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Derek R. Lovley - One of the best experts on this subject based on the ideXlab platform.
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Protozoan grazing reduces the current output of microbial fuel cells.
Bioresource technology, 2015Co-Authors: Dawn E Holmes, Kelly P Nevin, Trevor L. Woodard, Oona Snoeyenbos-west, Justin N. Strickland, Derek R. LovleyAbstract:Several experiments were conducted to determine whether protozoan grazing can reduce current output from sediment microbial fuel cells. When marine sediments were amended with eukaryotic inhibitors, the power output from the fuel cells increased 2-5-fold. Quantitative PCR showed that Geobacteraceae sequences were 120 times more abundant on anodes from treated fuel cells compared to untreated fuel cells, and that Spirotrichea sequences in untreated fuel cells were 200 times more abundant on anode surfaces than in the surrounding sediments. Defined studies with current-producing biofilms of Geobacter sulfurreducens and pure cultures of protozoa demonstrated that protozoa that were effective in consuming G. sulfurreducens reduced current production up to 91% when added to G. sulfurreducens fuel cells. These results suggest that anode biofilms are an attractive food source for protozoa and that protozoan grazing can be an important factor limiting the current output of sediment microbial fuel cells.
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Electrical conductivity in a mixed-species biofilm.
Applied and environmental microbiology, 2012Co-Authors: Nikhil S. Malvankar, Kelly P Nevin, Joanne Lau, Ashley E. Franks, Mark T. Tuominen, Derek R. LovleyAbstract:Geobacter sulfurreducens can form electrically conductive biofilms, but the potential for conductivity through mixed-species biofilms has not been examined. A current-producing biofilm grown from a wastewater sludge inoculum was highly conductive with low charge transfer resistance even though microorganisms other than Geobacteraceae accounted for nearly half the microbial community.
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Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens
Journal of Molecular Evolution, 2012Co-Authors: Julia Krushkal, Yanhua Qu, Derek R. Lovley, Ronald M. AdkinsAbstract:The protein family of LysR-type transcriptional regulators (LTTRs) is highly abundant among prokaryotes. We analyzed 10,145 non-redundant microbial sequences with homology to eight LysR family regulators of a model prokaryote, Geobacter sulfurreducens , and employed phylogenetic tree inference for LTTR classification. We also analyzed the arrangement of genome clusters containing G . sulfurreducens LTTR genes and searched for LTTR regulatory motifs, suggesting likely regulatory targets of G . sulfurreducens LTTRs . This is the first study to date providing a detailed classification of LTTRs in the deltaproteobacterial family Geobacteraceae .
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Genome diversity of the TetR family of transcriptional regulators in a metal-reducing bacterial family Geobacteraceae and other microbial species.
Omics : a journal of integrative biology, 2011Co-Authors: Julia Krushkal, Ronald M. Adkins, Sreedhar Sontineni, Ching Leang, Derek R. LovleyAbstract:Abstract Members of the TetR family of bacterial transcriptional regulators affect expression of genes whose products are involved in a variety of important functions, including osmotic stress, catabolic pathways, homeostasis, biosynthesis of antibiotics, expression of efflux pumps, multidrug resistance, and virulence of pathogenic bacteria. We used genome sequence information to carry out phylogenetic classification of 864 TetR family members with a special focus on TetR regulators in Geobacteraceae, an environmentally important family of delta-Proteobacteria. The genome of Geobacter sulfurreducens, a model representative of Geobacteraceae, contains nine genes from the tetR family. Several of these genes are located immediately upstream of operons encoding functionally important c-type cytochromes. Computational analyses identified the presence of conserved promoters and other regulatory binding sites upstream of several G. sulfurreducens tetR genes. This suggests the possibility of an intermediary role ...
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Constraint-based modeling analysis of the metabolism of two Pelobacter species
BMC Systems Biology, 2010Co-Authors: Shelley A. Haveman, Tom R Fahland, Derek R. LovleyAbstract: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.
Dawn E Holmes - One of the best experts on this subject based on the ideXlab platform.
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Protozoan grazing reduces the current output of microbial fuel cells.
Bioresource technology, 2015Co-Authors: Dawn E Holmes, Kelly P Nevin, Trevor L. Woodard, Oona Snoeyenbos-west, Justin N. Strickland, Derek R. LovleyAbstract:Several experiments were conducted to determine whether protozoan grazing can reduce current output from sediment microbial fuel cells. When marine sediments were amended with eukaryotic inhibitors, the power output from the fuel cells increased 2-5-fold. Quantitative PCR showed that Geobacteraceae sequences were 120 times more abundant on anodes from treated fuel cells compared to untreated fuel cells, and that Spirotrichea sequences in untreated fuel cells were 200 times more abundant on anode surfaces than in the surrounding sediments. Defined studies with current-producing biofilms of Geobacter sulfurreducens and pure cultures of protozoa demonstrated that protozoa that were effective in consuming G. sulfurreducens reduced current production up to 91% when added to G. sulfurreducens fuel cells. These results suggest that anode biofilms are an attractive food source for protozoa and that protozoan grazing can be an important factor limiting the current output of sediment microbial fuel cells.
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Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation
Environmental microbiology, 2008Co-Authors: Regina A. O'neil, Kelly P Nevin, Dawn E Holmes, Helen A. Vrionis, Joy E. Ward, Lorrie A. Adams, Trevor L. Woodard, Maddalena V. Coppi, M. Juliana Larrahondo, A. Lucie N'guessanAbstract:Summary 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 irondependent 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
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Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.
International journal of systematic and evolutionary microbiology, 2007Co-Authors: Kelly P Nevin, Dawn E Holmes, Trevor L. Woodard, Sean F Covalla, Derek R. LovleyAbstract:Reclassification of the species Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. is proposed on the basis of physiological traits and phylogenetic position. Characteristics additional to those provided in the original description revealed that the type strain (strain K1(T)=ATCC BAA-34(T)=JCM 14045(T)) has the ability to use Fe(III) as an electron acceptor for acetate oxidation and has an electron donor and acceptor profile typical of a Geobacter species, contains abundant c-type cytochromes, and has a temperature optimum of 30 degrees C and a pH optimum near pH 7.0; traits typical of members of the genus Geobacter. Phylogenetic analysis of nifD, recA, gyrB, rpoB, fusA and 16S rRNA genes further indicated that T. thiogenes falls within the Geobacter cluster of the family Geobacteraceae. Based on extensive phylogenetic evidence and the fact that T. thiogenes has the hallmark physiological characteristics of a Geobacter species, Trichlorobacter thiogenes should be reclassified as a member of the genus Geobacter.
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c-Type cytochromes in Pelobacter carbinolicus.
Applied and environmental microbiology, 2006Co-Authors: Shelley A. Haveman, Dawn E Holmes, Joy E. Ward, Yan-huai R. Ding, Raymond J. Didonato, Derek R. LovleyAbstract:Previous studies failed to detect c-type cytochromes in Pelobacter species despite the fact that other close relatives in the Geobacteraceae, such as Geobacter and Desulfuromonas species, have abundant c-type cytochromes. Analysis of the recently completed genome sequence of Pelobacter carbinolicus revealed 14 open reading frames that could encode c-type cytochromes. Transcripts for all but one of these open reading frames were detected in acetoin-fermenting and/or Fe(III)-reducing cells. Three putative c-type cytochrome genes were expressed specifically during Fe(III) reduction, suggesting that the encoded proteins may participate in electron transfer to Fe(III). One of these proteins was a periplasmic triheme cytochrome with a high level of similarity to PpcA, which has a role in Fe(III) reduction in Geobacter sulfurreducens. Genes for heme biosynthesis and system II cytochrome c biogenesis were identified in the genome and shown to be expressed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels of protein extracted from acetoin-fermenting P. carbinolicus cells contained three heme-staining bands which were confirmed by mass spectrometry to be among the 14 predicted c-type cytochromes. The number of cytochrome genes, the predicted amount of heme c per protein, and the ratio of heme-stained protein to total protein were much smaller in P. carbinolicus than in G. sulfurreducens. Furthermore, many of the c-type cytochromes that genetic studies have indicated are required for optimal Fe(III) reduction in G. sulfurreducens were not present in the P. carbinolicus genome. These results suggest that further evaluation of the functions of c-type cytochromes in the Geobacteraceae is warranted.
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Potential for Quantifying Expression of the Geobacteraceae Citrate Synthase Gene To Assess the Activity of Geobacteraceae in the Subsurface and on Current-Harvesting Electrodes
Applied and environmental microbiology, 2005Co-Authors: Dawn E Holmes, Kelly P Nevin, Helen A. Vrionis, Regina A. O'neil, Joy E. Ward, Lorrie A. Adams, Trevor L. Woodard, Derek R. LovleyAbstract:The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current production, whereas the expression of the constitutively expressed housekeeping genes recA, rpoD, and proC remained relatively constant. Analysis of mRNA extracted from groundwater collected from a U(VI)-contaminated site undergoing in situ uranium bioremediation revealed a remarkable correspondence between acetate levels in the groundwater and levels of transcripts of gltA. The expression of gltA was also significantly greater in RNA extracted from groundwater beneath a highway runoff recharge pool that was exposed to calcium magnesium acetate in June, when acetate concentrations were high, than in October, when the levels had significantly decreased. It was also possible to detect gltA transcripts on current-harvesting anodes deployed in freshwater sediments. These results suggest that it is possible to monitor the in situ metabolic rate of Geobacteraceae by tracking the expression of the citrate synthase gene.
Kelly P Nevin - One of the best experts on this subject based on the ideXlab platform.
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Protozoan grazing reduces the current output of microbial fuel cells.
Bioresource technology, 2015Co-Authors: Dawn E Holmes, Kelly P Nevin, Trevor L. Woodard, Oona Snoeyenbos-west, Justin N. Strickland, Derek R. LovleyAbstract:Several experiments were conducted to determine whether protozoan grazing can reduce current output from sediment microbial fuel cells. When marine sediments were amended with eukaryotic inhibitors, the power output from the fuel cells increased 2-5-fold. Quantitative PCR showed that Geobacteraceae sequences were 120 times more abundant on anodes from treated fuel cells compared to untreated fuel cells, and that Spirotrichea sequences in untreated fuel cells were 200 times more abundant on anode surfaces than in the surrounding sediments. Defined studies with current-producing biofilms of Geobacter sulfurreducens and pure cultures of protozoa demonstrated that protozoa that were effective in consuming G. sulfurreducens reduced current production up to 91% when added to G. sulfurreducens fuel cells. These results suggest that anode biofilms are an attractive food source for protozoa and that protozoan grazing can be an important factor limiting the current output of sediment microbial fuel cells.
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Electrical conductivity in a mixed-species biofilm.
Applied and environmental microbiology, 2012Co-Authors: Nikhil S. Malvankar, Kelly P Nevin, Joanne Lau, Ashley E. Franks, Mark T. Tuominen, Derek R. LovleyAbstract:Geobacter sulfurreducens can form electrically conductive biofilms, but the potential for conductivity through mixed-species biofilms has not been examined. A current-producing biofilm grown from a wastewater sludge inoculum was highly conductive with low charge transfer resistance even though microorganisms other than Geobacteraceae accounted for nearly half the microbial community.
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Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation
Environmental microbiology, 2008Co-Authors: Regina A. O'neil, Kelly P Nevin, Dawn E Holmes, Helen A. Vrionis, Joy E. Ward, Lorrie A. Adams, Trevor L. Woodard, Maddalena V. Coppi, M. Juliana Larrahondo, A. Lucie N'guessanAbstract:Summary 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 irondependent 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
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Characterizing Regulation of Metabolism in Geobacter sulfurreducens through Genome-Wide Expression Data and Sequence Analysis
Omics : a journal of integrative biology, 2008Co-Authors: Radhakrishnan Mahadevan, Kelly P Nevin, Regina A. O'neil, Bin Yan, Barbara A. Methé, Trevor L. Woodard, Maddalena V. Coppi, Brad Postier, Julia KrushkalAbstract:ABSTRACT Geobacteraceae are a family of metal reducing bacteria with important applications in bioremediation and electricity generation. G. sulfurreducens is a representative of Geobacteraceae that has been extensively studied with the goal of extending the understanding of this family of organisms for optimizing their practical applications. Here, we have analyzed gene expression data from 10 experiments involving environmental and genetic perturbations and have identified putative transcription factor binding sites (TFBS) involved in regulating key aspects of metabolism. Specifically, we considered data from both a subset of 10 microarray experiments (7 of 10) and all 10 experiments. The expression data from these two sets were independently clustered, and the upstream regions of genes and operons from the clusters in both sets were used to identify TFBS using the AlignACE program. This analysis resulted in the identification of motifs upstream of several genes involved in central metabolism, sulfate a...
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Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.
International journal of systematic and evolutionary microbiology, 2007Co-Authors: Kelly P Nevin, Dawn E Holmes, Trevor L. Woodard, Sean F Covalla, Derek R. LovleyAbstract:Reclassification of the species Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. is proposed on the basis of physiological traits and phylogenetic position. Characteristics additional to those provided in the original description revealed that the type strain (strain K1(T)=ATCC BAA-34(T)=JCM 14045(T)) has the ability to use Fe(III) as an electron acceptor for acetate oxidation and has an electron donor and acceptor profile typical of a Geobacter species, contains abundant c-type cytochromes, and has a temperature optimum of 30 degrees C and a pH optimum near pH 7.0; traits typical of members of the genus Geobacter. Phylogenetic analysis of nifD, recA, gyrB, rpoB, fusA and 16S rRNA genes further indicated that T. thiogenes falls within the Geobacter cluster of the family Geobacteraceae. Based on extensive phylogenetic evidence and the fact that T. thiogenes has the hallmark physiological characteristics of a Geobacter species, Trichlorobacter thiogenes should be reclassified as a member of the genus Geobacter.
Julia Krushkal - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic Classification of Diverse LysR-Type Transcriptional Regulators of a Model Prokaryote Geobacter sulfurreducens
Journal of Molecular Evolution, 2012Co-Authors: Julia Krushkal, Yanhua Qu, Derek R. Lovley, Ronald M. AdkinsAbstract:The protein family of LysR-type transcriptional regulators (LTTRs) is highly abundant among prokaryotes. We analyzed 10,145 non-redundant microbial sequences with homology to eight LysR family regulators of a model prokaryote, Geobacter sulfurreducens , and employed phylogenetic tree inference for LTTR classification. We also analyzed the arrangement of genome clusters containing G . sulfurreducens LTTR genes and searched for LTTR regulatory motifs, suggesting likely regulatory targets of G . sulfurreducens LTTRs . This is the first study to date providing a detailed classification of LTTRs in the deltaproteobacterial family Geobacteraceae .
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Genome diversity of the TetR family of transcriptional regulators in a metal-reducing bacterial family Geobacteraceae and other microbial species.
Omics : a journal of integrative biology, 2011Co-Authors: Julia Krushkal, Ronald M. Adkins, Sreedhar Sontineni, Ching Leang, Derek R. LovleyAbstract:Abstract Members of the TetR family of bacterial transcriptional regulators affect expression of genes whose products are involved in a variety of important functions, including osmotic stress, catabolic pathways, homeostasis, biosynthesis of antibiotics, expression of efflux pumps, multidrug resistance, and virulence of pathogenic bacteria. We used genome sequence information to carry out phylogenetic classification of 864 TetR family members with a special focus on TetR regulators in Geobacteraceae, an environmentally important family of delta-Proteobacteria. The genome of Geobacter sulfurreducens, a model representative of Geobacteraceae, contains nine genes from the tetR family. Several of these genes are located immediately upstream of operons encoding functionally important c-type cytochromes. Computational analyses identified the presence of conserved promoters and other regulatory binding sites upstream of several G. sulfurreducens tetR genes. This suggests the possibility of an intermediary role ...
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Bioinformatic analysis of gene regulation in the metal-reducing bacterial family Geobacteraceae
BMC Bioinformatics, 2010Co-Authors: Julia Krushkal, Ronald M. Adkins, Jeanette M. Peeples, Sreedhar Sontineni, Ching Leang, Peter Brown, Nelson D. Young, Toshiyuki Ueki, Katy JuárezAbstract:Background 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 energy production and removal of environmental pollutants. Materials and methods In this presentation, we describe computational analysis of gene regulation in multiple species from this family. Our ongoing analyses include cataloguing and integrating information about gene regulation, in silico prediction of transcription factor binding sites, and investigation of functional effects of genome-scale and single nucleotide and amino acid level changes in transcription factors, operons, and regulatory sequence elements in Geobacteraceae. Specifically, we discuss our computational pipeline for comparative analyses of variation in regulatory organization among species and strains of Geobacteraceae, which allows us to investigate changes in operon organization and to track the effects of operon rearrangements and individual single nucleotide base pair level changes on regulatory sequence elements. We also describe our computational analyses of two systems of gene expression, one of gene regulation by the PilR enhancer binding protein and another by the TetR family of transcriptional regulators. Finally, we describe our ongoing efforts to catalog available information on gene regulation and operon organization of Geobacter sulfurreducens, a model representative of the Geobacteraceae family.
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GSEL version 2, an online genome-wide query system of operon organization and regulatory sequence elements of Geobacter sulfurreducens.
Omics : a journal of integrative biology, 2009Co-Authors: Peter Brown, Derek R. Lovley, Ronald M. Adkins, Jose F. Barbe, Marko Puljic, Enrique Merino, Julia KrushkalAbstract:Abstract Geobacter sulfurreducens is a model organism within the delta-Proteobacterial family Geobacteraceae, members of which can participate in environmental bioremediation of metal and organic waste contaminants and in production of bioenergy. In this report, we describe a new, significantly expanded and updated, version 2 of the GSEL (Geobacter Sequence Elements) database (http://geobacter.org/research/gsel2/ and http://geobacter.org/refs/gsel2/) and its accompanying online query system, which compiles information on operon organization and regulatory sequence elements in the genome of G. sulfurreducens. It incorporates a new online graphical browser, provides novel search capabilities, and includes updated operon predictions along with new information on predicted and experimentally validated genome regulatory sites. The GSEL database and online search system provides a unique and comprehensive tool cataloging information about gene regulation in G. sulfurreducens, aiding in investigation of mechanis...
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Characterizing Regulation of Metabolism in Geobacter sulfurreducens through Genome-Wide Expression Data and Sequence Analysis
Omics : a journal of integrative biology, 2008Co-Authors: Radhakrishnan Mahadevan, Kelly P Nevin, Regina A. O'neil, Bin Yan, Barbara A. Methé, Trevor L. Woodard, Maddalena V. Coppi, Brad Postier, Julia KrushkalAbstract:ABSTRACT Geobacteraceae are a family of metal reducing bacteria with important applications in bioremediation and electricity generation. G. sulfurreducens is a representative of Geobacteraceae that has been extensively studied with the goal of extending the understanding of this family of organisms for optimizing their practical applications. Here, we have analyzed gene expression data from 10 experiments involving environmental and genetic perturbations and have identified putative transcription factor binding sites (TFBS) involved in regulating key aspects of metabolism. Specifically, we considered data from both a subset of 10 microarray experiments (7 of 10) and all 10 experiments. The expression data from these two sets were independently clustered, and the upstream regions of genes and operons from the clusters in both sets were used to identify TFBS using the AlignACE program. This analysis resulted in the identification of motifs upstream of several genes involved in central metabolism, sulfate a...
Helen A. Vrionis - One of the best experts on this subject based on the ideXlab platform.
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Gene transcript analysis of assimilatory iron limitation in Geobacteraceae during groundwater bioremediation
Environmental microbiology, 2008Co-Authors: Regina A. O'neil, Kelly P Nevin, Dawn E Holmes, Helen A. Vrionis, Joy E. Ward, Lorrie A. Adams, Trevor L. Woodard, Maddalena V. Coppi, M. Juliana Larrahondo, A. Lucie N'guessanAbstract:Summary 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 irondependent 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
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Potential for Quantifying Expression of the Geobacteraceae Citrate Synthase Gene To Assess the Activity of Geobacteraceae in the Subsurface and on Current-Harvesting Electrodes
Applied and environmental microbiology, 2005Co-Authors: Dawn E Holmes, Kelly P Nevin, Helen A. Vrionis, Regina A. O'neil, Joy E. Ward, Lorrie A. Adams, Trevor L. Woodard, Derek R. LovleyAbstract:The Geobacteraceae citrate synthase is phylogenetically distinct from those of other prokaryotes and is a key enzyme in the central metabolism of Geobacteraceae. Therefore, the potential for using levels of citrate synthase mRNA to estimate rates of Geobacter metabolism was evaluated in pure culture studies and in four different Geobacteraceae-dominated environments. Quantitative reverse transcription-PCR studies with mRNA extracted from cultures of Geobacter sulfurreducens grown in chemostats with Fe(III) as the electron acceptor or in batch with electrodes as the electron acceptor indicated that transcript levels of the citrate synthase gene, gltA, increased with increased rates of growth/Fe(III) reduction or current production, whereas the expression of the constitutively expressed housekeeping genes recA, rpoD, and proC remained relatively constant. Analysis of mRNA extracted from groundwater collected from a U(VI)-contaminated site undergoing in situ uranium bioremediation revealed a remarkable correspondence between acetate levels in the groundwater and levels of transcripts of gltA. The expression of gltA was also significantly greater in RNA extracted from groundwater beneath a highway runoff recharge pool that was exposed to calcium magnesium acetate in June, when acetate concentrations were high, than in October, when the levels had significantly decreased. It was also possible to detect gltA transcripts on current-harvesting anodes deployed in freshwater sediments. These results suggest that it is possible to monitor the in situ metabolic rate of Geobacteraceae by tracking the expression of the citrate synthase gene.
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Microbiological and Geochemical Heterogeneity in an in Situ Uranium Bioremediation Field Site
Applied and environmental microbiology, 2005Co-Authors: Helen A. Vrionis, Irene Ortiz-bernad, Robert T. Anderson, Charles T. Resch, Kathleen O'neill, Aaron D. Peacock, Richard Dayvault, David C. White, Philip E. Long, Derek R. LovleyAbstract:The geochemistry and microbiology of a uranium-contaminated subsurface environment that had undergone two seasons of acetate addition to stimulate microbial U(VI) reduction was examined. There were distinct horizontal and vertical geochemical gradients that could be attributed in large part to the manner in which acetate was distributed in the aquifer, with more reduction of Fe(III) and sulfate occurring at greater depths and closer to the point of acetate injection. Clone libraries of 16S rRNA genes derived from sediments and groundwater indicated an enrichment of sulfate-reducing bacteria in the order Desulfobacterales in sediment and groundwater samples. These samples were collected nearest the injection gallery where microbially reducible Fe(III) oxides were highly depleted, groundwater sulfate concentrations were low, and increases in acid volatile sulfide were observed in the sediment. Further down-gradient, metal-reducing conditions were present as indicated by intermediate Fe(II)/Fe(total) ratios, lower acid volatile sulfide values, and increased abundance of 16S rRNA gene sequences belonging to the dissimilatory Fe(III)- and U(VI)-reducing family Geobacteraceae. Maximal Fe(III) and U(VI) reduction correlated with maximal recovery of Geobacteraceae 16S rRNA gene sequences in both groundwater and sediment; however, the sites at which these maxima occurred were spatially separated within the aquifer. The substantial microbial and geochemical heterogeneity at this site demonstrates that attempts should be made to deliver acetate in a more uniform manner and that closely spaced sampling intervals, horizontally and vertically, in both sediment and groundwater are necessary in order to obtain a more in-depth understanding of microbial processes and the relative contribution of attached and planktonic populations to in situ uranium bioremediation.
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Vanadium Respiration by Geobacter metallireducens: Novel Strategy for In Situ Removal of Vanadium from Groundwater
Applied and environmental microbiology, 2004Co-Authors: Irene Ortiz-bernad, Robert T. Anderson, Helen A. Vrionis, Derek R. LovleyAbstract:Vanadium can be an important contaminant in groundwaters impacted by mining activities. In order to determine if microorganisms of the Geobacteraceae, the predominant dissimilatory metal reducers in many subsurface environments, were capable of reducing vanadium(V), Geobacter metallireducens was inoculated into a medium in which acetate was the electron donor and vanadium(V) was the sole electron acceptor. Reduction of vanadium(V) resulted in the production of vanadium(IV), which subsequently precipitated. Reduction of vanadium(V) was associated with cell growth with a generation time of 15 h. No vanadium(V) was reduced and no precipitate was formed in heat-killed or abiotic controls. Acetate was the most effective of all the electron donors evaluated. When acetate was injected into the subsurface to enhance the growth and activity of Geobacteraceae in an aquifer contaminated with uranium and vanadium, vanadium was removed from the groundwater even more effectively than uranium. These studies demonstrate that G. metallireducens can grow via vanadium(V) respiration and that stimulating the activity of Geobacteraceae, and hence vanadium(V) reduction, can be an effective strategy for in situ immobilization of vanadium in contaminated subsurface environments.