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

Pilot tests for the optimization of the bioremediation strategy of a multi-layered aquifer at a multi-focus site impacted with chlorinated ethenes

A multi-layered aquifer in an industrial area in the north of the Iberian Peninsula is severely contaminated with the chlorinated ethenes (CEs) tetrachloroethylene, trichloroethylene, cis-1,2-dichloroethylene, and vinyl chloride. Both shallow and deep aquifers are polluted, with two differentiated north and south CEs plumes. Hydrogeochemical and isotopic data (δ13C of CEs) evidenced natural attenuation of CEs. To select the optimal remediation strategy to clean-up the contamination plumes, laboratory treatability studies were performed, which confirmed the intrinsic biodegradation potential of the north and south shallow aquifers to fully dechlorinate CEs to ethene after injection of lactate, but also the combination of lactate and sulfidized mZVI as an alternative treatment for the north deep aquifer. In the lactate-amended microcosms, full dechlorination of CEs was accompanied by an increase in 16S rRNA gene copies of Dehalococcoides and Dehalogenimonas, and the tceA, vcrA and bvcA reductive dehalogenases. Three in situ pilot tests were implemented, which consisted in injections of lactate in the north and south shallow aquifers, and injections of lactate and sulfidized mZVI in the north deep aquifer. The hydrogeochemical, isotopic and molecular analyses used to monitor the pilot tests evidenced that results obtained mimicked the laboratory observations, albeit at different dechlorination rates. It is likely that the efficiency of the injections was affected by the amendment distribution. In addition, monitoring of the pilot tests in the shallow aquifers showed the release of CEs due to back diffusion from secondary sources, which limited the use of isotopic data for assessing treatment efficiency. In the pilot test that combined the injection of lactate and sulfidized mZVI, both biotic and abiotic pathways contributed to the production of ethene. This study demonstrates the usefulness of integrating different chemical, isotopic and biomolecular approaches for a more robust selection and implementation of optimal remediation strategies in CEs polluted sites.

Expanding the calibration range of compound-specific chlorine isotope analysis by the preparation of a 37 Cl-enriched tetrachloroethylene

RATIONALE

The recent development of reliable GC/qMS methods for δ³⁷ Cl compound-specific stable isotope analysis (CSIA) paves the way for dual carbon-chlorine isotope analysis of chlorinated ethenes and thus allows deeper insights into underlying transformation processes/mechanisms. A two-point calibration is indispensable for the precise and correct conversion of raw data to the international δ³⁷ Cl_SMOC scale. The currently available calibration standards for tetrachloroethylene (PCE) span only a very narrow range from -2.52‰ (EIL2) to +0.29‰ (EIL1), which is considerably smaller than observed δ³⁷ Cl isotope enrichment in (bio-)transformation studies (up to 12‰).

METHODS

We describe the preparation and evaluation of a new ³⁷ Cl-enriched PCE standard to avoid bias in δ³⁷ Cl CSIA arising from extrapolation beyond the calibration range. The preparation comprised: (i) partial PCE reduction by zero-valent zinc in a system of PCE, ethanol (initial volume ratio 3/5) and trace amounts of water followed by (ii) liquid-liquid extraction and (iii) a subsequent fractional distillation to purify the ³⁷ Cl-enriched PCE.

RESULTS

The obtained PCE (PCE_enriched ) showed a purity of 98.8% (mole fraction) and a δ³⁷ Cl_SMOC value of +10.8 ± 0.5‰. The evaluation of an experimental dataset with and without extrapolation showed no significant variation.

CONCLUSIONS

The new PCE standard (PCE_enriched ) expands the calibration range to 13.3‰ (previously 2.8‰) and thus prevents potential bias introduced by extrapolation beyond the calibration range.

Multi-element isotopic evidence for monochlorobenzene and benzene degradation under anaerobic conditions in contaminated sediments

Industrial chemicals are frequently detected in sediments due to a legacy of chemical spills. Globally, site remedies for groundwater and sediment decontamination include natural attenuation by in situ abiotic and biotic processes. Compound-specific isotope analysis (CSIA) is a diagnostic tool to identify, quantify, and characterize degradation processes in situ, and in some cases can differentiate between abiotic degradation and biodegradation. This study reports high-resolution carbon, chlorine, and hydrogen stable isotope profiles for monochlorobenzene (MCB), and carbon and hydrogen stable isotope profiles for benzene, coupled with measurements of pore water concentrations in contaminated sediments. Multi-element isotopic analysis of δ¹³C and δ³⁷Cl for MCB were used to generate dual-isotope plots, which for 2 locations at the study site resulted in Λ_C/Cl(130) values of 1.42 ± 0.19 and Λ_C/Cl(131) values of 1.70 ± 0.15, consistent with theoretical calculations for carbon-chlorine bond cleavage (Λ_T = 1.80 ± 0.31) via microbial reductive dechlorination. For benzene, significant δ²H (122‰) and δ¹³C (6‰) depletion trends, followed by enrichment trends in δ¹³C (1.6‰) in the upper part of the sediment, were observed at the same location, indicating not only production of benzene due to biodegradation of MCB, but subsequent biotransformation of benzene itself to nontoxic end-products. Degradation rate constants calculated independently using chlorine isotopic data and carbon isotopic data, respectively, agreed within uncertainty thus providing multiple lines of evidence for in situ contaminant degradation via reductive dechlorination and providing the foundation for a novel approach to determine site-specific in situ rate estimates essential for the prediction of remediation outcomes and timelines.

Simultaneous determination of stable chlorine and bromine isotopic ratios for bromochlorinated trihalomethanes using GC-qMS

Bromochlorinated compounds are organic contaminants originating from different natural and anthropic sources and increasingly found in different environmental compartments. This work presents an online approach for compound specific stable isotope analysis of chlorine and bromine isotope ratios for bromochlorinated trihalomethanes using gas chromatography coupled to quadrupole mass spectrometry (GC-qMS). An evaluation scheme was developed to simultaneously determine stable chlorine and bromine isotope ratios based on the mass spectral data of two target compounds: dibromochloromethane and dichlorobromomethane. The analytical technique was optimized by assessing the impact of different instrumental parameters, including dwell time, split ratios, and ionization energy. Successively, static headspace samples containing the two target compounds at aqueous concentrations ranging from 0.1 mg/L to 5 mg/L were analyzed in order to test the precision and reproducibility of the proposed approach. The results showed a good precision under the optimized instrumental conditions, with relative standard deviations ranging between 0.05% and 0.5% for chlorine and bromine isotope analysis. Finally, the method was tested in a source identification problem in which the simultaneous determination of chlorine and bromine stable isotope ratios allowed the clear distinction of dibromochloromethane from three different manufacturers.

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.

Deciphering the Variability of Stable Isotope (C, Cl) Fractionation of Tetrachloroethene Biotransformation by Desulfitobacterium strains Carrying Different Reductive Dehalogenases Enzymes

Kinetic isotope effects have been used successfully to prove and characterize organic contaminant transformation on various scales including field and laboratory studies. For tetrachloroethene (PCE) biotransformation, however, causes for the substantial variability of reported isotope enrichment factors (ε) are still not deciphered (ε_C = -0.4 to -19.0‰). Factors such as different reaction mechanisms and masking of isotope fractionation by either limited intracellular mass transfer or rate-limitations within the enzymatic multistep reaction are under discussion. This study evaluated the contribution of these factors to the magnitude of carbon and chlorine isotope fractionation of Desulfitobacterium strains harboring three different PCE-transforming enzymes (PCE-RdhA). Despite variable single element isotope fractionation (ε_C = -5.0 to -19.7‰; ε_Cl = -1.9 to -6.3‰), similar slopes of dual element isotope plots (Λ_C/Cl values of 2.4 ± 0.1 to 3.6 ± 0.1) suggest a common reaction mechanism for different PCE-RdhAs. Cell envelope properties of the Desulfitobacterium strains allowed to exclude masking effects due to PCE mass transfer limitation. Our results thus revealed that different rate-limiting steps (e.g., substrate channel diffusion) in the enzymatic multistep reactions of individual PCE-RdhAs rather than different reaction mechanisms determine the extent of PCE isotope fractionation in the Desulfitobacterium genus.

Integrative isotopic and molecular approach for the diagnosis and implementation of an efficient in-situ enhanced biological reductive dechlorination of chlorinated ethenes

Based on the previously observed intrinsic bioremediation potential of a site originally contaminated with perchloroethene (PCE), field-derived lactate-amended microcosms were performed to test different lactate isomers and concentrations, and find clearer isotopic and molecular parameters proving the feasibility of an in-situ enhanced reductive dechlorination (ERD) from PCE-to-ethene (ETH). According to these laboratory results, which confirmed the presence of Dehalococcoides sp. and the vcrA gene, an in-situ ERD pilot test consisting of a single injection of lactate in a monitoring well was performed and monitored for 190 days. The parameters used to follow the performance of the ERD comprised the analysis of i) hydrochemistry, including redox potential (Eh), and the concentrations of redox sensitive species, chlorinated ethenes (CEs), lactate, and acetate; ii) stable isotope composition of carbon of CEs, and sulphur and oxygen of sulphate; and iii) 16S rRNA gene sequencing from groundwater samples. Thus, it was proved that the injection of lactate promoted sulphate-reducing conditions, with the subsequent decrease in Eh, which allowed for the full reductive dechlorination of PCE to ETH in the injection well. The biodegradation of CEs was also confirmed by the enrichment in ¹³C and carbon isotopic mass balances. The metagenomic results evidenced the shift in the composition of the microbial population towards the predominance of fermentative bacteria. Given the success of the in-situ pilot test, a full-scale ERD with lactate was then implemented at the site. After one year of treatment, PCE and trichloroethene were mostly depleted, whereas vinyl chloride (VC) and ETH were the predominant metabolites. Most importantly, the shift of the carbon isotopic mass balances towards more positive values confirmed the complete reductive dechlorination, including the VC-to-ETH reaction step. The combination of techniques used here provides complementary lines of evidence for the diagnosis of the intrinsic biodegradation potential of a polluted site, but also to monitor the progress, identify potential difficulties, and evaluate the success of ERD at the field scale.

Chlorinated ethene plume evolution after source thermal remediation: Determination of degradation rates and mechanisms

The extent, mechanism(s), and rate of chlorinated ethene degradation in a large tetrachloroethene (PCE) plume were investigated in an extensive sampling campaign. Multiple lines of evidence for this degradation were explored, including compound-specific isotope analysis (CSIA), dual C-Cl isotope analysis, and quantitative real-time polymerase chain reaction (qPCR) analysis targeting the genera Dehalococcoides and Dehalogenimonas and the genes vcrA, bvcA, and cerA. A decade prior to this sampling campaign, the plume source was thermally remediated by steam injection. This released dissolved organic carbon (DOC) that stimulated microbial activity and created reduced conditions within the plume. Based on an inclusive analysis of minor and major sampling campaigns since the initial site characterization, it was estimated that reduced conditions peaked 4 years after the remediation event. At the time of this study, 11 years after the remediation event, the redox conditions in the aquifer are returning to their original state. However, the DOC released from the remediated source zone matches levels measured 3 years prior and plume conditions are still suitable for biotic reductive dechlorination. Dehalococcoides spp., Dehalogenimonas spp., and vcrA, bvcA, and cerA reductive dehalogenase genes were detected close to the source, and suggest that complete, biotic PCE degradation occurs here. Further downgradient, qPCR analysis and enriched δ¹³C values for cis-dichloroethene (cDCE) suggest that cDCE is biodegraded in a sulfate-reducing zone in the plume. In the most downgradient portion of the plume, lower levels of specific degraders supported by dual C-Cl analysis indicate that the biodegradation occurs in combination with abiotic degradation. Additionally, 16S rRNA gene amplicon sequencing shows that organizational taxonomic units known to contain organohalide-respiring bacteria are relatively abundant throughout the plume. Hydraulic conductivity testing was also conducted, and local degradation rates for PCE and cDCE were determined at various locations throughout the plume. PCE degradation rates from sampling campaigns after the thermal remediation event range from 0.11 to 0.35 yr^-1. PCE and cDCE degradation rates from the second to the third sampling campaigns ranged from 0.08 to 0.10 yr^-1 and 0.01 to 0.07 yr^-1, respectively. This is consistent with cDCE as the dominant daughter product in the majority of the plume and cDCE degradation as the time-limiting step. The extensive temporal and spatial analysis allowed for tracking the evolution of the plume and the lasting impact of the source remediation and illustrates that the multiple lines of evidence approach is essential to elucidate the primary degradation mechanisms in a plume of such size and complexity.

Mechanistic Dichotomy in Bacterial Trichloroethene Dechlorination Revealed by Carbon and Chlorine Isotope Effects

Tetrachloroethene (PCE) and trichloroethene (TCE) are significant groundwater contaminants. Microbial reductive dehalogenation at contaminated sites can produce nontoxic ethene but often stops at toxic cis-1,2-dichloroethene ( cis-DCE) or vinyl chloride (VC). The magnitude of carbon relative to chlorine isotope effects (as expressed by Λ_C/Cl, the slope of δ¹³C versus δ³⁷Cl regressions) was recently recognized to reveal different reduction mechanisms with vitamin B₁₂ as a model reactant for reductive dehalogenase activity. Large Λ_C/Cl values for cis-DCE reflected cob(I)alamin addition followed by protonation, whereas smaller Λ_C/Cl values for PCE evidenced cob(I)alamin addition followed by Cl^- elimination. This study addressed dehalogenation in actual microorganisms and observed identical large Λ_C/Cl values for cis-DCE (Λ_C/Cl = 10.0 to 17.8) that contrasted with identical smaller Λ_C/Cl for TCE and PCE (Λ_C/Cl = 2.3 to 3.8). For TCE, the trend of small Λ_C/Cl could even be reversed when mixed cultures were precultivated on VC or DCEs and subsequently confronted with TCE (Λ_C/Cl = 9.0 to 18.2). This observation provides explicit evidence that substrate adaptation must have selected for reductive dehalogenases with different mechanistic motifs. The patterns of Λ_C/Cl are consistent with practically all studies published to date, while the difference in reaction mechanisms offers a potential answer to the long-standing question of why bioremediation frequently stalls at cis-DCE.

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.

Stable carbon isotope fractionation of chlorinated ethenes by a microbial consortium containing multiple dechlorinating genes

The study aimed to determine the possible contribution of specific growth conditions and community structures to variable carbon enrichment factors (Ɛ-_carbon) values for the degradation of chlorinated ethenes (CEs) by a bacterial consortium with multiple dechlorinating genes. Ɛ-_carbon values for trichloroethylene, cis-1,2-dichloroethylene, and vinyl chloride were -7.24% ± 0.59%, -14.6% ± 1.71%, and -21.1% ± 1.14%, respectively, during their degradation by a microbial consortium containing multiple dechlorinating genes including tceA and vcrA. The Ɛ-_carbon values of all CEs were not greatly affected by changes in growth conditions and community structures, which directly or indirectly affected reductive dechlorination of CEs by this consortium. Stability analysis provided evidence that the presence of multiple dechlorinating genes within a microbial consortium had little effect on carbon isotope fractionation, as long as the genes have definite, non-overlapping functions.

Isotopic effects of PCE induced by organohalide-respiring bacteria

Reductive dechlorination performed by organohalide-respiring bacteria (OHRB) enables the complete detoxification of certain emerging groundwater pollutants such as perchloroethene (PCE). Environmental samples from a contaminated site incubated in a lab-scale microcosm (MC) study enable documentation of such reductive dechlorination processes. As compound-specific isotope analysis is used to monitor PCE degradation processes, nucleic acid analysis-like 16S-rDNA analysis-can be used to determine the key OHRB that are present. This study applied both methods to laboratory MCs prepared from environmental samples to investigate OHRB-specific isotope enrichment at PCE dechlorination. This method linkage can enhance the understanding of isotope enrichment patterns of distinct OHRB, which further contribute to more accurate evaluation, characterisation and prospection of natural attenuation processes. Results identified three known OHRB genera (Dehalogenimonas, Desulfuromonas, Geobacter) in diverse abundance within MCs. One species of Dehalogenimonas was potentially involved in complete reductive dechlorination of PCE to ethene. Furthermore, the isotopic effects of PCE degradation were clustered and two isotope enrichment factors (ε) (- 11.6‰, - 1.7‰) were obtained. Notably, ε values were independent of degradation rates and kinetics, but did reflect the genera of the dechlorinating OHRB.

Reductive Outer-Sphere Single Electron Transfer Is an Exception Rather than the Rule in Natural and Engineered Chlorinated Ethene Dehalogenation

Chlorinated ethenes (CEs) such as perchloroethylene, trichloroethylene and dichloroethylene are notorious groundwater contaminants. Although reductive dehalogenation is key to their environmental and engineered degradation, underlying reaction mechanisms remain elusive. Outer-sphere reductive single electron transfer (OS-SET) has been proposed for such different processes as Vitamin B₁₂-dependent biodegradation and zerovalent metal-mediated dehalogenation. Compound-specific isotope effect (¹³C/¹²C, ³⁷Cl/³⁵Cl) analysis offers a new opportunity to test these hypotheses. Defined OS-SET model reactants (CO₂ radical anions, S^2--doped graphene oxide in water) caused strong carbon (ε_C = -7.9‰ to -11.9‰), but negligible chlorine isotope effects (ε_Cl = -0.12‰ to 0.04‰) in CEs. Greater chlorine isotope effects were observed in CHCl₃ (ε_C = -7.7‰, ε_Cl = -2.6‰), and in CEs when the exergonicity of C-Cl bond cleavage was reduced in an organic solvent (reaction with arene radical anions in glyme). Together, this points to dissociative OS-SET (SET to a σ* orbital concerted with C-Cl breakage) in alkanes compared to stepwise OS-SET (SET to a π* orbital followed by C-Cl cleavage) in ethenes. The nonexistent chlorine isotope effects of chlorinated ethenes in all aqueous OS-SET experiments contrast strongly with pronounced Cl isotope fractionation in all natural and engineered reductive dehalogenations reported to date suggesting that OS-SET is an exception rather than the rule in environmental transformations of chlorinated ethenes.

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.

Calibration bias of experimentally determined chlorine isotope enrichment factors: the need for a two-point calibration in compound-specific chlorine isotope analysis

RATIONALE

The recent development of compound-specific online chlorine isotope analysis (³⁷ Cl-CSIA) methods has fostered dual chlorine-carbon isotope studies to gain better insights into sources and environmental transformation reactions of chlorinated ethenes. One-point and two-point calibration schemes are currently used to convert raw data to the international δ³⁷ Cl_SMOC scale, but a critical evaluation of best practices to arrive at reliable δ³⁷ Cl_SMOC signatures and enrichment factors was missing and is presented here.

METHODS

Aqueous solutions of neat perchloroethylene and trichloroethylene (TCE) and aqueous samples from a TCE biodegradation experiment with pure cultures of Desulfitobacterium hafniense Y51 were analysed for their chlorine isotope ratios using GC/qMS and GC/IRMS. The δ³⁷ Cl_SMOC values were obtained using one-point and two-point calibration schemes. Chlorine isotope enrichment factors, ε_Cl , were calculated using both approaches and the corresponding bias of δ³⁷ Cl_SMOC values introduced by the different types of calibration was determined.

RESULTS

Different calibration methods resulted in significant differences (up to 30%) in both δ³⁷ Cl signatures and ε_Cl values.

CONCLUSIONS

Our results demonstrate that a two-point calibration together with comprehensive information on reference materials is indispensable and should become standard practice for reliable ³⁷ Cl-CSIA of organic compounds. Copyright © 2016 John Wiley & Sons, Ltd.