@article {423,
	title = {Monitoring the metabolic status of geobacter species in contaminated groundwater by quantifying key metabolic proteins with Geobacter-specific antibodies.},
	journal = {Appl Environ Microbiol},
	volume = {77},
	year = {2011},
	month = {2011 Jul},
	pages = {4597-602},
	abstract = {Simple and inexpensive methods for assessing the metabolic status and bioremediation activities of subsurface microorganisms are required before bioremediation practitioners will adopt molecular diagnosis of the bioremediation community as a routine practice for guiding the development of bioremediation strategies. Quantifying gene transcripts can diagnose important aspects of microbial physiology during bioremediation but is technically challenging and does not account for the impact of translational modifications on protein abundance. An alternative strategy is to directly quantify the abundance of key proteins that might be diagnostic of physiological state. To evaluate this strategy, an antibody-based quantification approach was developed to investigate subsurface Geobacter communities. The abundance of citrate synthase corresponded with rates of metabolism of Geobacter bemidjiensis in chemostat cultures. During in situ bioremediation of uranium-contaminated groundwater the quantity of Geobacter citrate synthase increased with the addition of acetate to the groundwater and decreased when acetate amendments stopped. The abundance of the nitrogen-fixation protein, NifD, increased as ammonium became less available in the groundwater and then declined when ammonium concentrations increased. In a petroleum-contaminated aquifer, the abundance of BamB, an enzyme subunit involved in the anaerobic degradation of mono-aromatic compounds by Geobacter species, increased in zones in which Geobacter were expected to play an important role in aromatic hydrocarbon degradation. These results suggest that antibody-based detection of key metabolic proteins, which should be readily adaptable to standardized kits, may be a feasible method for diagnosing the metabolic state of microbial communities responsible for bioremediation, aiding in the rational design of bioremediation strategies.},
	keywords = {Acetates, Antibodies, Bacterial, Bacterial Proteins, Geobacter, Petroleum, Quaternary Ammonium Compounds, Soil Microbiology, Water Microbiology},
	issn = {1098-5336},
	doi = {10.1128/AEM.00114-11},
	author = {Yun, Jiae and Ueki, Toshiyuki and Miletto, Marzia and Lovley, Derek R}
}
@article {500,
	title = {Quantifying expression of a dissimilatory (bi)sulfite reductase gene in petroleum-contaminated marine harbor sediments.},
	journal = {Microb Ecol},
	volume = {55},
	year = {2008},
	month = {2008 Apr},
	pages = {489-99},
	abstract = {The possibility of quantifying in situ levels of transcripts for dissimilatory (bi)sulfite reductase (dsr) genes to track the activity of sulfate-reducing microorganisms in petroleum-contaminated marine harbor sediments was evaluated. Phylogenetic analysis of the cDNA generated from mRNA for a ca. 1.4 kbp portion of the contiguous dsrA and dsrB genes suggested that Desulfosarcina species, closely related to cultures known to anaerobically oxidize aromatic hydrocarbons, were active sulfate reducers in the sediments. The levels of dsrA transcripts (per mug total mRNA) were quantified in sediments incubated anaerobically at the in situ temperature as well as in sediments incubated at higher temperatures and/or with added acetate to increase the rate of sulfate reduction. Levels of dsrA transcripts were low when there was no sulfate reduction because the sediments were depleted of sulfate or if sulfate reduction was inhibited with added molybdate. There was a direct correlation between dsrA transcript levels and rates of sulfate reduction when sulfate was at ca. 10 mM in the various sediment treatments, but it was also apparent that within a given sediment, dsrA levels increased over time as long as sulfate was available, even when sulfate reduction rates did not increase. These results suggest that phylogenetic analysis of dsr transcript sequences may provide insight into the active sulfate reducers in marine sediments and that quantifying levels of dsrA transcripts can indicate whether sulfate reducers are active in particular sediment. Furthermore, it may only be possible to use dsrA transcript levels to compare the relative rates of sulfate reduction in sediments when sulfate concentrations, and possibly other environmental conditions, are comparable.},
	keywords = {Anaerobiosis, Desulfitobacterium, DNA, Bacterial, DNA, Ribosomal, Gene Expression, Geologic Sediments, Hydrogensulfite Reductase, Molecular Sequence Data, Petroleum, Phylogeny, RNA, Bacterial, RNA, Messenger, RNA, Ribosomal, 16S, Temperature},
	issn = {0095-3628},
	doi = {10.1007/s00248-007-9294-2},
	author = {Chin, Kuk-Jeong and Sharma, Manju L and Russell, Lyndsey A and O{\textquoteright}Neill, Kathleen R and Lovley, Derek R}
}
@article {493,
	title = {Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments.},
	journal = {ISME J},
	volume = {1},
	year = {2007},
	month = {2007 Dec},
	pages = {663-77},
	abstract = {There are distinct differences in the physiology of Geobacter species available in pure culture. Therefore, to understand the ecology of Geobacter species in subsurface environments, it is important to know which species predominate. Clone libraries were assembled with 16S rRNA genes and transcripts amplified from three subsurface environments in which Geobacter species are known to be important members of the microbial community: (1) a uranium-contaminated aquifer located in Rifle, CO, USA undergoing in situ bioremediation; (2) an acetate-impacted aquifer that serves as an analog for the long-term acetate amendments proposed for in situ uranium bioremediation and (3) a petroleum-contaminated aquifer in which Geobacter species play a role in the oxidation of aromatic hydrocarbons coupled with the reduction of Fe(III). The majority of Geobacteraceae 16S rRNA sequences found in these environments clustered in a phylogenetically coherent subsurface clade, which also contains a number of Geobacter species isolated from subsurface environments. Concatamers constructed with 43 Geobacter genes amplified from these sites also clustered within this subsurface clade. 16S rRNA transcript and gene sequences in the sediments and groundwater at the Rifle site were highly similar, suggesting that sampling groundwater via monitoring wells can recover the most active Geobacter species. These results suggest that further study of Geobacter species in the subsurface clade is necessary to accurately model the behavior of Geobacter species during subsurface bioremediation of metal and organic contaminants.},
	keywords = {Biodegradation, Environmental, Ecosystem, Ferric Compounds, Geobacter, Hydrocarbons, Aromatic, Molecular Sequence Data, Oxidation-Reduction, Petroleum, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Uranium},
	issn = {1751-7362},
	doi = {10.1038/ismej.2007.85},
	author = {Holmes, Dawn E and O{\textquoteright}Neil, Regina A and Vrionis, Helen A and N{\textquoteright}guessan, Lucie A and Ortiz-Bernad, Irene and Larrahondo, Maria J and Adams, Lorrie A and Ward, Joy A and Nicoll, Julie S and Nevin, Kelly P and Chavan, Milind A and Johnson, Jessica P and Long, Philip E and Lovley, Derek R}
}
@article {529,
	title = {Potential for quantifying expression of the Geobacteraceae citrate synthase gene to assess the activity of Geobacteraceae in the subsurface and on current-harvesting electrodes.},
	journal = {Appl Environ Microbiol},
	volume = {71},
	year = {2005},
	month = {2005 Nov},
	pages = {6870-7},
	abstract = {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.},
	keywords = {Acetates, Citrate (si)-Synthase, Deltaproteobacteria, DNA, Ribosomal, Electrodes, Ferric Compounds, Fresh Water, Geobacter, Geologic Sediments, Petroleum, Phylogeny, RNA, Ribosomal, 16S, Uranium, Water Pollutants, Chemical, Water Pollutants, Radioactive},
	issn = {0099-2240},
	doi = {10.1128/AEM.71.11.6870-6877.2005},
	author = {Holmes, Dawn E and Nevin, Kelly P and O{\textquoteright}Neil, Regina A and Ward, Joy E and Adams, Lorrie A and Woodard, Trevor L and Vrionis, Helen A and Lovley, Derek R}
}
@article {543,
	title = {In situ expression of nifD in Geobacteraceae in subsurface sediments.},
	journal = {Appl Environ Microbiol},
	volume = {70},
	year = {2004},
	month = {2004 Dec},
	pages = {7251-9},
	abstract = {In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 microM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.},
	keywords = {Acetates, Biodegradation, Environmental, Culture Media, DNA, Ribosomal, Fresh Water, Gene Expression Regulation, Bacterial, Geobacter, Geologic Sediments, Nitrogenase, Petroleum, Phylogeny, Polymerase Chain Reaction, Quaternary Ammonium Compounds, Rec A Recombinases, RNA, Ribosomal, 16S, Water Pollutants, Chemical},
	issn = {0099-2240},
	doi = {10.1128/AEM.70.12.7251-7259.2004},
	author = {Holmes, Dawn E and Nevin, Kelly P and Lovley, Derek R}
}
@article {575,
	title = {Anaerobic, sulfate-dependent degradation of polycyclic aromatic hydrocarbons in petroleum-contaminated harbor sediment.},
	journal = {Environ Sci Technol},
	volume = {36},
	year = {2002},
	month = {2002 Nov 15},
	pages = {4811-7},
	abstract = {It has previously been demonstrated that [14C]-labeled polycyclic aromatic hydrocarbons (PAHs) can be oxidized to 14CO2 in anoxic, PAH-contaminated, marine harbor sediments in which sulfate reduction is the terminal electron-accepting process. However, it has not previously been determined whether this degradation of [14C]-PAHs accurately reflects the degradation of the in situ pools of contaminant PAHs. In coal tar-contaminated sediments from Boston Harbor, [14C]-naphthalene was readily oxidized to 14CO2, but, after 95 d of incubation under anaerobic conditions, there was no significant decrease in the detectable pool of in situ naphthalene in these sediments. Therefore, to better evaluate the anaerobic biodegradation of the in situ PAH pools, the concentrations of these contaminants were monitored for ca. 1 year during which the sediments were incubated under conditions that mimicked those found in situ. There was loss of all of the PAHs that were monitored (2-5 ring congeners), including high molecular weight PAHs, such as benzo[a]pyrene, that have not previously been shown to be degraded under anaerobic conditions. There was no significant change in the PAH levels in the sediments amended with molybdate to inhibit sulfate-reducing bacteria or in sediments in which all microorganisms had been killed with glutaraldehyde. In some instances, over half of the detectable pools of in situ 2-3 ring PAHs were degraded. In general, the smaller PAHs were degraded more rapidly than the larger PAHs. A distinct exception in the Boston Harbor sediment was naphthalene which was degraded very slowly at a rate comparable to the larger PAHs. In a similar in situ-like study of fuel-contaminated sediments from Liepaja Harbor, Latvia, there was no decline in PAH levels in samples that were sulfate-depleted. However, when the Latvia sediments were supplemented with sufficient sodium sulfate or gypsum to elevate pore water levels of sulfate to approximately 14-25 mM there was a 90\% decline in the naphthalene and a 60\% decline in the 2-methylnaphthalene pool within 90 days. These studies demonstrate for the first time that degradation by anaerobic microorganisms can significantly impact the in situ pools of PAHs in petroleum-contaminated, anoxic, sulfate-reducing harbor sediments and suggest that the self-purification capacity of contaminated harbor sediments is greater than previously considered.},
	keywords = {Bacteria, Anaerobic, Biodegradation, Environmental, Environmental Monitoring, Geologic Sediments, Molecular Weight, Petroleum, Polycyclic Hydrocarbons, Aromatic, Ships, Sulfur-Reducing Bacteria, Transportation, Water Pollutants, Chemical},
	issn = {0013-936X},
	author = {Rothermich, Mary M and Hayes, Lory A and Lovley, Derek R}
}
@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}
}
