302-8933},
	author = {Newman, D K and Kennedy, E K and Coates, J D and Ahmann, D and Ellis, D J and Lovley, D R and Morel, F M}
}
@article {634,
	title = {Phylogenetic analysis of dissimilatory Fe(III)-reducing bacteria.},
	journal = {J Bacteriol},
	volume = {178},
	year = {1996},
	month = {1996 Apr},
	pages = {2402-8},
	abstract = {Evolutionary relationships among strictly anaerobic dissimilatory Fe(III)-reducing bacteria obtained from a diversity of sedimentary environments were examined by phylogenetic analysis of 16S rRNA gene sequences. Members of the genera Geobacter, Desulfuromonas, Pelobacter, and Desulfuromusa formed a monophyletic group within the delta subdivision of the class Proteobacteria. On the basis of their common ancestry and the shared ability to reduce Fe(III) and/or S0, we propose that this group be considered a single family, Geobacteraceae. Bootstrap analysis, characteristic nucleotides, and higher-order secondary structures support the division of Geobacteraceae into two subgroups, designated the Geobacter and Desulfuromonas clusters. The genus Desulfuromusa and Pelobacter acidigallici make up a distinct branch within the Desulfuromonas cluster. Several members of the family Geobacteraceae, none of which reduce sulfate, were found to contain the target sequences of probes that have been previously used to define the distribution of sulfate-reducing bacteria and sulfate-reducing bacterium-like microorganisms. The recent isolations of Fe(III)-reducing microorganisms distributed throughout the domain Bacteria suggest that development of 16S rRNA probes that would specifically target all Fe(III) reducers may not be feasible. However, all of the evidence suggests that if a 16S rRNA sequence falls within the family Geobacteraceae, then the organism has the capacity for Fe(III) reduction. The suggestion, based on geological evidence, that Fe(III) reduction was the first globally significant process for oxidizing organic matter back to carbon dioxide is consistent with the finding that acetate-oxidizing Fe(III) reducers are phylogenetically diverse.},
	keywords = {Bacteria, Anaerobic, Base Sequence, DNA, Ribosomal, Ferric Compounds, Iron, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid},
	issn = {0021-9193},
	author = {Lonergan, D J and Jenter, H L and Coates, J D and Phillips, E J and Schmidt, T M and Lovley, D R}
}
@article {639,
	title = {Fe(III) and S0 reduction by Pelobacter carbinolicus.},
	journal = {Appl Environ Microbiol},
	volume = {61},
	year = {1995},
	month = {1995 Jun},
	pages = {2132-8},
	abstract = {There is a close phylogenetic relationship between Pelobacter species and members of the genera Desulfuromonas and Geobacter, and yet there has been a perplexing lack of physiological similarities. Pelobacter species have been considered to have a fermentative metabolism. In contrast, Desulfuromonas and Geobacter species have a respiratory metabolism with Fe(III) serving as the common terminal electron acceptor in all species. However, the ability of Pelobacter species to reduce Fe(III) had not been previously evaluated. When a culture of Pelobacter carbinolicus that had grown by fermentation of 2,3-butanediol was inoculated into the same medium supplemented with Fe(III), the Fe(III) was reduced. There was less accumulation of ethanol and more production of acetate in the presence of Fe(III). P. carbinolicus grew with ethanol as the sole electron donor and Fe(III) as the sole electron acceptor. Ethanol was metabolized to acetate. Growth was also possible on Fe(III) with the oxidation of propanol to propionate or butanol to butyrate if acetate was provided as a carbon source. P. carbinolicus appears capable of conserving energy to support growth from Fe(III) respiration as it also grew with H2 or formate as the electron donor and Fe(III) as the electron acceptor. Once adapted to Fe(III) reduction, P. carbinolicus could also grow on ethanol or H2 with S0 as the electron acceptor. P. carbinolicus did not contain detectable concentrations of the c-type cytochromes that previous studies have suggested are involved in electron transport to Fe(III) in other organisms that conserve energy to support growth from Fe(III) reduction.(ABSTRACT TRUNCATED AT 250 WORDS)},
	keywords = {Bacteria, Anaerobic, Base Sequence, Butylene Glycols, Culture Media, Ethanol, Ferrous Compounds, Hydrogen, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S, Sulfur},
	issn = {0099-2240},
	author = {Lovley, D R and Phillips, E J and Lonergan, D J and Widman, P K}
}
