@article {3045, title = {H Is a Major Intermediate in Corrosion of Iron.}, journal = {mBio}, volume = {14}, year = {2023}, month = {2023 Apr 25}, pages = {e0007623}, abstract = {

Desulfovibrio vulgaris has been a primary pure culture sulfate reducer for developing microbial corrosion concepts. Multiple mechanisms for how it accepts electrons from Fe have been proposed. We investigated Fe oxidation with a mutant of in which hydrogenase genes were deleted. The hydrogenase mutant grew as well as the parental strain with lactate as the electron donor, but unlike the parental strain, it was not able to grow on H. The parental strain reduced sulfate with Fe as the sole electron donor, but the hydrogenase mutant did not. H accumulated over time in Fe cultures of the hydrogenase mutant and sterile controls but not in parental strain cultures. Sulfide stimulated H production in uninoculated controls apparently by both reacting with Fe to generate H and facilitating electron transfer from Fe to H. Parental strain supernatants did not accelerate H production from Fe, ruling out a role for extracellular hydrogenases. Previously proposed electron transfer between Fe and via soluble electron shuttles was not evident. The hydrogenase mutant did not reduce sulfate in the presence of Fe and either riboflavin or anthraquinone-2,6-disulfonate, and these potential electron shuttles did not stimulate parental strain sulfate reduction with Fe as the electron donor. The results demonstrate that primarily accepts electrons from Fe via H as an intermediary electron carrier. These findings clarify the interpretation of previous corrosion studies and suggest that H-mediated electron transfer is an important mechanism for iron corrosion under sulfate-reducing conditions. Microbial corrosion of iron in the presence of sulfate-reducing microorganisms is economically significant. There is substantial debate over how microbes accelerate iron corrosion. Tools for genetic manipulation have only been developed for a few Fe(III)-reducing and methanogenic microorganisms known to corrode iron and in each case those microbes were found to accept electrons from Fe via direct electron transfer. However, iron corrosion is often most intense in the presence of sulfate-reducing microbes. The finding that Desulfovibrio vulgaris relies on H to shuttle electrons between Fe and cells revives the concept, developed in some of the earliest studies on microbial corrosion, that sulfate reducers consumption of H is a major microbial corrosion mechanism. The results further emphasize that direct Fe-to-microbe electron transfer has yet to be rigorously demonstrated in sulfate-reducing microbes.

}, keywords = {Corrosion, Desulfovibrio, Desulfovibrio vulgaris, Hydrogenase, Iron, Lactic Acid, Oxidation-Reduction, Sulfates}, issn = {2150-7511}, doi = {10.1128/mbio.00076-23}, author = {Woodard, Trevor L and Ueki, Toshiyuki and Lovley, Derek R} } @article {3054, title = {Electrotrophy: Other microbial species, iron, and electrodes as electron donors for microbial respirations.}, journal = {Bioresour Technol}, volume = {345}, year = {2022}, month = {2022 Feb}, pages = {126553}, abstract = {

Electrotrophy, the growth of microbes on extracellular electron donors, drives important biogeochemical cycles and has practical applications. Studies of Fe(II)-based electrotrophy have provided foundational cytochrome-based mechanistic models for electron transport into cells. Direct electron uptake from other microbial species, Fe(0), or cathodes is of intense interest due to its potential roles in the production and anaerobic oxidation of methane, corrosion, and bioelectrochemical technologies. Other cells or Fe(0) can serve as the sole electron donor supporting the growth of several Geobacter and methanogen strains that are unable to use H as an electron donor, providing strong evidence for electrotrophy. Additional evidence for electrotrophy in Geobacter strains and Methanosarcina acetivorans is a requirement for outer-surface c-type cytochromes. However, in most instances claims for electrotrophy in anaerobes are based on indirect inference and the possibility that H is actually the electron donor supporting growth has not been rigorously excluded.

}, keywords = {Electrodes, Electron Transport, Electrons, Geobacter, Iron, Oxidation-Reduction, Soil Microbiology}, issn = {1873-2976}, doi = {10.1016/j.biortech.2021.126553}, author = {Lovley, Derek R} } @article {3047, title = {Genetic Manipulation of Desulfovibrio ferrophilus and Evaluation of Fe(III) Oxide Reduction Mechanisms.}, journal = {Microbiol Spectr}, volume = {10}, year = {2022}, month = {2022 Dec 21}, pages = {e0392222}, abstract = {

The sulfate-reducing microbe Desulfovibrio ferrophilus is of interest due to its relatively rare ability to also grow with Fe(III) oxide as an electron acceptor and its rapid corrosion of metallic iron. Previous studies have suggested multiple agents for extracellular electron exchange including a soluble electron shuttle, electrically conductive pili, and outer surface multiheme -type cytochromes. However, the previous lack of a strategy for genetic manipulation of limited mechanistic investigations. We developed an electroporation-mediated transformation method that enabled replacement of genes of interest with an antibiotic resistance gene via double-crossover homologous recombination. Genes were identified that are essential for flagellum-based motility and the expression of the two types of pili. Disrupting flagellum-based motility or expression of either of the two pili did not inhibit Fe(III) oxide reduction, nor did deleting genes for multiheme -type cytochromes predicted to be associated with the outer membrane. Although redundancies in cytochrome or pilus function might explain some of these phenotypes, overall, the results are consistent with primarily reducing Fe(III) oxide via an electron shuttle. The finding that is genetically tractable not only will aid in elucidating further details of its mechanisms for Fe(III) oxide reduction but also provides a new experimental approach for developing a better understanding of some of its other unique features, such as the ability to corrode metallic iron at high rates and accept electrons from negatively poised electrodes. is an important pure culture model for Fe(III) oxide reduction and the corrosion of iron-containing metals in anaerobic marine environments. This study demonstrates that is genetically tractable, an important advance for elucidating the mechanisms by which it interacts with extracellular electron acceptors and donors. The results demonstrate that there is not one specific outer surface multiheme -type cytochrome that is essential for Fe(III) oxide reduction. This finding, coupled with the lack of apparent porin-cytochrome conduits encoded in the genome and the finding that deleting genes for pilus and flagellum expression did not inhibit Fe(III) oxide reduction, suggests that has adopted strategies for extracellular electron exchange that are different from those of intensively studied electroactive microbes like and species. Thus, the ability to genetically manipulate is likely to lead to new mechanistic concepts in electromicrobiology.

}, keywords = {Cytochromes, Electron Transport, Ferric Compounds, Iron, Oxidation-Reduction, Oxides}, issn = {2165-0497}, doi = {10.1128/spectrum.03922-22}, author = {Ueki, Toshiyuki and Woodard, Trevor L and Lovley, Derek R} } @article {3062, title = {Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species.}, journal = {ISME J}, volume = {15}, year = {2021}, month = {2021 Oct}, pages = {3084-3093}, abstract = {

Microbial corrosion of iron-based materials is a substantial economic problem. A mechanistic understanding is required to develop mitigation strategies, but previous mechanistic studies have been limited to investigations with relatively pure Fe(0), which is not a common structural material. We report here that the mechanism for microbial corrosion of stainless steel, the metal of choice for many actual applications, can be significantly different from that~for Fe(0). Although H is often an intermediary electron carrier between the metal and microbes during Fe(0) corrosion, we found that H is not abiotically produced from stainless steel, making this corrosion mechanism unlikely. Geobacter sulfurreducens and Geobacter metallireducens, electrotrophs that are known to directly accept electrons from other microbes or electrodes, extracted electrons from stainless steel via direct iron-to-microbe electron transfer. Genetic modification to prevent H consumption did not negatively impact on stainless steel corrosion. Corrosion was inhibited when genes for outer-surface cytochromes that are key electrical contacts were deleted. These results indicate that a common model of microbial Fe(0) corrosion~by hydrogenase-positive microbes, in which H serves as an intermediary electron carrier between the metal surface and the microbe, may not apply to the microbial corrosion of stainless steel. However, direct iron-to-microbe electron transfer is a~feasible route for stainless steel corrosion.

}, keywords = {Corrosion, Electrons, Geobacter, Iron, Stainless Steel}, issn = {1751-7370}, doi = {10.1038/s41396-021-00990-2}, author = {Tang, Hai-Yan and Yang, Chuntian and Ueki, Toshiyuki and Pittman, Conor C and Xu, Dake and Woodard, Trevor L and Holmes, Dawn E and Gu, Tingyue and Wang, Fuhui and Lovley, Derek R} } @article {3077, title = {Iron Corrosion via Direct Metal-Microbe Electron Transfer.}, journal = {mBio}, volume = {10}, year = {2019}, month = {2019 May 14}, abstract = {

The concept that anaerobic microorganisms can directly accept electrons from Fe(0) has been controversial because direct metal-microbe electron transfer has previously only been indirectly inferred. Fe(0) oxidation was studied with strain ACL, an autotrophic strain that was previously shown to grow with electrons derived from a graphite cathode as the sole electron donor. Strain ACL grew with Fe(0) as the sole electron donor and fumarate as the electron acceptor. However, it appeared that at least a portion of the electron transfer was via H produced nonenzymatically from the oxidation of Fe(0) to Fe(II). H, which accumulated in abiotic controls, was consumed during the growth of strain ACL, the cells were predominately planktonic, and genes for the uptake hydrogenase were highly expressed. Strain ACL was constructed to prevent growth on H or formate by deleting the genes for the uptake of hydrogenase and formate dehydrogenases from strain ACL. Strain ACL also grew with Fe(0) as the sole electron donor, but H accumulated in the culture, and cells heavily colonized Fe(0) surfaces with no visible planktonic growth. Transcriptomics suggested that the outer surface -type cytochromes OmcS and OmcZ were important during growth of strain ACL on Fe(0). Strain ACL did not grow on Fe(0) if the gene for either of these cytochromes was deleted. The specific attachment of strain ACL to Fe(0), coupled with requirements for known extracellular electrical contacts, suggest that direct metal-microbe electron transfer is the most likely option for Fe(0) serving as an electron donor. The anaerobic corrosion of iron structures is expensive to repair and can be a safety and environmental concern. It has been known for over 100 years that the presence of anaerobic respiratory microorganisms can accelerate iron corrosion. Multiple studies have suggested that there are sulfate reducers, methanogens, and acetogens that can directly accept electrons from Fe(0) to support sulfate or carbon dioxide reduction. However, all of the strains studied can also use H as an electron donor for growth, which is known to be abiotically produced from Fe(0). Furthermore, no proteins definitely shown to function as extracellular electrical contacts with Fe(0) were identified. The studies described here demonstrate that direct electron transfer from Fe(0) can support anaerobic respiration. They also map out a simple genetic approach to the study of iron corrosion mechanisms in other microorganisms. A better understanding of how microorganisms promote iron corrosion is expected to lead to the development of strategies that can help reduce adverse impacts from this process.

}, keywords = {Anaerobiosis, Corrosion, Cytochromes, Electron Transport, Formate Dehydrogenases, Geobacter, Iron, Oxidation-Reduction, Oxidoreductases, Transcriptome}, issn = {2150-7511}, doi = {10.1128/mBio.00303-19}, author = {Tang, Hai-Yan and Holmes, Dawn E and Ueki, Toshiyuki and Palacios, Paola A and Lovley, Derek R} } @article {3121, title = {Centimeter-long electron transport in marine sediments via conductive minerals.}, journal = {ISME J}, volume = {9}, year = {2015}, month = {2015 Feb}, pages = {527-31}, abstract = {

Centimeter-long electron conduction through marine sediments, in which electrons derived from sulfide in anoxic sediments are transported to oxygen in surficial sediments, may have an important influence on sediment geochemistry. Filamentous bacteria have been proposed to mediate the electron transport, but the filament conductivity could not be verified and other mechanisms are possible. Surprisingly, previous investigations have never actually measured the sediment conductivity or its basic physical properties. Here we report direct measurements that demonstrate centimeter-long electron flow through marine sediments, with conductivities sufficient to account for previously estimated electron fluxes. Conductivity was lost for oxidized sediments, which contrasts with the previously described increase in the conductivity of microbial biofilms upon oxidation. Adding pyrite to the sediments significantly enhanced the conductivity. These results suggest that the role of conductive minerals, which are more commonly found in sediments than centimeter-long microbial filaments, need to be considered when modeling marine sediment biogeochemistry.

}, keywords = {Electron Transport, Geologic Sediments, Iron, Minerals, Oxidation-Reduction, Sulfides}, issn = {1751-7370}, doi = {10.1038/ismej.2014.131}, author = {Malvankar, Nikhil S and King, Gary M and Lovley, Derek R} } @article {1411, title = {Magnetite formation from ferrihydrite by hyperthermophilic archaea from Endeavour Segment, Juan de Fuca Ridge hydrothermal vent chimneys.}, journal = {Geobiology}, volume = {12}, year = {2014}, month = {2014 May}, pages = {200-11}, abstract = {

Hyperthermophilic iron reducers are common in hydrothermal chimneys found along the Endeavour Segment in the northeastern Pacific Ocean based on culture-dependent estimates. However, information on the availability of Fe(III) (oxyhydr) oxides within these chimneys, the types of Fe(III) (oxyhydr) oxides utilized by the organisms, rates and environmental constraints of hyperthermophilic iron reduction, and mineral end products is needed to determine their biogeochemical significance and are addressed in this study. Thin-section petrography on the interior of a hydrothermal chimney from the Dante edifice at Endeavour showed a thin coat of Fe(III) (oxyhydr) oxide associated with amorphous silica on the exposed outer surfaces of pyrrhotite, sphalerite, and chalcopyrite in pore spaces, along with anhydrite precipitation in the pores that is indicative of seawater ingress. The iron sulfide minerals were likely oxidized to Fe(III) (oxyhydr) oxide with increasing pH and Eh due to cooling and seawater exposure, providing reactants for bioreduction. Culture-dependent estimates of hyperthermophilic iron reducer abundances in this sample were 1740 and 10 cells per gram (dry weight) of material from the outer surface and the marcasite-sphalerite-rich interior, respectively. Two hyperthermophilic iron reducers, Hyperthermus sp. Ro04 and Pyrodictium sp. Su06, were isolated from other active hydrothermal chimneys on the Endeavour Segment. Strain Ro04 is a neutrophilic (pH opt 7-8) heterotroph, while strain Su06 is a mildly acidophilic (pH opt 5), hydrogenotrophic autotroph, both with optimal growth temperatures of 90-92 \°C. M\össbauer spectroscopy of the iron oxides before and after growth demonstrated that both organisms form nanophase (\<12 nm) magnetite [Fe3 O4 ] from laboratory-synthesized ferrihydrite [Fe10 O14 (OH)2 ] with no detectable mineral intermediates. They produced up to 40 mm Fe(2+) in a growth-dependent manner, while all abiotic and biotic controls produced \<3 mm Fe(2+) . Hyperthermophilic iron reducers may have a growth advantage over other hyperthermophiles in hydrothermal systems that are mildly acidic where mineral weathering at increased temperatures occurs.

}, keywords = {Ferric Compounds, Ferrosoferric Oxide, Hydrothermal Vents, Iron, Oxidation-Reduction, Pacific Ocean, Photomicrography, Pyrodictiaceae, Spectroscopy, Mossbauer, Sulfides}, issn = {1472-4669}, doi = {10.1111/gbi.12083}, author = {Lin, T Jennifer and Breves, E A and Dyar, M D and Ver Eecke, H C and Jamieson, J W and Holden, J F} } @article {1441, title = {Mycobacterial Esx-3 requires multiple components for iron acquisition.}, journal = {MBio}, volume = {5}, year = {2014}, month = {2014}, pages = {e01073-14}, abstract = {

ABSTRACT The type VII secretion systems are conserved across mycobacterial species and in many Gram-positive bacteria. While the well-characterized Esx-1 pathway is required for the virulence of pathogenic mycobacteria and conjugation in the model organism Mycobacterium smegmatis, Esx-3 contributes to mycobactin-mediated iron acquisition in these bacteria. Here we show that several Esx-3 components are individually required for function under low-iron conditions but that at least one, the membrane-bound protease MycP3 of M. smegmatis, is partially expendable. All of the esx-3 mutants tested, including the ΔmycP3ms mutant, failed to export the native Esx-3 substrates EsxHms and EsxGms to quantifiable levels, as determined by targeted mass spectrometry. Although we were able to restore low-iron growth to the esx-3 mutants by genetic complementation, we found a wide range of complementation levels for protein export. Indeed, minute quantities of extracellular EsxHms and EsxGms were sufficient for iron acquisition under our experimental conditions. The apparent separation of Esx-3 function in iron acquisition from robust EsxGms and EsxHms secretion in the ΔmycP3ms mutant and in some of the complemented esx-3 mutants compels reexamination of the structure-function relationships for type VII secretion systems. IMPORTANCE Mycobacteria have several paralogous type VII secretion systems, Esx-1 through Esx-5. Whereas Esx-1 is required for pathogenic mycobacteria to grow within an infected host, Esx-3 is essential for growth in vitro. We and others have shown that Esx-3 is required for siderophore-mediated iron acquisition. In this work, we identify individual Esx-3 components that contribute to this process. As in the Esx-1 system, most mutations that abolish Esx-3 protein export also disrupt its function. Unexpectedly, however, ultrasensitive quantitation of Esx-3 secretion by multiple-reaction-monitoring mass spectrometry (MRM-MS) revealed that very low levels of export were sufficient for iron acquisition under similar conditions. Although protein export clearly contributes to type VII function, the relationship is not absolute.

}, keywords = {Bacterial Secretion Systems, Gene Order, Genetic Loci, Iron, Mycobacterium, Oxazoles}, issn = {2150-7511}, doi = {10.1128/mBio.01073-14}, author = {Siegrist, M Sloan and Steigedal, Magnus and Ahmad, Rushdy and Mehra, Alka and Dragset, Marte S and Schuster, Brian M and Philips, Jennifer A and Carr, Steven A and Rubin, Eric J} } @article {3136, title = {Anaerobic benzene oxidation via phenol in Geobacter metallireducens.}, journal = {Appl Environ Microbiol}, volume = {79}, year = {2013}, month = {2013 Dec}, pages = {7800-6}, abstract = {

Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance. Therefore, benzene metabolism was investigated in Geobacter metallireducens, the only genetically tractable organism known to anaerobically degrade benzene. Trace amounts (<0.5 μM) of phenol accumulated in cultures of Geobacter metallireducens anaerobically oxidizing benzene to carbon dioxide with the reduction of Fe(III). Phenol was not detected in cell-free controls or in Fe(II)- and benzene-containing cultures of Geobacter sulfurreducens, a Geobacter species that cannot metabolize benzene. The phenol produced in G. metallireducens cultures was labeled with (18)O during growth in H2(18)O, as expected for anaerobic conversion of benzene to phenol. Analysis of whole-genome gene expression patterns indicated that genes for phenol metabolism were upregulated during growth on benzene but that genes for benzoate or toluene metabolism were not, further suggesting that phenol was an intermediate in benzene metabolism. Deletion of the genes for PpsA or PpcB, subunits of two enzymes specifically required for the metabolism of phenol, removed the capacity for benzene metabolism. These results demonstrate that benzene hydroxylation to phenol is an alternative to carboxylation for anaerobic benzene activation and suggest that this may be an important metabolic route for benzene removal in petroleum-contaminated groundwaters, in which Geobacter species are considered to play an important role in anaerobic benzene degradation.

}, keywords = {Anaerobiosis, Benzene, Carbon Dioxide, Gene Deletion, Gene Expression Profiling, Geobacter, Iron, Metabolic Networks and Pathways, Oxidation-Reduction, Phenol, Water}, issn = {1098-5336}, doi = {10.1128/AEM.03134-13}, author = {Zhang, Tian and Tremblay, Pier-Luc and Chaurasia, Akhilesh Kumar and Smith, Jessica A and Bain, Timothy S and Lovley, Derek R} } @article {3143, title = {Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013}, pages = {e57819}, abstract = {

While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux through Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III) reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.

}, keywords = {Biomass, Carbon, Environment, Gene Expression Regulation, Bacterial, Geobacter, Groundwater, Humic Substances, Iron, Oxidation-Reduction, Phosphates, Plankton, Proteomics, RNA, Ribosomal, 16S, Tandem Mass Spectrometry, Uranium, Vanadium, Water Microbiology}, issn = {1932-6203}, doi = {10.1371/journal.pone.0057819}, author = {Wilkins, Michael J and Wrighton, Kelly C and Nicora, Carrie D and Williams, Kenneth H and McCue, Lee Ann and Handley, Kim M and Miller, Chris S and Giloteaux, Ludovic and Montgomery, Alison P and Lovley, Derek R and Banfield, Jillian F and Long, Philip E and Lipton, Mary S} } @article {1563, title = {Interference of ferric ions with ferrous iron quantification using the ferrozine assay.}, journal = {J Microbiol Methods}, volume = {95}, year = {2013}, month = {2013 Dec}, pages = {366-7}, abstract = {

The ferrozine assay is a widely used colorimetric method for determining soluble iron concentrations. We provide evidence for a heretofore unrecognized interference of ferric ions (Fe(3+)) on ferrous iron (Fe(2+)) measurements performed in the dark. Fe(3+) concentrations affected the absorbance measurements, which linearly increased with incubation time.

}, keywords = {Chemistry Techniques, Analytical, Colorimetry, Darkness, Diagnostic Errors, Ferric Compounds, Ferrous Compounds, Ferrozine, Ions, Iron, Time Factors}, issn = {1872-8359}, doi = {10.1016/j.mimet.2013.10.005}, author = {Im, Jeongdae and Lee, Jaejin and L{\"o}ffler, Frank E} } @article {427, title = {Biochemical characterization of purified OmcS, a c-type cytochrome required for insoluble Fe(III) reduction in Geobacter sulfurreducens.}, journal = {Biochim Biophys Acta}, volume = {1807}, year = {2011}, month = {2011 Apr}, pages = {404-12}, abstract = {Previous studies with Geobacter sulfurreducens have demonstrated that OmcS, an abundant c-type cytochrome that is only loosely bound to the outer surface, plays an important role in electron transfer to Fe(III) oxides as well as other extracellular electron acceptors. In order to further investigate the function of OmcS, it was purified from a strain that overproduces the protein. Purified OmcS had a molecular mass of 47015 Da, and six low-spin bis-histidinyl hexacoordinated heme groups. Its midpoint redox potential was -212 mV. A thermal stability analysis showed that the cooperative melting of purified OmcS occurs in the range of 65-82 {\textdegree}C. Far UV circular dichroism spectroscopy indicated that the secondary structure of purified OmcS consists of about 10\% α-helix and abundant disordered structures. Dithionite-reduced OmcS was able to transfer electrons to a variety of substrates of environmental importance including insoluble Fe(III) oxide, Mn(IV) oxide and humic substances. Stopped flow analysis revealed that the reaction rate of OmcS oxidation has a hyperbolic dependence on the concentration of the studied substrates. A ten-fold faster reaction rate with anthraquinone-2,6-disulfonate (AQDS) (25.2 s$^{-}${\textonesuperior}) was observed as compared to that with Fe(III) citrate (2.9 s$^{-}${\textonesuperior}). The results, coupled with previous localization and gene deletion studies, suggest that OmcS is well-suited to play an important role in extracellular electron transfer.}, keywords = {Circular Dichroism, Cytochrome c Group, Geobacter, Heme, Iron, Kinetics, Molecular Weight, Oxidation-Reduction, Solubility}, issn = {0006-3002}, doi = {10.1016/j.bbabio.2011.01.003}, author = {Qian, Xinlei and Mester, T{\"u}nde and Morgado, Leonor and Arakawa, Tsutomu and Sharma, Manju L and Inoue, Kengo and Joseph, Crisjoe and Salgueiro, Carlos A and Maroney, Michael J and Lovley, Derek R} } @article {434, title = {The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments.}, journal = {BMC Genomics}, volume = {11}, year = {2010}, month = {2010}, pages = {490}, abstract = {BACKGROUND: Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. RESULTS: Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced non-subsurface Geobacteraceae, which will be useful for in silico metabolic modeling of subsurface bioremediation processes involving Geobacter species. Pathways can now be predicted for the use of various carbon sources such as propionate by G. bemidjiensis. Additional metabolic capabilities such as carbon dioxide fixation and growth on glucose were predicted from the genome annotation. The presence of different dicarboxylic acid transporters and two oxaloacetate decarboxylases in G. bemidjiensis may explain its ability to grow by disproportionation of fumarate. Although benzoate is the only aromatic compound that G. bemidjiensis is known or predicted to utilize as an electron donor and carbon source, the genome suggests that this species may be able to detoxify other aromatic pollutants without degrading them. Furthermore, G. bemidjiensis is auxotrophic for 4-aminobenzoate, which makes it the first Geobacter species identified as having a vitamin requirement. Several features of the genome indicated that G. bemidjiensis has enhanced abilities to respire, detoxify and avoid oxygen. CONCLUSION: Overall, the genome sequence of G. bemidjiensis offers surprising insights into the metabolism and physiology of Geobacteraceae in subsurface environments, compared to non-subsurface Geobacter species, such as the ability to disproportionate fumarate, more efficient oxidation of propionate, enhanced responses to oxygen stress, and dependence on the environment for a vitamin requirement. Therefore, an understanding of the activity of Geobacter species in the subsurface is more likely to benefit from studies of subsurface isolates such as G. bemidjiensis than from the non-subsurface model species studied so far.}, keywords = {Aldehyde Oxidoreductases, Biodegradation, Environmental, Carbohydrate Metabolism, Carbon Dioxide, Cell Wall, Electrons, Environmental Microbiology, Fatty Acids, Frameshift Mutation, Fumarates, Genes, Bacterial, Genome, Bacterial, Geobacter, Glucose, Iron, Metabolic Networks and Pathways, Multienzyme Complexes, Multigene Family, Osmosis, Oxidation-Reduction, Oxo-Acid-Lyases, Propionic Acids, Pyruvic Acid, Species Specificity, Surface Properties}, issn = {1471-2164}, doi = {10.1186/1471-2164-11-490}, author = {Aklujkar, Muktak and Young, Nelson D and Holmes, Dawn and Chavan, Milind and Risso, Carla and Kiss, Hajnalka E and Han, Cliff S and Land, Miriam L and Lovley, Derek R} } @article {376, title = {Microbial communities acclimate to recurring changes in soil redox potential status.}, journal = {Environ Microbiol}, volume = {12}, year = {2010}, month = {2010 Dec}, pages = {3137-49}, abstract = {Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA-based) and active (RNA-based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO$_{2}$ respiration, methanogenesis, N$_{2}$O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4-day redox potential fluctuations did not. Using RNA:DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbial community adapted to fluctuating redox potential.}, keywords = {Acclimatization, Archaea, Bacteria, Carbon Dioxide, DNA, Archaeal, DNA, Bacterial, Iron, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, RNA, Archaeal, RNA, Bacterial, Soil, Soil Microbiology, Trees}, issn = {1462-2920}, doi = {10.1111/j.1462-2920.2010.02286.x}, author = {Deangelis, Kristen M and Silver, Whendee L and Thompson, Andrew W and Firestone, Mary K} } @article {464, title = {Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.}, journal = {Microb Biotechnol}, volume = {2}, year = {2009}, month = {2009 Mar}, pages = {274-86}, abstract = {The increasing availability of the genome sequences of microorganisms involved in important bioremediation processes makes it feasible to consider developing genome-scale models that can aid in predicting the likely outcome of potential subsurface bioremediation strategies. Previous studies of the in situ bioremediation of uranium-contaminated groundwater have demonstrated that Geobacter species are often the dominant members of the groundwater community during active bioremediation and the primary organisms catalysing U(VI) reduction. Therefore, a genome-scale, constraint-based model of the metabolism of Geobacter sulfurreducens was coupled with the reactive transport model HYDROGEOCHEM in an attempt to model in situ uranium bioremediation. In order to simplify the modelling, the influence of only three growth factors was considered: acetate, the electron donor added to stimulate U(VI) reduction; Fe(III), the electron acceptor primarily supporting growth of Geobacter; and ammonium, a key nutrient. The constraint-based model predicted that growth yields of Geobacter varied significantly based on the availability of these three growth factors and that there are minimum thresholds of acetate and Fe(III) below which growth and activity are not possible. This contrasts with typical, empirical microbial models that assume fixed growth yields and the possibility for complete metabolism of the substrates. The coupled genome-scale and reactive transport model predicted acetate concentrations and U(VI) reduction rates in a field trial of in situ uranium bioremediation that were comparable to the predictions of a calibrated conventional model, but without the need for empirical calibration, other than specifying the initial biomass of Geobacter. These results suggest that coupling genome-scale metabolic models with reactive transport models may be a good approach to developing models that can be truly predictive, without empirical calibration, for evaluating the probable response of subsurface microorganisms to possible bioremediation approaches prior to implementation.}, keywords = {Acetates, Biodegradation, Environmental, Biological Transport, Genome, Bacterial, Geobacter, Iron, Models, Biological, Uranium}, issn = {1751-7915}, doi = {10.1111/j.1751-7915.2009.00087.x}, author = {Scheibe, Timothy D and Mahadevan, Radhakrishnan and Fang, Yilin and Garg, Srinath and Long, Philip E and Lovley, Derek R} } @article {466, title = {Genome-scale constraint-based modeling of Geobacter metallireducens.}, journal = {BMC Syst Biol}, volume = {3}, year = {2009}, month = {2009}, pages = {15}, abstract = {BACKGROUND: Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III) oxide serving as electron acceptor. Geobacter species, including G. sulfurreducens and G. metallireducens, are used for bioremediation and electricity generation from waste organic matter and renewable biomass. The constraint-based modeling approach enables the development of genome-scale in silico models that can predict the behavior of complex biological systems and their responses to the environments. Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens. RESULTS: The genome-scale metabolic model of G. metallireducens was constructed to include 747 genes and 697 reactions. Compared to the G. sulfurreducens model, the G. metallireducens metabolic model contains 118 unique reactions that reflect many of G. metallireducens{\textquoteright} specific metabolic capabilities. Detailed examination of the G. metallireducens model suggests that its central metabolism contains several energy-inefficient reactions that are not present in the G. sulfurreducens model. Experimental biomass yield of G. metallireducens growing on pyruvate was lower than the predicted optimal biomass yield. Microarray data of G. metallireducens growing with benzoate and acetate indicated that genes encoding these energy-inefficient reactions were up-regulated by benzoate. These results suggested that the energy-inefficient reactions were likely turned off during G. metallireducens growth with acetate for optimal biomass yield, but were up-regulated during growth with complex electron donors such as benzoate for rapid energy generation. Furthermore, several computational modeling approaches were applied to accelerate G. metallireducens research. For example, growth of G. metallireducens with different electron donors and electron acceptors were studied using the genome-scale metabolic model, which provided a fast and cost-effective way to understand the metabolism of G. metallireducens. CONCLUSION: We have developed a genome-scale metabolic model for G. metallireducens that features both metabolic similarities and differences to the published model for its close relative, G. sulfurreducens. Together these metabolic models provide an important resource for improving strategies on bioremediation and bioenergy generation.}, keywords = {Biodegradation, Environmental, Biomass, Computer Simulation, Ecosystem, Electron Transport, Energy Metabolism, Genome, Bacterial, Geobacter, Iron, Metabolic Networks and Pathways, Models, Biological, Models, Genetic, Mutation, Phenotype, Species Specificity, Systems Biology}, issn = {1752-0509}, doi = {10.1186/1752-0509-3-15}, author = {Sun, Jun and Sayyar, Bahareh and Butler, Jessica E and Pharkya, Priti and Fahland, Tom R and Famili, Iman and Schilling, Christophe H and Lovley, Derek R and Mahadevan, Radhakrishnan} } @article {1447, title = {Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition.}, journal = {Proc Natl Acad Sci U S A}, volume = {106}, year = {2009}, month = {2009 Nov 3}, pages = {18792-7}, abstract = {

The Esx secretion pathway is conserved across Gram-positive bacteria. Esx-1, the best-characterized system, is required for virulence of Mycobacterium tuberculosis, although its precise function during infection remains unclear. Esx-3, a paralogous system present in all mycobacterial species, is required for growth in vitro. Here, we demonstrate that mycobacteria lacking Esx-3 are defective in acquiring iron. To compete for the limited iron available in the host and the environment, these organisms use mycobactin, high-affinity iron-binding molecules. In the absence of Esx-3, mycobacteria synthesize mycobactin but are unable to use the bound iron and are impaired severely for growth during macrophage infection. Mycobacteria thus require a specialized secretion system for acquiring iron from siderophores.

}, keywords = {Animals, Bacterial Proteins, Genome, Bacterial, Iron, Macrophages, Mice, Mutation, Mycobacterium, Mycobacterium Infections, Oxazoles, Protein Binding, Secretory Pathway, Siderophores, Transcription, Genetic, Up-Regulation}, issn = {1091-6490}, doi = {10.1073/pnas.0900589106}, author = {Siegrist, M Sloan and Unnikrishnan, Meera and McConnell, Matthew J and Borowsky, Mark and Cheng, Tan-Yun and Siddiqi, Noman and Fortune, Sarah M and Moody, D Branch and Rubin, Eric J} } @article {1210, title = {Constraints on anaerobic respiration in the hyperthermophilic Archaea Pyrobaculum islandicum and Pyrobaculum aerophilum.}, journal = {Appl Environ Microbiol}, volume = {74}, year = {2008}, month = {2008 Jan}, pages = {396-402}, abstract = {

Pyrobaculum islandicum uses iron, thiosulfate, and elemental sulfur for anaerobic respiration, while Pyrobaculum aerophilum uses iron and nitrate; however, the constraints on these processes and their physiological mechanisms for iron and sulfur reduction are not well understood. Growth rates on sulfur compounds are highest at pH 5 to 6 and highly reduced (<-420-mV) conditions, while growth rates on nitrate and iron are highest at pH 7 to 9 and more-oxidized (>-210-mV) conditions. Growth on iron expands the known pH range of growth for both organisms. P. islandicum differs from P. aerophilum in that it requires direct contact with insoluble iron oxide for growth, it did not produce any extracellular compounds when grown on insoluble iron, and it lacked 2,6-anthrahydroquinone disulfonate oxidase activity. Furthermore, iron reduction in P. islandicum appears to be completely independent of c-type cytochromes. Like that in P. aerophilum, NADH-dependent ferric reductase activity in P. islandicum increased significantly in iron-grown cultures relative to that in non-iron-grown cultures. Proteomic analyses showed that there were significant increases in the amounts of a putative membrane-bound thiosulfate reductase in P. islandicum cultures grown on thiosulfate relative to those in cultures grown on iron and elemental sulfur. This is the first evidence of this enzyme being used in either a hyperthermophile or an archaeon. Pyrobaculum arsenaticum and Pyrobaculum calidifontis also grew on Fe(III) citrate and insoluble iron oxide, but only P. arsenaticum could grow on insoluble iron without direct contact.

}, keywords = {Anaerobiosis, FMN Reductase, Hydrogen-Ion Concentration, Iron, Nitrates, Oxidation-Reduction, Pyrobaculum, Species Specificity, Sulfur, Sulfurtransferases, Thiosulfates}, issn = {1098-5336}, doi = {10.1128/AEM.02033-07}, author = {Feinberg, Lawrence F and Srikanth, R and Vachet, Richard W and Holden, James F} } @article {488, title = {Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation.}, journal = {Environ Microbiol}, volume = {10}, year = {2008}, month = {2008 May}, pages = {1218-30}, abstract = {Limitations on the availability of Fe(III) as an electron acceptor are thought to play an important role in restricting the growth and activity of Geobacter species during bioremediation of contaminated subsurface environments, but the possibility that these organisms might also be limited in the subsurface by the availability of iron for assimilatory purposes was not previously considered because copious quantities of Fe(II) are produced as the result of Fe(III) reduction. Analysis of multiple Geobacteraceae genomes revealed the presence of a three-gene cluster consisting of homologues of two iron-dependent regulators, fur and dtxR (ideR), separated by a homologue of feoB, which encodes an Fe(II) uptake protein. This cluster appears to be conserved among members of the Geobacteraceae and was detected in several environments. Expression of the fur-feoB-ideR cluster decreased as Fe(II) concentrations increased in chemostat cultures. The number of Geobacteraceae feoB transcripts in groundwater samples from a site undergoing in situ uranium bioremediation was relatively high until the concentration of dissolved Fe(II) increased near the end of the field experiment. These results suggest that, because much of the Fe(II) is sequestered in solid phases, Geobacter species, which have a high requirement for iron for iron-sulfur proteins, may be limited by the amount of iron available for assimilatory purposes. These results demonstrate the ability of transcript analysis to reveal previously unsuspected aspects of the in situ physiology of microorganisms in subsurface environments.}, keywords = {Bacterial Proteins, Biodegradation, Environmental, Culture Media, Ferric Compounds, Ferrous Compounds, Fresh Water, Gene Expression Regulation, Bacterial, Geobacter, Iron, Multigene Family, Phylogeny, Polymerase Chain Reaction, Repressor Proteins, Reverse Transcriptase Polymerase Chain Reaction, Transcription, Genetic, Uranium, Water Pollution, Radioactive}, issn = {1462-2920}, doi = {10.1111/j.1462-2920.2007.01537.x}, author = {O{\textquoteright}Neil, Regina A and Holmes, Dawn E and Coppi, Maddalena V and Adams, Lorrie A and Larrahondo, M Juliana and Ward, Joy E and Nevin, Kelly P and Woodard, Trevor L and Vrionis, Helen A and N{\textquoteright}guessan, Lucie A and Lovley, Derek R} } @article {481, title = {Genome-wide gene expression patterns and growth requirements suggest that Pelobacter carbinolicus reduces Fe(III) indirectly via sulfide production.}, journal = {Appl Environ Microbiol}, volume = {74}, year = {2008}, month = {2008 Jul}, pages = {4277-84}, abstract = {Although Pelobacter species are closely related to Geobacter species, recent studies suggested that Pelobacter carbinolicus may reduce Fe(III) via a different mechanism because it lacks the outer-surface c-type cytochromes that are required for Fe(III) reduction by Geobacter sulfurreducens. Investigation into the mechanisms for Fe(III) reduction demonstrated that P. carbinolicus had growth yields on both soluble and insoluble Fe(III) consistent with those of other Fe(III)-reducing bacteria. Comparison of whole-genome transcript levels during growth on Fe(III) versus fermentative growth demonstrated that the greatest apparent change in gene expression was an increase in transcript levels for four contiguous genes. These genes encode two putative periplasmic thioredoxins; a putative outer-membrane transport protein; and a putative NAD(FAD)-dependent dehydrogenase with homology to disulfide oxidoreductases in the N terminus, rhodanese (sulfurtransferase) in the center, and uncharacterized conserved proteins in the C terminus. Unlike G. sulfurreducens, transcript levels for cytochrome genes did not increase in P. carbinolicus during growth on Fe(III). P. carbinolicus could use sulfate as the sole source of sulfur during fermentative growth, but required elemental sulfur or sulfide for growth on Fe(III). The increased expression of genes potentially involved in sulfur reduction, coupled with the requirement for sulfur or sulfide during growth on Fe(III), suggests that P. carbinolicus reduces Fe(III) via an indirect mechanism in which (i) elemental sulfur is reduced to sulfide and (ii) the sulfide reduces Fe(III) with the regeneration of elemental sulfur. This contrasts with the direct reduction of Fe(III) that has been proposed for Geobacter species.}, keywords = {Acetoin, Cytochrome c Group, Deltaproteobacteria, Ethanol, Fermentation, Ferric Compounds, Gene Expression Profiling, Genome, Bacterial, Iron, Nitrilotriacetic Acid, Oligonucleotide Array Sequence Analysis, Oxidation-Reduction, Reverse Transcriptase Polymerase Chain Reaction, RNA, Bacterial, Substrate Specificity, Sulfides, Sulfur, Sulfur-Reducing Bacteria, Thioredoxins}, issn = {1098-5336}, doi = {10.1128/AEM.02901-07}, author = {Haveman, Shelley A and Didonato, Raymond J and Villanueva, Laura and Shelobolina, Evgenya S and Postier, Bradley L and Xu, Bo and Liu, Anna and Lovley, Derek R} } @article {524, title = {Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.}, journal = {Appl Environ Microbiol}, volume = {72}, year = {2006}, month = {2006 Feb}, pages = {1558-68}, abstract = {Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae, which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism and electron transport, a metabolic model which integrated genome-based predictions with available genetic and physiological data was developed via the constraint-based modeling approach. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed that energy conservation with extracellular electron acceptors, such as Fe(III), was limited relative to that associated with intracellular acceptors. This limitation was attributed to lack of cytoplasmic proton consumption during reduction of extracellular electron acceptors. Model-based analysis of the metabolic cost of producing an extracellular electron shuttle to promote electron transfer to insoluble Fe(III) oxides demonstrated why Geobacter species, which do not produce shuttles, have an energetic advantage over shuttle-producing Fe(III) reducers in subsurface environments. In silico analysis also revealed that the metabolic network of G. sulfurreducens could synthesize amino acids more efficiently than that of Escherichia coli due to the presence of a pyruvate-ferredoxin oxidoreductase, which catalyzes synthesis of pyruvate from acetate and carbon dioxide in a single step. In silico phenotypic analysis of deletion mutants demonstrated the capability of the model to explore the flexibility of G. sulfurreducens central metabolism and correctly predict mutant phenotypes. These results demonstrate that iterative modeling coupled with experimentation can accelerate the understanding of the physiology of poorly studied but environmentally relevant organisms and may help optimize their practical applications.}, keywords = {Amino Acids, Electron Transport, Escherichia coli, Fumarates, Geobacter, Iron, Models, Biological, Mutation, Oxidation-Reduction, Phenotype, Protons, Quinones, Species Specificity}, issn = {0099-2240}, doi = {10.1128/AEM.72.2.1558-1568.2006}, author = {Mahadevan, R and Bond, D R and Butler, J E and Esteve-Nu{\~n}ez, A and Coppi, M V and Palsson, B O and Schilling, C H and Lovley, D R} } @article {556, title = {Preferential reduction of FeIII over fumarate by Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {186}, year = {2004}, month = {2004 May}, pages = {2897-9}, abstract = {The presence of Fe(III), but not that of Fe(II), resulted in ca. 20-fold-lower levels of mRNA for fumarate reductase, inhibiting fumarate reduction and favoring utilization of fumarate as an electron donor in chemostat cultures of Geobacter sulfurreducens, despite the fact that growth yield with fumarate was 3-fold higher than with Fe(III).}, keywords = {Electrons, Fumarates, Geobacter, Iron, Oxidation-Reduction, Succinate Dehydrogenase}, issn = {0021-9193}, author = {Esteve-N{\'u}{\~n}ez, Abraham and N{\'u}{\~n}ez, Cinthia and Lovley, Derek R} } @article {564, title = {Electricity generation by direct oxidation of glucose in mediatorless microbial fuel cells.}, journal = {Nat Biotechnol}, volume = {21}, year = {2003}, month = {2003 Oct}, pages = {1229-32}, abstract = {Abundant energy, stored primarily in the form of carbohydrates, can be found in waste biomass from agricultural, municipal and industrial sources as well as in dedicated energy crops, such as corn and other grains. Potential strategies for deriving useful forms of energy from carbohydrates include production of ethanol and conversion to hydrogen, but these approaches face technical and economic hurdles. An alternative strategy is direct conversion of sugars to electrical power. Existing transition metal-catalyzed fuel cells cannot be used to generate electric power from carbohydrates. Alternatively, biofuel cells in which whole cells or isolated redox enzymes catalyze the oxidation of the sugar have been developed, but their applicability has been limited by several factors, including (i) the need to add electron-shuttling compounds that mediate electron transfer from the cell to the anode, (ii) incomplete oxidation of the sugars and (iii) lack of long-term stability of the fuel cells. Here we report on a novel microorganism, Rhodoferax ferrireducens, that can oxidize glucose to CO(2) and quantitatively transfer electrons to graphite electrodes without the need for an electron-shuttling mediator. Growth is supported by energy derived from the electron transfer process itself and results in stable, long-term power production.}, keywords = {Bioelectric Energy Sources, Bioreactors, Carbon Dioxide, Comamonadaceae, Electrodes, Energy Transfer, Equipment Design, Equipment Failure Analysis, Glucose, Iron, Oxidation-Reduction}, issn = {1087-0156}, doi = {10.1038/nbt867}, author = {Chaudhuri, Swades K and Lovley, Derek R} } @article {571, title = {OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens.}, journal = {J Bacteriol}, volume = {185}, year = {2003}, month = {2003 Apr}, pages = {2096-103}, abstract = {Microorganisms in the family Geobacteraceae are the predominant Fe(III)-reducing microorganisms in a variety of subsurface environments in which Fe(III) reduction is an important process, but little is known about the mechanisms for electron transport to Fe(III) in these organisms. The Geobacter sulfurreducens genome was found to contain a 10-kb chromosomal duplication consisting of two tandem three-gene clusters. The last genes of the two clusters, designated omcB and omcC, encode putative outer membrane polyheme c-type cytochromes which are 79\% identical. The role of the omcB and omcC genes in Fe(III) reduction in G. sulfurreducens was investigated. OmcB and OmcC were both expressed during growth with acetate as the electron donor and either fumarate or Fe(III) as the electron acceptor. OmcB was ca. twofold more abundant under both conditions. Disrupting omcB or omcC by gene replacement had no impact on growth with fumarate. However, the OmcB-deficient mutant was greatly impaired in its ability to reduce Fe(III) both in cell suspensions and under growth conditions. In contrast, the ability of the OmcC-deficient mutant to reduce Fe(III) was similar to that of the wild type. When omcB was reintroduced into the OmcB-deficient mutant, the capacity for Fe(III) reduction was restored in proportion to the level of OmcB production. These results indicate that OmcB, but not OmcC, has a major role in electron transport to Fe(III) and suggest that electron transport to the outer membrane is an important feature in Fe(III) reduction in this organism.}, keywords = {Amino Acid Sequence, Bacterial Outer Membrane Proteins, Bacterial Proteins, Cytochrome c Group, Deltaproteobacteria, Gene Expression Regulation, Bacterial, Iron, Molecular Sequence Data, Multigene Family, Mutation, Oxidation-Reduction, Sequence Homology, Amino Acid}, issn = {0021-9193}, author = {Leang, Ching and Coppi, M V and Lovley, D R} } @article {569, title = {Thermophily in the Geobacteraceae: Geothermobacter ehrlichii gen. nov., sp. nov., a novel thermophilic member of the Geobacteraceae from the "Bag City" hydrothermal vent.}, journal = {Appl Environ Microbiol}, volume = {69}, year = {2003}, month = {2003 May}, pages = {2985-93}, abstract = {Little is known about the microbiology of the "Bag City" hydrothermal vent, which is part of a new eruption site on the Juan de Fuca Ridge and which is notable for its accumulation of polysaccharide on the sediment surface. A pure culture, designated strain SS015, was recovered from a vent fluid sample from the Bag City site through serial dilution in liquid medium with malate as the electron donor and Fe(III) oxide as the electron acceptor and then isolation of single colonies on solid Fe(III) oxide medium. The cells were gram-negative rods, about 0.5 micro m by 1.2 to 1.5 micro m, and motile and contained c-type cytochromes. Analysis of the 16S ribosomal DNA (rDNA) sequence of strain SS015 placed it in the family Geobacteraceae in the delta subclass of the Proteobacteria. Unlike previously described members of the Geobacteraceae, which are mesophiles, strain SS015 was a thermophile and grew at temperatures of between 35 and 65 degrees C, with an optimum temperature of 55 degrees C. Like many previously described members of the Geobacteraceae, strain SS015 grew with organic acids as the electron donors and Fe(III) or nitrate as the electron acceptor, with nitrate being reduced to ammonia. Strain SS015 was unique among the Geobacteraceae in its ability to use sugars, starch, or amino acids as electron donors for Fe(III) reduction. Under stress conditions, strain SS015 produced copious quantities of extracellular polysaccharide, providing a model for the microbial production of the polysaccharide accumulation at the Bag City site. The 16S rDNA sequence of strain SS015 was less than 94\% similar to the sequences of previously described members of the Geobacteraceae; this fact, coupled with its unique physiological properties, suggests that strain SS015 represents a new genus in the family Geobacteraceae. The name Geothermobacter ehrlichii gen. nov., sp. nov., is proposed (ATCC BAA-635 and DSM 15274). Although strains of Geobacteraceae are known to be the predominant Fe(III)-reducing microorganisms in a variety of Fe(III)-reducing environments at moderate temperatures, strain SS015 represents the first described thermophilic member of the Geobacteraceae and thus extends the known environmental range of this family to hydrothermal environments.}, keywords = {Base Composition, Cytochromes, Deltaproteobacteria, DNA, Bacterial, DNA, Ribosomal, Drug Resistance, Bacterial, Ecosystem, Electron Transport, Geologic Sediments, Hot Temperature, Hydrogen-Ion Concentration, Iron, Microscopy, Electron, Molecular Sequence Data, Oxidation-Reduction, Pacific Ocean, Phylogeny, Seawater, Sodium Chloride, Species Specificity}, issn = {0099-2240}, author = {Kashefi, Kazem and Holmes, Dawn E and Baross, John A and Lovley, Derek R} } @article {583, title = {Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments.}, journal = {Appl Environ Microbiol}, volume = {68}, year = {2002}, month = {2002 May}, pages = {2300-6}, abstract = {Stimulating microbial reduction of soluble U(VI) to insoluble U(IV) shows promise as a strategy for immobilizing uranium in uranium-contaminated subsurface environments. In order to learn more about which microorganisms might be involved in U(VI) reduction in situ, the changes in the microbial community when U(VI) reduction was stimulated with the addition of acetate were monitored in sediments from three different uranium-contaminated sites in the floodplain of the San Juan River in Shiprock, N.Mex. In all three sediments U(VI) reduction was accompanied by concurrent Fe(III) reduction and a dramatic enrichment of microorganisms in the family Geobacteraceae, which are known U(VI)- and Fe(III)-reducing microorganisms. At the point when U(VI) reduction and Fe(III) reduction were nearing completion, Geobacteraceae accounted for ca. 40\% of the 16S ribosomal DNA (rDNA) sequences recovered from the sediments with bacterial PCR primers, whereas Geobacteraceae accounted for fewer than 5\% of the 16S rDNA sequences in control sediments that were not amended with acetate and in which U(VI) and Fe(III) reduction were not stimulated. Between 55 and 65\% of these Geobacteraceae sequences were most similar to sequences from Desulfuromonas species, with the remainder being most closely related to Geobacter species. Quantitative analysis of Geobacteraceae sequences with most-probable-number PCR and TaqMan analyses indicated that the number of Geobacteraceae sequences increased from 2 to 4 orders of magnitude over the course of U(VI) and Fe(III) reduction in the acetate-amended sediments from the three sites. No increase in Geobacteraceae sequences was observed in control sediments. In contrast to the predominance of Geobacteraceae sequences, no sequences related to other known Fe(III)-reducing microorganisms were detected in sediments. These results compare favorably with an increasing number of studies which have demonstrated that Geobacteraceae are important components of the microbial community in a diversity of subsurface environments in which Fe(III) reduction is an important process. The combination of these results with the finding that U(VI) reduction takes place during Fe(III) reduction and prior to sulfate reduction suggests that Geobacteraceae will be responsible for much of the Fe(III) and U(VI) reduction during uranium bioremediation in these sediments.}, keywords = {Gene Library, Geologic Sediments, Iron, Oxidation-Reduction, Proteobacteria, RNA, Ribosomal, 16S, Soil Pollutants, Uranium}, issn = {0099-2240}, author = {Holmes, Dawn E and Finneran, Kevin T and O{\textquoteright}Neil, Regina A and Lovley, Derek R} } @article {578, title = {Fulvic acid oxidation state detection using fluorescence spectroscopy.}, journal = {Environ Sci Technol}, volume = {36}, year = {2002}, month = {2002 Jul 15}, pages = {3170-5}, abstract = {Humic substances are a heterogeneous class of moderate molecular weight, yellow-colored biomolecules present in all soils, sediments, and natural waters. Although humic substances are generally resistant to microbial degradation under anaerobic conditions, some microorganisms in soils and sediments can use quinone moieties in humic substances as electron acceptors. Laboratory experiments have shown that humic substances can act as electron shuttles in the microbial reduction of ferric iron. Field studies of electron shuttling processes have been constrained by the lack of methods to characterize the oxidation state of quinone moieties in humic substances at natural concentrations. All humic substances have fluorescent properties, and fluorescence spectroscopy can indicate differences in precursor organic source of humic substances. Here we show that the quinone moieties responsible for electron transfer reactions contribute significantly to the fluorescence of humic substances. Further we use fluorescence spectroscopy to elucidate the oxidation state of quinone moieties in humic substances at natural concentrations found in sediment interstitial waters.}, keywords = {Benzopyrans, Environmental Monitoring, Iron, Oxidation-Reduction, Spectrometry, Fluorescence}, issn = {0013-936X}, author = {Klapper, Lisa and McKnight, Diane M and Fulton, J Robin and Blunt-Harris, Elizabeth L and Nevin, Kelly P and Lovley, Derek R and Hatcher, Patrick G} } @article {579, title = {Rapid evolution of redox processes in a petroleum hydrocarbon-contaminated aquifer.}, journal = {Ground Water}, volume = {40}, year = {2002}, month = {2002 Jul-Aug}, pages = {353-60}, abstract = {Ground water chemistry data collected over a six-year period show that the distribution of contaminants and redox processes in a shallow petroleum hydrocarbon-contaminated aquifer has changed rapidly over time. Shortly after a gasoline release occurred in 1990, high concentrations of benzene were present near the contaminant source area. In this contaminated zone, dissolved oxygen in ground water was depleted, and by 1994 Fe(III) reduction and sulfate reduction were the predominant terminal electron accepting processes. Significantly, dissolved methane was below measurable levels in 1994, indicating the absence of significant methanogenesis. By 1996, however, depletion of solid-phase Fe(III)-oxyhydrox ides in aquifer sediments and depletion of dissolved sulfate in ground water resulted in the onset of methanogenesis. Between 1996 and 2000, water-chemistry data indicated that methanogenic metabolism became increasingly prevalent. Molecular analysis of 16S-rDNA extracted from sediments shows the presence of a more diverse methanogenic community inside as opposed to outside the plume core, and is consistent with water-chemistry data indicating a shift toward methanogenesis over time. This rapid evolution of redox processes reflects several factors including the large amounts of contaminants, relatively rapid ground water flow (approximately 0.3 m/day [approximately foot/day]), and low concentrations of microbially reducible Fe(III) oxyhydroxides ( approximately 1 micromol/g) initially present in aquifer sediments. These results illustrate that, under certain hydrologic conditions, redox conditions in petroleum hydrocarbon-contaminated aquifers can change rapidly in time and space, and that the availability of solid-phase Fe(III)-oxyhydroxides affects this rate of change.}, keywords = {Hydrocarbons, Iron, Methane, Oxidation-Reduction, Petroleum, Soil Pollutants, Solubility, Sulfates, Water Pollutants, Water Supply}, issn = {0017-467X}, author = {Chapelle, Francis H and Bradley, Paul M and Lovley, Derek R and O{\textquoteright}Neill, Kathleen and Landmeyer, James E} } @article {601, title = {Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers.}, journal = {Int J Syst Evol Microbiol}, volume = {51}, year = {2001}, month = {2001 Mar}, pages = {581-8}, abstract = {Recent studies on the diversity and ubiquity of Fe(III)-reducing organisms in different environments led to the isolation and identification of four new dissimilatory Fe(III)-reducers (strains H-2T, 172T, TACP-2T and TACP-5). All four isolates are non-motile, Gram-negative, freshwater, mesophilic, strict anaerobes with morphology identical to that of Geobacter metallireducens strain GS-15T. Analysis of the 16S rRNA sequences indicated that the new isolates belong to the genus Geobacter, in the delta-Proteobacteria. Significant differences in phenotypic characteristics, DNA-DNA homology and G+C content indicated that the four isolates represent three new species of the genus. The names Geobacter hydrogenophilus sp. nov. (strain H-2T), Geobacter chapellei sp. nov. (strain 172T) and Geobacter grbiciae sp. nov. (strains TACP-2T and TACP-5) are proposed. Geobacter hydrogenophilus and Geobacter chapellei were isolated from a petroleum-contaminated aquifer and a pristine, deep, subsurface aquifer, respectively. Geobacter grbiciae was isolated from aquatic sediments. All of the isolates can obtain energy for growth by coupling the oxidation of acetate to the reduction of Fe(III). The four isolates also coupled Fe(III) reduction to the oxidation of other simple, volatile fatty acids. In addition, Geobacter hydrogenophilus and Geobacter grbiciae were able to oxidize aromatic compounds such as benzoate, whilst Geobacter grbiciae was also able to use the monoaromatic hydrocarbon toluene.}, keywords = {Base Composition, Deltaproteobacteria, Ferric Compounds, Gram-Negative Anaerobic Straight, Curved, and Helical Rods, Hydrocarbons, Iron, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, RNA, Ribosomal, 16S}, issn = {1466-5026}, author = {Coates, J D and Bhupathiraju, V K and Achenbach, L A and Mclnerney, M J and Lovley, D R} } @article {611, title = {Lack of production of electron-shuttling compounds or solubilization of Fe(III) during reduction of insoluble Fe(III) oxide by Geobacter metallireducens.}, journal = {Appl Environ Microbiol}, volume = {66}, year = {2000}, month = {2000 May}, pages = {2248-51}, abstract = {Studies with the dissimilatory Fe(III)-reducing microorganism Geobacter metallireducens demonstrated that the common technique of separating Fe(III)-reducing microorganisms and Fe(III) oxides with semipermeable membranes in order to determine whether the Fe(III) reducers release electron-shuttling compounds and/or Fe(III) chelators is invalid. This raised doubts about the mechanisms for Fe(III) oxide reduction by this organism. However, several experimental approaches indicated that G. metallireducens does not release electron-shuttling compounds and does not significantly solubilize Fe(III) during Fe(III) oxide reduction. These results suggest that G. metallireducens directly reduces insoluble Fe(III) oxide.}, keywords = {Deltaproteobacteria, Electron Transport, Ferric Compounds, Iron, Kinetics, Oxidation-Reduction, Solubility}, issn = {0099-2240}, author = {Nevin, K P and Lovley, D R} } @article {604, title = {N2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species.}, journal = {Environ Microbiol}, volume = {2}, year = {2000}, month = {2000 Jun}, pages = {266-73}, abstract = {Cells of Geobacter metallireducens, Magnetospirillum strain AMB-1, Magnetospirillum magnetotacticum and Magnetospirillum gryphiswaldense showed N2-dependent growth, the first anaerobically with Fe(III) as the electron acceptor, and the latter three species microaerobically in semi-solid oxygen gradient cultures. Cells of the Magnetospirillum species grown with N2 under microaerobic conditions were magnetotactic and therefore produced magnetosomes. Cells of Geobacter metallireducens reduced acetylene to ethylene (11.5+/-5.9 nmol C2H4 produced min(-1) mg(-1) cell protein) while growing with Fe(III) as the electron acceptor in anaerobic growth medium lacking a fixed nitrogen source. Cells of the Magnetospirillum species, grown in a semi-solid oxygen gradient medium, also reduced acetylene at comparable rates. Uncut chromosomal and fragments from endonuclease-digested chromosomal DNA from these species, as well as Geobacter sulphurreducens organisms, hybridized with a nifHDK probe from Rhodospirillum rubrum, indicating the presence of these nitrogenase structural genes in these organisms. The evidence presented here shows that members of the metal-metabolizing genera, Geobacter and Magnetospirillum, fix atmospheric dinitrogen.}, keywords = {Acetylene, DNA, Bacterial, Ethylenes, Genes, Bacterial, Iron, Nitrogen Fixation, Nitrogenase, Oxidation-Reduction, Oxidoreductases, Proteobacteria, Rhodospirillaceae}, issn = {1462-2912}, author = {Bazylinski, D A and Dean, A J and Sch{\"u}ler, D and Phillips, E J and Lovley, D R} } @article {614, title = {Reduction of Fe(III), Mn(IV), and toxic metals at 100 degrees C by Pyrobaculum islandicum.}, journal = {Appl Environ Microbiol}, volume = {66}, year = {2000}, month = {2000 Mar}, pages = {1050-6}, abstract = {It has recently been noted that a diversity of hyperthermophilic microorganisms have the ability to reduce Fe(III) with hydrogen as the electron donor, but the reduction of Fe(III) or other metals by these organisms has not been previously examined in detail. When Pyrobaculum islandicum was grown at 100 degrees C in a medium with hydrogen as the electron donor and Fe(III)-citrate as the electron acceptor, the increase in cell numbers of P. islandicum per mole of Fe(III) reduced was found to be ca. 10-fold higher than previously reported. Poorly crystalline Fe(III) oxide could also serve as the electron acceptor for growth on hydrogen. The stoichiometry of hydrogen uptake and Fe(III) oxide reduction was consistent with the oxidation of 1 mol of hydrogen resulting in the reduction of 2 mol of Fe(III). The poorly crystalline Fe(III) oxide was reduced to extracellular magnetite. P. islandicum could not effectively reduce the crystalline Fe(III) oxide minerals goethite and hematite. In addition to using hydrogen as an electron donor for Fe(III) reduction, P. islandicum grew via Fe(III) reduction in media in which peptone and yeast extract served as potential electron donors. The closely related species P. aerophilum grew via Fe(III) reduction in a similar complex medium. Cell suspensions of P. islandicum reduced the following metals with hydrogen as the electron donor: U(VI), Tc(VII), Cr(VI), Co(III), and Mn(IV). The reduction of these metals was dependent upon the presence of cells and hydrogen. The metalloids arsenate and selenate were not reduced. U(VI) was reduced to the insoluble U(IV) mineral uraninite, which was extracellular. Tc(VII) was reduced to insoluble Tc(IV) or Tc(V). Cr(VI) was reduced to the less toxic, less soluble Cr(III). Co(III) was reduced to Co(II). Mn(IV) was reduced to Mn(II) with the formation of manganese carbonate. These results demonstrate that biological reduction may contribute to the speciation of metals in hydrothermal environments and could account for such phenomena as magnetite accumulation and the formation of uranium deposits at ca. 100 degrees C. Reduction of toxic metals with hyperthermophilic microorganisms or their enzymes might be applied to the remediation of metal-contaminated waters or waste streams.}, keywords = {Chromium, Cobalt, Energy Metabolism, Ferric Compounds, Geological Phenomena, Geology, Iron, Manganese, Metals, Heavy, Oxidation-Reduction, Technetium, Thermoproteaceae, Uranium, Water Pollutants, Chemical}, issn = {0099-2240}, author = {Kashefi, K and Lovley, D R} } @article {617, title = {Role of humic-bound iron as an electron transfer agent in dissimilatory Fe(III) reduction.}, journal = {Appl Environ Microbiol}, volume = {65}, year = {1999}, month = {1999 Sep}, pages = {4252-4}, abstract = {The dissimilatory Fe(III) reducer Geobacter metallireducens reduced Fe(III) bound in humic substances, but the concentrations of Fe(III) in a wide range of highly purified humic substances were too low to account for a significant portion of the electron-accepting capacities of the humic substances. Furthermore, once reduced, the iron in humic substances could not transfer electrons to Fe(III) oxide. These results suggest that other electron-accepting moieties in humic substances, such as quinones, are the important electron-accepting and shuttling agents under Fe(III)-reducing conditions.}, keywords = {Deltaproteobacteria, Electron Transport, Ferric Compounds, Humic Substances, Iron, Oxidation-Reduction}, issn = {0099-2240}, author = {Lovley, D R and Blunt-Harris, E L} } @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 {625, title = {Recovery of humic-reducing bacteria from a diversity of environments.}, journal = {Appl Environ Microbiol}, volume = {64}, year = {1998}, month = {1998 Apr}, pages = {1504-9}, abstract = {To evaluate which microorganisms might be responsible for microbial reduction of humic substances in sedimentary environments, humic-reducing bacteria were isolated from a variety of sediment types. These included lake sediments, pristine and contaminated wetland sediments, and marine sediments. In each of the sediment types, all of the humic reducers recovered with acetate as the electron donor and the humic substance analog, 2,6-anthraquinone disulfonate (AQDS), as the electron acceptor were members of the family Geobacteraceae. This was true whether the AQDS-reducing bacteria were enriched prior to isolation on solid media or were recovered from the highest positive dilutions of sediments in liquid media. All of the isolates tested not only conserved energy to support growth from acetate oxidation coupled to AQDS reduction but also could oxidize acetate with highly purified soil humic acids as the sole electron acceptor. All of the isolates tested were also able to grow with Fe(III) serving as the sole electron acceptor. This is consistent with previous studies that have suggested that the capacity for Fe(III) reduction is a common feature of all members of the Geobacteraceae. These studies demonstrate that the potential for microbial humic substance reduction can be found in a wide variety of sediment types and suggest that Geobacteraceae species might be important humic-reducing organisms in sediments.}, keywords = {Acetic Acid, Anthraquinones, Base Sequence, DNA Primers, Electron Transport, Fresh Water, Gram-Negative Anaerobic Bacteria, Humic Substances, Iron, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial, RNA, Ribosomal, 16S, Seawater, Sulfur-Reducing Bacteria, Water Microbiology}, issn = {0099-2240}, author = {Coates, J D and Ellis, D J and Blunt-Harris, E L and Gaw, C V and Roden, E E and Lovley, D R} } @article {630, title = {Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium.}, journal = {Arch Microbiol}, volume = {165}, year = {1996}, month = {1996 Jun}, pages = {370-6}, abstract = {A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAl-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAl-1 differs from all other described bacteria, and represents the type strain of a new genus and species, Geovibrio ferrireducens.}, keywords = {Bacteria, Base Composition, Iron, Phylogeny}, issn = {0302-8933}, author = {Caccavo, F and Coates, J D and Rossello-Mora, R A and Ludwig, W and Schleifer, K H and Lovley, D R and McInerney, M J} } @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 {641, title = {Bioremediation of organic and metal contaminants with dissimilatory metal reduction.}, journal = {J Ind Microbiol}, volume = {14}, year = {1995}, month = {1995 Feb}, pages = {85-93}, abstract = {Dissimilatory metal reduction has the potential to be a helpful mechanism for both intrinsic and engineered bioremediation of contaminated environments. Dissimilatory Fe(III) reduction is an important intrinsic process for removing organic contaminants from aquifers contaminated with petroleum or landfill leachate. Stimulation of microbial Fe(III) reduction can enhance the degradation of organic contaminants in ground water. Dissimilatory reduction of uranium, selenium, chromium, technetium, and possibly other metals, can convert soluble metal species to insoluble forms that can readily be removed from contaminated waters or waste streams. Reduction of mercury can volatilize mercury from waters and soils. Despite its potential, there has as yet been limited applied research into the use of dissimilatory metal reduction as a bioremediation tool.}, keywords = {Bacteria, Biodegradation, Environmental, Chromium, Hydrocarbons, Iron, Mercury, Metals, Oxidation-Reduction, Selenium, Uranium}, issn = {0169-4146}, author = {Lovley, D R} } @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 {651, title = {Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals.}, journal = {Arch Microbiol}, volume = {159}, year = {1993}, month = {1993}, pages = {336-44}, abstract = {The gram-negative metal-reducing microorganism, previously known as strain GS-15, was further characterized. This strict anaerobe oxidizes several short-chain fatty acids, alcohols, and monoaromatic compounds with Fe(III) as the sole electron acceptor. Furthermore, acetate is also oxidized with the reduction of Mn(IV), U(VI), and nitrate. In whole cell suspensions, the c-type cytochrome(s) of this organism was oxidized by physiological electron acceptors and also by gold, silver, mercury, and chromate. Menaquinone was recovered in concentrations comparable to those previously found in gram-negative sulfate reducers. Profiles of the phospholipid ester-linked fatty acids indicated that both the anaerobic desaturase and the branched pathways for fatty acid biosynthesis were operative. The organism contained three lipopolysaccharide hydroxy fatty acids which have not been previously reported in microorganisms, but have been observed in anaerobic freshwater sediments. The 16S rRNA sequence indicated that this organism belongs in the delta proteobacteria. Its closest known relative is Desulfuromonas acetoxidans. The name Geobacter metallireducens is proposed.}, keywords = {Cytochrome c Group, Fatty Acids, Gram-Negative Anaerobic Bacteria, Iron, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S}, issn = {0302-8933}, author = {Lovley, D R and Giovannoni, S J and White, D C and Champine, J E and Phillips, E J and Gorby, Y A and Goodwin, S} } @article {1741, title = {Hydrogen peroxide and iron: a microbial cellulolytic system?}, journal = {Biotechnol Bioeng Symp}, year = {1975}, month = {1975}, pages = {151-9}, keywords = {Cellulase, Cellulose, Glycoside Hydrolases, Hydrogen Peroxide, Hydrogen-Ion Concentration, Iron, Kinetics, Mitosporic Fungi, Structure-Activity Relationship, Trichoderma}, issn = {0572-6565}, author = {Koenigs, J W} } @article {1726, title = {Studies of oxygen binding energy to hemoglobin molecule.}, journal = {Biochem Biophys Res Commun}, volume = {66}, year = {1975}, month = {1975 Oct 27}, pages = {1424-31}, keywords = {Binding Sites, Cobalt, Hemoglobins, Humans, Hydrogen-Ion Concentration, Iron, Ligands, Mathematics, Oxygen, Oxyhemoglobins, Protein Binding, Spectrum Analysis}, issn = {0006-291X}, author = {Chow, Y W and Pietranico, R and Mukerji, A} }