Final Technical Report for DOE Award DE-FG02-07ER64403 [Modeling of Microbially Induced Calcite Precipitation for the Immobilization of Strontium-90 Using a Variable Velocity Streamtube Ensemble]

Biogeochemical modeling using PHREEQC2 and a streamtube ensemble approach is utilized to understand a well-to-well subsurface treatment system at the Vadose Zone Research Park (VZRP) near Idaho Falls, Idaho. Treatment involves in situ microbially-mediated ureolysis to induce calcite precipitation for the immobilization of strontium-90. PHREEQC2 is utilized to model the kinetically-controlled ureolysis and consequent calcite precipitation. Reaction kinetics, equilibrium phases, and cation exchange are used within PHREEQC2 to track pH and levels of calcium, ammonium, urea, and calcite precipitation over time, within a series of one-dimensional advective-dispersive transport paths creating a streamtube ensemble representation of the well-to-well transport. An understanding of the impact of physical heterogeneities within this radial flowfield is critical for remediation design; we address this via the streamtube approach: instead of depicting spatial extents of solutes in the subsurface we focus on their arrival distribution at the control well(s). Traditionally, each streamtube maintains uniform velocity; however in radial flow in homogeneous media, the velocity within any given streamtube is spatially-variable in a common way, being highest at the input and output wells and approaching a minimum at the midpoint between the wells. This idealized velocity variability is of significance in the case of ureolytically driven calcite precipitation. Streamtube velocity patterns for any particular configuration of injection and withdrawal wells are available as explicit calculations from potential theory, and also from particle tracking programs. To approximate the actual spatial distribution of velocity along streamtubes, we assume idealized radial non-uniform velocity associated with homogeneous media. This is implemented in PHREEQC2 via a non-uniform spatial discretization within each streamtube that honors both the streamtube’s travel time and the idealized “fast-slow-fast” pattern of non-uniform velocity along the streamline. Breakthrough curves produced by each simulation are weighted by the path-respective flux fractions (obtained by deconvolution of tracer tests conducted at the VZRP) to obtain the flux-average of flow contributions to the observation well

Final report for DOE Grant No. DE-FG02-07ER64404 - Field Investigations of Microbially Facilitated Calcite Precipitation for Immobilization of Strontium-90 and Other Trace Metals in the Subsurface

Subsurface radionuclide and metal contaminants throughout the U.S. Department of Energy (DOE) complex pose one of DOEâÃÂÃÂs greatest challenges for long-term stewardship. One promising stabilization mechanism for divalent ions, such as the short-lived radionuclide 90Sr, is co-precipitation in calcite. We have previously found that that nutrient addition can stimulate microbial ureolytic activity that this activity accelerates calcite precipitation and co-precipitation of Sr, and that higher calcite precipitation rates can result in increased Sr partitioning. We have conducted integrated field, laboratory, and computational research to evaluate the relationships between ureolysis and calcite precipitation rates and trace metal partitioning under environmentally relevant conditions, and investigated the coupling between flow/flux manipulations and precipitate distribution. A field experimental campaign conducted at the Integrated Field Research Challenge (IFRC) site located at Rifle, CO was based on a continuous recirculation design; water extracted from a down-gradient well was amended with urea and molasses (a carbon and electron donor) and re-injected into an up-gradient well. The goal of the recirculation design and simultaneous injection of urea and molasses was to uniformly accelerate the hydrolysis of urea and calcite precipitation over the entire inter-wellbore zone. The urea-molasses recirculation phase lasted, with brief interruptions for geophysical surveys, for 12 days followed by long-term monitoring which continued for 13 months. Following the recirculation phase we found persistent increases in urease activity (as determined from 14C labeled laboratory urea hydrolysis rates) in the upper portion of the inter-wellbore zone. We also observed an initial increase (approximately 2 weeks) in urea concentration associated with injection activities followed by decreasing urea concentration and associated increases in ammonium and dissolved inorganic carbon (DIC) following the termination of injection. Based on the loss of urea and the appearance of ammonium, a first order rate constant for urea hydrolysis of 0.18 day-1 rate with an associate Rf for ammonium of 11 were estimated. This rate constant is approximately 6 times higher than estimated for previous field experiments conducted in eastern Idaho. Additionally, DIC carbon isotope ratios were measured for the groundwater. Injected urea had a ÃÂô13C of 40.7ÃÂñ0.4 âÃÂð compared to background groundwater DIC of ÃÂô13C of -16.6ÃÂñ0.2âÃÂð. Observed decreases in groundwater DIC ÃÂô13C of up to -19.8âÃÂð followed temporal trends similar to those observed for ammonium and suggest that both the increase in ammonium and the sift in ÃÂô13C are the result of urea hydrolysis. Although direct observation of calcite precipitation was not possible because of the high pre-existing calcite content in the site sediments, an observed ÃÂô13C decrease for solid carbonates from sediment samples collect following urea injection (compared to pre-injection values) is likely the result of the incorporation of inorganic carbon derived from urea hydrolysis into newly formed solid carbonates

Subsurface Uranium Fate and Transport: Integrated Experiments and Modeling of Coupled Biogeochemical Mechanisms of Nanocrystalline Uraninite Oxidation by Fe(III)-(hydr)oxides - Project Final Report

Subsurface bacteria including sulfate reducing bacteria (SRB) reduce soluble U(VI) to insoluble U(IV) with subsequent precipitation of UO2. We have shown that SRB reduce U(VI) to nanometer-sized UO2 particles (1-5 nm) which are both intra- and extracellular, with UO2 inside the cell likely physically shielded from subsequent oxidation processes. We evaluated the UO2 nanoparticles produced by Desulfovibrio desulfuricans G20 under growth and non-growth conditions in the presence of lactate or pyruvate and sulfate, thiosulfate, or fumarate, using ultrafiltration and HR-TEM. Results showed that a significant mass fraction of bioreduced U (35-60%) existed as a mobile phase when the initial concentration of U(VI) was 160 µM. Further experiments with different initial U(VI) concentrations (25 - 900 M) in MTM with PIPES or bicarbonate buffers indicated that aggregation of uraninite depended on the initial concentrations of U(VI) and type of buffer. It is known that under some conditions SRB-mediated UO2 nanocrystals can be reoxidized (and thus remobilized) by Fe(III)-(hydr)oxides, common constituents of soils and sediments. To elucidate the mechanism of UO2 reoxidation by Fe(III) (hydr)oxides, we studied the impact of Fe and U chelating compounds (citrate, NTA, and EDTA) on reoxidation rates. Experiments were conducted in anaerobic batch systems in PIPES buffer. Results showed EDTA significantly accelerated UO2 reoxidation with an initial rate of 9.5M day-1 for ferrihydrite. In all cases, bicarbonate increased the rate and extent of UO2 reoxidation with ferrihydrite. The highest rate of UO2 reoxidation occurred when the chelator promoted UO2 and Fe(III) (hydr)oxide dissolution as demonstrated with EDTA. When UO2 dissolution did not occur, UO2 reoxidation likely proceeded through an aqueous Fe(III) intermediate as observed for both NTA and citrate. To complement to these laboratory studies, we collected U-bearing samples from a surface seep at the Rifle field site and have measured elevated U concentrations in oxic iron-rich sediments. To translate experimental results into numerical analysis of U fate and transport, a reaction network was developed based on Sani et al. (2004) to simulate U(VI) bioreduction with concomitant UO2 reoxidation in the presence of hematite or ferrihydrite. The reduction phase considers SRB reduction (using lactate) with the reductive dissolution of Fe(III) solids, which is set to be microbially mediated as well as abiotically driven by sulfide. Model results show the oxidation of HS– by Fe(III) directly competes with UO2 reoxidation as Fe(III) oxidizes HS– preferentially over UO2. The majority of Fe reduction is predicted to be abiotic, with ferrihydrite becoming fully consumed by reaction with sulfide. Predicted total dissolved carbonate concentrations from the degradation of lactate are elevated (log(pCO2) ~ –1) and, in the hematite system, yield close to two orders-of-magnitude higher U(VI) concentrations than under initial carbonate concentrations of 3 mM. Modeling of U(VI) bioreduction with concomitant reoxidation of UO2 in the presence of ferrihydrite was also extended to a two-dimensional field-scale groundwater flow and biogeochemically reactive transport model for the South Oyster site in eastern Virginia. This model was developed to simulate the field-scale immobilization and subsequent reoxidation of U by a biologically mediated reaction network

Impact of different environmental conditions on the aggregation of biogenic U(IV) nanoparticles synthesized by Desulfovibrio alaskensis G20

This study investigates the impact of specific environmental conditions on the formation of colloidal U(IV) nanoparticles by the sulfate reducing bacteria (SRB, Desulfovibrio alaskensis G20). The reduction of soluble U(VI) to less soluble U(IV) was quantitatively investigated under growth and non-growth conditions in bicarbonate or 1,4-piperazinediethanesulfonic acid (PIPES) buffered environments. The results showed that under non-growth conditions, the majority of the reduced U nanoparticles aggregated and precipitated out of solution. High resolution transmission electron microscopy revealed that only a very small fraction of cells had reduced U precipitates in the periplasmic spaces in the presence of PIPES buffer, whereas in the presence of bicarbonate buffer, reduced U was also observed in the cytoplasm with greater aggregation of biogenic U(IV) particles at higher initial U(VI) concentrations. The same experiments were repeated under growth conditions using two different electron donors (lactate and pyruvate) and three electron acceptors (sulfate, fumarate, and thiosulfate). In contrast to the results of the non-growth experiments, even after 0.2 mu m filtration, the majority of biogenic U(IV) remained in the aqueous phase resulting in potentially mobile biogenic U(IV) nanoparticles. Size fractionation results showed that U(IV) aggregates were between 18 and 200 nm in diameter, and thus could be very mobile. The findings of this study are helpful to assess the size and potential mobility of reduced U nanoparticles under different environmental conditions, and would provide insights on their potential impact affecting U(VI) bioremediation efforts at subsurface contaminated sites

Dynamics of Coupled Microbial and Contaminant Transport.

Dynamic microbial attachment/detachment occurs in subsurface systems in response to changing environmental conditions caused by contaminant movement and degradation. This project's objective is to develop the understanding of the environmental conditions and mechanisms by which anaerobic bacteria partition between aqueous and solid phases. In particular this interdisciplinary research project provides fundamental information on the attachment/detachment dynamics of anaerobic bacteria in heterogeneous porous media under growth and growth-limiting conditions. This is a critical requirement for designing and evaluating in situ bioremediation efforts

Detectors for the James Webb Space Telescope Near-Infrared Spectrograph I: Readout Mode, Noise Model, and Calibration Considerations

We describe how the James Webb Space Telescope (JWST) Near-Infrared Spectrograph's (NIRSpec's) detectors will be read out, and present a model of how noise scales with the number of multiple non-destructive reads sampling-up-the-ramp. We believe that this noise model, which is validated using real and simulated test data, is applicable to most astronomical near-infrared instruments. We describe some non-ideal behaviors that have been observed in engineering grade NIRSpec detectors, and demonstrate that they are unlikely to affect NIRSpec sensitivity, operations, or calibration. These include a HAWAII-2RG reset anomaly and random telegraph noise (RTN). Using real test data, we show that the reset anomaly is: (1) very nearly noiseless and (2) can be easily calibrated out. Likewise, we show that large-amplitude RTN affects only a small and fixed population of pixels. It can therefore be tracked using standard pixel operability maps.Comment: 55 pages, 10 figure

Reduced Diversity and High Sponge Abundance on a Sedimented Indo-Pacific Reef System: Implications for Future Changes in Environmental Quality

Although coral reef health across the globe is declining as a result of anthropogenic impacts, relatively little is known of how environmental variability influences reef organisms other than corals and fish. Sponges are an important component of coral reef fauna that perform many important functional roles and changes in their abundance and diversity as a result of environmental change has the potential to affect overall reef ecosystem functioning. In this study, we examined patterns of sponge biodiversity and abundance across a range of environments to assess the potential key drivers of differences in benthic community structure. We found that sponge assemblages were significantly different across the study sites, but were dominated by one species Lamellodysidea herbacea (42% of all sponges patches recorded) and that the differential rate of sediment deposition was the most important variable driving differences in abundance patterns. Lamellodysidea herbacea abundance was positively associated with sedimentation rates, while total sponge abundance excluding Lamellodysidea herbacea was negatively associated with rates of sedimentation. Overall variation in sponge assemblage composition was correlated with a number of variables although each variable explained only a small amount of the overall variation. Although sponge abundance remained similar across environments, diversity was negatively affected by sedimentation, with the most sedimented sites being dominated by a single sponge species. Our study shows how some sponge species are able to tolerate high levels of sediment and that any transition of coral reefs to more sedimented states may result in a shift to a low diversity sponge dominated system, which is likely to have subsequent effects on ecosystem functioning. © 2014 Powell et al

Final Technical Report for DOE Award DE-FG02-07ER64403 [Modeling of Microbially Induced Calcite Precipitation for the Immobilization of Strontium-90 Using a Variable Velocity Streamtube Ensemble]

Biogeochemical modeling using PHREEQC2 and a streamtube ensemble approach is utilized to understand a well-to-well subsurface treatment system at the Vadose Zone Research Park (VZRP) near Idaho Falls, Idaho. Treatment involves in situ microbially-mediated ureolysis to induce calcite precipitation for the immobilization of strontium-90. PHREEQC2 is utilized to model the kinetically-controlled ureolysis and consequent calcite precipitation. Reaction kinetics, equilibrium phases, and cation exchange are used within PHREEQC2 to track pH and levels of calcium, ammonium, urea, and calcite precipitation over time, within a series of one-dimensional advective-dispersive transport paths creating a streamtube ensemble representation of the well-to-well transport. An understanding of the impact of physical heterogeneities within this radial flowfield is critical for remediation design; we address this via the streamtube approach: instead of depicting spatial extents of solutes in the subsurface we focus on their arrival distribution at the control well(s). Traditionally, each streamtube maintains uniform velocity; however in radial flow in homogeneous media, the velocity within any given streamtube is spatially-variable in a common way, being highest at the input and output wells and approaching a minimum at the midpoint between the wells. This idealized velocity variability is of significance in the case of ureolytically driven calcite precipitation. Streamtube velocity patterns for any particular configuration of injection and withdrawal wells are available as explicit calculations from potential theory, and also from particle tracking programs. To approximate the actual spatial distribution of velocity along streamtubes, we assume idealized radial non-uniform velocity associated with homogeneous media. This is implemented in PHREEQC2 via a non-uniform spatial discretization within each streamtube that honors both the streamtube’s travel time and the idealized “fast-slow-fast” pattern of non-uniform velocity along the streamline. Breakthrough curves produced by each simulation are weighted by the path-respective flux fractions (obtained by deconvolution of tracer tests conducted at the VZRP) to obtain the flux-average of flow contributions to the observation well

Subsurface Uranium Fate and Transport: Integrated Experiments and Modeling of Coupled Biogeochemical Mechanisms of Nanocrystalline Uraninite Oxidation by Fe(III)-(hydr)oxides - Project Final Report

Subsurface bacteria including sulfate reducing bacteria (SRB) reduce soluble U(VI) to insoluble U(IV) with subsequent precipitation of UO2. We have shown that SRB reduce U(VI) to nanometer-sized UO2 particles (1-5 nm) which are both intra- and extracellular, with UO2 inside the cell likely physically shielded from subsequent oxidation processes. We evaluated the UO2 nanoparticles produced by Desulfovibrio desulfuricans G20 under growth and non-growth conditions in the presence of lactate or pyruvate and sulfate, thiosulfate, or fumarate, using ultrafiltration and HR-TEM. Results showed that a significant mass fraction of bioreduced U (35-60%) existed as a mobile phase when the initial concentration of U(VI) was 160 µM. Further experiments with different initial U(VI) concentrations (25 - 900 M) in MTM with PIPES or bicarbonate buffers indicated that aggregation of uraninite depended on the initial concentrations of U(VI) and type of buffer. It is known that under some conditions SRB-mediated UO2 nanocrystals can be reoxidized (and thus remobilized) by Fe(III)-(hydr)oxides, common constituents of soils and sediments. To elucidate the mechanism of UO2 reoxidation by Fe(III) (hydr)oxides, we studied the impact of Fe and U chelating compounds (citrate, NTA, and EDTA) on reoxidation rates. Experiments were conducted in anaerobic batch systems in PIPES buffer. Results showed EDTA significantly accelerated UO2 reoxidation with an initial rate of 9.5M day-1 for ferrihydrite. In all cases, bicarbonate increased the rate and extent of UO2 reoxidation with ferrihydrite. The highest rate of UO2 reoxidation occurred when the chelator promoted UO2 and Fe(III) (hydr)oxide dissolution as demonstrated with EDTA. When UO2 dissolution did not occur, UO2 reoxidation likely proceeded through an aqueous Fe(III) intermediate as observed for both NTA and citrate. To complement to these laboratory studies, we collected U-bearing samples from a surface seep at the Rifle field site and have measured elevated U concentrations in oxic iron-rich sediments. To translate experimental results into numerical analysis of U fate and transport, a reaction network was developed based on Sani et al. (2004) to simulate U(VI) bioreduction with concomitant UO2 reoxidation in the presence of hematite or ferrihydrite. The reduction phase considers SRB reduction (using lactate) with the reductive dissolution of Fe(III) solids, which is set to be microbially mediated as well as abiotically driven by sulfide. Model results show the oxidation of HS– by Fe(III) directly competes with UO2 reoxidation as Fe(III) oxidizes HS– preferentially over UO2. The majority of Fe reduction is predicted to be abiotic, with ferrihydrite becoming fully consumed by reaction with sulfide. Predicted total dissolved carbonate concentrations from the degradation of lactate are elevated (log(pCO2) ~ –1) and, in the hematite system, yield close to two orders-of-magnitude higher U(VI) concentrations than under initial carbonate concentrations of 3 mM. Modeling of U(VI) bioreduction with concomitant reoxidation of UO2 in the presence of ferrihydrite was also extended to a two-dimensional field-scale groundwater flow and biogeochemically reactive transport model for the South Oyster site in eastern Virginia. This model was developed to simulate the field-scale immobilization and subsequent reoxidation of U by a biologically mediated reaction network