Chlorinated Ethene Reactivity with Vitamin B12 Is Governed by Cobalamin Chloroethylcarbanions as Crossroads of Competing Pathways

Controlled electrocatalysis of the dechlorination and detoxification of chlorinated ethylenes to avoid production of highly toxic intermediates

In this study, electrochemical dechlorination and detoxification of a mixture of chlorinated ethylenes was investigated under various conditions using a double monoatomic synergistic metal catalytic cathode. Electrocatalytic degradation of mixed chlorinated with stepwise voltage and alternating current exhibited excellent dechlorination efficiency. The removal ratios of 1,2-dichloroethylene (1,2-DCE), trichloroethylene (TCE), and tetrachloroethylene (PCE) reached 78.79 %, 79.27 %, and 93.44 % in 10 min, and 98.14 %, 97.56 %, and 98.70 % in 30 min, respectively. The toxicity was evaluated using a quantitative structure-activity relationship model. The cumulative toxicity was reduced to 8.00 % of the initial cumulative toxicity in 30 min. An electrochemical dechlorination strategy for selective degradation and detoxification of mixtures of chlorinated pollutants is proposed. Controlled dechlorination and detoxification under low-voltage control avoided the accumulation of toxic intermediates. Cumulative toxicity was reduced by strategies of selective dechlorination, and segmented and alternating current decreased the energy consumption. The strategy provides a basis for alternating current electrocatalytic dechlorination associated with mixed chlorinated pollutants treatment.

Understanding the sources, function, and irreplaceable role of cobamides in organohalide-respiring bacteria

Halogenated organic compounds are persistent pollutants that pose a serious threat to human health and the safety of ecosystems. Cobamides are essential cofactors for reductive dehalogenases (RDase) in organohalide-respiring bacteria (OHRB), which catalyze the dehalogenation process. This review systematically summarizes the impact of cobamides on organohalide respiration. The catalytic processes of cobamide in dehalogenation processes are also discussed. Additionally, we examine OHRB, which cannot synthesize cobamide and must obtain it from the environment through a salvage pathway; the co-culture with cobamide producer is more beneficial and possible. This review aims to help readers better understand the importance and function of cobamides in reductive dehalogenation. The presented information can aid in the development of bioremediation strategies.

Comprehensive exploration of the anaerobic biotransformation of polychlorinated biphenyls in Dehalococcoides mccartyi CG1: Kinetics, enantioselectivity, and isotope fractionation

Anaerobic microbial transformation is a key pathway in the natural attenuation of polychlorinated biphenyls (PCBs). Much less is known about the transformation behaviors induced by pure organohalide-respiring bacteria, especially kinetic isotope effects. Therefore, the kinetics, pathways, enantioselectivity, and carbon and chlorine isotope fractionation of PCBs transformation by Dehalococcoides mccartyi CG1 were comprehensively explored. The results indicated that the PCBs were mainly dechlorinated via removing their double-flanked meta-chlorine, with their first-order kinetic constants following the order of PCB132 > PCB174 > PCB85 > PCB183 > PCB138. However, PCBs occurred great loss of stoichiometric mass balance during microbial transformation, suggesting the generation of other non-dehalogenation products and/or stable intermediates. The preferential transformation of (-)-atropisomers and generation of (+)-atropisomers were observed during PCB132 and PCB174 biotransformation with the enantiomeric enrichment factors of -0.8609 ± 0.1077 and -0.4503 ± 0.1334 (first half incubation times)/-0.1888 ± 0.1354 (second half incubation times), respectively, whereas no enantioselectivity occurred during PCB183 biotransformation. More importantly, although there was no carbon and chlorine isotope fractionation occurring for studied substrates, the δ13C values of dechlorination products, including PCB47 (-28.15 ± 0.35‰ ∼ -27.77 ± 0.20‰), PCB91 (-36.36 ± 0.09‰ ∼ -34.71 ± 0.49‰), and PCB149 (-28.08 ± 0.26‰ ∼ -26.83 ± 0.10‰), were all significantly different from those of their corresponding substrates (PCB85: -30.81 ± 0.02‰ ∼ -30.22 ± 0.21‰, PCB132: -33.57 ± 0.15‰ ∼ -33.13 ± 0.14‰, and PCB174: -26.30 ± 0.09‰ ∼ -26.01 ± 0.07‰), which further supported the generation of other non-dehalogenation products and/or stable intermediates with enrichment or depletion of 13C. These findings provide deeper insights into the anaerobic microbial transformation behaviors of PCBs.

Insight into the Mechanism Underlying Dehalococcoides mccartyi Strain CBDB1-Mediated B12-Dependent Aromatic Reductive Dehalogenation

Anaerobic bacteria transform aromatic halides through reductive dehalogenation. This dehalorespiration is catalyzed by the supernucleophilic coenzyme vitamin B₁₂, cob(I)alamin, in reductive dehalogenases. So far, the underlying inner-sphere electron transfer (ET) mechanism has been discussed controversially. In the present study, all 36 chloro-, bromo-, and fluorobenzenes and full-size cobalamin are analyzed at the quantum chemical density functional theory level with respect to a wide range of theoretically possible inner-sphere ET mechanisms. The calculated reaction free energies within the framework of Co^I···X (X = F, Cl, and Br) attack rule out most of the inner-sphere pathways. The only route with feasible energetics is a proton-coupled two-ET mechanism that involves a B₁₂ side-chain tyrosine (modeled by phenol) as a proton donor. For 12 chlorobenzenes and 9 bromobenzenes with experimental data from Dehalococcoides mccartyi strain CBDB1, the newly proposed PC-TET mechanism successfully discriminates 16 of 17 active from 4 inactive substrates and correctly predicts the observed regiospecificity to 100%. Moreover, fluorobenzenes are predicted to be recalcitrant in agreement with experimental findings. Conceptually, based on the Bell-Evans-Polanyi principle, the computational approach provides novel mechanistic insights and may serve as a tool for predicting the energetic feasibility of reductive aromatic dehalogenation.

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.

Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review

Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.

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.

Exploring Mechanisms of Biotic Chlorinated Alkane Reduction: Evidence of Nucleophilic Substitution (SN2) with Vitamin B12

Chlorinated alkanes are notorious groundwater contaminants. Their natural reductive dechlorination by microorganisms involves reductive dehalogenases (RDases) containing cobamide as a cofactor. However, underlying mechanisms of reductive dehalogenation have remained uncertain. Here, observed products, radical trap experiments, UV-vis, and mass spectra demonstrate that (i) reduction by cobalamin (vitamin B₁₂) involved chloroalkyl-cobalamin complexes (ii) whose formation involved a second-order nucleophilic substitution (S_N2). Dual element isotope analysis subsequently linked insights from our model system to microbial reductive dehalogenation. Identical observed isotope effects in reduction of trichloromethane by Dehalobacter CF and cobalamin (Dehalobacter CF, ε_C = -27.9 ± 1.7‰; ε_Cl = -4.2 ± 0.‰; λ = 6.6 ± 0.1; cobalamin, ε_C = -26.0 ± 0.9‰; ε_Cl = -4.0 ± 0.2‰; λ = 6.5 ± 0.2) indicated the same underlying mechanism, as did identical isotope effects in the reduction of 1,2-dichloroethane by Dehalococcoides and cobalamin (Dehalococcoides, ε_C = -33.0 ± 0.4‰; ε_Cl = -5.1 ± 0.1‰; λ = 6.5 ± 0.2; cobalamin, ε_C = -32.8 ± 1.7‰; ε_Cl = -5.1 ± 0.2‰; λ = 6.4 ± 0.2). In contrast, a different, non-S_N2 reaction was evidenced by different isotope effects in reaction of 1,2-dichloroethane with Dehalogenimonas (ε_C = -23.0 ± 2.0‰; ε_Cl = -12.0 ± 0.8‰; λ = 1.9 ± 0.02) illustrating a diversity of biochemical reaction mechanisms manifested even within the same class of enzymes (RDases). This study resolves open questions in our understanding of bacterial reductive dehalogenation and, thereby, provides important information on the biochemistry of bioremediation.

Reactivity of chloroacetamides toward sulfide + black carbon: Insights from structural analogues and dynamic NMR spectroscopy

Chloroacetamides are commonly used in herbicide formulations, and their occurrence has been reported in soils and groundwater. However, how their chemical structures affect transformation kinetics and pathways in the presence of environmental reagents such as hydrogen sulfide species and black carbon has not been investigated. In this work, we assessed the impact of increasing Cl substituents on reaction kinetics and pathways of six chloroacetamides. The contribution of individual pathways (reductive dechlorination vs. nucleophilic substitution) to the overall decay of selected chloroacetamides was differentiated using various experimental setups; both the transformation rates and product distributions were characterized. Our results suggest that the number of Cl substituents affected reaction pathways and kinetics: trichloroacetamides predominantly underwent reductive dechlorination whereas mono- and dichloroacetamides transformed via nucleophilic substitution. Furthermore, we synthesized eight dichloroacetamide analogs (Cl₂CHC(=O)NRR') with differing R groups and characterized their transformation kinetics. Dynamic NMR spectroscopy was employed to quantify the rotational energy barriers of dichloroacetamides. Our results suggest that adsorption of dichloroacetamides on black carbon constrained R groups from approaching the dichloromethyl carbon and subsequently favored nucleophilic attack. This study provides new insights to better predict the fate of chloroacetamides in subsurface environments by linking their structural characteristics to transformation kinetics and pathways.

Application of dual carbon-bromine stable isotope analysis to characterize anaerobic micro-degradation mechanisms of PBDEs in wetland bottom-water

Polybrominated diphenyl ethers (PBDEs), one kind of persistent organic pollutants, were widely detected in coastal wetlands. Microbial reductive debromination is one of the most important attenuation processes for PBDEs in anaerobic environment, whereas the underlying reaction mechanisms remain elusive. Dual-element stable isotope analysis was recently recognized to distinguish different reaction mechanism for degradation of organic pollutants. In this study, the dual carbon-bromine isotope effects associated with the anaerobic microbial degradation were first investigated to characterize the reaction mechanisms for BDE-47 and BDE-153. Presence of lower brominated congeners indicated stepwise debromination as the main degradation pathway, with the preferential removal of bromine in para position > meta/ortho position. The pronounced isotope fractionation was observed for both carbon and bromine, with similar carbon (ε_C) and bromine isotope enrichment factor (ε_Br) between BDE-47 (ε_C = -5.98‰, ε_Br = -2.44‰) and BDE-153 (ε_C = -5.57‰, ε_Br = -2.06‰) during the microbial degradation. Compared to ε_C and ε_Br, the correlation of carbon and isotope effects (Λ_C/Br = Δδ⁸¹Br/Δδ¹³C) was almost the same between BDE-47 (0.436) and BDE-153 (0.435), indicating the similar reaction mechanism. The calculated carbon and bromine apparent kinetic isotope effects (AKIE_C and AKIE_Br) were 1.0773 and 1.0098 for BDE-47 and 1.0716 and 1.0125 for BDE-153, within range reported for degradation of halogenated compounds following nucleophilic substitution. Combination analysis of degradation products, Λ_C/Br and AKIE, all the results pointed to that the anaerobic reductive debromination of BDE-47 and BDE-153 followed the nucleophilic aromatic substitution, with the addition of cofactor to the benzene ring concomitant with dissociation of carbon-bromine bond via the inner-sphere electron transfer, and the cleavage of C-Br bond was the rate-determining step. This study contributed to the development of dual carbon-bromine isotope analysis as a robust approach to probe the fate of PBDEs in contaminated sites.

Outer-sphere electron transfer does not underpin B12-dependent olefinic reductive dehalogenation in anaerobes

Anaerobic microbial B₁₂-dependent reductive dehalogenation may pave a way to remediate soil, sediment, and underground water contaminated with halogenated olefins. The chemical reaction is initiated by electron transfer (ET) from supernucleophilic cob(I)alamin (B_12s). However, the inherent mechanism as outer-sphere or inner-sphere route is still under debate. To clarify the possibility of an outer-sphere pathway, we calculated free energy barriers of the initial steps of all outer-sphere ET routes by Marcus theory employing density functional theory (DFT). For 18 fluorinated, chlorinated, and brominated ethenes as representative olefins, 164 of 165 reactions with free energy barriers larger than 20 kcal mol^-1 are not feasible under physiological dehalogenase conditions. Moreover, electronic structure analysis of perbromoethene with an outer-sphere free energy barrier of 18.2 kcal mol^-1 reveals no ET initiation down to Co⋯Br and Co⋯C distances of 3.15 Å. The results demonstrate that the B₁₂-catalyzed reductive dechlorination of olefins in microbes should proceed through an inner-sphere ET pathway.

Insights into carbon isotope fractionation on trichloroethene degradation in base activated persulfate process: The role of multiple reactive oxygen species

Understanding the role of reactive oxygen species (ROS) is essential to elucidate the mechanism of contaminants degradation in in-situ chemical oxidation (ISCO). In this study, compound specific isotope analysis (CSIA) and radicals quenching methods were integrated to investigate the roles of hydroxyl radical (HO), sulfate radical (SO₄^-), and superoxide radical (O₂^-) on trichloroethene (TCE) degradation during persulfate (PS) activated with base. The carbon isotope fractionation of TCE was found to be dependent of the base:PS ratios, yielding carbon enrichment factors (ε values) from -9.8 ± 0.5‰ to -16.7 ± 1.0‰ at base:PS molar ratios between 0.5:1 and 10:1, which was attributed to multi-pathways degradation of TCE by multiple ROS. The expected ε value (-31.6 ± 1.6‰) for TCE degradation via O₂^- attacking pathway, was more negative than those values via SO₄^- or HO pathways. The relative contributions of HO, SO₄^- and O₂^- for TCE degradation during base activated PS were estimated with observed ε values. HO and O₂^- were the predominant ROS for TCE degradation (with the relative contribution of 55-69% and 22-45%, respectively) in base activated PS. This work highlights the prospect of CSIA application for identifying degradation pathways of contaminants with ROS in environment.

A Spectroscopically Validated Computational Investigation of Viable Reaction Intermediates in the Catalytic Cycle of the Reductive Dehalogenase PceA

Organisms that produce reductive dehalogenases utilize halogenated aromatic and aliphatic substances as terminal electron acceptors in a process termed organohalide respiration. These organisms can couple the reduction of halogenated substances with the production of ATP. Tetrachloroethylene reductive dehalogenase (PceA) catalyzes the reductive dehalogenation of per- and trichloroethylenes (PCE and TCE, respectively) to primarily cis-dichloroethylene (DCE). The enzymatic conversion of PCE to TCE (and subsequently DCE) could potentially proceed via a mechanism in which the first step involves a single-electron transfer, nucleophilic addition followed by chloride elimination or protonation, or direct attack at the halogen. Difficulties with producing adequate quantities of PceA have greatly hampered direct experimental studies of the reaction mechanism. To overcome these challenges, we have generated computational models of resting and TCE-bound PceA using quantum mechanics/molecular mechanics (QM/MM) calculations and validated these models on the basis of experimental data. Notably, the norpseudo-cob(II)alamin [Co(II)Cbl*] cofactor remains five-coordinate upon binding of the substrate to the enzyme, retaining a loosely bound water on the lower face. Thus, the mechanism for the thermodynamically challenging Co(II) → Co(I)Cbl* reduction used by PceA differs fundamentally from that utilized by adenosyltransferases, which generate four-coordinate Co(II)Cbl species to facilitate access to the Co(I) oxidation state. The same QM/MM computational methodology was then applied to viable reaction intermediates in the catalytic cycle of PceA. The intermediate predicted to possess the lowest energy is that resulting from electron transfer from Co(I)Cbl* to the substrate to yield Co(II)Cbl*, a chloride ion, and a vinylic radical.

Groundwater geochemical constituents controlling the reductive dechlorination of TCE by nZVI: Evidence from diverse anaerobic corrosion mechanisms of nZVI

The corrosion mechanisms of nanoscale zero-valent iron (nZVI) vary with different geochemical constituents, which affect the reductive dechlorination process of trichloroethylene (TCE). In this study, the effect of nZVI anaerobic corrosion on the reductive dechlorination of TCE with different groundwater geochemical constituents (Ca²⁺-SO₄^2-, Ca²⁺-HCO₃^-, Na⁺-NO₃^-) was investigated. Microscopic characterization by X-ray diffraction (XRD) and transmission electron microscopy (TEM) combined with pH, oxidation-reduction potential (ORP) and dissolved Fe²⁺ in solutions to illustrate the corrosion mechanism of nZVI. In the four systems including ultrapure water (UPW), the reduction of TCE conformed to pseudo-first-order kinetics, the generation of Cl^- accorded with zero-order kinetics, and multi-step reaction kinetics was used to fit the generation and degradation of chlorinated byproducts (Dichloroethylene, DCEs). Compared with UPW system, the dissolution corrosion of Ca²⁺-HCO₃^- and Ca²⁺-SO₄^2- promoted the reductive dechlorination of TCE (k_{obs, TCE} = 0.658 ± 0.010 & 0.245 ± 0.028 d^-1 and k_{obs, Cl-} = 41.682 ± 1.016 & 20.623 ± 1.923 μM⋅d^-1 for Ca²⁺-HCO₃^- & Ca²⁺-SO₄^2-, respectively) and the degradation of DCEs (0.444 ± 0.036 & 0.244 ± 0.040 μM⋅d^-1 for Ca²⁺-HCO₃^- & Ca²⁺-SO₄^2-, respectively); redox-active NO₃^- competed for electrons and passivated the surface of nZVI, which limited the reductive dechlorination of TCE (k_{obs, TCE} = 0.111 ± 0.025 d^-1 & k_{obs, Cl-} = 14.943 ± 0.664 μM⋅d^-1) and the degradation of DCEs (0.078 ± 0.018 μM⋅d^-1), and the passivation layer promoted the adsorption of TCE. This study from the perspective of nZVI corrosion provides a theoretical basis for the long-term application of nZVI technology in the remediation of TCE-contaminated sites with different groundwater geochemical types.

Genetic Analysis of Citrobacter sp.86 Reveals Involvement of Corrinoids in Chlordecone and Lindane Biotransformations

Chlordecone (Kepone®) and γ-hexachlorocyclohexane (γ-HCH or lindane) have been used for decades in the French West Indies (FWI) resulting in long-term soil and water pollution. In a previous work, we have identified a new Citrobacter species (sp.86) that is able to transform chlordecone into numerous products under anaerobic conditions. No homologs to known reductive dehalogenases or other candidate genes were found in the genome sequence of Citrobacter sp.86. However, a complete anaerobic pathway for cobalamin biosynthesis was identified. In this study, we investigated whether cobalamin or intermediates of cobalamin biosynthesis was required for chlordecone microbiological transformation. For this purpose, we constructed a set of four Citrobacter sp.86 mutant strains defective in several genes belonging to the anaerobic cobalamin biosynthesis pathway. We monitored chlordecone and its transformation products (TPs) during long-term incubation in liquid cultures under anaerobic conditions. Chlordecone TPs were detected in the case of cobalamin-producing Citrobacter sp.86 wild-type strain but also in the case of mutants able to produce corrinoids devoid of lower ligand. In contrast, mutants unable to insert the cobalt atom in precorrin-2 did not induce any transformation of chlordecone. In addition, it was found that lindane, previously shown to be anaerobically transformed by Citrobacter freundii without evidence of a mechanism, was also degraded in the presence of the wild-type strain of Citrobacter sp.86. The lindane degradation abilities of the various Citrobacter sp.86 mutant strains paralleled chlordecone transformation. The present study shows the involvement of cobalt-containing corrinoids in the microbial degradation of chlorinated compounds with different chemical structures. Their increased production in contaminated environments could accelerate the decontamination processes.

Dual Element (C/Cl) Isotope Analysis Indicates Distinct Mechanisms of Reductive Dehalogenation of Chlorinated Ethenes and Dichloroethane in Dehalococcoides mccartyi Strain BTF08 With Defined Reductive Dehalogenase Inventories

Dehalococcoides mccartyi strain BTF08 has the unique property to couple complete dechlorination of tetrachloroethene and 1,2-dichloroethane to ethene with growth by using the halogenated compounds as terminal electron acceptor. The genome of strain BTF08 encodes 20 genes for reductive dehalogenase homologous proteins (RdhA) including those described for dehalogenation of tetrachloroethene (PceA, PteA), trichloroethene (TceA) and vinyl chloride (VcrA). Thus far it is unknown under which conditions the different RdhAs are expressed, what their substrate specificity is and if different reaction mechanisms are employed. Here we found by proteomic analysis from differentially activated batches that PteA and VcrA were expressed during dechlorination of tetrachloroethene to ethene, while TceA was expressed during 1,2-dichloroethane dehalogenation. Carbon and chlorine compound-specific stable isotope analysis suggested distinct reaction mechanisms for the dechlorination of (i) cis-dichloroethene and vinyl chloride versus (ii) tetrachloroethene. This differentiation was observed independent of the expressed RdhA proteins. Differently, two stable isotope fractionation patterns were observed for 1,2-dichloroethane transformation, for cells with distinct RdhA inventories. Conclusively, we could link specific RdhA expression with functions and provide an insight into the apparently substrate-specific reaction mechanisms in the pathway of reductive dehalogenation in D. mccartyi strain BTF08. Data are available via ProteomeXchange with identifiers PXD018558 and PXD018595.

Dual C-Cl Isotope Analysis for Characterizing the Reductive Dechlorination of α- and γ-Hexachlorocyclohexane by Two Dehalococcoides mccartyi Strains and an Enrichment Culture

Hexachlorocyclohexanes (HCHs) are persistent organic contaminants that threaten human health. Microbial reductive dehalogenation is one of the most important attenuation processes in contaminated environments. This study investigated carbon and chlorine isotope fractionation of α- and γ-HCH during the reductive dehalogenation by three anaerobic cultures. The presence of tetrachlorocyclohexene (TeCCH) indicated that reductive dichloroelimination was the first step of bond cleavage. Isotope enrichment factors (ε_C and ε_Cl) were derived from the transformation of γ-HCH (ε_C, from -4.0 ± 0.5 to -4.4 ± 0.6 ‰; ε_Cl, from -2.9 ± 0.4 to -3.3 ± 0.4 ‰) and α-HCH (ε_C, from -2.4 ± 0.2 to -3.0 ± 0.4 ‰; ε_Cl, from -1.4 ± 0.3 to -1.8 ± 0.2 ‰). During α-HCH transformation, no enantioselectivity was observed, and similar ε_c values were obtained for both enantiomers. The correlation of ¹³C and ³⁷Cl fractionation (Λ = Δδ¹³C/Δδ³⁷Cl ≈ ε_C/ε_Cl) of γ-HCH (from 1.1 ± 0.3 to 1.2 ± 0.1) indicates similar bond cleavage during the reductive dichloroelimination by the three cultures, similar to α-HCH (1.7 ± 0.2 to 2.0 ± 0.3). The different isotope fractionation patterns during reductive dichloroelimination and dehydrochlorination indicates that dual-element stable isotope analysis can potentially be used to evaluate HCH transformation pathways at contaminated field sites.

Compound-specific chlorine isotope fractionation in biodegradation of atrazine

Atrazine is a frequently detected groundwater contaminant. It can be microbially degraded by oxidative dealkylation or by hydrolytic dechlorination. Compound-specific isotope analysis is a powerful tool to assess its transformation. In previous work, carbon and nitrogen isotope effects were found to reflect these different transformation pathways. However, chlorine isotope fractionation could be a particularly sensitive indicator of natural transformation since chlorine isotope effects are fully represented in the molecular average while carbon and nitrogen isotope effects are diluted by non-reacting atoms. Therefore, this study explored chlorine isotope effects during atrazine hydrolysis with Arthrobacter aurescens TC1 and oxidative dealkylation with Rhodococcus sp. NI86/21. Dual element isotope slopes of chlorine vs. carbon isotope fractionation (Λ = 1.7 ± 0.9 vs. Λ = 0.6 ± 0.1) and chlorine vs. nitrogen isotope fractionation (Λ = -1.2 ± 0.7 vs. Λ = 0.4 ± 0.2) provided reliable indicators of different pathways. Observed chlorine isotope effects in oxidative dealkylation (ε_Cl = -4.3 ± 1.8‰) were surprisingly large, whereas in hydrolysis (ε_Cl = -1.4 ± 0.6‰) they were small, indicating that C-Cl bond cleavage was not the rate-determining step. This demonstrates the importance of constraining expected isotope effects of new elements before using the approach in the field. Overall, the triple element isotope information brought forward here enables a more reliable identification of atrazine sources and degradation pathways.

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.

Requirements for Chromium Reactors for Use in the Determination of H Isotopes in Compound-Specific Stable Isotope Analysis of Chlorinated Compounds

There is a strong need for careful quality control in hydrogen compound-specific stable isotope analysis (CSIA) of halogenated compounds. This arises in part due to the lack of universal design of the chromium (Cr) reactors. In this study, factors that optimize the critical performance parameter, linearity, for the Cr reduction method for hydrogen isotope analysis were identified and evaluated. These include the effects of short and long vertically mounted reactors and temperature profiles on trapping of Cl to ensure accurate and precise hydrogen isotope measurements. This paper demonstrates the critical parameters that need consideration to optimize any Cr reactor applications to ensure the accuracy of δ²H analysis for organic compounds and to enhance intercomparability for both international standards and reference materials run by continuous flow versus an elemental analyzer.

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.

Isotope fractionation in atrazine degradation reveals rate-limiting, energy-dependent transport across the cell membrane of gram-negative rhizobium sp. CX-Z

In the biological mass transfer of organic contaminants like atrazine, the cellular membrane limits bioavailability of pesticides. We aimed to illustrate the roles of cellular membrane physiology and substrate uptake (e.g., passive diffusion and energy-dependent transport) on the limitations of bioavailability in atrazine biodegradation by Gram-negative strain Rhizobium sp. CX-Z. Compound-specific stable isotope analysis revealed energy-dependent transport across cellular membrane led to bioavailability limitations in atrazine biotransformation. Carbon isotope fractionation (ε_(C) = -1.8 ± 0.3‰) was observed and significantly smaller in atrazine biodegradation by Rhizobium sp. CX-Z than that expected in acid hydrolysis (ε_(C) = -4.8 ± 0.4‰) and hydrolysis by the pure enzyme TrzN (ε_(C) = -5.0 ± 0.2‰). However, isotope fractionation was restored in membrane-free cells of Rhizobium sp. CX-Z (ε_(C) = -5.4 ± 0.2‰) where no cellular membrane limits substrate uptake. When respiratory chain was inhibited by rotenone, the pseudo-first order kinetic rate constants (0.08 ± 0.03 h^-1, 0.09 ± 0.03 h^-1) was observed to be statistically less than in the control group (0.23 ± 0.02 h^-1, 0.33 ± 0.02 h^-1), demonstrating that energy-dependent transport dominated atrazine transfer across the cellular membrane. Therefore, our results revealed energy-dependent transport across cellular membrane existing in Gram-negative strain Rhizobium sp. CX-Z determines bioavailability of atrazine in biotransformation process even at high concentration.

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.

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.

Diversity and Niche of Archaea in Bioremediation

Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.