Advanced methods for RNA recovery from petroleum impacted soils.

Microbially-mediated hydrocarbon degradation is well documented. However, how these microbial processes occur in complex subsurface petroleum impacted systems remains unclear, and this knowledge is needed to guide technologies to enhance microbial degradation effectively. Analysis of RNA derived from soils impacted by petroleum liquids would allow for analysis of active microbial communities, and a deeper understanding of the dynamic biochemistry occurring during site remediation. However, RNA analysis in soils impacted with petroleum liquids is challenging due to: (A) RNA being inherently unstable, and (B) petroleum impacted soils containing problematic levels of polymerase chain reaction (PCR) inhibitors that must be removed to yield high-purity RNA for downstream analysis. A previously published soil wash pretreatment step and a commercially available DNA extraction kit protocol were combined and modified to be able to purify RNA from soils containing petroleum liquids.•A key modification involved reformulation of the pretreatment solution via replacing water as the diluent with a commercially-available RNA preservation solution.•Methods were developed and demonstrated using cryogenically preserved soils from three former petroleum refineries. Results showed the new soil washing approach had no adverse effects on RNA recovery but did improve RNA quality, by PCR inhibitor removal, which in turn allows for characterization of active microbial communities present in petroleum impacted soils.•In summary, our method for extracting RNA from petroleum-impacted soils provides a promising new tool for resolving metabolic processes at sites as they progress toward restoration via natural and/or engineered remediation.

Real-time soil and groundwater monitoring via spatial and temporal resolution of biogeochemical potentials.

Oxidation-reduction potentials (ORP) govern the transformation of organic compounds in water and soils. Standard methods for measurements of ORPs in subsurface setting are deeply flawed due to heterogeneous samples from wells, failure to capture weakly poised redox couples, and biases with ex-situ measurements. In this study, we developed a real-time in-situ ORP sensor system that continuously measures biogeochemical electrical potentials using vertically distributed point sensing electrodes in direct contact with the soil. Three hundred thousand data points, providing a full range of aqueous ORP values (+ 600 to - 600 mV vs. Ag/AgCl) were collected over 513 days to spatially and temporally resolve subsurface biogeochemical processes at a former petroleum refinery. Water quality and microbial community data support the validity of the ORP data. In locations impacted by petroleum light non-aqueous phase liquids (LNAPLs), barometric pumping and ebullition events drive near-daily cycles of ORP changes in the vadose zone of 400 mV. When only dissolved phase hydrocarbons are present, near-daily redox cycles are absent and values for ORP indicate methanogenic conditions immediately about the water table. When hydrocarbons are not present, redox conditions are more oxidizing by + 400 to + 700 mV. The embedded electrodes revealed variations in hydrocarbon biodegradation in time and space that cannot be resolved by collection and analysis of conventional samples of groundwater and soil gas.

The Mechanism of C-H Bond Oxidation by Aqueous Permanganate.

The permanganate ion (MnO4-) has been widely used as a reagent for water treatment for over a century. It is a strong enough oxidant to activate carbon-hydrogen bonds, one of the most important reactions in biological and chemical systems. Our current textbook understanding of the oxidation mechanism in aqueous solution involves an initial, rate-limiting hydride abstraction by permanganate followed by reaction of the carbocation with bulk water to form an alcohol. This mechanism fits well into the classic oxidation sequence of alkane → alcohol → aldehyde → carboxylate, the central paradigm for both abiotic and biotic alkane oxidation in aqueous environments. In this study, we provide three lines of evidence through (1) a broken-symmetry density functional theory approach, (2) isotope labeling experiments, and (3) kinetic network modeling to demonstrate that aqueous permanganate can circumvent prior alcohol formation and produce aldehydes directly via a reaction path that bifurcates after the initial transition state. In contrast to classic transition state theory, the rate-limiting step is found to not determine product distribution, bearing critical implications for pathway and rate predictions. This complex reaction network provides new insights into the oxidation mechanisms of organic compounds involving transition metal complexes as well as enzyme or metal oxide surface active sites.

Mechanism for detecting NAPL using electrical resistivity imaging.

The detection of non-aqueous phase liquid (NAPL) related impacts in freshwater environments by electrical resistivity imaging (ERI) has been clearly demonstrated in field conditions, but the mechanism generating the resistive signature is poorly understood. An electrical barrier mechanism which allows for detecting NAPLs with ERI is tested by developing a theoretical basis for the mechanism, testing the mechanism in a two-dimensional sand tank with ERI, and performing forward modeling of the laboratory experiment. The NAPL barrier theory assumes at low bulk soil NAPL concentrations, thin saturated NAPL barriers can block pore throats and generate a detectable electrically resistive signal. The sand tank experiment utilized a photographic technique to quantify petroleum saturation, and to help determine whether ERI can detect and quantify NAPL across the water table. This experiment demonstrates electrical imaging methods can detect small quantities of NAPL of sufficient thickness in formations. The bulk volume of NAPL is not the controlling variable for the amount of resistivity signal generated. The resistivity signal is primarily due to a zone of high resistivity separate phase liquid blocking current flow through the fully NAPL saturated pores spaces. For the conditions in this tank experiment, NAPL thicknesses of 3.3cm and higher in the formation was the threshold for detectable changes in resistivity of 3% and greater. The maximum change in resistivity due to the presence of NAPL was an increase of 37%. Forward resistivity models of the experiment confirm the barrier mechanism theory for the tank experiment.

Advanced Electrochemical Oxidation of 1,4-Dioxane via Dark Catalysis by Novel Titanium Dioxide (TiO2) Pellets.

1,4-dioxane is an emerging groundwater contaminant with significant regulatory implications. Because it is resistant to traditional groundwater treatments, remediation of 1,4-dioxane is often limited to costly ex situ UV-based advanced oxidation. By varying applied voltage, electrical conductivity, seepage velocity, and influent contaminant concentration in flow-through reactors, we show that electrochemical oxidation is a viable technology for in situ and ex situ treatment of 1,4-dioxane under a wide range of environmental conditions. Using novel titanium dioxide (TiO2) pellets, we demonstrate for the first time that this prominent catalyst can be activated in the dark even when electrically insulated from the electrodes. TiO2-catalyzed reactors achieved efficiencies of greater than 97% degradation of 1,4-dioxane, up to 4.6 times higher than noncatalyzed electrolytic reactors. However, the greatest catalytic enhancement (70% degradation versus no degradation without catalysis) was observed in low-ionic-strength water, where conventional electrochemical approaches notoriously fail. The TiO2 pellet's dark-catalytic oxidation activity was confirmed on the pharmaceutical lamotrigine and the industrial solvent chlorobenzene, signifying that electrocatalytic treatment has tremendous potential as a transformative remediation technology for persistent organic pollutants in groundwater and other aqueous environments.

Implications of soil mixing for NAPL source zone remediation: Column studies and modeling of field-scale systems.

Soil remediation is often inhibited by subsurface heterogeneity, which constrains contaminant/reagent contact. Use of soil mixing techniques for reagent delivery provides a means to overcome contaminant/reagent contact limitations. Furthermore, soil mixing reduces the permeability of treated soils, thus extending the time for reactions to proceed. This paper describes research conducted to evaluate implications of soil mixing on remediation of non-aqueous phase liquid (NAPL) source zones. The research consisted of column studies and subsequent modeling of field-scale systems. For column studies, clean influent water was flushed through columns containing homogenized soils, granular zero valent iron (ZVI), and trichloroethene (TCE) NAPL. Within the columns, NAPL depletion occurred due to dissolution, followed by either column-effluent discharge or ZVI-mediated degradation. Complete removal of TCE NAPL from the columns occurred in 6-8 pore volumes of flow. However, most of the TCE (>96%) was discharged in the column effluent; less than 4% of TCE was degraded. The low fraction of TCE degraded is attributed to the short hydraulic residence time (<4 days) in the columns. Subsequently, modeling was conducted to scale up column results. By scaling up to field-relevant system sizes (>10 m) and reducing permeability by one-or-more orders of magnitude, the residence time could be greatly extended, potentially for periods of years to decades. Model output indicates that the fraction of TCE degraded can be increased to >99.9%, given typical post-mixing soil permeability values. These results suggest that remediation performance can be greatly enhanced by combining contaminant degradation with an extended residence time.

Measurement of Natural Losses of LNAPL Using CO2 Traps.

Efflux of CO2 above releases of petroleum light nonaqueous phase liquids (LNAPLs) has emerged as a critical parameter for resolving natural losses of LNAPLs and managing LNAPL sites. Current approaches for resolving CO2 efflux include gradient, flux chamber, and mass balance methods. Herein a new method for measuring CO2 efflux above LNAPL bodies, referred to as CO2 traps, is introduced. CO2 traps involve an upper and a lower solid phase sorbent elements that convert CO2 gas into solid phase carbonates. The sorbent is placed in an open vertical section of 10 cm ID polyvinyl chloride (PVC) pipe located at grade. The lower sorbent element captures CO2 released from the subsurface via diffusion and advection. The upper sorbent element prevents atmospheric CO2 from reaching the lower sorbent element. CO2 traps provide integral measurement of CO2 efflux based over the period of deployment, typically 2 to 4 weeks. Favorable attributes of CO2 traps include simplicity, generation of integral (time averaged) measurement, and a simple means of capturing CO2 for carbon isotope analysis. Results from open and closed laboratory experiments indicate that CO2 traps quantitatively capture CO2 . Results from the deployment of 23 CO2 traps at a former refinery indicate natural loss rates of LNAPL (measured in the fall, likely concurrent with high soil temperatures and consequently high degradation rates) ranging from 13,400 to 130,000 liters per hectare per year (L/Ha/year). A set of field triplicates indicates a coefficient of variation of 18% (resulting from local spatial variations and issues with measurement accuracy).

Testing high resolution numerical models for analysis of contaminant storage and release from low permeability zones.

It is now widely recognized that contaminant release from low permeability zones can sustain plumes long after primary sources are depleted, particularly for chlorinated solvents where regulatory limits are orders of magnitude below source concentrations. This has led to efforts to appropriately characterize sites and apply models for prediction incorporating these effects. A primary challenge is that diffusion processes are controlled by small-scale concentration gradients and capturing mass distribution in low permeability zones requires much higher resolution than commonly practiced. This paper explores validity of using numerical models (HydroGeoSphere, FEFLOW, MODFLOW/MT3DMS) in high resolution mode to simulate scenarios involving diffusion into and out of low permeability zones: 1) a laboratory tank study involving a continuous sand body with suspended clay layers which was 'loaded' with bromide and fluorescein (for visualization) tracers followed by clean water flushing, and 2) the two-layer analytical solution of Sale et al. (2008) involving a relatively simple scenario with an aquifer and underlying low permeability layer. All three models are shown to provide close agreement when adequate spatial and temporal discretization are applied to represent problem geometry, resolve flow fields and capture advective transport in the sands and diffusive transfer with low permeability layers and minimize numerical dispersion. The challenge for application at field sites then becomes appropriate site characterization to inform the models, capturing the style of the low permeability zone geometry and incorporating reasonable hydrogeologic parameters and estimates of source history, for scenario testing and more accurate prediction of plume response, leading to better site decision making.

A mass balance approach to resolving LNAPL stability.

This article explores the hypothesis that natural losses of light nonaqueous phase liquids (LNAPLs) through dissolution and evaporation can control the overall extent of LNAPL bodies and LNAPL fluxes observed within LNAPL bodies. First, a proof-of-concept sand tank experiment is presented. An LNAPL (methyl tert-butyl ether) was injected into a sand tank at five constant injection rates that were increased stepwise. Initially, for each injection rate the LNAPL bodies expanded quickly. With time the rate of expansion of the LNAPL bodies slowed and at extended times the extent of the LNAPL became constant. Attainment of a stable LNAPL extent is attributed to rates of LNAPL addition being equal to rates of LNAPL losses through dissolution and evaporation. Secondly, analytical solutions are developed to extrapolate the processes observed in the proof-of-concept experiment to dimensions and time frames that are consistent with field-scale LNAPL bodies. Three LNAPL body geometries that are representative of common field conditions are considered including one-dimensional, circular, and oblong shapes. Using idealized conditions, the solutions describe volumetric LNAPL fluxes as a function of position in LNAPL bodies and the overall extent of LNAPL bodies as a function of time. Results from both the proof-of-concept experiment and the mathematical developments illustrate that natural losses of LNAPL can play an important role in governing LNAPL fluxes within LNAPL bodies and the overall extent of LNAPL bodies.

Chlorinated ethene source remediation: lessons learned.

Chlorinated solvents such as trichloroethene (TCE) and tetrachloroethene (PCE) are widespread groundwater contaminants often released as dense nonaqueous phase liquids (DNAPLs). These contaminants are difficult to remediate, particularly their source zones. This review summarizes the progress made in improving DNAPL source zone remediation over the past decade, and is structured to highlight the important practical lessons learned for improving DNAPL source zone remediation. Experience has shown that complete restoration is rare, and alternative metrics such as mass discharge are often useful for assessing the performance of partial restoration efforts. Experience also has shown that different technologies are needed for different times and locations, and that deliberately combining technologies may improve overall remedy performance. Several injection-based technologies are capable of removing a large fraction of the total contaminant mass, and reducing groundwater concentrations and mass discharge by 1 to 2 orders of magnitude. Thermal treatment can remove even more mass, but even these technologies generally leave some contamination in place. Research on better delivery techniques and characterization technologies will likely improve treatment, but managers should anticipate that source treatment will leave some contamination in place that will require future management.

Measurement of LNAPL flux using single-well intermittent mixing tracer dilution tests.

The stability of subsurface Light Nonaqueous Phase Liquids (LNAPLs) is a key factor driving expectations for remedial measures at LNAPL sites. The conventional approach to resolving LNAPL stability has been to apply Darcy's Equation. This paper explores an alternative approach wherein single-well tracer dilution tests with intermittent mixing are used to resolve LNAPL stability. As a first step, an implicit solution for single-well intermittent mixing tracer dilution tests is derived. This includes key assumptions and limits on the allowable time between intermittent mixing events. Second, single-well tracer dilution tests with intermittent mixing are conducted under conditions of known LNAPL flux. This includes a laboratory sand tank study and two field tests at active LNAPL recovery wells. Results from the sand tank studies indicate that LNAPL fluxes in wells can be transformed into formation fluxes using corrections for (1) LNAPL thicknesses in the well and formation and (2) convergence of flow to the well. Using the apparent convergence factor from the sand tank experiment, the average error between the known and measured LNAPL fluxes is 4%. Results from the field studies show nearly identical known and measured LNAPL fluxes at one well. At the second well the measured fluxes appear to exceed the known value by a factor of two. Agreement between the known and measured LNAPL fluxes, within a factor of two, indicates that single-well tracer dilution tests with intermittent mixing can be a viable means of resolving LNAPL stability.

Use of single-well tracer dilution tests to evaluate LNAPL flux at seven field sites.

Petroleum liquids, referred to as light non-aqueous phase liquids (LNAPLs), are commonly found beneath petroleum facilities. Concerns with LNAPLs include migration into clean soils, migration beyond property boundaries, and discharges to surface water. Single-well tracer dilution techniques were used to measure LNAPL fluxes through 50 wells at 7 field sites. A hydrophobic tracer was mixed into LNAPL in a well. Intensities of fluorescence associated with the tracer were measured over time using a spectrometer and a fiber optic cable. LNAPL fluxes were estimated using observed changes in the tracer concentrations over time. Measured LNAPL fluxes range from 0.006 to 2.6 m/year with a mean and median of 0.15 and 0.064 m/year, respectively. Measured LNAPL fluxes are two to four orders of magnitude smaller than a common groundwater flux of 30 m/year. Relationships between LNAPL fluxes and possible governing parameters were evaluated. Observed LNAPL fluxes are largely independent of LNAPL thickness in wells. Natural losses of LNAPL through dissolution, evaporation, and subsequent biodegradation, were estimated using a simple mass balance, measured LNAPL fluxes in wells, and an assumed stable LNAPL extent. The mean and median of the calculated loss rates were found to be 24.0 and 5.0 m3/ha/year, respectively. Mean and median losses are similar to values reported by others. Coupling observed LNAPL fluxes to observed rates of natural LNAPL depletion suggests that natural losses of LNAPL may be an important parameter controlling the overall extent of LNAPL bodies.

Prediction of contaminant persistence in aqueous phase: a quantum chemical approach.

At contaminated field sites where active remediation measures are not feasible, monitored natural attenuation is sometimes the only alternative for surface water or groundwater decontamination. However, due to slow degradation rates of some contaminants under natural conditions, attenuation processes and their performance assessment can take several years to decades to complete. Here, we apply quantum chemical calculations to predict contaminant persistence in the aqueous phase. For the test compound hexamethylphosphoramide (HMPA), P-N bond hydrolysis is the only thermodynamically favorable reaction that may lead to its degradation under reducing conditions. Through calculation of aqueous Gibbs free energies of activation for all potential reaction mechanisms, it is predicted that HMPA hydrolyzes via an acid-catalyzed mechanism at pH < 8.2, and an uncatalyzed mechanism at pH 8.2-8.5. The estimated half-lives of thousands to hundreds of thousands of years over the groundwater-typical pH range of 6.0 to 8.5 indicate that HMPA will be persistent in the absence of suitable oxidants. At pH 0, where the hydrolysis reaction is rapid enough to enable measurement, the experimentally determined rate constant and half-life are in excellent agreement with the predicted values. Since the quantum chemical methodology described herein can be applied to virtually any contaminant or reaction of interest, it is especially valuable for the prediction of persistence when slow reaction rates impede experimental investigations and appropriate QSARs are unavailable.

Quantum chemical prediction of redox reactivity and degradation pathways for aqueous phase contaminants: an example with HMPA.

Models used to predict the fate of aqueous phase contaminants are often limited by their inability to address the widely varying redox conditions in natural and engineered systems. Here, we present a novel approach based on quantum chemical calculations that identifies the thermodynamic conditions necessary for redox-promoted degradation and predicts potential degradation pathways. Hexamethylphosphoramide (HMPA), a widely used solvent and potential groundwater contaminant, is used as a test case. Its oxidation is estimated to require at least iron-reducing conditions at low to neutral pH and nitrate-reducing conditions at high pH. Furthermore, the transformation of HMPA by permanganate is predicted to proceed through sequential N-demethylation. Experimental validation based on LC/TOF-MS analysis confirms the predicted pathways of HMPA oxidation by permanganate to phosphoramide via the formation of less methylated as well as singly and multiply oxygenated reaction intermediates. Pathways predicted to be thermodynamically or kinetically unfavorable are similarly absent in the experimental studies. Our newly developed methodology will enable scientists and engineers to estimate the favorability of contaminant degradation at a specific field site, suitable approaches to enhance degradation, and the persistence of a contaminant and its reaction intermediates.

Effects of reduced contaminant loading on downgradient water quality in an idealized two-layer granular porous media.

The following explores the issue of how reductions in contaminant loading to plumes will effect downgradient water quality. An idealized scenario of two adjacent layers of uniform geologic media, one transmissive and the other low permeability, is considered. A high concentration source, similar to a thin DNAPL pool, is introduced in the transmissive layer immediately above the low permeability layer. While the source is active, dissolved constituents are driven along the contact by advection and into the low permeability layer by transverse diffusion. Removing the source reverses the concentration gradient between the layers, driving back diffusion of contaminants from the low permeability layer. Laboratory studies involving four contaminants demonstrate that 15 to 44% of the introduced contaminant moves into the low permeability zone (along a distance of 87 cm in a sand tank) over a period of 25 days. The greatest movement of contaminants into the low permeability zone is seen with the contaminants with the greatest sorption coefficients. A unique two-dimensional analytical solution is developed for the two-layer scenario. Processes addressed include advection; transverse dispersion; adsorption and degradation in the transmissive zones; and diffusion, adsorption, and degradation in the low permeability layer. Laboratory data agree favorably with the analytical solutions. Collectively, the laboratory results and analytical solutions provide a basis for testing other modeling approaches that can be applied to more complex problems. A set of field-scale scenarios are considered using the analytical solutions. Results indicate that improvement in water quality associated with source removal diminish with distance downgradient of the source. Furthermore, contaminant degradation and contaminant adsorption in the stagnant zone are shown to be critical factors governing the timing and magnitude of downgradient improvements in water quality. For five of six scenarios considered, observed improvements in water quality 100 m downgradient of the source fall in the range of 1 to 2 orders of magnitude 15 years after complete source removal. The sixth scenario, involving a contaminant half-life of three years and no adsorption, shows greater than three order of magnitude improvements in downgradient water quality within one year of source removal.

Measurement of LNAPL flow using single-well tracer dilution techniques.

This paper describes the use of single-well tracer dilution techniques to resolve the rate of light nonaqueous phase liquid (LNAPL) flow through wells and the adjacent geologic formation. Laboratory studies are presented in which a fluorescing tracer is added to LNAPL in wells. An in-well mixer keeps the tracer well mixed in the LNAPL. Tracer concentrations in LNAPL are measured through time using a fiber optic cable and a spectrometer. Results indicate that the rate of tracer depletion is proportional to the rate of LNAPL flow through the well and the adjacent formation. Tracer dilution methods are demonstrated for vertically averaged LNAPL Darcy velocities of 0.00048 to 0.11 m/d and LNAPL thicknesses of 9 to 24 cm. Over the range of conditions studied, results agree closely with steady-state LNAPL flow rates imposed by pumping. A key parameter for estimating LNAPL flow rates in the formation is the flow convergence factor alpha. Measured convergence factors for 0.030-inch wire wrap, 0.030-inch-slotted polyvinyl chloride (PVC), and 0.010-inch-slotted PVC are 1.7, 0.91, and 0.79, respectively. In addition, methods for using tracer dilution data to determine formation transmissivity to LNAPL are presented. Results suggest that single-well tracer dilution techniques are a viable approach for measuring in situ LNAPL flow and formation transmissivity to LNAPL.

Sequential electrolytic oxidation and reduction of aqueous phase energetic compounds.

Contamination of soils and groundwater with energetic compounds has been documented at many former ammunition manufacturing plants and ranges. Recent research at Colorado State University (CSU) has demonstrated the potential utility of electrolytic degradation of organic compounds using an electrolytic permeable reactive barrier (e-barrier). In principle, an electrolytic approach to degrade aqueous energetic compounds such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) or 2,4,6-trinitrotoluene (TNT) can overcome limitations of management strategies that involve solely oxidation or reduction, through sequential oxidation-reduction or reduction-oxidation. The objective of this proof-of-concept research was to evaluate transformation of aqueous phase RDX and TNT in flow-through electrolytic reactors. Laboratory experiments were conducted using six identical column reactors containing porous media and expanded titanium-mixed-metal-oxide electrodes. Three columns tested TNT transformation and three tested RDXtransformation. Electrode sequence was varied between columns and one column for each contaminant acted as a no-voltage control. Over 97% of TNT and 93% of RDX was transformed in the reactors under sequential oxidation-reduction. Significant accumulation of known degradation intermediates was not observed under sequential oxidation-reduction. Removal of approximately 90% of TNT and 40% of RDX was observed under sequential reduction-oxidation. Power requirements on the order of 3 W/m2 were measured during the experiment. This suggests that an in-situ electrolytic approach may be cost-practical for managing groundwater contaminated with explosive compounds.