Insights into enzyme kinetics of chloroethane biodegradation using compound specific stable isotopes

Dual C-Cl isotope fractionation offers potential to assess biodegradation of 1,2-dichloropropane and 1,2,3-trichloropropane by Dehalogenimonas cultures

1,2-dichloropropane (1,2-DCP) and 1,2,3-trichloropropane (1,2,3-TCP) are hazardous chemicals frequently detected in groundwater near agricultural zones due to their historical use in chlorinated fumigant formulations. In this study, we show that the organohalide-respiring bacterium Dehalogenimonas alkenigignens strain BRE15 M can grow during the dihaloelimination of 1,2-DCP and 1,2,3-TCP to propene and allyl chloride, respectively. Our work also provides the first application of dual isotope approach to investigate the anaerobic reductive dechlorination of 1,2-DCP and 1,2,3-TCP. Stable carbon and chlorine isotope fractionation values for 1,2-DCP (ƐC = -13.6 ± 1.4 ‰ and ƐCl = -27.4 ± 5.2 ‰) and 1,2,3-TCP (ƐC = -3.8 ± 0.6 ‰ and ƐCl = -0.8 ± 0.5 ‰) were obtained resulting in distinct dual isotope slopes (Λ12DCP = 0.5 ± 0.1, Λ123TCP = 4 ± 2). However direct comparison of ΛC-Cl among different substrates is not possible and investigation of the C and Cl apparent kinetic isotope effects lead to the hypothesis that concerted dichloroelimination mechanism is more likely for both compounds. In fact, whole cell activity assays using cells suspensions of the Dehalogenimonas-containing culture grown with 1,2-DCP and methyl viologen as electron donor suggest that the same set of reductive dehalogenases was involved in the transformation of 1,2-DCP and 1,2,3-TCP. This study opens the door to the application of isotope techniques for evaluating biodegradation of 1,2-DCP and 1,2,3-TCP, which often co-occur in groundwaters near agricultural fields.

Investigation of Active Site Amino Acid Influence on Carbon and Chlorine Isotope Fractionation during Reductive Dechlorination

Reductive dehalogenases (RDases) are corrinoid-dependent enzymes that reductively dehalogenate organohalides in respiratory processes. By comparing isotope effects in biotically-catalyzed reactions to reference experiments with abiotic corrinoid-catalysts, compound-specific isotope analysis (CSIA) has been shown to yield valuable insights into enzyme mechanisms and kinetics, including RDases. Here, we report isotopic fractionation (ε) during biotransformation of chloroform (CF) for carbon (εC = -1.52 ± 0.34‰) and chlorine (εCl = -1.84 ± 0.19‰), corresponding to a ΛC/Cl value of 1.13 ± 0.35. These results are highly suppressed compared to isotope effects observed both during CF biotransformation by another organism with a highly similar RDase (> 95% sequence identity) at the amino acid level, and to those observed during abiotic dehalogenation of CF. Amino acid differences occur at four locations within the two different RDases' active sites, and this study examines whether these differences potentially affect the observed εC, εCl, and ΛC/Cl. Structural protein models approximating the locations of the residues elucidate possible controls on reaction mechanisms and/or substrate binding efficiency. These four locations are not conserved among other chloroalkane reducing RDases with high amino acid similarity (> 90%), suggesting that these locations may be important in determining isotope fractionation within this homologous group of RDases.

Implications of regression bias for multi-element isotope analysis for environmental remediation

Measuring changes in the stable isotope ratios of multiple elements (e.g. Δδ¹³C, Δδ³⁷Cl, and Δδ²H) during the (bio)transformation of environmental contaminants has provided new insights into reaction mechanisms and tools to optimize remediation efforts. Dual-isotope analysis, wherein changes in one isotopic system are plotted against another (to derive an interpretational parameter expressed as Λ), is a key tool in multi-element isotopic assessment. To date, most dual-isotope analyses use ordinary linear regression (OLR) for the calculation, which can be subject to regression attenuation and thus an inherent artifact that depresses slope values, expressed as Λ. Here, a series of Monte Carlo simulations were constructed to represent common data conditions and variations within dual-isotope data to test the degree of bias when deriving Λ using OLR compared to an alternative regression technique, the York method. The degree of bias was quantified compared to the modeled or "true" Λ value. For all simulations, the York method provided the least bias in slope estimates (<1%) over all data conditions tested. In contrast, OLR produced unbiased estimates only under a limited set of conditions, which was validated through a mathematical model proof. Both the mathematical model and simulations show that bias of at least 5% in OLR occurs when the extent of enrichment in the x-variable (X_M) is equal to or less than ≈15 times the 1σ precision in the isotope measurement (σ_X), for both Cl/C and C/H plots. The results give practitioners tools to evaluate whether bias is present in data and to estimate the extent to which this negatively impacts the interpretations and predictions of remediation potential for new and previously published datasets. This study demonstrates that integration of such robust statistical tools is essential for dual-isotope interpretations widely used in contaminant hydrogeology but relevant to other disciplines including environmental chemistry and ecology.

Dual C-Cl isotope analysis for characterizing the anaerobic transformation of α, β, γ, and δ-hexachlorocyclohexane in contaminated aquifers

Hexachlorocyclohexanes (HCHs) are widespread and persistent environmental pollutants, which cause heavy contamination in soil, sediment and groundwater. An anaerobic consortium, which was enriched on β-HCH using a soil sample from a contaminated area of a former pesticide factory, was capable to transform α, β, γ, and δ-HCH via tetrachlorocyclohexene isomers stoichiometrically to benzene and chlorobenzene. The carbon and chlorine isotope enrichment factors (ε_C and ε_Cl) of the dehalogenation of the four isomers ranged from -1.9 ± 0.3 to -6.4 ± 0.7‰ and from -1.6 ± 0.2 to -3.2 ± 0.6‰, respectively, and the correlation of δ³⁷Cl and δ¹³C (Λ values) of the four isomers ranged from 1.1 ± 0.1 to 2.4 ± 0.2. The evaluation of Λ and the apparent kinetic isotope effects (AKIE) for carbon and chlorine may lead to the hypothesis that the two eliminated chlorine atoms of α- and γ-HCH were in axial positions, the same as for the β-HCH conformer which has six chlorine atoms in axial positions after ring flip. The dichloroelimination of δ-HCH resulted in distinct AKIE and Λ values as one chlorine atom is in axial whereas the other chlorine atoms are in the equatorial positions. Significant chlorine and carbon isotope fractionations of HCH isomers were observed in the samples from a contaminated aquifer (Bitterfeld, Germany). The ³⁷Cl/³⁵Cl and ¹³C/¹²C isotope fractionation patterns of HCH isomers from laboratory experiments were used diagnostically in a model to characterize microbial dichloroelimination in the field study. The comparison of isotope fractionation patterns indicates that the transformation of HCH isomers at the field was mainly governed by microbial dichloroelimination transformation.

Multi-element (C, H, Cl, Br) stable isotope fractionation as a tool to investigate transformation processes for halogenated hydrocarbons

Compound-specific isotope analysis (CSIA) is a powerful tool to evaluate transformation processes of halogenated compounds. Many halogenated hydrocarbons allow for multiple stable isotopic systems (C, H, Cl, Br) to be measured for a single compound. This has led to a large body of literature describing abiotic and biotic transformation pathways and reaction mechanisms for contaminants such as chlorinated alkenes and alkanes as well as brominated hydrocarbons. Here, the current literature is reviewed and a new compilation of Λ values for multi-isotopic systems for halogenated hydrocarbons is presented. Case studies of each compound class are discussed and thereby the current strengths of multi-element isotope analysis, continuing challenges, and gaps in our current knowledge are identified for practitioners of multi-element CSIA to address in the near future.

Reductive Dehalogenation of Trichloromethane by Two Different Dehalobacter restrictus Strains Reveal Opposing Dual Element Isotope Effects

Trichloromethane (TCM) is a frequently detected and persistent groundwater contaminant. Recent studies have reported that two closely related Dehalobacter strains (UNSWDHB and CF) transform TCM to dichloromethane, with inconsistent carbon isotope effects (ε¹³C_UNSWDHB = -4.3 ± 0.45‰; ε¹³C_CF = -27.5 ± 0.9‰). This study uses dual element compound specific isotope analysis (C; Cl) to explore the underlying differences. TCM transformation experiments using strain CF revealed pronounced normal carbon and chlorine isotope effects (ε¹³C_CF = -27.9 ± 1.7‰; ε³⁷Cl_CF = -4.2 ± 0.2‰). In contrast, small carbon and unprecedented inverse chlorine isotope effects were observed for strain UNSWDHB (ε¹³C_UNSWDHB = -3.1 ± 0.5‰; ε³⁷Cl_UNSWDHB = 2.5 ± 0.3‰) leading to opposing dual element isotope slopes (λ_CF = 6.64 ± 0.14 vs λ_UNSWDHB = -1.20 ± 0.18). Isotope effects of strain CF were identical to experiments with TCM and Vitamin B₁₂ (ε¹³C_Vitamin B12 = -26.0 ± 0.9‰, ε³⁷Cl_Vitamin B12 = -4.0 ± 0.2‰, λ_Vitamin B12 = 6.46 ± 0.20). Comparison to previously reported isotope effects suggests outer-sphere-single-electron transfer or S_N2 as possible underlying mechanisms. Cell suspension and cell free extract experiments with strain UNSWDHB were both unable to unmask the intrinsic KIE of the reductive dehalogenase (TmrA) suggesting that enzyme binding and/or mass-transfer into the periplasm were rate-limiting. Nondirected intermolecular interactions of TCM with cellular material were ruled out as reason for the inverse isotope effect by gas/water and gas/hexadecane partitioning experiments indicating specific, yet uncharacterized interactions must be operating prior to catalysis.

Dual carbon - chlorine isotope fractionation during dichloroelimination of 1,1,2-trichloroethane by an enrichment culture containing Dehalogenimonas sp

Chlorinated ethanes are frequent groundwater contaminants but compound specific isotope analysis (CSIA) has been scarcely applied to investigate their degradation pathways. In this study, dual carbon and chlorine isotope fractionation was used to investigate for the first time the anoxic biodegradation of 1,1,2-trichloroethane (1,1,2-TCA) using a Dehalogenimonas-containing culture. The isotopic fractionation values obtained for the biodegradation of 1,1,2-TCA were ɛ_C = -6.9 ± 0.4‰ and ɛ_Cl = -2.7 ± 0.3‰. The detection of vinyl chloride (VC) as unique byproduct and a closed carbon isotopic mass balance corroborated that dichloroelimination was the degradation pathway used by this strain. Combining the values of δ¹³C and δ³⁷Cl resulted in a dual element C-Cl isotope slope of Λ = 2.5 ± 0.2‰. Investigation of the apparent kinetic isotope effects (AKIEs) expected for cleavage of a CCl bond showed an important masking of the intrinsic isotope fractionation. Theoretical calculation of Λ suggested that dichloroelimination of 1,1,2-TCA was taking place via simultaneous cleavage of two CCl bonds (concerted reaction mechanism). The isotope data obtained in this study can be useful to monitor natural attenuation of 1,1,2-TCA via dichloroelimination and provide insights into the source and fate of VC in contaminated groundwaters.

Two-stage chromium isotope fractionation during microbial Cr(VI) reduction

Chromium isotope fractionation analysis is a promising approach for the assessment of microbial Cr(VI) reduction in groundwater. Understanding the mechanisms and other parameters that control Cr isotope fractionation factors (between the product Cr(III) and reactant Cr (VI)) in microbial Cr(VI) reduction is critical to this application. To date, such studies are very limited. Here, the influence of critical factors on observed Cr isotope fractionation during Cr(VI) reduction by Shewanella oneidensis MR-1 under various conditions was investigated. The Cr(VI) concentration and Cr isotope ratio measurements were conducted on unreacted Cr(VI) remaining in solution to determine Cr isotope fractionation factors. The changes in ambient environmental conditions (e.g., pH, temperature) have limited influence on Cr isotope fractionation factors. However, as a result of Cr(VI) consumption as the experiments proceed, the change in bioavailability of Cr(VI) has a significant impact on Cr isotope fractionation factors. For example, in temperature-controlled experiments, Cr isotope fractionation showed two-stage behavior: during Stage I, the values of ε were -2.81 ± 0.19‰ and -2.60 ± 0.14‰ at 18 °C and 34 °C, respectively; during Stage II, as Cr(VI) reduction progressed, Cr isotope fractionation was significantly masked, and the ε values decreased to -0.98 ± 0.49‰ and -1.01 ± 0.11‰ at 18 °C and 34 °C, respectively. Similar two-stage isotope fractionation behaviors were observed in pH-controlled experiments (pH = 6.0 and 7.2) and in experiments with and without the addition of a competing electron acceptor (nitrate). Masking of isotope fractionation in Stage II indicated restrictions on the bioavailability of Cr(VI) and mass-transfer limitations. This study provides an explanation for the variation in Cr isotope fractionation factors during microbial Cr(VI) reduction in the environment, furthering the viability of Cr isotope ratio analysis as an approach in understanding Cr biogeochemical cycling.

Dual Carbon-Chlorine Isotope Analysis Indicates Distinct Anaerobic Dichloromethane Degradation Pathways in Two Members of Peptococcaceae

Dichloromethane (DCM) is a probable human carcinogen and frequent groundwater contaminant and contributes to stratospheric ozone layer depletion. DCM is degraded by aerobes harboring glutathione-dependent DCM dehalogenases; however, DCM contamination occurs in oxygen-deprived environments, and much less is known about anaerobic DCM metabolism. Some members of the Peptococcaceae family convert DCM to environmentally benign products including acetate, formate, hydrogen (H₂), and inorganic chloride under strictly anoxic conditions. The current study applied stable carbon and chlorine isotope fractionation measurements to the axenic culture Dehalobacterium formicoaceticum and to the consortium RM comprising DCM degrader Candidatus Dichloromethanomonas elyunquensis. Degradation-associated carbon and chlorine isotope enrichment factors (ε_C and ε_Cl) of -42.4 ± 0.7‰ and -5.3 ± 0.1‰, respectively, were measured in D. formicoaceticum cultures. A similar ε_Cl of -5.2 ± 0.1‰, but a substantially lower ε_C of -18.3 ± 0.2‰, were determined for Ca. Dichloromethanomonas elyunquensis. The ε_C and ε_Cl values resulted in distinctly different dual element C-Cl isotope correlations (Λ^C/Cl = Δδ¹³C/Δδ³⁷Cl) of 7.89 ± 0.12 and 3.40 ± 0.03 for D. formicoaceticum and Ca. Dichloromethanomonas elyunquensis, respectively. The distinct Λ^C/Cl values obtained for the two cultures imply mechanistically distinct C-Cl bond cleavage reactions, suggesting that members of Peptococcaceae employ different pathways to metabolize DCM. These findings emphasize the utility of dual carbon-chlorine isotope analysis to pinpoint DCM degradation mechanisms and to provide an additional line of evidence that detoxification is occurring at DCM-contaminated sites.

Branched pathways in the degradation of cDCE by cytochrome P450 in Polaromonas sp. JS666

Compound specific isotope analysis (CSIA) is widely used to monitor contaminant remediation in groundwater. CSIA-based approaches that use enrichment (ε) values to assess degradative processes rely on the assumption that the contaminant being investigated will have an ε value that is constant and specific to a catalytic pathway of a microorganism. Distinct ε values have been reported for aerobic degradation of cis-dichloroethene (cDCE), which has led to a number of proposed degradation mechanisms; however, cytochrome P450 catalyzed oxidation is the only biochemical mechanism that has been established in Polaromonas sp. JS666. Using CSIA we measured the ε values for microbial oxidation of cDCE (-18.8‰±1.5‰) and 1,2-dichloroethane (1,2-DCA) (-16.6‰±0.9‰) in wild-type JS666 and the oxidation of cDCE (-13.5‰±2.3‰) from a recombinant E. coli strain expressing the cytochrome P450 enzyme from JS666. This study supports the hypothesis that cytochrome P450 catalyzes the initial step in the degradation pathway of both cDCE and 1,2-DCA and provides evidence that a single enzyme can catalyze multiple pathways with different products and distinct ε values for a single substrate. Therefore, in cases where the products of the reaction cannot, or have not been characterized, caution must be used when employing ε values to interpret mechanisms, pathways, and their applications to environmental contaminant remediation.

Determining Carbon Kinetic Isotope Effects Using Headspace Analysis of Evolved CO2

Isotope ratio mass spectrometry (IRMS) provides accurate measurements of relative abundance of isotopes of heavy atoms for reactions that are subject to kinetic isotope effects (KIEs). The recent development of compound-specific isotope analysis (CSIA) allows the use of multiple time points that provide data for a rate plot as well as isotope ratios. Utilizing CSIA in enzymology presents opportunities for obtaining heavy atom KIEs in diverse areas.

Distinct Dual C-Cl Isotope Fractionation Patterns during Anaerobic Biodegradation of 1,2-Dichloroethane: Potential To Characterize Microbial Degradation in the Field

This study investigates, for the first time, dual C-Cl isotope fractionation during anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) via dihaloelimination by Dehalococcoides and Dehalogenimonas-containing enrichment cultures. Isotopic fractionation of 1,2-DCA (ε_bulk^C and ε_bulk^Cl) for Dehalococcoides (-33.0 ± 0.4‰ and -5.1 ± 0.1‰) and Dehalogenimonas-containing microcosms (-23 ± 2‰ and -12.0 ± 0.8‰) resulted in distinctly different dual element C-Cl isotope correlations (Λ = Δδ¹³C/Δδ³⁷Cl ≈ ε_bulk^C/ε_bulk^Cl), 6.8 ± 0.2 and 1.89 ± 0.02, respectively. Determined isotope effects and detected products suggest that the difference on the obtained Λ values for biodihaloelimination could be associated with a different mode of concerted bond cleavage rather than two different reaction pathways (i.e., stepwise vs concerted). Λ values of 1,2-DCA were, for the first time, determined in two field sites under reducing conditions (2.1 ± 0.1 and 2.2 ± 2.9). They were similar to the one obtained for the Dehalogenimonas-containing microcosms (1.89 ± 0.02) and very different from those reported for aerobic degradation pathways in a previous laboratory study (7.6 ± 0.1 and 0.78 ± 0.03). Thus, this study illustrates the potential of a dual isotope analysis to differentiate between aerobic and anaerobic biodegradation pathways of 1,2-DCA in the field and suggests that this approach might also be used to characterize dihaloelimination of 1,2-DCA by different bacteria, which needs to be confirmed in future studies.

Experimental Determination of Isotope Enrichment Factors - Bias from Mass Removal by Repetitive Sampling

Application of compound-specific stable isotope approaches often involves comparisons of isotope enrichment factors (ε). Experimental determination of ε-values is based on the Rayleigh equation, which relates the change in measured isotope ratios to the decreasing substrate fractions and is valid for closed systems. Even in well-controlled batch experiments, however, this requirement is not necessarily fulfilled, since repetitive sampling can remove a significant fraction of the analyte. For volatile compounds the need for appropriate corrections is most evident, and various methods have been proposed to account for mass removal and for volatilization into the headspace. In this study we use both synthetic and experimental data to demonstrate that the determination of ε-values according to current correction methods is prone to considerable systematic errors even in well-designed experimental setups. Application of inappropriate methods may lead to incorrect and inconsistent ε-values entailing misinterpretations regarding the processes underlying isotope fractionation. In fact, our results suggest that artifacts arising from inappropriate data evaluation might contribute to the variability of published ε-values. In response, we present novel, adequate methods to eliminate systematic errors in data evaluation. A model-based sensitivity analysis serves to reveal the most crucial experimental parameters and can be used for future experimental design to obtain correct ε-values allowing mechanistic interpretations.

Concentration effects on biotic and abiotic processes in the removal of 1,1,2-trichloroethane and vinyl chloride using carbon-amended ZVI

A permeable reactive barrier, consisting of both zero valent iron (ZVI) and a biodegradable organic carbon, was evaluated for the remediation of 1,1,2-trichloroethane (1,1,2-TCA) contaminated groundwater. During an 888 day laboratory column study, degradation rates initially stabilized with a degradation half-life of 4.4±0.4 days. Based on the accumulation of vinyl chloride (VC) and limited production of 1,1-dichloroethene (1,1-DCE) and 1,2-dichloroethane (1,2-DCA), the dominant degradation pathway was likely abiotic dichloroelimination to form VC. Degradation of VC was not observed based on the accumulation of VC and limited ethene production. After a step reduction in the influent concentration of 1,1,2-TCA from 170±20 mg L(-1) to 39±11 mg L(-1), the degradation half-life decreased 5-fold to 0.83±0.17 days. The isotopic enrichment factor of 1,1,2-TCA also changed after the step reduction from -14.6±0.7‰ to -0.72±0.12‰, suggesting a possible change in the degradation mechanism from abiotic reductive degradation to biodegradation. Microbiological data suggested a co-culture of Desulfitobacterium and Dehalococcoides was responsible for the biodegradation of 1,1,2-TCA to ethene.

Use of dual carbon-chlorine isotope analysis to assess the degradation pathways of 1,1,1-trichloroethane in groundwater

Compound-specific isotope analysis (CSIA) is a powerful tool to track contaminant fate in groundwater. However, the application of CSIA to chlorinated ethanes has received little attention so far. These compounds are toxic and prevalent groundwater contaminants of environmental concern. The high susceptibility of chlorinated ethanes like 1,1,1-trichloroethane (1,1,1-TCA) to be transformed via different competing pathways (biotic and abiotic) complicates the assessment of their fate in the subsurface. In this study, the use of a dual C-Cl isotope approach to identify the active degradation pathways of 1,1,1-TCA is evaluated for the first time in an aerobic aquifer impacted by 1,1,1-TCA and trichloroethylene (TCE) with concentrations of up to 20 mg/L and 3.4 mg/L, respectively. The reaction-specific dual carbon-chlorine (C-Cl) isotope trends determined in a recent laboratory study illustrated the potential of a dual isotope approach to identify contaminant degradation pathways of 1,1,1-TCA. Compared to the dual isotope slopes (Δδ(13)C/Δδ(37)Cl) previously determined in the laboratory for dehydrohalogenation/hydrolysis (DH/HY, 0.33 ± 0.04) and oxidation by persulfate (∞), the slope determined from field samples (0.6 ± 0.2, r(2) = 0.75) is closer to the one observed for DH/HY, pointing to DH/HY as the predominant degradation pathway of 1,1,1-TCA in the aquifer. The observed deviation could be explained by a minor contribution of additional degradation processes. This result, along with the little degradation of TCE determined from isotope measurements, confirmed that 1,1,1-TCA is the main source of the 1,1-dichlorethylene (1,1-DCE) detected in the aquifer with concentrations of up to 10 mg/L. This study demonstrates that a dual C-Cl isotope approach can strongly improve the qualitative and quantitative assessment of 1,1,1-TCA degradation processes in the field.

Resiliency of Stable Isotope Fractionation (δ(13)C and δ(37)Cl) of Trichloroethene to Bacterial Growth Physiology and Expression of Key Enzymes

Quantification of in situ (bio)degradation using compound-specific isotope analysis requires a known and constant isotope enrichment factor (ε). Because reported isotope enrichment factors for microbial dehalogenation of chlorinated ethenes vary considerably we studied the potential effects of metabolic adaptation to TCE respiration on isotope fractionation (δ(13)C and δ(37)Cl) using a model organism (Desulfitobacterium hafniesne Y51), which only has one reductive dehalogenase (PceA). Cells grown on TCE for the first time showed exponential growth until 10(9) cells/mL. During exponential growth, the cell-normalized amount of PceA enzyme increased steadily in the presence of TCE (up to 21 pceA transcripts per cell) but not with alternative substrates (<1 pceA transcript per cell). Cultures initially transferred or subcultivated on TCE showed very similar isotope fractionation, both for carbon (εcarbon: -8.6‰ ± 0.3‰ or -8.8‰ ± 0.2‰) and chlorine (εchlorine: -2.7‰ ± 0.3‰) with little variation (0.7‰) for the different experimental conditions. Thus, TCE isotope fractionation by D. hafniense strain Y51 was affected by neither growth phase, pceA transcription, or translation, nor by PceA content per cell, suggesting that transport limitations did not affect isotope fractionation. Previously reported variable ε values for other organohalide-respiring bacteria might thus be attributed to different expression levels of their multiple reductive dehalogenases.

Carbon isotopic fractionation during biodegradation of phthalate esters in anoxic condition

Here we evaluate the quantitative relationship between carbon isotopic fractionation and anoxic biodegradation of phthalate esters (PAEs), a kind of endocrine disruptors. The stable carbon isotope delta values (δ(13)C) of 4 PAEs, i.e. di-methyl phthalate (DMP), di-ethyl phthalate (DEP), di-n-butyl phthalate (DBP), and di-iso-butyl phthalate (DiBP), were analyzed during biodegradation by a pure bacteria strain isolated from the shallow aquifer sediment in anoxic condition. Results showed that the carbon isotopic fractionation in the initial degradation of PAEs was well-described by the Rayleigh equation model with R(2) from 0.8885 to 0.9821. The carbon isotopic fractionation (ε) for DMP and DEP were -4.6±0.4‰ and -2.9±0.1‰, respectively, while DBP and DiBP showed limited isotopic fractionation. A linear relationship between ε values and the total carbon atoms present in straight-carbon-chain PAE molecules with R(2) of 0.9918. The apparent kinetic isotope effects (AKIEs) were calculated for proposed 4 initial transformation pathways of PAEs. The high carbon AKIEs of 1.048 and 1.036 were obtained for single enzymatic hydrolysis of DMP and DEP, respectively, and fell in the expected KIE range of 1.03-1.09. However, the intrinsic carbon isotope effects for enzymatic hydrolysis of DBP and DiBP might be masked.

Substrate hydrophobicity and cell composition influence the extent of rate limitation and masking of isotope fractionation during microbial reductive dehalogenation of chlorinated ethenes

This study investigated the effect of intracellular microscale mass transfer on microbial carbon isotope fractionation of tetrachloroethene (PCE) and trichloroethene (TCE). Significantly stronger isotope fractionation was observed for crude extracts vs intact cells of Sulfurospirillum multivorans, Geobacter lovleyi, Desulfuromonas michiganensis, Desulfitobacterium hafniense strain PCE-S, and Dehalobacter restrictus. Furthermore, carbon stable isotope fractionation was stronger for microorganisms with a Gram-positive cell envelope compared to those with a Gram-negative cell envelope. Significant differences were observed between model organisms in cellular sorption capacity for PCE (S. multivorans-K(d-PCE) = 0.42-0.51 L g(-1); D. hafniense-K(d-PCE) = 0.13 L g(-1)), as well as in envelope hydrophobicity (S. multivorans 33.0° to 72.2°; D. hafniense 59.1° to 60.8°) when previously cultivated with fumarate or PCE as electron acceptor, but not for TCE. Cell envelope properties and the tetrachloroethene reductive dehalogenase (PceA-RDase) localization did not result in significant effects on observed isotope fractionation of TCE. For PCE, however, systematic masking of isotope effects as a result of microscale mass transfer limitation at microbial membranes was observed, with carbon isotope enrichment factors of -2.2‰, -1.5 to -1.6‰, and -1.0‰ (CI95% < ± 0.2‰) for no membrane, hydrophilic outer membrane, and outer + cytoplasmic membrane, respectively. Conclusively, rate-limiting mass transfer barriers were (a) the outer membrane or cell wall and (b) the cytoplasmic membrane in case of a cytoplasmic location of the RDase enzyme. Overall, our results indicate that masking of isotope fractionation is determined by (1) hydrophobicity of the degraded compound, (2) properties of the cell envelope, and (3) the localization of the reacting enzyme.

C and Cl isotope fractionation of 1,2-dichloroethane displays unique δ¹³C/δ³⁷Cl patterns for pathway identification and reveals surprising C-Cl bond involvement in microbial oxidation

This study investigates dual element isotope fractionation during aerobic biodegradation of 1,2-dichloroethane (1,2-DCA) via oxidative cleavage of a C-H bond (Pseudomonas sp. strain DCA1) versus C-Cl bond cleavage by S(N)2 reaction (Xanthobacter autotrophicus GJ10 and Ancylobacter aquaticus AD20). Compound-specific chlorine isotope analysis of 1,2-DCA was performed for the first time, and isotope fractionation (ε(bulk)(Cl)) was determined by measurements of the same samples in three different laboratories using two gas chromatography-isotope ratio mass spectrometry systems and one gas chromatography-quadrupole mass spectrometry system. Strongly pathway-dependent slopes (Δδ13C/Δδ37Cl), 0.78 ± 0.03 (oxidation) and 7.7 ± 0.2 (S(N)2), delineate the potential of the dual isotope approach to identify 1,2-DCA degradation pathways in the field. In contrast to different ε(bulk)(C) values [-3.5 ± 0.1‰ (oxidation) and -31.9 ± 0.7 and -32.0 ± 0.9‰ (S(N)2)], the obtained ε(bulk)(Cl) values were surprisingly similar for the two pathways: -3.8 ± 0.2‰ (oxidation) and -4.2 ± 0.1 and -4.4 ± 0.2‰ (S(N)2). Apparent kinetic isotope effects (AKIEs) of 1.0070 ± 0.0002 (13C-AKIE, oxidation), 1.068 ± 0.001 (13C-AKIE, S(N)2), and 1.0087 ± 0.0002 (37Cl-AKIE, S(N)2) fell within expected ranges. In contrast, an unexpectedly large secondary 37Cl-AKIE of 1.0038 ± 0.0002 reveals a hitherto unrecognized involvement of C-Cl bonds in microbial C-H bond oxidation. Our two-dimensional isotope fractionation patterns allow for the first time reliable 1,2-DCA degradation pathway identification in the field, which unlocks the full potential of isotope applications for this important groundwater contaminant.

Stable carbon isotope analysis to distinguish biotic and abiotic degradation of 1,1,1-trichloroethane in groundwater sediments

The fate and treatability of 1,1,1-TCA by natural and enhanced reductive dechlorination was studied in laboratory microcosms. The study shows that compound-specific isotope analysis (CSIA) identified an alternative 1,1,1-TCA degradation pathway that cannot be explained by assuming biotic reductive dechlorination. In all biotic microcosms 1,1,1-TCA was degraded with no apparent increase in the biotic degradation product 1,1-DCA. 1,1,1-TCA degradation was documented by a clear enrichment in (13)C in all biotic microcosms, but not in the abiotic control, which suggests biotic or biotically mediated degradation. Biotic degradation by reductive dechlorination of 1,1-DCA to CA only occurred in bioaugmented microcosms and in donor stimulated microcosms with low initial 1,1,1-TCA or after significant decrease in 1,1,1-TCA concentration (after∼day 200). Hence, the primary degradation pathway for 1,1,1-TCA does not appear to be reductive dechlorination via 1,1-DCA. In the biotic microcosms, the degradation of 1,1,1-TCA occurred under iron and sulfate reducing conditions. Biotic reduction of iron and sulfate likely resulted in formation of FeS, which can abiotically degrade 1,1,1-TCA. Hence, abiotic degradation of 1,1,1-TCA mediated by biotic FeS formation constitute an explanation for the observed 1,1,1-TCA degradation. This is supported by a high 1,1,1-TCA (13)C enrichment factor consistent with abiotic degradation in biotic microcosms. 1,1-DCA carbon isotope field data suggest that this abiotic degradation of 1,1,1-TCA is a relevant process also at the field site.

Distinct carbon isotope fractionation during anaerobic degradation of dichlorobenzene isomers

Chlorinated benzenes are ubiquitous organic contaminants found in groundwater and soils. Compound specific isotope analysis (CSIA) has been increasingly used to assess natural attenuation of chlorinated contaminants, in which anaerobic reductive dechlorination plays an essential role. In this work, carbon isotope fractionation of the three dichlorobenzene (DCB) isomers was investigated during anaerobic reductive dehalogenation in methanogenic laboratory microcosms. Large isotope fractionation of 1,3-DCB and 1,4-DCB was observed while only a small isotope effect occurred for 1,2-DCB. Bulk enrichment factors (εbulk) were determined from a Rayleigh model: -0.8 ± 0.1 ‰ for 1,2-DCB, -5.4 ± 0.4 ‰ for 1,3-DCB, and -6.3 ± 0.2 ‰ for 1,4-DCB. εbulk values were converted to apparent kinetic isotope effects for carbon (AKIE) in order to characterize the carbon isotope effect at the reactive positions for the DCB isomers. AKIE values are 1.005 ± 0.001, 1.034 ± 0.003, and 1.039 ± 0.001 for 1,2-DCB, 1,3-DCB, and 1,4-DCB, respectively. The large difference in AKIE values between 1,2-DCB and 1,3-DCB (or 1,4-DCB) suggests distinct reaction pathways may be involved for different DCB isomers during microbial reductive dechlorination by the methanogenic cultures.

Carbon isotope fractionation of 1,1,1-trichloroethane during base-catalyzed persulfate treatment

The extent of carbon isotope fractionation during degradation of 1,1,1-trichloroethane (1,1,1-TCA) by a base-catalyzed persulfate (S₂O₈(2-)) treatment system was investigated. Significant destruction of 1,1,1-TCA was observed at a pH of ∼12. An increase in the NaOH:S₂O₈(2-) molar ratio from 0.2:1 to 8:1 enhanced the reaction rate of 1,1,1-TCA by a factor of ∼5 to yield complete (>99.9%) destruction. An average carbon isotope enrichment fractionation factor which was independent of the NaOH:S₂O₈(2-) molar ratio of -7.0 ± 0.2‰ was obtained. This significant carbon isotope fractionation and the lack of dependence on changes in the NaOH:S₂O₈(2-) molar ratio demonstrates that carbon isotope analysis can potentially be used in situ as a performance assessment tool to estimate the degradation effectiveness of 1,1,1-TCA by a base-catalyzed persulfate system.

Pressure-monitored headspace analysis combined with compound-specific isotope analysis to measure isotope fractionation in gas-producing reactions

RATIONALE

Processes that lead to pressure changes in closed experimental systems can dramatically increase the total uncertainty in enrichment factors (ε) based on headspace analysis and compound-specific isotope analysis (CSIA). We report: (1) A new technique to determine ε values for non-isobaric processes, and (2) a general approach to evaluate the experimental error in calculated ε values.

METHODS

ε values were determined by monitoring the change in headspace pressure from the production of CO2 in a decarboxylation reaction using a pressure gauge and measuring the δ(13) C values using CSIA. The statistical error was assessed over shorter reaction progress intervals to evaluate the impact of experimental error on the total uncertainty associated with calculated ε values.

RESULTS

As an alternative to conventional compositional analysis, calculation of CO2 produced during the reaction monitored with a pressure gauge resulted in rate constants and ε values with improved correlation coefficients and confidence intervals for a non-isobaric process in a closed system. Further, statistical evaluation of the ε values as a function of reaction progress showed that uncertainty in data points for reaction progress (f) at late stages of the reaction can have a significant impact on the reported ε value.

CONCLUSIONS

Pressure-monitored headspace analysis reduces the uncertainty associated with monitoring the reaction progress (f) based on estimating substrate removal and headspace dilution during sampling. Statistical calculations over shorter intervals should be used to evaluate the total error for reported ε values.

Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis

The degradation of chlorinated ethenes and ethanes in clay till was investigated at a contaminated site (Vadsby, Denmark) by high resolution sampling of intact cores combined with groundwater sampling. Over decades of contamination, bioactive zones with degradation of trichloroethene (TCE) and 1,1,1-trichloroethane (1,1,1-TCA) to 1,2-cis-dichloroethene (cis-DCE) and 1,1-dichloroethane, respectively, had developed in most of the clay till matrix. Dehalobacter dominated over Dehalococcoides (Dhc) in the clay till matrix corresponding with stagnation of sequential dechlorination at cis-DCE. Sporadically distributed bioactive zones with partial degradation to ethene were identified in the clay till matrix (thickness from 0.10 to 0.22 m). In one sub-section profile the presence of Dhc with the vcrA gene supported the occurrence of degradation of cis-DCE and VC, and in another enriched δ(13)C for TCE, cis-DCE and VC documented degradation. Highly enriched δ(13)C for 1,1,1-TCA (25‰) and cis-DCE (-4‰) suggested the occurrence of abiotic degradation in a third sub-section profile. Due to fine scale heterogeneity the identification of active degradation zones in the clay till matrix depended on high resolution subsampling of the clay till cores. The study demonstrates that an integrated approach combining chemical analysis, molecular microbial tools and compound specific isotope analysis (CSIA) was required in order to document biotic and abiotic degradations in the clay till system.

Large carbon isotope fractionation during biodegradation of chloroform by Dehalobacter cultures

Compound specific isotope analysis (CSIA) has been applied to monitor bioremediation of groundwater contaminants and provide insight into mechanisms of transformation of chlorinated ethanes. To date there is little information on its applicability for chlorinated methanes. Moreover, published enrichment factors (ε) observed during the biotic and abiotic degradation of chlorinated alkanes, such as carbon tetrachloride (CT); 1,1,1-trichloroethane (1,1,1-TCA); and 1,1-dichloroethane (1,1-DCA), range from -26.5‰ to -1.8‰ and illustrate a system where similar C-Cl bonds are cleaved but significantly different isotope enrichment factors are observed. In the current study, biotic degradation of chloroform (CF) to dichloromethane (DCM) was carried out by the Dehalobacter containing culture DHB-CF/MEL also shown to degrade 1,1,1-TCA and 1,1-DCA. The carbon isotope enrichment factor (ε) measured during biodegradation of CF was -27.5‰ ± 0.9‰, consistent with the theoretical maximum kinetic isotope effect for C-Cl bond cleavage. Unlike 1,1,1-TCA and 1,1-DCA, reductive dechlorination of CF by the Dehalobacter-containing culture shows no evidence of suppression of the intrinsic maximum kinetic isotope effect. Such a large fractionation effect, comparable to those published for cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC) suggests CSIA has significant potential to identify and monitor biodegradation of CF, as well as important implications for recent efforts to fingerprint natural versus anthropogenic sources of CF in soils and groundwater.

Monitoring biodegradation of ethene and bioremediation of chlorinated ethenes at a contaminated site using compound-specific isotope analysis (CSIA)

Chlorinated ethenes are commonly found in contaminated groundwater. Remediation strategies focus on transformation processes that will ultimately lead to nontoxic products. A major concern with these strategies is the possibility of incomplete dechlorination and accumulation of toxic daughter products (cis-1,2-dichloroethene (cDCE), vinyl chloride (VC)). Ethene mass balance can be used as a direct indicator to assess the effectiveness of dechlorination. However, the microbial processes that affect ethene are not well characterized and poor mass balance may reflect biotransformation of ethene rather than incomplete dechlorination. Microbial degradation of ethene is commonly observed in aerobic systems but fewer cases have been reported in anaerobic systems. Limited information is available on the isotope enrichment factors associated with these processes. Using compound-specific isotope analysis (CSIA) we determined the enrichment factors associated with microbial degradation of ethene in anaerobic microcosms (ε = -6.7‰ ± 0.4‰, and -4.0‰ ± 0.8‰) from cultures collected from the Twin Lakes wetland area at the Savannah River site in Georgia (United States), and in aerobic microcosms (ε = -3.0‰ ± 0.3‰) from Mycobacterium sp. strain JS60. Under anaerobic and aerobic conditions, CSIA can be used to determine whether biotransformation of ethene is occurring in addition to biodegradation of the chlorinated ethenes. Using δ(13)C values determined for ethene and for chlorinated ethenes at a contaminated field site undergoing bioremediation, this study demonstrates how CSIA of ethene can be used to reduce uncertainty and risk at a site by distinguishing between actual mass balance deficits during reductive dechlorination and apparent lack of mass balance that is related to biotransformation of ethene.

Pathway-dependent isotope fractionation during aerobic and anaerobic degradation of monochlorobenzene and 1,2,4-trichlorobenzene

Stable carbon isotope fractionation is a valuable tool for monitoring natural attenuation and to establish the fate of groundwater contaminants. In this study, we measured carbon isotope fractionation during aerobic and anaerobic degradation of two chlorinated benzenes: monochlorobenzene (MCB) and 1,2,4-trichlorobenzene (1,2,4-TCB). MCB isotope fractionation was measured in anaerobic methanogenic microcosms, while 1,2,4-TCB isotope experiments were carried out in both aerobic and anaerobic microcosms. Large isotope fractionation was observed in both the anaerobic microcosm experiments. Enrichment factors (ε) for anaerobic reductive dechlorination of MCB and 1,2,4-TCB were -5.0‰ ± 0.2‰ and -3.0‰ ± 0.4‰, respectively. In contrast, no significant isotope fractionation was found during aerobic microbial degradation of 1,2,4-TCB. The cleavage of a C-Cl σ bond occurs during anaerobic reductive dechlorination of MCB and 1,2,4-TCB, while no σ bond cleavage is involved during aerobic degradation via dioxygenase. The difference in isotope fractionation for aerobic versus anaerobic biodegradation of MCB and 1,2,4-TCB can be explained by the difference in the initial step of aerobic versus anaerobic biodegradation pathways.

Natural and enhanced anaerobic degradation of 1,1,1-trichloroethane and its degradation products in the subsurface--a critical review

1,1,1-Trichloroethane (TCA) in groundwater is susceptible to a variety of natural degradation mechanisms. Evidence of intrinsic decay of TCA in aquifers is commonly observed; however, TCA remains a persistent pollutant at many sites and some of the daughter products that accumulate from intrinsic decay of TCA have been determined to be more toxic than the parent compound. Research advances from the past decade indicate that in situ enhanced reductive dechlorination (ERD) offers promise as a cost-effective solution toward the cleanup of groundwater contaminated with TCA and its transformation daughter products. Laboratory studies have demonstrated that pure or mixed cultures containing certain Dehalobacter (Dhb) bacteria can catalyze respiratory dechlorination of TCA and 1,1-dichloroethane (1,1-DCA) to monochloroethane (CA) in groundwater systems. 16S rRNA Dhb gene probes have been used as biomarkers in groundwater samples to both assess ERD potential and quantify growth of Dhb in ERD applications at TCA sites. Laboratory findings suggest that iron-bearing minerals and methanogenic bacteria that co-occur in reduced aquifers may synergistically affect dechlorination of TCA. Despite these advances, a number of significant challenges remain, including an inability of any known cultures to completely dechlorinate TCA to ethane. CA is commonly observed as a terminal product of the biological reductive dechlorination of TCA and 1,1-DCA. Also important is the lack of rigorous field studies demonstrating the utility of bioaugmentation with Dhb cultures for remediation of TCA in the field. In this paper we review the state-of-the-science of TCA degradation in aquifers, examining results from both laboratory experiments and twenty-two field case studies, focusing on the capabilities and limits of ERD technology, and identifying aspects of the technology that warrant further development.