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.

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.

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.

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.

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.

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.

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.