@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 {560,
	title = {Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses.},
	journal = {Microb Ecol},
	volume = {46},
	year = {2003},
	month = {2003 Aug},
	pages = {257-69},
	abstract = {The abundance, distribution, and phylogenetic diversity of members of the Fe(III)-reducing family Geobacteraceae were studied along a gradient of metal contaminants in Lake Coeur d{\textquoteright}Alene, Idaho. Partial 16S rRNA gene fragments were amplified by PCR using primers directed toward conserved regions of the gene within the family Geobacteraceae. Analysis of amplicons separated by denaturing gradient gel electrophoresis (DGGE) suggested within-site variation was as great as between-site variation. Amplicons were cloned and grouped by RFLP type and DGGE migration distance and representatives were sequenced. Grouping clones with 3\% or less sequence dissimilarity, 15 distinct phylotypes were identified compared to 16 distinct DGGE bands. Only 1 phylotype was recovered from all sites. This clone, B14, is most closely related to Geobacter metallireducens and constituted a greater portion of the pristine community than of the contaminated communities. A second phylotype, Q2, predominated in the contaminated communities and was notably absent from the pristine libraries. Clone Q2 presents a high degree of sequence similarity to two Geobacter spp. previously isolated from this region of Lake Coeur d{\textquoteright}Alene. Six phylotypes were unique to the contaminated sediments, whereas two were found only in the pristine sediments. Indices of diversity (Shannon and Simpson) were consistently higher when calculated with DGGE data than when clone library data were used. Most-probable-number PCR and real-time PCR suggested that the Geobacteraceae phylotypes were spread relatively evenly across all three sites along the gradient. Our data indicate that the Geobacteraceae are diverse and abundant in Lake Coeur d{\textquoteright}Alene sediments, regardless of metals content. These results provide insight into the ability of dissimilatory Fe(III)-reducing bacteria to colonize habitats with elevated metal concentrations, and they have important implications for the management and remediation of metal-contaminated sites.},
	keywords = {Cloning, Molecular, Geobacter, Geologic Sediments, Phylogeny, Polymerase Chain Reaction, Population Dynamics, RNA, Ribosomal, 16S, Water Pollutants, Water Supply},
	issn = {0095-3628},
	author = {Cummings, D E and Snoeyenbos-West, O L and Newby, D T and Niggemyer, A M and Lovley, D R and Achenbach, L A and Rosenzweig, R F}
}
@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 {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 {612,
	title = {Hexadecane decay by methanogenesis.},
	journal = {Nature},
	volume = {404},
	year = {2000},
	month = {2000 Apr 13},
	pages = {722-3},
	keywords = {Alkanes, Anaerobiosis, Bacteria, Biodegradation, Environmental, Geologic Sediments, Methane, Petroleum},
	issn = {0028-0836},
	doi = {10.1038/35008145},
	author = {Anderson, R T and Lovley, D R}
}
@article {616,
	title = {Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer.},
	journal = {Int J Syst Bacteriol},
	volume = {49 Pt 4},
	year = {1999},
	month = {1999 Oct},
	pages = {1615-22},
	abstract = {In an attempt to understand better the micro-organisms involved in anaerobic degradation of aromatic hydrocarbons in the Fe(III)-reducing zone of petroleum-contaminated aquifers, Fe(III)-reducing micro-organisms were isolated from contaminated aquifer material that had been adapted for rapid oxidation of toluene coupled to Fe(III) reduction. One of these organisms, strain H-5T, was enriched and isolated on acetate/Fe(III) medium. Strain H-5T is a Gram-negative strict anaerobe that grows with various simple organic acids such as acetate, propionate, lactate and fumarate as alternative electron donors with Fe(III) as the electron acceptor. In addition, strain H-5T also oxidizes long-chain fatty acids such as palmitate with Fe(III) as the sole electron acceptor. Strain H-5T can also grow by fermentation of citrate or fumarate in the absence of an alternative electron acceptor. The primary end-products of citrate fermentation are acetate and succinate. In addition to various forms of soluble and insoluble Fe(III), strain H-5T grows with nitrate, Mn(IV), fumarate and the humic acid analogue 2,6-anthraquinone disulfonate as alternative electron acceptors. As with other organisms that can oxidize organic compounds completely with the reduction of Fe(III), cell suspensions of strain H-5T have absorbance maxima indicative of a c-type cytochrome(s). It is proposed that strain H-5T represents a novel genus in the Holophaga-Acidobacterium phylum and that it should be named Geothrix fermentans sp. nov., gen. nov.},
	keywords = {Biodegradation, Environmental, DNA, Bacterial, DNA, Ribosomal, Ferric Compounds, Geologic Sediments, Gram-Negative Anaerobic Bacteria, Molecular Sequence Data, Oxidation-Reduction, Petroleum, Phylogeny, RNA, Ribosomal, 16S, Water Microbiology, Water Pollutants, Chemical, Water Supply},
	issn = {0020-7713},
	author = {Coates, J D and Ellis, D J and Gaw, C V and Lovley, D 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 {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 {622,
	title = {Humic acids as electron acceptors for anaerobic microbial oxidation of vinyl chloride and dichloroethene.},
	journal = {Appl Environ Microbiol},
	volume = {64},
	year = {1998},
	month = {1998 Aug},
	pages = {3102-5},
	abstract = {Anaerobic oxidation of [1,2-14C]vinyl chloride and [1, 2-14C]dichloroethene to 14CO2 under humic acid-reducing conditions was demonstrated. The results indicate that waterborne contaminants can be oxidized by using humic acid compounds as electron acceptors and suggest that natural aquatic systems have a much larger capacity for contaminant oxidation than previously thought.},
	keywords = {Aerobiosis, Anaerobiosis, Bacteria, Biodegradation, Environmental, Geologic Sediments, Humic Substances, Oxidation-Reduction, Vinyl Chloride, Water Microbiology, Water Pollutants},
	issn = {0099-2240},
	author = {Bradley, P M and Chapelle, F H and Lovley, D R}
}
@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}
}
