@article {498,
	title = {The degree of redundancy in metabolic genes is linked to mode of metabolism.},
	journal = {Biophys J},
	volume = {94},
	year = {2008},
	month = {2008 Feb 15},
	pages = {1216-20},
	abstract = {An understanding of the factors favoring the maintenance of duplicate genes in microbial genomes is essential for developing models of microbial evolution. A genome-scale flux-balance analysis of the metabolic network of Saccharomyces cerevisiae has suggested that gene duplications primarily provide increased enzyme dosage to enhance metabolic flux because the incidence of gene duplications in essential genes is no higher than that in nonessential genes. Here, we used genome-scale metabolic models to analyze the extent of genetic and biochemical redundancy in prokaryotes that are either specialists, with one major mode of energy generation, or generalists, which have multiple metabolic strategies for conservation of energy. Surprisingly, the results suggest that generalists, such as Escherichia coli and Bacillus subtilis, are similar to the eukaryotic generalist, S. cerevisiae, in having a low percentage (<10\%) of essential genes and few duplications of these essential genes, whereas metabolic specialists, such as Geobacter sulfurreducens and Methanosarcina barkeri, have a high percentage (>30\%) of essential genes and a high degree of genetic redundancy in these genes compared to nonessential genes. Furthermore, the specialist organisms appear to rely more on gene duplications rather than alternative-but-equivalent metabolic pathways to provide resilience to gene loss. Generalists rely more on alternative pathways. Thus, the concept that the role of gene duplications is to boost enzymatic flux rather than provide metabolic resilience may not be universal. Rather, the degree of gene duplication in microorganisms may be linked to mode of metabolism and environmental niche.},
	keywords = {Bacterial Physiological Phenomena, Bacterial Proteins, Computer Simulation, Gene Expression Regulation, Bacterial, Genes, Duplicate, Models, Biological, Signal Transduction},
	issn = {1542-0086},
	doi = {10.1529/biophysj.107.118414},
	author = {Mahadevan, 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 {595,
	title = {Development of a genetic system for Geobacter sulfurreducens.},
	journal = {Appl Environ Microbiol},
	volume = {67},
	year = {2001},
	month = {2001 Jul},
	pages = {3180-7},
	abstract = {Members of the genus Geobacter are the dominant metal-reducing microorganisms in a variety of anaerobic subsurface environments and have been shown to be involved in the bioremediation of both organic and metal contaminants. To facilitate the study of the physiology of these organisms, a genetic system was developed for Geobacter sulfurreducens. The antibiotic sensitivity of this organism was characterized, and optimal conditions for plating it at high efficiency were established. A protocol for the introduction of foreign DNA into G. sulfurreducens by electroporation was also developed. Two classes of broad-host-range vectors, IncQ and pBBR1, were found to be capable of replication in G. sulfurreducens. In particular, the IncQ plasmid pCD342 was found to be a suitable expression vector for this organism. When the information and novel methods described above were utilized, the nifD gene of G. sulfurreducens was disrupted by the single-step gene replacement method. Insertional mutagenesis of this key gene in the nitrogen fixation pathway impaired the ability of G. sulfurreducens to grow in medium lacking a source of fixed nitrogen. Expression of the nifD gene in trans complemented this phenotype. This paper constitutes the first report of genetic manipulation of a member of the Geobacter genus.},
	keywords = {Anti-Bacterial Agents, Bacterial Proteins, Blotting, Southern, Culture Media, Deltaproteobacteria, Electroporation, Fimbriae Proteins, Genetic Complementation Test, Genetic Vectors, Microbial Sensitivity Tests, Mutagenesis, Insertional, Nitrogen Fixation, Plasmids, Transformation, Bacterial},
	issn = {0099-2240},
	doi = {10.1128/AEM.67.7.3180-3187.2001},
	author = {Coppi, M V and Leang, C and Sandler, S J and Lovley, D R}
}
@article {606,
	title = {Differences in Fe(III) reduction in the hyperthermophilic archaeon, Pyrobaculum islandicum, versus mesophilic Fe(III)-reducing bacteria.},
	journal = {FEMS Microbiol Lett},
	volume = {195},
	year = {2001},
	month = {2001 Feb 20},
	pages = {253-8},
	abstract = {The discovery that all hyperthermophiles that have been evaluated have the capacity to reduce Fe(III) has raised the question of whether mechanisms for dissimilatory Fe(III) reduction have been conserved throughout microbial evolution. Many studies have suggested that c-type cytochromes are integral components in electron transport to Fe(III) in mesophilic dissimilatory Fe(III)-reducing microorganisms. However, Pyrobaculum islandicum, the hyperthermophile in which Fe(III) reduction has been most intensively studied, did not contain c-type cytochromes. NADPH was a better electron donor for the Fe(III) reductase activity in P. islandicum than NADH. This is the opposite of what has been observed with mesophiles. Thus, if previous models for dissimilatory Fe(III) reduction by mesophilic bacteria are correct, then it is unlikely that a single strategy for electron transport to Fe(III) is present in all dissimilatory Fe(III)-reducing microorganisms.},
	keywords = {Cytochrome c Group, Electron Transport, Ferric Compounds, FMN Reductase, NADH, NADPH Oxidoreductases, NADP, Oxidation-Reduction, Temperature, Thermoproteaceae},
	issn = {0378-1097},
	author = {Childers, S E and Lovley, D R}
}
@article {607,
	title = {Direct and Fe(II)-mediated reduction of technetium by Fe(III)-reducing bacteria.},
	journal = {Appl Environ Microbiol},
	volume = {66},
	year = {2000},
	month = {2000 Sep},
	pages = {3743-9},
	abstract = {The dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens reduced and precipitated Tc(VII) by two mechanisms. Washed cell suspensions coupled the oxidation of hydrogen to enzymatic reduction of Tc(VII) to Tc(IV), leading to the precipitation of TcO(2) at the periphery of the cell. An indirect, Fe(II)-mediated mechanism was also identified. Acetate, although not utilized efficiently as an electron donor for direct cell-mediated reduction of technetium, supported the reduction of Fe(III), and the Fe(II) formed was able to transfer electrons abiotically to Tc(VII). Tc(VII) reduction was comparatively inefficient via this indirect mechanism when soluble Fe(III) citrate was supplied to the cultures but was enhanced in the presence of solid Fe(III) oxide. The rate of Tc(VII) reduction was optimal, however, when Fe(III) oxide reduction was stimulated by the addition of the humic analog and electron shuttle anthaquinone-2,6-disulfonate, leading to the rapid formation of the Fe(II)-bearing mineral magnetite. Under these conditions, Tc(VII) was reduced and precipitated abiotically on the nanocrystals of biogenic magnetite as TcO(2) and was removed from solution to concentrations below the limit of detection by scintillation counting. Cultures of Fe(III)-reducing bacteria enriched from radionuclide-contaminated sediment using Fe(III) oxide as an electron acceptor in the presence of 25 microM Tc(VII) contained a single Geobacter sp. detected by 16S ribosomal DNA analysis and were also able to reduce and precipitate the radionuclide via biogenic magnetite. Fe(III) reduction was stimulated in aquifer material, resulting in the formation of Fe(II)-containing minerals that were able to reduce and precipitate Tc(VII). These results suggest that Fe(III)-reducing bacteria may play an important role in immobilizing technetium in sediments via direct and indirect mechanisms.},
	keywords = {Culture Media, Deltaproteobacteria, Ferric Compounds, Ferrous Compounds, Fresh Water, Oxidation-Reduction, Technetium},
	issn = {0099-2240},
	author = {Lloyd, J R and Sole, V A and Van Praagh, C V 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}
}
@article {637,
	title = {Desulfuromonas palmitatis sp. nov., a marine dissimilatory Fe(III) reducer that can oxidize long-chain fatty acids.},
	journal = {Arch Microbiol},
	volume = {164},
	year = {1995},
	month = {1995 Dec},
	pages = {406-13},
	abstract = {Studies on the microorganisms living in hydrocarbon-contaminated sediments in San Diego Bay, California led to the isolation of a novel Fe(III)-reducing microorganism. This organism, designated strain SDBY1, was an obligately anaerobic, non-motile, non-flagellated, gram-negative rod. Strain SDBY1 conserves energy to support growth from the oxidation of acetate, lactate, succinate, fumarate, laurate, palmitate, or stearate. H2 was also oxidized with the reduction of Fe(III), but growth with H2 as the sole electron donor was not observed. In addition to various forms of soluble and insoluble Fe(III), strain SDBY1 also coupled growth to the reduction of fumarate, Mn(IV), or S0. Air-oxidized minus dithionite-reduced difference spectra exhibited peaks at 552.8, 523.6, and 422.8 nm, indicative of c-type cytochrome(s). Strain SDBY1 shares physiological characteristics with organisms in the genera Geobacter, Pelobacter, and Desulfuromonas. Detailed analysis of the 16S rRNA sequence indicated that strain SDBY1 should be placed in the genus Desulfuromonas. The new species name Desulfuromonas palmitatis is proposed. D. palmitatis is only the second marine organism found (after D. acetoxidans) to oxidize multicarbon organic compounds completely to carbon dioxide with Fe(III) as an electron acceptor and provides the first pure culture model for the oxidation of long-chain fatty acids coupled to Fe(III) reduction.},
	keywords = {Electron Transport, Fatty Acids, Gram-Negative Anaerobic Bacteria, Iron, Microscopy, Electron, Scanning, Oxidation-Reduction, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Water Microbiology},
	issn = {0302-8933},
	author = {Coates, J D and Lonergan, D J and Philips, E J and Jenter, H and Lovley, D R}
}
@article {650,
	title = {Dissimilatory Fe(III) Reduction by the Marine Microorganism Desulfuromonas acetoxidans.},
	journal = {Appl Environ Microbiol},
	volume = {59},
	year = {1993},
	month = {1993 Mar},
	pages = {734-42},
	abstract = {The ability of the marine microorganism Desulfuromonas acetoxidans to reduce Fe(III) was investigated because of its close phylogenetic relationship with the freshwater dissimilatory Fe(III) reducer Geobacter metallireducens. Washed cell suspensions of the type strain of D. acetoxidans reduced soluble Fe(III)-citrate and Fe(III) complexed with nitriloacetic acid. The c-type cytochrome(s) of D. acetoxidans was oxidized by Fe(III)-citrate and Mn(IV)-oxalate, as well as by two electron acceptors known to support growth, colloidal sulfur and malate. D. acetoxidans grew in defined anoxic, bicarbonate-buffered medium with acetate as the sole electron donor and poorly crystalline Fe(III) or Mn(IV) as the sole electron acceptor. Magnetite (Fe(3)O(4)) and siderite (FeCO(3)) were the major end products of Fe(III) reduction, whereas rhodochrosite (MnCO(3)) was the end product of Mn(IV) reduction. Ethanol, propanol, pyruvate, and butanol also served as electron donors for Fe(III) reduction. In contrast to D. acetoxidans, G. metallireducens could only grow in freshwater medium and it did not conserve energy to support growth from colloidal S reduction. D. acetoxidans is the first marine microorganism shown to conserve energy to support growth by coupling the complete oxidation of organic compounds to the reduction of Fe(III) or Mn(IV). Thus, D. acetoxidans provides a model enzymatic mechanism for Fe(III) or Mn(IV) oxidation of organic compounds in marine and estuarine sediments. These findings demonstrate that 16S rRNA phylogenetic analyses can suggest previously unrecognized metabolic capabilities of microorganisms.},
	issn = {0099-2240},
	author = {Roden, E E and Lovley, D R}
}
@article {652,
	title = {Dissimilatory metal reduction.},
	journal = {Annu Rev Microbiol},
	volume = {47},
	year = {1993},
	month = {1993},
	pages = {263-90},
	abstract = {Microorganisms can enzymatically reduce a variety of metals in metabolic processes that are not related to metal assimilation. Some microorganisms can conserve energy to support growth by coupling the oxidation of simple organic acids and alcohols, H2, or aromatic compounds to the reduction of Fe(III) or Mn(IV). This dissimilatory Fe(III) and Mn(IV) reduction influences the organic as well as the inorganic geochemistry of anaerobic aquatic sediments and ground water. Microorganisms that use U(VI) as a terminal electron acceptor play an important role in uranium geochemistry and may be a useful tool for removing uranium from contaminated environments. Se(VI) serves as a terminal electron acceptor to support anaerobic growth of some microorganisms. Reduction of Se(VI) to Se(O) is an important mechanism for the precipitation of selenium from contaminated waters. Enzymatic reduction of Cr(VI) to the less mobile and less toxic Cr(III), and reduction of soluble Hg(II) to volatile Hg(O) may affect the fate of these compounds in the environment and might be used as a remediation strategy. Microorganisms can also enzymatically reduce other metals such as technetium, vanadium, molybdenum, gold, silver, and copper, but reduction of these metals has not been studied extensively.},
	keywords = {Bacteria, Metals, Oxidation-Reduction},
	issn = {0066-4227},
	doi = {10.1146/annurev.mi.47.100193.001403},
	author = {Lovley, D R}
}
@article {656,
	title = {Dissimilatory Fe(III) and Mn(IV) reduction.},
	journal = {Microbiol Rev},
	volume = {55},
	year = {1991},
	month = {1991 Jun},
	pages = {259-87},
	abstract = {The oxidation of organic matter coupled to the reduction of Fe(III) or Mn(IV) is one of the most important biogeochemical reactions in aquatic sediments, soils, and groundwater. This process, which may have been the first globally significant mechanism for the oxidation of organic matter to carbon dioxide, plays an important role in the oxidation of natural and contaminant organic compounds in a variety of environments and contributes to other phenomena of widespread significance such as the release of metals and nutrients into water supplies, the magnetization of sediments, and the corrosion of metal. Until recently, much of the Fe(III) and Mn(IV) reduction in sedimentary environments was considered to be the result of nonenzymatic processes. However, microorganisms which can effectively couple the oxidation of organic compounds to the reduction of Fe(III) or Mn(IV) have recently been discovered. With Fe(III) or Mn(IV) as the sole electron acceptor, these organisms can completely oxidize fatty acids, hydrogen, or a variety of monoaromatic compounds. This metabolism provides energy to support growth. Sugars and amino acids can be completely oxidized by the cooperative activity of fermentative microorganisms and hydrogen- and fatty-acid-oxidizing Fe(III) and Mn(IV) reducers. This provides a microbial mechanism for the oxidation of the complex assemblage of sedimentary organic matter in Fe(III)- or Mn(IV)-reducing environments. The available evidence indicates that this enzymatic reduction of Fe(III) or Mn(IV) accounts for most of the oxidation of organic matter coupled to reduction of Fe(III) and Mn(IV) in sedimentary environments. Little is known about the diversity and ecology of the microorganisms responsible for Fe(III) and Mn(IV) reduction, and only preliminary studies have been conducted on the physiology and biochemistry of this process.},
	keywords = {Bacteria, Electron Transport, Ferric Compounds, Fungi, Geological Phenomena, Geology, Manganese, Oxidation-Reduction, Soil Microbiology, Water Microbiology},
	issn = {0146-0749},
	author = {Lovley, D R}
}
