@article {420,
	title = {Molecular analysis of the metabolic rates of discrete subsurface populations of sulfate reducers.},
	journal = {Appl Environ Microbiol},
	volume = {77},
	year = {2011},
	month = {2011 Sep},
	pages = {6502-9},
	abstract = {Elucidating the in situ metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of dsrAB sequences prior to the addition of acetate indicated that Desulfobacteraceae, Desulfobulbaceae, and Syntrophaceae-related sulfate reducers were the most abundant. Quantifying dsrB transcripts of the individual populations suggested that Desulfobacteraceae initially had higher dsrB transcripts per cell than Desulfobulbaceae or Syntrophaceae populations and that the activity of Desulfobacteraceae increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast, dsrB transcript abundance in Desulfobulbaceae and Syntrophaceae remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the Desulfobacteraceae was consistent with the finding that Desulfobacteraceae became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in dsrB transcript abundance in the Desulfobacteraceae. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.},
	keywords = {Biodiversity, Deltaproteobacteria, DNA, Bacterial, Gene Expression Profiling, Hydrogensulfite Reductase, Molecular Sequence Data, Oxidation-Reduction, Sequence Analysis, DNA, Soil Microbiology, Sulfates, Water Microbiology},
	issn = {1098-5336},
	doi = {10.1128/AEM.00576-11},
	author = {Miletto, M and Williams, K H and N{\textquoteright}Guessan, A L and Lovley, D R}
}
@article {544,
	title = {Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments.},
	journal = {Microb Ecol},
	volume = {48},
	year = {2004},
	month = {2004 Aug},
	pages = {178-90},
	abstract = {The microbial communities associated with electrodes from underwater fuel cells harvesting electricity from five different aquatic sediments were investigated. Three fuel cells were constructed with marine, salt-marsh, or freshwater sediments incubated in the laboratory. Fuel cells were also deployed in the field in salt marsh sediments in New Jersey and estuarine sediments in Oregon, USA. All of the sediments produced comparable amounts of power. Analysis of 16S rRNA gene sequences after 3-7 months of incubation demonstrated that all of the energy-harvesting anodes were highly enriched in microorganisms in the delta-Proteobacteria when compared with control electrodes not connected to a cathode. Geobacteraceae accounted for the majority of delta-Proteobacterial sequences or all of the energy-harvesting anodes, except the one deployed at the Oregon estuarine site. Quantitative PCR analysis of 16S rRNA genes and culturing studies indicated that Geobacteraceae were 100-fold more abundant on the marine-deployed anodes versus controls. Sequences most similar to microorganisms in the family Desulfobulbaceae predominated on the anode deployed in the estuarine sediments, and a significant proportion of the sequences recovered from the freshwater anodes were closely related to the Fe(III)-reducing isolate, Geothrix fermentans. There was also a specific enrichment of microorganisms on energy harvesting cathodes, but the enriched populations varied with the sediment/water source. Thus, future studies designed to help optimize the harvesting of electricity from aquatic sediments or waste organic matter should focus on the electrode interactions of these microorganisms which are most competitive in colonizing anodes and cathodes.},
	keywords = {Base Sequence, Biodiversity, Bioelectric Energy Sources, Cloning, Molecular, DNA Primers, Electrodes, Gammaproteobacteria, Geologic Sediments, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Restriction Mapping, RNA, Ribosomal, 16S, Sequence Analysis, DNA},
	issn = {0095-3628},
	doi = {10.1007/s00248-003-0004-4},
	author = {Holmes, D E and Bond, D R and O{\textquoteright}Neil, R A and Reimers, C E and Tender, L R and Lovley, D R}
}
@article {596,
	title = {Microbial detoxification of metals and radionuclides.},
	journal = {Curr Opin Biotechnol},
	volume = {12},
	year = {2001},
	month = {2001 Jun},
	pages = {248-53},
	abstract = {Microorganisms have important roles in the biogeochemical cycling of toxic metals and radionuclides. Recent advances have been made in understanding metal-microbe interactions and new applications of these processes to the detoxification of metal and radionuclide contamination have been developed.},
	keywords = {Bacteria, Biodegradation, Environmental, Biotechnology, Environmental Pollution, Genetic Engineering, Geologic Sediments, Metals, Heavy, Radioisotopes},
	issn = {0958-1669},
	author = {Lloyd, J R and Lovley, D R}
}
@article {609,
	title = {Microbes with a mettle for bioremediation.},
	journal = {Nat Biotechnol},
	volume = {18},
	year = {2000},
	month = {2000 Jun},
	pages = {600-1},
	keywords = {Bacterial Adhesion, Cadmium, Cupriavidus necator, Industrial Waste, Metallothionein, Metals, Heavy, Soil Microbiology, Soil Pollutants},
	issn = {1087-0156},
	doi = {10.1038/76433},
	author = {Lovley, D R and Lloyd, J R}
}
@article {619,
	title = {Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer.},
	journal = {Appl Environ Microbiol},
	volume = {65},
	year = {1999},
	month = {1999 Jul},
	pages = {3056-63},
	abstract = {Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn., was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial or Geobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number-PCR enumeration, which indicated that members of the family Geobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxus is known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest that Geobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site{\textquoteright}s capacity for anaerobic benzene degradation.},
	keywords = {Anaerobiosis, Benzene, Biodegradation, Environmental, Culture Media, DNA, Bacterial, DNA, Ribosomal, Fresh Water, Geologic Sediments, Gram-Negative Anaerobic Bacteria, Molecular Sequence Data, Oxidation-Reduction, Petroleum, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Water Pollutants},
	issn = {0099-2240},
	author = {Rooney-Varga, J N and Anderson, R T and Fraga, J L and Ringelberg, D and Lovley, D R}
}
@article {620,
	title = {Microbiological evidence for Fe(III) reduction on early Earth.},
	journal = {Nature},
	volume = {395},
	year = {1998},
	month = {1998 Sep 3},
	pages = {65-7},
	abstract = {It is generally considered that sulphur reduction was one of the earliest forms of microbial respiration, because the known microorganisms that are most closely related to the last common ancestor of modern life are primarily anaerobic, sulphur-reducing hyperthermophiles. However, geochemical evidence indicates that Fe(III) is more likely than sulphur to have been the first external electron acceptor of global significance in microbial metabolism. Here we show that Archaea and Bacteria that are most closely related to the last common ancestor can reduce Fe(III) to Fe(II) and conserve energy to support growth from this respiration. Surprisingly, even Thermotoga maritima, previously considered to have only a fermentative metabolism, could grow as a respiratory organism when Fe(III) was provided as an electron acceptor. These results provide microbiological evidence that Fe(III) reduction could have been an important process on early Earth and suggest that microorganisms might contribute to Fe(III) reduction in modern hot biospheres. Furthermore, our discovery that hyperthermophiles that had previously been thought to require sulphur for cultivation can instead be grown without the production of toxic and corrosive sulphide, should aid biochemical investigations of these poorly understood organisms.},
	keywords = {Earth (Planet), Electron Transport, Environmental Microbiology, Ferric Compounds, Gram-Negative Anaerobic Bacteria, Oxidation-Reduction, Thermoproteaceae},
	issn = {0028-0836},
	doi = {10.1038/25720},
	author = {Vargas, M and Kashefi, K and Blunt-Harris, E L and Lovley, D R}
}
@article {632,
	title = {Microbial degradation of hydrochlorofluorocarbons (CHCl2F and CHCl2CF3) in soils and sediments.},
	journal = {Appl Environ Microbiol},
	volume = {62},
	year = {1996},
	month = {1996 May},
	pages = {1818-21},
	abstract = {The ability of microorganisms to degrade trace levels of the hydrochlorofluorocarbons HCFC-21 and HCFC-123 was investigated. Methanotroph-linked oxidation of HCFC-21 was observed in aerobic soils, and anaerobic degradation of HCFC-21 occurred in freshwater and salt marsh sediments. Microbial degradation of HCFC-123 was observed in anoxic freshwater and salt marsh sediments, and the recovery of 1,1,1-trifluoro-2-chloroethane indicated the involvement of reductive dechlorination. No degradation of HCFC-123 was observed in aerobic soils. In some experiments, HCFCs were degraded at low (parts per billion) concentrations, raising the possibility that bacteria in nature remove HCFCs from the atmosphere.},
	keywords = {Biodegradation, Environmental, Chlorofluorocarbons, Soil Microbiology},
	issn = {0099-2240},
	author = {Oremland, R S and Lonergan, D J and Culbertson, C W and Lovley, D R}
}
@article {667,
	title = {Minimum threshold for hydrogen metabolism in methanogenic bacteria.},
	journal = {Appl Environ Microbiol},
	volume = {49},
	year = {1985},
	month = {1985 Jun},
	pages = {1530-1},
	abstract = {Methanogenic isolates did not consume hydrogen below partial pressures of 6.5 Pa. Thus, in contrast to a previous report, results from pure-culture studies do not invalidate the threshold model for methane production from hydrogen in sediments.},
	issn = {0099-2240},
	author = {Lovley, D R}
}
@article {671,
	title = {Metabolism of acetate, methanol, and methylated amines in intertidal sediments of lowes cove, maine.},
	journal = {Appl Environ Microbiol},
	volume = {45},
	year = {1983},
	month = {1983 Jun},
	pages = {1848-53},
	abstract = {The fates and the rates of metabolism of acetate, trimethylamine, methylamine, and methanol were examined to determine the significance of these compounds as in situ methane precursors in surface sediments of an intertidal zone in Maine. Concentrations of these potential methane precursors were generally <3 muM, with the exception of sediments containing fragments of the seaweed Ascophyllum nodosum, in which acetate was 96 muM. [2-C]acetate turnover in all samples was rapid (turnover time <2 h), with CO(2) as the primary product. [C]trimethylamine and methylamine turnover times were slower (>8 h) and were characterized by formation of both CH(4) and CO(2). Ratios of CH(4)/CO(2) from [C]trimethylamine and methylamine in uninhibited sediments indicated that a significant fraction of these substrates were catabolized via a non-methanogenic process. Data from inhibition experiments involving sodium molybdate and 2-bromoethanesulfonic acid supported this interpretation. [C]methanol was oxidized relatively slowly compared with the other substrates and was catabolized mainly to CO(2). Results from experiments with molybdate and 2-bromoethanesulfonic acid suggested that methanol was oxidized primarily through sulfate reduction. In Lowes Cove sediments, trimethylamine accounted for 35.1 to 61.1\% of total methane production.},
	issn = {0099-2240},
	author = {King, G M and Klug, M J and Lovley, D R}
}
@article {672,
	title = {Methanogenesis from methanol and methylamines and acetogenesis from hydrogen and carbon dioxide in the sediments of a eutrophic lake.},
	journal = {Appl Environ Microbiol},
	volume = {45},
	year = {1983},
	month = {1983 Apr},
	pages = {1310-5},
	abstract = {C-tracer techniques were used to examine the metabolism of methanol and methylamines and acetogenesis from hydrogen and carbon dioxide in sediments from the profundal and littoral zones of eutrophic Wintergreen Lake, Michigan. Methanogens were primarily responsible for the metabolism of methanol, monomethylamine, and trimethylamine and maintained the pool size of these substrates below 10 muM in both sediment types. Methanol and methylamines were the precursors for less than 5 and 1\%, respectively, of the total methane produced. Methanol and methylamines continued to be metabolized to methane when the sulfate concentration in the sediment was increased to 20 mM. Less than 2\% of the total acetate production was derived from carbon dioxide reduction. Hydrogen consumption by hydrogen-oxidizing acetogens was 5\% or less of the total hydrogen uptake by acetogens and methanogens. These results, in conjunction with previous studies, emphasize that acetate and hydrogen are the major methane precursors and that methanogens are the predominant hydrogen consumers in the sediments of this eutrophic lake.},
	issn = {0099-2240},
	author = {Lovley, D R and Klug, M J}
}
