Life Sciences Commons^™

Proteogenomic Monitoring Of Geobacter Physiology During Stimulated Uranium Bioremdiation, Michael J. Wilkins, Nathan C. Verberkmes, Kenneth H. Williams, Stephen J. Callister, Paula J. Mouser, Hila Elifantz, A. Lucie N'Guessan, Brian C. Thomas, Carrie D. Nicora, Manesh B. Shah, Paul Abraham, Mary S. Lipton, Derek Lovley, Robert L. Hettich, Philip E. Long, Jillian F. Banfield

Derek Lovley

Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides …

Coupling A Genome-Scale Metabolic Model With A Reactive Transport Model To Describe In Situ Uranium Bioremediation, Derek Lovley, Timothy D. Scheibe, Radhakrishnan Mahadeven, Yilin Fang, Srinath Garg, Philip E. Long

Derek Lovley

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 …

Future Shock From The Microbe Electric (In Crystal Ball), Derek Lovley

Derek Lovley

No abstract provided.

Genome-Scale Constraint-Based Modeling Of Geobacter Metallireducens, Derek Lovley, Jun Sun, Bahareh Sayyar, Jessica E. Butler, Priti Pharkya, Tom R. Fahland, Iman Famili, Christophe H. Schillng

Derek Lovley

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. …

Genome-Scale Comparison And Constraint-Based Metabolic Reconstruction Of The Facilitative Anaerobic Fe(Iii)-Reducer Rhodoferax Ferrireducens, Derek Lovley, Carla Risso, Jun Sun, Kai Zhuang, Radhakrishnan Mahadevan, Robert Deboy, Wael Ismail, Susmita Shrivastava, Heather Huot, Sagar Kothari, Sean Daughtry, Olivia Bui, Christophe H. Schilling, Barbara A. Methѐ

Derek Lovley

Background Rhodoferax ferrireducens is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about R. ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies. Results The iterative modeling and …

Evolution From A Respiratory Ancestor To Fill Syntrophic And Fermentative Niches: Comparative Genomics Of Six Geobacteraceae Species, Derek Lovley, Jessica E. Butler, Nelson D. Young

Derek Lovley

Background The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration. Results In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the …

The Genome Sequence Of Geobacter Metallireducens: Features Of Metabolism, Physiology And Regulation Common And Dissimilar To Geobacter Sulfurreducens, Derek Lovley, Muktak Aklujkar, Julia Krushkal, Genevieve Dibartolo, Alla Lapidus, Miriam L. Land

Derek Lovley

BACKGROUND: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. RESULTS: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until …

Anode Biofilm Transcriptomics Reveals Outer Surface Components Essential For High Density Current Production In Geobacter Sulfurreducens Fuel Cells, Derek Lovley, Kelly P. Nevin, Byoung-Chan Kim, Richard H. Glaven, Jessica P. Johnson, Trevor L. Woodard, Barbara A. Methѐ, Raymond J. Didonato Jr., Sean F. Covalla, Ashley E. Franks, Anna Liu

Derek Lovley

The mechanisms by which Geobacter sulfurreducens transfers electrons through relatively thick (>50 µm) biofilms to electrodes acting as a sole electron acceptor were investigated. Biofilms of Geobacter sulfurreducens were grown either in flow-through systems with graphite anodes as the electron acceptor or on the same graphite surface, but with fumarate as the sole electron acceptor. Fumarate-grown biofilms were not immediately capable of significant current production, suggesting substantial physiological differences from current-producing biofilms. Microarray analysis revealed 13 genes in current-harvesting biofilms that had significantly higher transcript levels. The greatest increases were for pilA, the gene immediately downstream of pilA, and …

Novel Strategy For Three-Dimensional Real-Time Imaging Of Microbial Fuel Cell Communities: Monitoring The Inhibitory Effects Of Proton Accumulation Within The Anode Biofilm, Derek Lovley, Ashley E. Franks, Kelly P. Nevin, Hongfei Jia, Mounir Izallalen, Trevor L. Woodard

Derek Lovley

Harvesting electricity from the environment, organic wastes, or renewable biomass with microbial fuel cells (MFCs) is an appealing strategy, but the destructive sampling required to investigate the anode-associated biofilms has hampered research designed to better understand and optimize microbe–anode interactions. Therefore, a MFC that permits real-time imaging of the anode biofilm with confocal scanning laser microscopy was developed. In this new MFC Geobacter sulfurreducens, an organism closely related to those often found on MFC anodes and capable of high current densities, produced current comparable to that previously reported with other MFC designs. G. sulfurreducens engineered to produce the fluorescent protein …

Genome-Wide Analysis Of The Rpon Regulon In Geobacter Sulfurreducens, Derek Lovley, Ching Leang, Julia Krushkal, Toshiyuki Ueki, Marko Puljic, Jun Sun, Katy Juárez, Chinthia Núñez, Gemma Reguera, Raymond Didonato, Bradley Postier, Ronald M. Adkins

Derek Lovley

Background The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production. Results An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a …

Bioinformatic Analysis Of Gene Regulation In Geobacter Sulfurreducens, Derek Lovley, Julia Krushkal, Yanhua Qu, Peter Brown, Sreedhar Sontineni, Toshiyuki Ueki, Katy Juarez, Ching Leang, Enrique Merino, Jeanette Peeples, Jose F. Barbe, Ronald M. Adkins

Derek Lovley

Background Geobacteraceae are a family of microorganisms from the delta subdivision of Proteobacteria. They have potential for environmental bioremediation and electricity generation. In this presentation, we describe our recent bioinformatic analyses of gene regulation in Geobacter sulfurreducens, a model representative of this family. Results and conclusion We have developed an online database, GSEL (Geobacter Sequence Elements), which compiles regulatory information for G. sulfurreducens. We have recently completed the development of a new, significantly expanded and updated, relational version 2 of the GSEL database and its accompanying online query system, which compiles manually curated information on operon organization and transcription regulatory …

Cyclic Voltammetry Of Biofilms Of Wild Type And Mutant Geobacter Sulfurreducens On Fuel Cell Anodes Indicates Possible Roles Of Omcb, Omcz, Type Iv Pili, And Protons In Extracellular Electron Transfer, Derek Lovley, Hanno Richter, Kelly P. Nevin, Hongfei Jia, Daniel A. Lowy, Leonard M. Tender

Derek Lovley

Geobacteracea are distinct for their ability to reduce insoluble oxidants including minerals and electrodes without apparent reliance on soluble extracellular electron transfer (ET) mediators. This property makes them important anode catalysts in new generation microbial fuel cells (MFCs) because it obviates the need to replenish ET mediators otherwise necessary to sustain power. Here we report cyclic voltammetry (CV) of biofilms of wild type (WT) and mutant G. sulfurreducens strains grown on graphite cloth anodes acting as electron acceptors with acetate as the electron donor. Our analysis indicates that WT biofilms contain a conductive network of bound ET mediators in which …