In Situ Bioremediation of a Gasoline-Contaminated Vadose Zone: Implications from Direct Observations

In situ bioremediation of a contaminated vadose zone requires implementing hydraulic and chemical conditions that stimulate the development of indigenous bacteria capable of degrading contaminants in the subsurface. We investigated enhanced biostimulation of a gasoline-contaminated deep vadose zone through nutrient- and O–amended water infiltration. A vadose zone monitoring system (VMS) provided real-time observations of the treatment process’s effect on hydrocarbon attenuation. The VMS data included continuous measurements of variations in water content, concentrations and isotopic compositions of methyl -butyl ether and benzene, toluene, ethylbenzene, and xylene in pore-water and gas phases, and concentrations of O and CO in the vadose zone gas phase. Real-time observations from the unsaturated zone enabled interactive adjustment of the remediation strategy and improved biostimulation conditions for biodegradation of the target compounds. In the course of three infiltration events that included infiltration of an O– and nutrient-enriched water solution, a significant reduction in contaminant mass was observed across the unsaturated zone

Bromine and Carbon Isotope Effects during Photolysis of Brominated Phenols

In the present study, carbon and bromine isotope effects during UV-photodegradation of bromophenols in aqueous and ethanolic solutions were determined. An anomalous relatively high inverse bromine isotope fractionation (ε_{reactive position} up to +5.1‰) along with normal carbon isotope effect (ε_{reactive position} of −12.6‰ to −23.4‰) observed in our study may be attributed to coexistence of both mass-dependent and mass-independent isotope fractionation of C–Br bond cleavage. Isotope effects of a similar scale were observed for all the studied reactions in ethanol, and for 4-bromophenol in aqueous solution. This may point out related radical mechanism for these processes. The lack of any carbon and bromine isotope effects during photodegradation of 2-bromophenol in aqueous solution possibly indicates that C–Br bond cleavage is not a rate-limiting step in the reaction. The bromine isotope fractionation, without any detectable carbon isotope effect, that was observed for 3-bromophenol photolysis in aqueous solution probably originates from mass-independent fractionation

A Benchmark Study of Kinetic Isotope Effects and Barrier Heights for the Finkelstein Reaction

Herein, we present a combined (experimental and computational) study of the Finkelstein reaction in condensed phase, where bromine is substituted by iodine in 2-bromoethylbenzene, in the presence of either acetone or acetonitrile as a solvent. Performance of various density functional theory and ab initio methods were tested for reaction barrier heights as well as for bromine and carbon kinetic isotope effects (KIEs). Two different implicit solvation models were examined (PCM and SMD). Theoretically predicted KIEs were compared with experimental values, while reaction barrier heights were assessed using the CCSD­(T)-level and experimental energies as reference. In general, although the tested parameters (energies and KIEs) do not exhibit any substantial difference upon a change of the solvent, the different behavior of the theoretical methods was observed depending on the solvent. With respect to isotope effects, both PCM and SMD seem to perform very similarly, though results obtained with PCM are slightly closer to the experimental values. For predicting reaction barriers, utilization of either PCM or SMD solvation models yielded different results. Functionals from the ωB97 family: ωB97, ωB97X, and ωB97X-D provide the most accurate results for the studied system

The Spatial Distribution of the Microbial Community in a Contaminated Aquitard below an Industrial Zone

The industrial complex Neot Hovav, in Israel, is situated above an anaerobic fractured chalk aquitard, which is polluted by a wide variety of hazardous organic compounds. These include volatile and non-volatile, halogenated, organic compounds. In this study, we characterized the indigenous bacterial population in 17 boreholes of the groundwater environment, while observing the spatial variations in the population and structure as a function of distance from the polluting source. In addition, the de-halogenating potential of the microbial groundwater population was tested through a series of lab microcosm experiments, thus exemplifying the potential and limitations for bioremediation of the site. In all samples, the dominant phylum was Proteobacteria. In the production plant area, the non-obligatory organo-halide respiring bacteria (OHRB) Firmicutes Phylum was also detected in the polluted water, in abundancies of up to 16 %. Non-metric multidimensional scaling (NMDS) analysis of the microbial community structure in the groundwater exhibited clusters of distinct populations following the location in the industrial complex and distance from the polluting source. Dehalogenation of halogenated ethylene was demonstrated in contrast to the persistence of brominated alcohols. Persistence is likely due to the chemical characteristics of brominated alcohols, and not because of the absence of active de-halogenating bacteria

Insights into Generalization of the Rate-Limiting Steps of the Dehalogenation by LinB and DhaA: A Computational Approach

LinB and DhaA are well-known haloalkane dehalogenases (HLDs) capable of converting a plethora of halogenated alkanes, also those considered persistent pollutants. The dehalogenation reaction that these two enzymes catalyze has been studied to determine its rate-limiting step (rls) for the last two decades now. As a result, it has been determined that HLDs can show different rate-limiting steps for individual substrates, and at this point we do not have a basis for any generalization in this matter. Therefore, in this work we aimed at gaining insights into the enzymatic dehalogenation of selected dibromo- and bromochloro- ethanes and propanes by LinB and DhaA using computational approach to determine whether defined structural similarities of the substrates result in a unified mechanism and the same rls. By predicting halogen binding isotope effects (BIEs) as well as computing interaction energy for each HLD-ligand complex the nature of the protein-ligand interactions has been characterized. Furthermore, C and Br kinetic isotope effects (KIEs) as well as the minimum free energy paths (MFEPs) were computed to investigate the chemical reaction for the selected systems. Accuracy of the approach and robustness of the computational predictions were validated by measuring KIEs on the selected reactions. Overall results strongly indicate that any generalization with respect to the enzymatic process involving various ligands in the case of DhaA is impossible, even if the considered ligands are structurally similar as those analyzed in the present study. Moreover, even small structural differences such as changing of one of the (non-leaving) halogen substituents may lead to significant changes in the enzymatic process and result in a different rls in the case of LinB. It has also been demonstrated that KIEs themselves cannot be used as rls indicators in the reactions catalyzed by the studied HLDs

Can Path Integral Molecular Dynamics Make a Good Approximation for Vapor Pressure Isotope Effects Prediction for Organic Solvents? A Comparison to ONIOM QM/MM and QM Cluster Calculation

Isotopic fractionation of volatile organic compounds (VOCs), which are under strict measures of control because of their potential harm to the environment and humans, has an important ecological aspect, as the isotopic composition of compounds may depend on the conditions in which such compounds are distributed in Nature. Therefore, detailed knowledge on isotopic fractionation, not only experimental but also based on theoretical models, is crucial to follow conditions and pathways within which these contaminants are spread throughout the ecosystems. In this work, we present carbon and, for the first time, bromine vapor pressure isotope effect (VPIE) on the evaporation process from pure-phase systemsdibromomethane and bromobenzene, the representatives of aliphatic and aromatic brominated VOCs. We combine isotope effects measurements with their theoretical prediction using three computational techniques, namely path integral molecular dynamics, QM cluster, and hybrid ONIOM models. While evaporation of both compounds resulted in normal bromine VPIEs, the difference in the direction of carbon isotopic fractionation is observed for the aliphatic and aromatic compounds, where VPIEs are inverse and normal, respectively. Even though theoretical models tested here turned out to be insufficient for quantitative agreement with the experimental values, cluster electronic structure calculations, as well as two-layer ONIOM computations, provided better reproduction of experimental trends

Geochemical evidence for iron-mediated anaerobic oxidation of methane

Anaerobic oxidation of methane (AOM) by sulfate has been recognized as a critical process to maintain this greenhouse gas stability by limiting methane flux to the atmosphere. We show geochemical evidence for AOM in deep lake sediments and demonstrate that AOM is likely driven by iron (Fe) reduction. Pore-water profiles from Lake Kinneret (Sea of Galilee, Israel) show that this sink for methane is located below the 20-cm depth in the sediment, which is well below the depths at which nitrate and sulfate are completely exhausted, as well as below the zone of methanogenesis. Iron-dependant AOM was verified by Fe(III)-amended mesocosm studies using intact sediment cores, and native iron oxides were detectable throughout the sediments. Because anaerobic Fe(III) respiration is thermodynamically more favorable than both sulfate-dependent methanotrophy and methanogenesis, its occurrence below the zone of methane production supports the idea that reduction of sedimentary iron oxides is kinetically or biologically limited. Similar conditions are likely to prevail in other incompletely pyritized aquatic sediments, indicating that AOM with Fe(III) is an important global sink for methane

δ¹³C and δ³⁷Cl Isotope Fractionation To Characterize Aerobic vs Anaerobic Degradation of Trichloroethylene

Trichloroethylene (TCE) is a carcinogenic organic chemical impacting water resources worldwide. Its breakdown by reductive vs oxidative degradation involves different types of chemical bonds. Hence, if distinct isotope effects are reflected in dual element (carbon and chlorine) isotope values, such trends could help distinguishing both processes in the environment. This work explored dual element isotope trends associated with TCE oxidation by two pure bacterial cultures: Pseudomonas putida F1 and Methylosinus trichosporium OB3b, where the latter expresses either soluble methane-monooxygenase (sMMO) or particulate methane-monooxygenase (pMMO). Carbon and chlorine isotope enrichment factors of TCE (ε¹³C = −11.5, −2.4, and −4.2‰; ε³⁷Cl = 0.3, −1.3, and −2.4‰, respectively) differed strongly between the strains. The dual element isotope trend for strain F1 (ε¹³C/ε³⁷Cl = −38) reflected, as expected, primary carbon and negligible chlorine isotope effects, whereas unexpectedly large chlorine isotope effects became apparent in the trend obtained with strain OB3b (ε¹³C/ε³⁷Cl = +1.7 for sMMO and pMMO). Therefore, although dual element isotope analysis partly reflects predicted differences in oxidative vs reductive (ε¹³C/ε³⁷Cl = 3.4–5.7) degradation, the unexpected OB3b fractionation data may challenge field interpretation