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Full-Text Articles in Life Sciences
Expression Of Acetate Permease-Like (Apl) Genes In Subsurface Communities Of Geobacter Species Under Fluctuating Acetate Concentrations, Derek Lovley, Hila Elifantz, Lucie N'Guessan, Paula Mouser, Kenneth Williams, Michael Wilkins, Carla Risso, Dawn Holmes, Philip Long
Expression Of Acetate Permease-Like (Apl) Genes In Subsurface Communities Of Geobacter Species Under Fluctuating Acetate Concentrations, Derek Lovley, Hila Elifantz, Lucie N'Guessan, Paula Mouser, Kenneth Williams, Michael Wilkins, Carla Risso, Dawn Holmes, Philip Long
Carla Risso
The addition of acetate to uranium-contaminated aquifers in order to stimulate the growth and activity of Geobacter species that reduce uranium is a promising in situ bioremediation option. Optimizing this bioremediation strategy requires that sufficient acetate be added to promote Geobacter species growth. We hypothesized that under acetate-limiting conditions, subsurface Geobacter species would increase the expression of either putative acetate symporters genes (aplI and aplII). Acetate was added to a uranium-contaminated aquifer (Rifle, CO) in two continuous amendments separated by 5 days of groundwater flush to create changing acetate concentrations. While the expression of aplI in monitoring well D04 (high …
Genome-Scale Dynamics Modeling Of The Competition Between Rhodoferax And Geobacter In Anoxic Subsurface Environments, Derek Lovley, Kai Zhuang, Mounir Izallalen, Paula Museor, Hanno Richter, Carla Risso, Radhakrishnan Mahadevan
Genome-Scale Dynamics Modeling Of The Competition Between Rhodoferax And Geobacter In Anoxic Subsurface Environments, Derek Lovley, Kai Zhuang, Mounir Izallalen, Paula Museor, Hanno Richter, Carla Risso, Radhakrishnan Mahadevan
Carla Risso
The advent of rapid complete genome sequencing, and the potential to capture this information in genome-scale metabolic models, provide the possibility of comprehensively modeling microbial community interactions. For example, Rhodoferax and Geobacter species are acetate-oxidizing Fe(III)-reducers that compete in anoxic subsurface environments and this competition may have an influence on the in situ bioremediation of uranium-contaminated groundwater. Therefore, genome-scale models of Geobacter sulfurreducens and Rhodoferax ferrireducens were used to evaluate how Geobacter and Rhodoferax species might compete under diverse conditions found in a uranium-contaminated aquifer in Rifle, CO. The model predicted that at the low rates of acetate flux expected …
Anaerobic Oxidation Of Benzene By The Hyperthermophilic Archaeon Ferroglobus Placidus, Derek Lovley, Dawn E. Holmes, Carla Risso, Jessica A. Smith
Anaerobic Oxidation Of Benzene By The Hyperthermophilic Archaeon Ferroglobus Placidus, Derek Lovley, Dawn E. Holmes, Carla Risso, Jessica A. Smith
Carla Risso
Anaerobic benzene oxidation coupled to the reduction of Fe(III) was studied in Ferroglobus placidus in order to learn more about how such a stable molecule could be metabolized under strict anaerobic conditions. F. placidus conserved energy to support growth at 85°C in a medium with benzene provided as the sole electron donor and Fe(III) as the sole electron acceptor. The stoichiometry of benzene loss and Fe(III) reduction, as well as the conversion of [14C]benzene to [14C]carbon dioxide, was consistent with complete oxidation of benzene to carbon dioxide with electron transfer to Fe(III). Benzoate, but not phenol or toluene, accumulated at …
The Genome Of Geobacter Bemidjiensis, Exemplar For The Subsurface Clade Of Geobacter Species That Predominate In Fe(Iii)-Reducing Subsurface Enviorments, Derek Lovley, Muktak Aklujkar, Nealson D. Young, Dawn Holmes, Milind Chavan, Carla Risso, Hajnalka E. Kiss, Cliff S. Han, Miriam L. Land
The Genome Of Geobacter Bemidjiensis, Exemplar For The Subsurface Clade Of Geobacter Species That Predominate In Fe(Iii)-Reducing Subsurface Enviorments, Derek Lovley, Muktak Aklujkar, Nealson D. Young, Dawn Holmes, Milind Chavan, Carla Risso, Hajnalka E. Kiss, Cliff S. Han, Miriam L. Land
Carla Risso
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 …
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 Schilling, Barbara Methѐ
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 Schilling, Barbara Methѐ
Carla Risso
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 …
Highly Conserved Genes In Geobacter Species With Expression Patterns Indicative Of Acetate Limitation, Derek Lovley, Carla Risso, Barbara A. Methé, Hila Elifantz, Dawn E. Holmes
Highly Conserved Genes In Geobacter Species With Expression Patterns Indicative Of Acetate Limitation, Derek Lovley, Carla Risso, Barbara A. Methé, Hila Elifantz, Dawn E. Holmes
Carla Risso
Analysis of the genome of Geobacter sulfurreducens revealed four genes encoding putative symporters with homology to ActP, an acetate transporter in Escherichia coli. Three of these genes, aplA, aplB and aplC, are highly similar (over 90 % identical) and fell within a tight phylogenetic cluster (Group I) consisting entirely of Geobacter homologues. Transcript levels for all three genes increased in response to acetate limitation. The fourth gene, aplD, is phylogenetically distinct (Group II) and its expression was not influenced by acetate availability. Deletion of any one of the three genes in Group I did not significantly affect acetate-dependent growth, suggesting …
Elucidation Of An Alternate Isoleucine Biosynthesis Pathway In Geobacter Sulfurreducens, Derek Lovley, Carla Risso, Stephen J. Van Dien, Amber Orloff, Maddalena V. Coppi
Elucidation Of An Alternate Isoleucine Biosynthesis Pathway In Geobacter Sulfurreducens, Derek Lovley, Carla Risso, Stephen J. Van Dien, Amber Orloff, Maddalena V. Coppi
Carla Risso
The central metabolic model for Geobacter sulfurreducens included a single pathway for the biosynthesis of isoleucine that was analogous to that of Escherichia coli, in which the isoleucine precursor 2-oxobutanoate is generated from threonine. 13C labeling studies performed in G. sulfurreducens indicated that this pathway accounted for a minor fraction of isoleucine biosynthesis and that the majority of isoleucine was instead derived from acetyl-coenzyme A and pyruvate, possibly via the citramalate pathway. Genes encoding citramalate synthase (GSU1798), which catalyzes the first dedicated step in the citramalate pathway, and threonine ammonia-lyase (GSU0486), which catalyzes the conversion of threonine to 2-oxobutanoate, were …