Jonathan D. Istok

A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity

Here, we report a catalytic beacon sensor for uranyl (UO22+) based on an in vitro-selected UO22+-specific DNAzyme. The sensor consists of a DNA enzyme strand with a 3′ quencher and a DNA substrate with a ribonucleotide adenosine (rA) in the middle and a fluorophore and a quencher at the 5′ and 3′ ends, respectively. The presence of UO22+ causes catalytic cleavage of the DNA substrate strand at the rA position and release of the fluorophore and thus dramatic increase of fluorescence intensity. The sensor has a detection limit of 11 parts per trillion (45 pM), a dynamic range up to 400 nM, and selectivity of >1-million-fold over other metal ions. The most interfering metal ion, Th(IV), interacts with the fluorescein fluorophore, causing slightly enhanced fluorescence intensity, with an apparent dissociation constant of ≈230 μM. This sensor rivals the most sensitive analytical instruments for uranium detection, and its application in detecting uranium in contaminated soil samples is also demonstrated. This work shows that simple, cost-effective, and portable metal sensors can be obtained with similar sensitivity and selectivity as much more expensive and sophisticated analytical instruments. Such a sensor will play an important role in environmental remediation of radionuclides such as uranium.

Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate

ABSTRACT Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells. In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed that sediment pH increased substantially (by 1 to 2 pH units) while nitrate was largely depleted. A large diversity of 16S rRNA gene sequences were retrieved from subsurface sediments, including species from the α, β, δ, and γ subdivisions of the class Proteobacteria, as well as low- and high-G+C gram-positive species. Following in situ biostimulation of microbial communities within contaminated sediments, sequences related to previously cultured metal-reducing δ-Proteobacteria increased from 5% to nearly 40% of the clone libraries. Quantitative PCR revealed that Geobacter-type 16S rRNA gene sequences increased in biostimulated sediments by 1 to 2 orders of magnitude at two of the four sites tested. Evidence from the quantitative PCR analysis corroborated information obtained from 16S rRNA gene clone libraries, indicating that members of the δ-Proteobacteria subdivision, including Anaeromyxobacter dehalogenans-related and Geobacter-related sequences, are important metal-reducing organisms in acidic subsurface sediments. This study provides the first cultivation-independent analysis of the change in metal-reducing microbial communities in subsurface sediments during an in situ bioremediation experiment.

Utilization of Microbial Biofilms as Monitors of Bioremediation

A down-well aquifer microbial sampling system was developed using glass wool or Bio-Sep beads as a solid-phase support matrix. Here we describe the use of these devices to monitor the groundwater microbial community dynamics during field bioremediation experiments at the U.S. Department of Energy Natural and Accelerated Bioremediation Research Program’s Field Research Center at the Oak Ridge National Laboratory. During the 6-week deployment, microbial biofilms colonized glass wool and bead internal surfaces. Changes in viable biomass, community composition, metabolic status, and respiratory state were reflected in sampler composition, type of donor, and groundwater pH. Biofilms that formed on Bio-Sep beads had 2–13 times greater viable biomass; however, the bead communities were less metabolically active [higher cyclopropane/monoenoic phospholipid fatty acid (PLFA) ratios] and had a lower aerobic respiratory state (lower total respiratory quinone/PLFA ratio and ubiquinone/menaquinone ratio) than the biofilms formed on glass wool. Anaerobic growth in these systems was characterized by plasmalogen phospholipids and was greater in the wells that received electron donor additions. Partial 16S rDNA sequences indicated that Geobacter and nitrate-reducing organisms were induced by the acetate, ethanol, or glucose additions. DNA and lipid biomarkers were extracted and recovered without the complications that commonly plague sediment samples due to the presence of clay or dissolved organic matter. Although microbial community composition in the groundwater or adjacent sediments may differ from those formed on down-well biofilm samplers, the metabolic activity responses of the biofilms to modifications in groundwater geochemistry record the responses of the microbial community to biostimulation while providing integrative sampling and ease of recovery for biomarker analysis.

Precipitation estimation in mountainous terrain using multivariate geostatistics. Part II: isohyetal maps

Abstract Values of average annual precipitation (AAP) may be important for hydrologic characterization of a potential high-level nuclear-waste repository site at Yucca Mountain, Nevada. Reliable measurements of AAP are sparse in the vicinity of Yucca Mountain, and estimates of AAP were needed for an isohyetal mapping over a 2600-square-mile watershed containing Yucca Mountain. Estimates were obtained with a multivariate geostatistical model developed using AAP and elevation data from a network of 42 precipitation stations in southern Nevada and southeastern California. An additional 1531 elevations were obtained to improve estimation accuracy. Isohyets representing estimates obtained using univariate geostatistics (kriging) defined a smooth and continuous surface. Isohyets representing estimates obtained using multivariate geostatistics (cokriging) defined an irregular surface that more accurately represented expected local orographic influences on AAP. Cokriging results included a maximum estimate within...

In-situ oxidation of trichloroethene by permanganate: effects on porous medium hydraulic properties.

In-situ oxidation of dense nonaqueous-phase liquids (DNAPLs) by strong oxidants such as potassium permanganate (KMnO4) has been proposed as a possible DNAPL remediation strategy. In this study, we investigated the effects of in-situ trichloroethene (TCE) oxidation by KMnO4 on porous medium hydraulic properties. In particular, we wanted to determine the overall effects of concurrent solid phase (MnO2) precipitation, gas (CO2) evolution and TCE dissolution resulting from the oxidation reaction on the porous mediums aqueous-phase relative permeability, krw. Three TCE removal experiments were conducted in a 95-cm long, 5.1-cm i.d. glass column, which was homogeneously packed with well-characterized 30/40-mesh silica sand. TCE was emplaced in the sand-pack in residual, entrapped form through a sequence of water/TCE imbibition and drainage steps. The column was then flushed under constant aqueous flux conditions for up to 104 h with either deionized water (reference experiment), deionized water containing 5 mM KMnO4 or deionized water containing 5 mM KMnO4 and 300 mM Na2HPO4. Aqueous-phase relative permeabilities were computed from measured flow rates and measurements of aqueous-phase pressure head, h obtained using pressure transducers connected to tensiometers distributed along the column length. A dual-energy gamma radiation system was used to monitor changes in fluid saturation that occurred during each experiment. In addition, column effluent samples were collected for chemical analyses. Dissolution of TCE during deionized water flushing led to an increase in krw by approximately 22% and a local reduction in h. On the other hand, vigorous CO2 gas production and precipitation of MnO2 was visually observed during flushing with deionized water that contained 5 mM KMnO4. As a consequence, krw declined by approximately 96% and h increased locally by more than 1000 cm H2O during the first 24 h of the experiment, causing sand-pack ruptures and pump failure. Conversely, less CO2 gas production and MnO2 precipitation was visually observed during flushing with deionized water that contained 5 mM KMnO4 and 300 mM Na2HPO4. Consequently, only small increases in h (< 15 cm H2O) were observed in this experiment due to a reduction in krw of approximately 53%. While we must attribute changes in h due to variations in krw to our specific experimental design (constant aqueous flux, one-dimensional flow experiments), these experiments nevertheless confirm that successful application of in situ chemical oxidation of TCE requires consideration of detrimental processes such as MnO2 precipitation and CO2 gas formation. In addition, our results indicate that utilization of a buffered oxidant solution may improve the effectiveness of in-situ oxidation of TCE by KMnO4 in otherwise weakly buffered porous media.

In situ evaluation of solute retardation using single-well push–pull tests

Abstract More efficient methods are needed for the in situ evaluation of solute sorption to aquifer sediments. The objective of this study was to develop a simplified method for estimating retardation factors for injected solutes from “push–pull” test extraction phase breakthrough curves (BTCs). Sensitivity analyses based on numerical simulations were used to evaluate the method performance for a variety of test conditions. Simulations were conducted for varying retardation factors, aquifer parameters and injection phase durations, for tests performed under nonideal transport conditions such as nonlinear equilibrium and linear nonequilibrium sorption, and for a test performed in a physically heterogeneous aquifer. Predicted retardation factors showed errors ⩽14% in tests performed under ideal transport conditions (physically homogeneous aquifer with spatially uniform dispersivity that does not vary from solute to solute, spatially uniform linear equilibrium sorption). The method performed more poorly for solutes with large retardation factors ( R >20) and for tests conducted under nonideal transport conditions, and is expected to perform poorly in aquifers with highly heterogeneous sorption. In an example application, we used the method to estimate the distribution coefficient for 85 Sr using data from a field test performed by Pickens JF, Jackson RE, Inch KJ, Merritt WF. (Water Resour Res 1981;17:529–44). Reasonable agreement was found between distribution coefficients obtained using the simplified method of estimation and those obtained by Pickens et al. (1981).

Geometry and position of light nonaqueous-phase liquid lenses in water-wetted porous media

Predicting the movement of LNAPLs (light nonaqueous-phase liquids) in the subsurface environment is critical for the design of effective remediatory action. The objective of this study was to develop a method for predicting the shape and extent of LNAPL lenses in the capillary fringe of the vadose zone. Two-dimensional experiments were performed in a glass chamber (50 cm × 60 cm × 0.95 cm) using four Miller-similar silica sands (1220, 2030, 3040 and 4050 sieve sizes) and two LNAPLs (Soltrol® 220 and Duoprime® 55 mineral oil). LNAPLs were released in water-wetted sands to simulate a point-source discharge above a water table. Observation of light transmission was used to delineate the changing LNAPL lens boundary during infiltration until equilibrium was established. At equilibrium, no zone above the capillary fringe remained at a NAPL saturation higher than the residual saturation. A previously published model for predicting vertical lens dimensions was tested and good agreement was found between measured and predicted lens thicknesses when the time-dependent nature of LNAPL—water interfacial tensions was considered. Less agreement between measured and predicted lens thicknesses was found when model equations were modified to a fully explicit, predictive form. Observed spatial variability in the emplacement of LNAPLs in the capillary fringe, compounded by the strong time dependence of a key variable, limits the use of the model as a predictive tool, but provides important insight into the low precision in prediction which is attainable even if a more complete model was developed. The results provide a means to better understand LNAPL behavior in the subsurface environment.

An analytical solution to the solute transport equation with rate‐limited desorption and decay

An analytical solution is derived for the advection-dispersion equation with rate-limited desorption and first-order decay, using an eigenfunction integral equations method. The model equations represent one-dimensional solute transport in a homogeneous isotropic porous medium where the porous medium is saturated with the aqueous solution. The flow field is uniform. Rate-limited desorption is described as a first-order process where the rate is proportional to the difference in concentration between the sorbed phase and the aqueous phase. The solution was verified for the limiting case of equilibrium desorption using the solution of van Genuchten and Alves (1982). Example calculations are presented to show the effect of the desorption rate, decay rate, and distribution coefficient on the rate of contaminant removal from both the aqueous and sorbed phases of a groundwater aquifer. The solution quantifies the expected results, where the larger the desorption and decay rate and the smaller the distribution coefficient, the faster the rate of contaminant removal from the aqueous and sorbed phases.

Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquifer

ABSTRACT Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.

Effects of rate-limited desorption on the feasibility of in situ bioremediation

Remediation of contaminated groundwater aquifers can be extremely difficult when desorption of the contaminant from the solid phase to the aqueous phase is slow. The effects of desorption rates on the feasibility of in situ bioremediation are investigated using an analytical solution to the solute transport equation with rate-limited desorption and first-order decay. Sensitivity analyses are used to identify when desorption or degradation is the rate-limiting process for bioremediation for the range of desorption rates, degradation rates, and equilibrium distribution coefficients reported in the literature. The results show that when the desorption coefficient is large relative to the degradation coefficient (degradation is rate limiting), the performance of in situ bioremediation compared to groundwater extraction is improved as the degradation rate increases. Degradation in the aqueous phase increases the concentration gradient between solid and aqueous phases, increasing the rate of desorption and thus the rate of remediation. However, when the desorption coefficient is small relative to the degradation coefficient (desorption is rate limiting), increasing the degradation rate any further will not improve the performance of in situ bioremediation. For sites that conform to the assumptions of the model and for which model parameters can be measured or estimated, the results can be used to perform a preliminary assessment of the feasibility of in situ bioremediation.