@article {531,
	title = {Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens.},
	journal = {J Bacteriol},
	volume = {187},
	year = {2005},
	month = {2005 Sep},
	pages = {5918-26},
	abstract = {Previous studies demonstrated that an outer membrane c-type cytochrome, OmcB, was involved in Fe(III) reduction in Geobacter sulfurreducens. An OmcB-deficient mutant was greatly impaired in its ability to reduce both soluble and insoluble Fe(III). Reintroducing omcB restored the capacity for Fe(III) reduction at a level proportional to the level of OmcB production. Here, we report that the OmcB-deficient mutant gradually adapted to grow on soluble Fe(III) but not insoluble Fe(III). The adapted OmcB-deficient mutant reduced soluble Fe(III) at a rate comparable to that of the wild type, but the cell yield of the mutant was only ca. 60\% of that of the wild type under steady-state culturing conditions. Analysis of proteins and transcript levels demonstrated that expression of several membrane-associated cytochromes was higher in the adapted mutant than in the wild type. Further comparison of transcript levels during steady-state growth on Fe(III) citrate with a whole-genome DNA microarray revealed a significant shift in gene expression in an apparent attempt to adapt metabolism to the impaired electron transport to Fe(III). These results demonstrate that, although there are many other membrane-bound c-type cytochromes in G. sulfurreducens, increased expression of these cytochromes cannot completely compensate for the loss of OmcB. The concept that outer membrane cytochromes are promiscuous reductases that are interchangeable in function appears to be incorrect. Furthermore, the results indicate that there may be different mechanisms for electron transfer to soluble Fe(III) and insoluble Fe(III) oxides in G. sulfurreducens, which emphasizes the importance of studying electron transport to the environmentally relevant Fe(III) oxides.},
	keywords = {Adaptation, Physiological, Bacterial Outer Membrane Proteins, Base Sequence, Cytochromes c, DNA Primers, Electron Transport, Ferric Compounds, Gene Expression Regulation, Bacterial, Geobacter, Kinetics, Oxidation-Reduction, Reverse Transcriptase Polymerase Chain Reaction},
	issn = {0021-9193},
	doi = {10.1128/JB.187.17.5918-5926.2005},
	author = {Leang, Ching and Adams, L A and Chin, K-J and Nevin, K P and Meth{\'e}, B A and Webster, J and Sharma, M L and Lovley, D R}
}
@article {603,
	title = {Acetate oxidation coupled to Fe(iii) reduction in hyperthermophilic microorganisms.},
	journal = {Appl Environ Microbiol},
	volume = {67},
	year = {2001},
	month = {2001 Mar},
	pages = {1363-5},
	abstract = {No hyperthermophilic microorganisms have previously been shown to anaerobically oxidize acetate, the key extracellular intermediate in the anaerobic oxidation of organic matter. Here we report that two hyperthermophiles, Ferroglobus placidus and "Geoglobus ahangari," grow at 85 degrees C by oxidizing acetate to carbon dioxide, with Fe(III) serving as the electron acceptor. These results demonstrate that acetate could potentially be metabolized within the hot microbial ecosystems in which hyperthermophiles predominate, rather than diffusing to cooler environments prior to degradation as has been previously proposed.},
	keywords = {Acetates, Anaerobiosis, Archaea, Ferric Compounds, Hot Temperature, Oxidation-Reduction},
	issn = {0099-2240},
	doi = {10.1128/AEM.67.3.1363-1365.2001},
	author = {Tor, J M and Kashefi, K and Lovley, D 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 {599,
	title = {Anaerobic degradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA).},
	journal = {Environ Sci Technol},
	volume = {35},
	year = {2001},
	month = {2001 May 1},
	pages = {1785-90},
	abstract = {The potential for anaerobic degradation of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA) was investigated in laboratory incubations of sediments from a petroleum-contaminated aquifer and in aquatic sediments. The addition of humic substances (HS) stimulated the anaerobic degradation of MTBE in aquifer sediments in which Fe(III) was available as an electron acceptor. This is attributed to the fact that HS and other extracellular quinones can stimulate the activity of Fe(III)-reducing microorganisms by acting as an electron shuttle between Fe(III)-reducing microorganisms and insoluble Fe(III) oxides. MTBE was not degraded in aquifer sediments without Fe(III) and HS. [14C]-MTBE added to aquatic sediments adapted for anaerobic MTBE degradation was converted to 14CO2 in the presence or absence of HS or the HS analog, anthraquione-2,6-disulfonate. Unamended aquatic sediments produced 14CH4 as well as 14CO2 from [14C]-MTBE. The aquatic sediments also rapidly consumed TBA under anaerobic conditions and converted [14C]-TBA to 14CH4 and 14CO2. An adaptation period of ca. 250-300 days was required prior to the most rapid anaerobic MTBE degradation in both sediment types, whereas TBA was metabolized in the aquatic sediments without a lag. These results demonstrate that, under the appropriate conditions, MTBE and TBA can be degraded in the absence of oxygen. This suggests that it may be possible to design strategies for the anaerobic remediation of MTBE in petroleum-contaminated subsurface environments.},
	keywords = {Anaerobiosis, Biodegradation, Environmental, Carbon Dioxide, Geologic Sediments, Methane, Methyl Ethers, tert-Butyl Alcohol, Water Pollutants, Chemical},
	issn = {0013-936X},
	author = {Finneran, K T and Lovley, D R}
}
@article {597,
	title = {Application of the 5{\textquoteright} fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments.},
	journal = {Appl Environ Microbiol},
	volume = {67},
	year = {2001},
	month = {2001 Jun},
	pages = {2781-9},
	abstract = {In this study, we report on the development of quantitative PCR and reverse transcriptase PCR assays for the 16S rRNA of Geobacter spp. and identify key issues related to fluorogenic reporter systems for nucleic acid analyses of sediments. The lower detection limit of each assay was 5 to 50 fg of genomic DNA or < or =2 pg of 16S rRNA. TaqMan PCR spectral traces from uncontaminated, amended aquifer sediments were significantly lower (P < 0.0002) than traces for the external standard curve. We also observed a similar, significant decrease in mean quencher emissions for undiluted extracts relative to those for diluted extracts (P < 0.0001). If PCR enumerations were based solely upon the undiluted sample eluant, the TaqMan assay generated an inaccurate result even though the threshold cycle (C(t)) measurements were precise and reproducible in the sediment extracts. Assay accuracy was significantly improved by employing a system of replicate dilutions and replicate analyses for both DNA and rRNA quantitation. Our results clearly demonstrate that fluorescence quenching and autofluorescence can significantly affect TaqMan PCR enumeration accuracy, with subsequent implications for the design and implementation of TaqMan PCR to sediments and related environmental samples.},
	keywords = {Deltaproteobacteria, DNA, Ribosomal, Fluorescent Dyes, Geologic Sediments, Polymerase Chain Reaction, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sensitivity and Specificity, Taq Polymerase},
	issn = {0099-2240},
	doi = {10.1128/AEM.67.6.2781-2789.2001},
	author = {Stults, J R and Snoeyenbos-West, O and Methe, B and Lovley, D R and Chandler, D P}
}
@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 {626,
	title = {Anaerobic benzene degradation in petroleum-contaminated aquifer sediments after inoculation with a benzene-oxidizing enrichment.},
	journal = {Appl Environ Microbiol},
	volume = {64},
	year = {1998},
	month = {1998 Feb},
	pages = {775-8},
	abstract = {Sediments from the sulfate-reduction zone of a petroleum-contaminated aquifer, in which benzene persisted, were inoculated with a benzene-oxidizing, sulfate-reducing enrichment from aquatic sediments. Benzene was degraded, with apparent growth of the benzene-degrading population over time. These results suggest that the lack of benzene degradation in the sulfate-reduction zones of some aquifers may result from the failure of the appropriate benzene-degrading sulfate reducers to colonize the aquifers rather than from environmental conditions that are adverse for anaerobic benzene degradation.},
	keywords = {Anaerobiosis, Benzene, Biodegradation, Environmental, Fresh Water, Geologic Sediments, Iron, Oxidation-Reduction, Petroleum, Sulfates},
	issn = {0099-2240},
	author = {Weiner, JM and Lovley, D R}
}
@article {628,
	title = {Anaerobic degradation of polycyclic aromatic hydrocarbons and alkanes in petroleum-contaminated marine harbor sediments.},
	journal = {Appl Environ Microbiol},
	volume = {63},
	year = {1997},
	month = {1997 Sep},
	pages = {3589-93},
	abstract = {Although polycyclic aromatic hydrocarbons (PAHs) have usually been found to persist under strict anaerobic conditions, in a previous study an unusual site was found in San Diego Bay in which two PAHs, naphthalene and phenanthrene, were oxidized to carbon dioxide under sulfate-reducing conditions. Further investigations with these sediments revealed that methylnaphthalene, fluorene, and fluoranthene were also anaerobically oxidized to carbon dioxide in these sediments, while pyrene and benzo[a]pyrene were not. Studies with naphthalene indicated that PAH oxidation was sulfate dependent. Incubating the sediments with additional naphthalene for 1 month resulted in a significant increase in the oxidation of [14C]naphthalene. In sediments from a less heavily contaminated site in San diego Bay where PAHs were not readily degraded, naphthalene degradation could be stimulated through inoculation with active PAH-degrading sediments from the most heavily contaminated site. Sediments from the less heavily contaminated site that had been adapted for rapid anaerobic degradation of high concentrations of benzene did not oxidize naphthalene, suggesting that the benzene- and naphthalene-degrading populations were different. When fuels containing complex mixtures of alkanes were added to sediments from the two sites, there was significant degradation in the alkanes. [14C]hexadecane was also anaerobically oxidized to 14CO2 in these sediments. Molybdate, a specific inhibitor of sulfate reduction, inhibited hexadecane oxidation. These results demonstrate that a wide variety of hydrocarbon contaminants can be degraded under sulfate-reducing conditions in hydrocarbon-contaminated sediments, and they suggest that it may be possible to use sulfate reduction rather than aerobic respiration as a treatment strategy for hydrocarbon-contaminated dredged sediments.},
	keywords = {Alkanes, Anaerobiosis, Biodegradation, Environmental, California, Naphthalenes, Oxidation-Reduction, Petroleum, Polycyclic Hydrocarbons, Aromatic, Sulfates, Water Microbiology, Water Pollutants, Chemical},
	issn = {0099-2240},
	author = {Coates, J D and Woodward, J and Allen, J and Philp, P and Lovley, D R}
}
@article {649,
	title = {Anaerobes into heavy metal: Dissimilatory metal reduction in anoxic environments.},
	journal = {Trends Ecol Evol},
	volume = {8},
	year = {1993},
	month = {1993 Jun},
	pages = {213-7},
	abstract = {Within the last decade, a novel form of microbial metabolism of major environmental significance has been elucidated. In this process, known as dissimilatory metal reduction, specialized microorganisms, living in anoxic aquatic sediments and ground water, oxidize organic compounds to carbon dioxide with metals serving as the oxidant. Recent studies have demonstrated that this metabolism explains a number of important geochemical phenomena in ancient and modern sedimentary environments, affecting not only the cycling of metals but also the fate of organic matter. Furthermore, this metabolism may have practical application in remediation of environments contaminated with toxic metals and/or organics.},
	issn = {0169-5347},
	doi = {10.1016/0169-5347(93)90102-U},
	author = {Lovley, D R}
}
@article {654,
	title = {Acetate oxidation by dissimilatory Fe(III) reducers.},
	journal = {Appl Environ Microbiol},
	volume = {58},
	year = {1992},
	month = {1992 Sep},
	pages = {3205-8},
	keywords = {Acetates, Ferric Compounds, Gram-Negative Bacteria, Oxidation-Reduction},
	issn = {0099-2240},
	author = {Lovley, D R and Phillips, E J and Caccavo, F}
}
@article {659,
	title = {Anaerobic Oxidation of Toluene, Phenol, and p-Cresol by the Dissimilatory Iron-Reducing Organism, GS-15.},
	journal = {Appl Environ Microbiol},
	volume = {56},
	year = {1990},
	month = {1990 Jun},
	pages = {1858-64},
	abstract = {The dissimilatory Fe(III) reducer, GS-15, is the first microorganism known to couple the oxidation of aromatic compounds to the reduction of Fe(III) and the first example of a pure culture of any kind known to anaerobically oxidize an aromatic hydrocarbon, toluene. In this study, the metabolism of toluene, phenol, and p-cresol by GS-15 was investigated in more detail. GS-15 grew in an anaerobic medium with toluene as the sole electron donor and Fe(III) oxide as the electron acceptor. Growth coincided with Fe(III) reduction. [ring-C]toluene was oxidized to CO(2), and the stoichiometry of CO(2) production and Fe(III) reduction indicated that GS-15 completely oxidized toluene to carbon dioxide with Fe(III) as the electron acceptor. Magnetite was the primary iron end product during toluene oxidation. Phenol and p-cresol were also completely oxidized to carbon dioxide with Fe(III) as the sole electron acceptor, and GS-15 could obtain energy to support growth by oxidizing either of these compounds as the sole electron donor. p-Hydroxybenzoate was a transitory extracellular intermediate of phenol and p-cresol metabolism but not of toluene metabolism. GS-15 oxidized potential aromatic intermediates in the oxidation of toluene (benzylalcohol and benzaldehyde) and p-cresol (p-hydroxybenzylalcohol and p-hydroxybenzaldehyde). The metabolism described here provides a model for how aromatic hydrocarbons and phenols may be oxidized with the reduction of Fe(III) in contaminated aquifers and petroleum-containing sediments.},
	issn = {0099-2240},
	author = {Lovley, D R and Lonergan, D J}
}
@article {665,
	title = {Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal potomac river.},
	journal = {Appl Environ Microbiol},
	volume = {52},
	year = {1986},
	month = {1986 Oct},
	pages = {751-7},
	abstract = {The distribution of Fe(III), its availability for microbial reduction, and factors controlling Fe(III) availability were investigated in sediments from a freshwater site in the Potomac River Estuary. Fe(III) reduction in sediments incubated under anaerobic conditions and depth profiles of oxalate-extractable Fe(III) indicated that Fe(III) reduction was limited to depths of 4 cm or less, with the most intense Fe(III) reduction in the top 1 cm. In incubations of the upper 4 cm of the sediments, Fe(III) reduction was as important as methane production as a pathway for anaerobic electron flow because of the high rates of Fe(III) reduction in the 0- to 0.5-cm interval. Most of the oxalate-extractable Fe(III) in the sediments was not reduced and persisted to a depth of at least 20 cm. The incomplete reduction was not the result of a lack of suitable electron donors. The oxalate-extractable Fe(III) that was preserved in the sediments was considered to be in a form other than amorphous Fe(III) oxyhydroxide, since synthetic amorphous Fe(III) oxyhydroxide, amorphous Fe(III) oxyhydroxide adsorbed onto clay, and amorphous Fe(III) oxyhydroxide saturated with adsorbed phosphate or fulvic acids were all readily reduced. Fe(3)O(4) and the mixed Fe(III)-Fe(II) compound(s) that were produced during the reduction of amorphous Fe(III) oxyhydroxide in an enrichment culture were oxalate extractable but were not reduced, suggesting that mixed Fe(III)-Fe(II) compounds might account for the persistence of oxalate-extractable Fe(III) in the sediments. The availability of microbially reducible Fe(III) in surficial sediments demonstrates that microbial Fe(III) reduction can be important to organic matter decomposition and iron geochemistry. However, the overall extent of microbial Fe(III) reduction is governed by the inability of microorganisms to reduce most of the Fe(III) in the sediment.},
	issn = {0099-2240},
	author = {Lovley, D R and Phillips, E J}
}
