Showing papers by "Kenneth H. Williams published in 2009"

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

Abstract: 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 indicate early proliferation of multiple M21 and Geobacter bemidjiensis-like strains and later possible emergence of M21 and G. bemidjiensis-like strains more closely related to Geobacter lovleyi. Throughout biostimulation, the proteome is dominated by enzymes that convert acetate to acetyl-coenzyme A and pyruvate for central metabolism, while abundant peptides matching tricarboxylic acid cycle proteins and ATP synthase subunits were also detected, indicating the importance of energy generation during the period of rapid growth following the start of biostimulation. Evolving Geobacter strain composition may be linked to changes in protein abundance over the course of biostimulation and may reflect changes in metabolic functioning. Thus, metagenomics-independent community proteogenomics can be used to diagnose the status of the subsurface consortia upon which remediation biotechnology relies.

Geophysical monitoring of coupled microbial and geochemical processes during stimulated subsurface bioremediation.

Abstract: Understanding how microorganisms alter their physical and chemical environment during bioremediation is hindered by our inability to resolve subsurface microbial activity with high spatial resolution. Here we demonstrate the use of a minimally invasive geophysical technique to monitor stimulated microbial activity during acetate amendment in an aquifer near Rifle, Colorado. During electrical induced polarization (IP) measurements, spatiotemporal variations in the phase response between imposed electric current and the resultant electric field correlated with changes in groundwater geochemistry accompanying stimulated iron and sulfate reduction and sulfide mineral precipitation. The magnitude of the phase response varied with measurement frequency (0.125 and 1 Hz) and was dependent upon the dominant metabolic process. The spectral effect was corroborated using a biostimulated column experiment containing Rifle sediments and groundwater. Fluids and sediments recovered from regions exhibiting an anomalous ph...

Mineral transformation and biomass accumulation associated with uranium bioremediation at Rifle, Colorado

Abstract: Injection of organic carbon into the subsurface as an electron donor for bioremediation of redox-sensitive contaminants like uranium often leads to mineral transformation and biomass accumulation, both of which can alter the flow field and potentially bioremediation efficacy. This work combines reactive transport modeling with a column experiment and field measurements to understand the biogeochemical processes and to quantify the biomass and mineral transformation/accumulation during a bioremediation experiment at a uranium contaminated site near Rifle, Colorado. We use the reactive transport model CrunchFlow to explicitly simulate microbial community dynamics of iron and sulfate reducers, and their impacts on reaction rates. The column experiment shows clear evidence of mineral precipitation, primarily in the form of calcite and iron monosulfide. At the field scale, reactive transport simulations suggest that the biogeochemical reactions occur mostly close to the injection wells where acetate concentrations are highest, with mineral precipitate and biomass accumulation reaching as high as 1.5% of the pore space. This work shows that reactive transport modeling coupled with field data can be an effective tool for quantitative estimation of mineral transformation and biomass accumulation, thus improving the design of bioremediation strategies.

Influence of Heterogeneous Ammonium Availability on Bacterial Community Structure and the Expression of Nitrogen Fixation and Ammonium Transporter Genes during in Situ Bioremediation of Uranium-Contaminated Groundwater

Abstract: The influence of ammonium availability on bacterial community structure and the physiological status of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by 2 orders of magnitude (<4 to 400 μM) across the study site. Analysis of 16S rRNA sequences suggested that ammonium may have been one factor influencing the community composition prior to acetate amendment with Rhodoferax species predominating over Geobacter species with higher ammonium and Dechloromonas species dominating at the site with lowest ammonium. However, once acetate was added and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to acetate concentrations rather than ammonium levels. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium transporter gene, amtB, in Geobacter species indicated that ammonium was the p...

Feedbacks between hydrological heterogeneity and bioremediation induced biogeochemical transformations.

Abstract: For guiding optimal design and interpretation of in-situ treatments that strongly perturb subsurface systems, knowledge about the spatial and temporal patterns of mass transport and reaction intensities are important. Here, a procedure was developed and applied to time-lapse concentrations of a conservative tracer (bromide), an injected amendment (acetate) and reactive species (iron(II), uranium(VI) and sulfate) associated with two field scale biostimulation experiments, which were conducted successively at the same field location over two years. The procedure is based on a temporal moment analysis approach that relies on a streamtube approximation. The study shows that biostimulated reactions can be considerably influenced by subsurface hydrological and geochemical heterogeneities: the delivery of bromide and acetate and the intensity of the sulfate reduction is interpreted to be predominantly driven by the hydrological heterogeneity, while the intensity of the iron reduction is interpreted to be primarily controlled by the geochemical heterogeneity. The intensity of the uranium(VI) reduction appears to be impacted by both the hydrological and geochemical heterogeneity. Finally, the study documents the existence of feedbacks between hydrological heterogeneity and remediation-induced biogeochemical transformations at the field scale, particularly the development of precipitates that may cause clogging and flow rerouting.

Field-Based Detection and Monitoring of Uranium in Contaminated Groundwater using Two Immunosensors

Abstract: Field-based monitoring of environmental contaminants has long been a need for environmental scientists. Described herein are two kinetic exclusion-based immunosensors, a field portable sensor (FPS) and an inline senor, that were deployed at the Integrated Field Research Challenge Site of the U.S. Department of Energy in Rifle, CO. Both sensors utilized a monoclonal antibody that binds to a U(VI)-dicarboxyphenanthroline complex (DCPI in a kinetic exclusion immunoassay format These sensors were able to monitor changes of uranium in groundwater samples from approximately 1 microM to below the regulated drinking water limit of 126 nM (30 ppb). The FPS is a battery-operated sensor platform that can determine the uranium level in a single sample in 5-10 min, if the instrument has been previously calibrated with standards. The average minimum detection level (MDL) in this assay was 0.33 nM (79 ppt), and the MDL in the sample (based on a 1:200-1:400 dilution) was 66-132 nM (15.7-31.4 ppb). The inline sensor, while requiring a grounded power source, has the ability to autonomously analyze multiple samples in a single experiment The average MDL in this assay was 0.12 nM (29 ppt), and the MDL in the samples (based on 1:200 or 1:400 dilutions) was 24-48 nM (5.7-11.4 ppb). Both sensor platforms showed an acceptable level of agreement (9 = 0.94 and 0.76, for the inline and FPS, respectively) with conventional methods for uranium quantification.

A state-space Bayesian framework for estimating biogeochemical transformations using time-lapse geophysical data

Abstract: [1] We develop a state-space Bayesian framework to combine time-lapse geophysical data with other types of information for quantitative estimation of biogeochemical parameters during bioremediation. We consider characteristics of end products of biogeochemical transformations as state vectors, which evolve under constraints of local environments through evolution equations, and consider time-lapse geophysical data as available observations, which could be linked to the state vectors through petrophysical models. We estimate the state vectors and their associated unknown parameters over time using Markov chain Monte Carlo sampling methods. To demonstrate the use of the state-space approach, we apply it to complex resistivity data collected during laboratory column biostimulation experiments that were poised to precipitate iron and zinc sulfides during sulfate reduction. We develop a petrophysical model based on sphere-shaped cells to link the sulfide precipitate properties to the time-lapse geophysical attributes and estimate volume fraction of the sulfide precipitates, fraction of the dispersed, sulfide-encrusted cells, mean radius of the aggregated clusters, and permeability over the course of the experiments. Results of the case study suggest that the developed state-space approach permits the use of geophysical data sets for providing quantitative estimates of end-product characteristics and hydrological feedbacks associated with biogeochemical transformations. Although tested here on laboratory column experiment data sets, the developed framework providesthe foundation neededfor quantitative field-scale estimation of biogeochemical parameters over space and time using direct, but often sparse wellbore data with indirect, but more spatially extensive geophysical data sets.

Hanford 100-D Area Biostimulation Treatability Test Results

Abstract: Pacific Northwest National Laboratory conducted a treatability test designed to demonstrate that in situ biostimulation can be applied to help meet cleanup goals in the Hanford Site 100-D Area. In situ biostimulation has been extensively researched and applied for aquifer remediation over the last 20 years for various contaminants. In situ biostimulation, in the context of this project, is the process of amending an aquifer with a substrate that induces growth and/or activity of indigenous bacteria for the purpose of inducing a desired reaction. For application at the 100-D Area, the purpose of biostimulation is to induce reduction of chromate, nitrate, and oxygen to remove these compounds from the groundwater. The in situ biostimulation technology is intended to provide supplemental treatment upgradient of the In Situ Redox Manipulation (ISRM) barrier previously installed in the Hanford 100-D Area and thereby increase the longevity of the ISRM barrier. Substrates for the treatability test were selected to provide information about two general approaches for establishing and maintaining an in situ permeable reactive barrier based on biological reactions, i.e., a biobarrier. These approaches included 1) use of a soluble (miscible) substrate that is relatively easy to distribute over a large areal extent, is inexpensive, and is expected to have moderate longevity; and 2) use of an immiscible substrate that can be distributed over a reasonable areal extent at a moderate cost and is expected to have increased longevity.