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Full-Text Articles in Microbiology
Application Of Cyclic Voltammetry To Investigate Enhanced Catalytic Current Generation By Biofilm-Modified Anodes Of Geobacter Sulfurreducens Strain Dl1 Vs. Variant Strain Kn400, Sarah M. Strycharz, Anthony P. Malanoski, Rachel M. Snider, Hana Yi, Derek Lovley, Leonard M. Tender
Application Of Cyclic Voltammetry To Investigate Enhanced Catalytic Current Generation By Biofilm-Modified Anodes Of Geobacter Sulfurreducens Strain Dl1 Vs. Variant Strain Kn400, Sarah M. Strycharz, Anthony P. Malanoski, Rachel M. Snider, Hana Yi, Derek Lovley, Leonard M. Tender
Derek Lovley
A biofilm of Geobacter sulfurreducens will grow on an anode surface and catalyze the generation of an electrical current by oxidizing acetate and utilizing the anode as its metabolic terminal electron acceptor. Here we report qualitative analysis of cyclic voltammetry of anodes modified with biofilms of G. sulfurreducens strains DL1 and KN400 to predict possible rate-limiting steps in current generation. Strain KN400 generates approximately 2 to 8-fold greater current than strain DL1 depending upon the electrode material, enabling comparative electrochemical analysis to study the mechanism of current generation. This analysis is based on our recently reported electrochemical model for biofilm-catalyzed …
Bioinformatic Analysis Of Gene Regulation In The Metal-Reducing Bacteria Family, Derek Lovley, Julia Krushkal, Ronald M. Adkins, Yanhua Qu, Jeanette Peeples, Sreedhar Sontineni, Ching Leang, Peter Brown, Nelson D. Young, Toshiyuki Ueki, Katy Juarez
Bioinformatic Analysis Of Gene Regulation In The Metal-Reducing Bacteria Family, Derek Lovley, Julia Krushkal, Ronald M. Adkins, Yanhua Qu, Jeanette Peeples, Sreedhar Sontineni, Ching Leang, Peter Brown, Nelson D. Young, Toshiyuki Ueki, Katy Juarez
Derek Lovley
Knowledge of how structural genome differences among microorganisms lead to variation in gene regulation is fundamentally important for our understanding of the functioning of gene regulatory pathways and their individual components. This knowledge is also necessary for our better understanding of the genomic changes leading to adaptation to diverse and changing environments. Our research focuses on Geobacteraceae, a metal-reducing family of delta-Proteobacteria, which are capable of harvesting electricity from organic matter and environmental bioremediation of organic and metal pollutants. We are investigating molecular mechanisms which allow these species to adapt and regulate their responses to environmental stimuli, which result in …
Novel Regulatory Cascades Controlling Expression Of Nitrogen Fixation Genes, Toshiyuki Ueki, Derek Lovley
Novel Regulatory Cascades Controlling Expression Of Nitrogen Fixation Genes, Toshiyuki Ueki, Derek Lovley
Derek Lovley
Geobacter species often play an important role in bioremediation of environments contaminated with metals or organics and show promise for harvesting electricity from waste organic matter in microbial fuel cells. The ability of Geobacter species to fix atmospheric nitrogen is an important metabolic feature for these applications. We identified novel regulatory cascades controlling nitrogen-fixation gene expression in Geobacter sulfurreducens. Unlike the regulatory mechanisms known in other nitrogen-fixing microorganisms, nitrogen-fixation gene regulation in G. sulfurreducens is controlled by two two-component His-Asp phosphorelay systems. One of these systems appears to be the master regulatory system that activates transcription of the majority of …
Electrodic Voltages Accompanying Stimulated Bioremediation Of A Uranium-Contaminated Aquifer, Kenneth H. Williams, A. Lucie N'Guessan, Jennifer Druhan, Philip E. Long, Susan S. Hubbard, Derek Lovley, Jillian F. Banfield
Electrodic Voltages Accompanying Stimulated Bioremediation Of A Uranium-Contaminated Aquifer, Kenneth H. Williams, A. Lucie N'Guessan, Jennifer Druhan, Philip E. Long, Susan S. Hubbard, Derek Lovley, Jillian F. Banfield
Derek Lovley
The inability to track the products of subsurface microbial activity during stimulated bioremediation has limited its implementation. We used spatiotemporal changes in electrodic potentials (EP) to track the onset and persistence of stimulated sulfate-reducing bacteria in a uranium-contaminated aquifer undergoing acetate amendment. Following acetate injection, anomalous voltages approaching −900 mV were measured between copper electrodes within the aquifer sediments and a single reference electrode at the ground surface. Onset of EP anomalies correlated in time with both the accumulation of dissolved sulfide and the removal of uranium from groundwater. The anomalies persisted for 45 days after halting acetate injection. Current-voltage …
Role Of Geobacter Sulfurreducens Outer-Surface C-Type Cytochromes In Reduction Of Soil Humic Acid And Anthraquinone-2,6-Disulfonate, James W. Voordeckers, Byoung-Chan Kim, Mounir Izallalen, Derek Lovley
Role Of Geobacter Sulfurreducens Outer-Surface C-Type Cytochromes In Reduction Of Soil Humic Acid And Anthraquinone-2,6-Disulfonate, James W. Voordeckers, Byoung-Chan Kim, Mounir Izallalen, Derek Lovley
Derek Lovley
Deleting individual genes for outer surface c-type cytochromes in Geobacter sulfurreducens partially inhibited the reduction of humic substances and anthraquinone-2,6,-disulfonate. Complete inhibition was obtained only when five of these genes were simultaneously deleted, suggesting that diverse outer surface cytochromes can contribute to the reduction of humic substances and other extracellular quinones.
Microbial Electrosynthesis:Feeding Microbes Electricity To Convert Carbon Dioxide And Water To Multi Carbon Extracellular Organic Compounds, Derek Lovley, Kelly P. Nevin, Trevor L. Woodward, Ashley E. Franks, Zarath M. Summers
Microbial Electrosynthesis:Feeding Microbes Electricity To Convert Carbon Dioxide And Water To Multi Carbon Extracellular Organic Compounds, Derek Lovley, Kelly P. Nevin, Trevor L. Woodward, Ashley E. Franks, Zarath M. Summers
Derek Lovley
The possibility of providing the acetogenic microorganism Sporomusa ovata with electrons delivered directly to the cells with a graphite electrode for the reduction of carbon dioxide to organic compounds was investigated. Biofilms of S. ovata growing on graphite cathode surfaces consumed electrons with the reduction of carbon dioxide to acetate and small amounts of 2-oxobutyrate. Electrons appearing in these products accounted for over 85% of the electrons consumed. These results demonstrate that microbial production of multicarbon organic compounds from carbon dioxide and water with electricity as the energy source is feasible. Importance Reducing carbon dioxide to multicarbon organic chemicals and …
Metabolic Response Of Geobacter Sulfurreducens Towards Electron Donor/Acceptor Variation, Derek Lovley, Tae Hoon Yang, Maddalena V. Coppi, Jun Sun
Metabolic Response Of Geobacter Sulfurreducens Towards Electron Donor/Acceptor Variation, Derek Lovley, Tae Hoon Yang, Maddalena V. Coppi, Jun Sun
Derek Lovley
Background Geobacter sulfurreducens is capable of coupling the complete oxidation of organic compounds to iron reduction. The metabolic response of G. sulfurreducens towards variations in electron donors (acetate, hydrogen) and acceptors (Fe(III), fumarate) was investigated via 13C-based metabolic flux analysis. We examined the 13C-labeling patterns of proteinogenic amino acids obtained from G. sulfurreducens cultured with 13C-acetate. Results Using 13C-based metabolic flux analysis, we observed that donor and acceptor variations gave rise to differences in gluconeogenetic initiation, tricarboxylic acid cycle activity, and amino acid biosynthesis pathways. Culturing G. sulfurreducens cells with Fe(III) as the electron acceptor and acetate as the electron …
Evolution Of Electron Transfer Out Of The Cell: Comparative Genomics Of Six Geobacter Genomes, Jessica E. Butler, Nelson D. Young, Derek Lovley
Evolution Of Electron Transfer Out Of The Cell: Comparative Genomics Of Six Geobacter Genomes, Jessica E. Butler, Nelson D. Young, Derek Lovley
Derek Lovley
Background: Geobacter species grow by transferring electrons out of the cell - either to Fe(III)-oxides or to manmade substances like energy-harvesting electrodes. Study of Geobacter sulfurreducens has shown that TCA cycle enzymes, inner-membrane respiratory enzymes, and periplasmic and outer-membrane cytochromes are required. Here we present comparative analysis of six Geobacter genomes, including species from the clade that predominates in the subsurface. Conservation of proteins across the genomes was determined to better understand the evolution of Geobacter species and to create a metabolic model applicable to subsurface environments. Results: The results showed that enzymes for acetate transport and oxidation, and for …
Interference With Histidyl-Trna Synthetase By A Crispr Spacer Sequence As A Factor In The Evolution Of Pelobacter Carbinolicus, Derek Lovley, Muktak Aklujkar
Interference With Histidyl-Trna Synthetase By A Crispr Spacer Sequence As A Factor In The Evolution Of Pelobacter Carbinolicus, Derek Lovley, Muktak Aklujkar
Derek Lovley
BACKGROUND: Pelobacter carbinolicus, a bacterium of the family Geobacteraceae, cannot reduce Fe(III) directly or produce electricity like its relatives. How P. carbinolicus evolved is an intriguing problem. The genome of P. carbinolicus contains clustered regularly interspaced short palindromic repeats (CRISPR) separated by unique spacer sequences, which recent studies have shown to produce RNA molecules that interfere with genes containing identical sequences. RESULTS: CRISPR spacer #1, which matches a sequence within hisS, the histidyl-tRNA synthetase gene of P. carbinolicus, was shown to be expressed. Phylogenetic analysis and genetics demonstrated that a gene paralogous to hisS in the genomes of Geobacteraceae is …
Constraint-Based Modeling Analysis Of The Metabolism Of Two Pelobacter Species, Derek Lovley, Jun Sun, Shelly A. Haveman, Olivia Bui, Tom R. Fahland
Constraint-Based Modeling Analysis Of The Metabolism Of Two Pelobacter Species, Derek Lovley, Jun Sun, Shelly A. Haveman, Olivia Bui, Tom R. Fahland
Derek Lovley
BACKGROUND: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. RESULTS: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter …
De Novo Assembly Of The Complete Genome Of An Enhanced Electricity-Producing Variant Of Geobacter Sulfurreducens Using Only Short Reads, Derek Lovley, Harish Nagarajan, Jessica E. Butler, Anna Klimes, Yu Qiu, Karsten Zengler, Joy Ward, Nelson D. Young, Barbara A. Methe, Bernhard Ø. Palsson, Christian L. Barrett
De Novo Assembly Of The Complete Genome Of An Enhanced Electricity-Producing Variant Of Geobacter Sulfurreducens Using Only Short Reads, Derek Lovley, Harish Nagarajan, Jessica E. Butler, Anna Klimes, Yu Qiu, Karsten Zengler, Joy Ward, Nelson D. Young, Barbara A. Methe, Bernhard Ø. Palsson, Christian L. Barrett
Derek Lovley
State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated. We have successfully developed a four-phase strategy for using only next-generation sequencing technologies (Illumina and 454) to assemble …
Genome-Wide Gene Regulation Of Biosynthesis And Energy Generation By A Novel Transcriptional Repressor In Geobacter Species, Derek Lovley, Toshiyuki Ueki
Genome-Wide Gene Regulation Of Biosynthesis And Energy Generation By A Novel Transcriptional Repressor In Geobacter Species, Derek Lovley, Toshiyuki Ueki
Derek Lovley
Geobacter species play important roles in bioremediation of contaminated environments and in electricity production from waste organic matter in microbial fuel cells. To better understand physiology of Geobacter species, expression and function of citrate synthase, a key enzyme in the TCA cycle that is important for organic acid oxidation in Geobacter species, was investigated. Geobacter sulfurreducens did not require citrate synthase for growth with hydrogen as the electron donor and fumarate as the electron acceptor. Expression of the citrate synthase gene, gltA, was repressed by a transcription factor under this growth condition. Functional and comparative genomics approaches, coupled with genetic …
The Genome Of Geobacter Bemidjiensis, Exemplar For The Subsurface Clade Of Geobacter Species That Predominate In Fe(Iii)-Reducing Subsurface Enviorments, Muktak Aklujkar, Nealson D. Young, Dawn Holmes, Milind Chavan, Carla Risso, Hajnalka E. Kiss, Cliff S. Han, Miriam L. Land, Derek Lovley
The Genome Of Geobacter Bemidjiensis, Exemplar For The Subsurface Clade Of Geobacter Species That Predominate In Fe(Iii)-Reducing Subsurface Enviorments, Muktak Aklujkar, Nealson D. Young, Dawn Holmes, Milind Chavan, Carla Risso, Hajnalka E. Kiss, Cliff S. Han, Miriam L. Land, Derek Lovley
Derek Lovley
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 …