Kinetic Isotope Effects of the Enzymatic Transformation of γ-Hexachlorocyclohexane by the Lindane Dehydrochlorinase Variants LinA1 and LinA2

Enhanced aerobic bioremediation of an aquifer heavily contaminated with a mixture of chlorobenzenes and hexachlorocyclohexanes at the Sardas landfill (Spain)

The groundwater at the Sardas landfill in Huesca, Spain, is contaminated with benzene, chlorobenzenes, and hexachlorocyclohexane (HCH) isomers due to illegal waste dumping from a former lindane factory. In this study, microcosms using field-derived groundwater to evaluate in situ bioremediation were constructed. Anaerobic biostimulation with lactate successfully transformed α-, β-, δ-, and γ-HCH within two weeks, but failed to degrade benzene and less chlorinated benzenes, even with nutrient addition. In contrast, aerobic biostimulation led to rapid degradation of benzene, chlorobenzenes, and α-, δ-, and γ-HCH. Notably, adding a phosphorus source significantly increased the degradation rates. Following these laboratory results, an in situ pilot test using the oxygen-releasing compound CaO2 was conducted at two site injection wells. The field results mirrored those from the microcosms, showing a marked reduction in contaminants at both the injection wells and surrounding wells. Bacterial community analysis based on the 16S rRNA genes in samples derived from aerobic microcosms and groundwater before and after the biostimulation test revealed a marked increase in the genus Pseudomonas, suggesting its potential role as biodegrading agent. This study illustrates the effectiveness of biostimulation as a viable strategy for treating groundwater contaminated with HCH isomers, benzene, and chlorobenzenes.

Degradation study of δ-hexachlorocyclohexane by iron sulfide nanoparticles: Elucidation of reaction pathway using compound specific isotope analysis and pH variation

pH influences the reactivity of iron (II) minerals towards halogenated pollutants like hexachlorocyclohexanes (HCHs). To explore these incompletely understood interactions, we investigated the carbon isotope fractionation of the δ-HCH isomer during dehalogenation by iron sulfide at pHs spanning a pH range across slightly acidic to alkaline domains (5.8-9.6). The δ-1,3,4,5,6-pentachlorocyclohex-1-ene (δ-PCCH) was the intermediate degradation product, while benzene, monochlorobenzene (MCB), but especially 1,2-dichlorobenzene (1,2-DCB), and 1,2,4-trichlorobenzene (1,2,4-TCB), were the main degradation products of δ-HCH. These degradation products suggested dehydrochlorination as the main degradation pathway of δ-HCH by iron sulfide. Different kinetic experiments indicate that the rate constants (ka) during dechlorination of δ-HCH by iron sulfide rose with pH: 0.003 d-1 (pH 5.8) < 0.034 d-1 (pH 8) < 0.085 (pH 9.3) < 0.286 d-1 (pH 9.6). Upon Rayleigh model calculations, an enrichment factor (εC) of -7.8 ± 1.0 ‰ was calculated for δ-HCH dehalogenation by FeS at pH 8.0. This suggests an apparent kinetic isotope effect (AKIEC) value of 1.049 ± 0.006 for dehydrohalogenation. The magnitude of the isotope effect from this paper furthermore supports dehydrohalogenation and opens the possibility to study the degradation of HCHs by iron (II) minerals containing FeS as mackinawite in oxygen-deprived environments.

Recent progresses in compound specific isotope analysis of halogenated persistent organic pollutants. Assessing the transformation of halogenated persistent organic pollutants at contaminated sites

Compound specific isotope analysis was extensively used to characterise the environmental processes associated with the abiotic and biotic transformation of persistent halogenated organic pollutants including those of contaminants of emerging concern (CECs). In the last years, the compound specific isotope analysis was applied as tool to evaluate the environmental fate and was expanded to larger molecules like brominated flame retardants and polychlorinated biphenyls. Multi-element (C, H, Cl, Br) CSIA methods have been also employed both in laboratory and field experiments. Nevertheless, despite the instrumental advances of isotope ratio mass spectrometers systems, the instrumental detection limit for gas chromatography-combustion-isotope ratio mass spectrometer (GC-C-IRMS) systems is challenging, especially when it is utilized to δ13C analysis. Liquid chromatography-combustion isotope ratio mass spectrometry methods are challenging, taking into consideration the chromatographic resolution required when analysing complex mixtures. For chiral contaminants, enantioselective stable isotope analysis (ESIA) has turned up as alternative approach but, up to now, it has been used for a limited number of compounds. Taking into consideration the occurrence of new emerging halogenated organic contaminants, new GC and LC methods for non-target screening using high resolution mass spectrometry are needed to be developed prior to the compound specific isotope analysis (CSIA) methods.

Determination of Stable Hydrogen Isotopic Composition and Isotope Enrichment Factor at Low Hydrogen Concentration

Determination of stable hydrogen isotopic compositions (δ2H) is currently challenged to achieve a high detection limit for reaching the linear range where δ2H values are independent of concentration. Therefore, it is difficult to assess precise δ2H values for calculating the hydrogen isotope enrichment factor (εH) and for field application where the concentrations of contaminants are relatively low. In this study, a data treatment approach was developed to obtain accurate δ2H values below the linear range. The core concept was to use a logarithmic function to fit the δ2H values below the linear range and then adjust the δ2H values below the linear range into the linear range by using the fitted logarithmic equation. Moreover, the adjusted δ2H values were calibrated by using laboratory reference materials, e.g., n-alkanes. Tris(2-chloroethyl) phosphate (TCEP) and hexachlorocyclohexane (HCH) isomers were selected as examples of complex heteroatom-bearing compounds to develop the data treatment approach. This data treatment approach was then tested using δ2H values from a TCEP transformation experiment with OH radicals. Comparable δ2H values and εH between the low-concentration experiment and the reference experiment were obtained using the developed approach. Therefore, the developed data treatment approach enables a possibility of determining the hydrogen isotopic compositions of organic components in low concentrations. It is especially valuable for determining organic contaminants in environmental samples, which are usually present in low concentrations.

Conductive Materials on Biocathodes Altered the Electron-Transfer Paths and Modulated γ-HCH Dechlorination and CH4 Production in Microbial Electrochemical Systems

Adding conductive materials to the cathode of a microbial electrochemical system (MES) can alter the route of interspecies electron transfer and the kinetics of reduction reactions. We tested reductive dechlorination of γ-hexachlorocyclohexane (γ-HCH), along with CH₄ production, in MES systems whose cathodes were coated with conductive magnetite nanoparticles (NaFe), biochar (BC), magnetic biochar (FeBC), or anti-conductive silica biochar (SiBC). Coating with NaFe enriched electroactive microorganisms, boosted electro-bioreduction, and accelerated γ-HCH dechlorination and CH₄ production. In contrast, BC only accelerated dechlorination, while FeBC only accelerated methanogenesis, because of their assemblies of functional taxa that selectively transferred electrons to those electron sinks. SiBC, which decreased electro-bioreduction, yielded the highest CH₄ production and increased methanogens and the mcrA gene. This study provides a strategy to selectively control the distribution of electrons between reductive dechlorination and methanogenesis by adding conductive or anti-conductive materials to the MES's cathode. If the goal is to maximize dechlorination and minimize methane generation, then BC is the optimal conductive material. If the goal is to accelerate electro-bioreduction, then the best addition is NaFe. If the goal is to increase the rate of methanogenesis, adding anti-conductive SiBC is the best.

Citrobacter sp. Y3 harbouring novel gene HBCD-hd-1 mineralizes hexabromocyclododecane via new metabolic pathways according to multi-omics characterization

Hexabromocyclododecane (HBCD) is a typical persistent organic pollutant that is widely detected in the environment. Despite the significant efforts put into its mineralisation, there is still a lack of microorganism resources that can completely mineralise HBCD. Stable isotope analysis revealed that the Citrobacter sp. Y3 can use [¹³C]HBCD as its sole carbon source and degrade or even mineralise it into ¹³CO₂, with a maximum conversion rate of 100% in approximately 14 days. Strain Y3 could completely mineralise HBCD, which it used as its only carbon source, and six debromination enzymes related to HBCD degradation were found in Y3, including haloalkane dehalogenase (DhaA), haloacid dehalogenase (HAD), etc. A functional gene named HBCD-hd-1, encoding a HAD, was found to be upregulated during HBCD degradation and heterologously expressed in Escherichia coli. Recombinant E. coli with the HBCD-hd-1 gene transformed the typical intermediate 4-bromobutyric acid to 4-hydroxybutanoic acid and showed excellent degradation performance on HBCD, accompanied by nearly 100% bromine (Br) ion generation. The expression of HBCD-hd-1 in Y3 rapidly accelerated the biodegradation of HBCD. With HBCD as its sole carbon source, strain Y3 could potentially degrade HBCD, especially in a low-nutrient environment.

Characterization of Hexachlorocyclohexane Isomer Dehydrochlorination by LinA1 and LinA2 Using Multi-element Compound-Specific Stable Isotope Analysis

Dehydrochlorination is one of the main (thus far discovered) processes for aerobic microbial transformation of hexachlorocyclohexane (HCH) which is mainly catalyzed by LinA enzymes. In order to gain a better understanding of the reaction mechanisms, multi-element compound-specific stable isotope analysis was applied for evaluating α- and γ-HCH transformations catalyzed by LinA1 and LinA2 enzymes. The isotopic fractionation (ε_E) values for particular elements of (+)α-HCH (ε_C = -10.8 ± 1.0‰, ε_Cl = -4.2 ± 0.5‰, ε_H = -154 ± 16‰) were distinct from the values for (-)α-HCH (ε_C = -4.1 ± 0.7‰, ε_Cl = -1.6 ± 0.2‰, ε_H = -68 ± 10‰), whereas the dual-isotope fractionation patterns were almost identical for both enantiomers (Λ_C-Cl = 2.4 ± 0.4 and 2.5 ± 0.2, Λ_H-C = 12.9 ± 2.4 and 14.9 ± 1.1). The ε_E of γ-HCH transformation by LinA1 and LinA2 were -7.8 ± 1.0‰ and -7.5 ± 0.8‰ (ε_C), -2.7 ± 0.3‰ and -2.5 ± 0.4‰ (ε_Cl), -170 ± 25‰ and -150 ± 13‰ (ε_H), respectively. Similar Λ_C-Cl values (2.7 ± 0.2 and 2.9 ± 0.2) were observed as well as similar Λ_H-C values (20.1 ± 2.0 and 18.4 ± 1.9), indicating a similar reaction mechanism by both enzymes during γ-HCH transformation. This is the first data set on 3D isotope fractionation of α- and γ-HCH enzymatic dehydrochlorination, which gave a more precise characterization of the bond cleavages, highlighting the potential of multi-element compound-specific stable isotope analysis to characterize different transformation processes (e.g., dehydrochlorination and reductive dehalogenation).

Perfluoroalkyl and polyfluoroalkyl substances (PFASs) in groundwater: current understandings and challenges to overcome

Perfluoroalkyl and polyfluoroalkyl substances (PFASs) have been frequently detected in groundwater globally. With the phase-out of perfluorooctane sulfonate (PFOS) and perfluorooctanate (PFOA) due to their risk to the ecosystem and human population, various novel PFASs have been used as replacements and detected in groundwater. In order to summarize the current understanding and knowledge gaps on PFASs in groundwater, we reviewed the studies about environmental occurrence, transport, and risk of legacy and novel PFASs in groundwater published from 1999 to 2021. Our review suggests that PFOS and PFOA could still be detected in groundwater due to the long residence time and the retention in the soil-groundwater system. Firefighting training sites, industrial parks, and landfills were commonly hotspots of PFASs in groundwater. More novel PFASs have been detected via nontarget analysis using high-resolution mass spectrometry. Some novel PFASs had concentrations comparable to that of PFOS and PFOA. Both legacy and novel PFASs can pose a risk to human population who rely on contaminated groundwater as drinking water. Transport of PFASs to groundwater is influenced by various factors, i.e., the compound structure, the hydrochemical condition, and terrain. The exchange of PFASs between groundwater and surface water needs to be better characterized. Field monitoring, isotope tracing, nontarget screening, and modeling are useful approaches and should be integrated to get a comprehensive understanding of PFASs sources and behaviors in groundwater.

Kinetic isotope effects of C and N indicate different transformation mechanisms between atzA- and trzN-harboring strains in dechlorination of atrazine

Compound-specific stable isotope analysis provides an alternative method to insight into the biotransformation mechanisms of diffuse organic pollutants in the environment, e.g., the endocrine disruptor herbicide atrazine. Biotic hydrolysis process catalyzed by chlorohydrolase AtzA and TrzN plays an important role in the detoxification of atrazine, while the catalytic mechanism of AtzA is still speculative. To investigate the catalytic mechanism of AtzA and answer whether both enzymes catalyze hydrolytic dechlorination of atrazine by the same mechanism, in this study, apparent kinetic isotope effects (AKIE) for carbon and nitrogen were observed by three atzA-harboring bacterial isolates and their membrane-free extracts. The AKIEs obtained from atzA-harboring bacterial isolates (AKIEC = 1.021 ± 0.010, AKIEN = 0.992 ± 0.003) were statistically different from that of trzN-harboring strains (AKIEC = 1.040 ± 0.006, AKIEN = 0.983 ± 0.006), confirming the different activation mechanisms of atrazine preceding to nucleophilic aromatic substitution of Cl atom in actual enzymatic reaction catalyzed by AtzA and TrzN, despite the limitation of variable dual-element isotope plots. The lower degree of normal carbon and inverse nitrogen isotope fractionation observed from atzA-harboring strains, suggesting AtzA catalyzing hydrolytic dechlorination of atrazine by coordination of Cl and one aromatic N to the Fe2+ drawing electron density from carbon-chlorine bond that facilitating the nucleophilic attack, rather than in TrzN case that protonation of aromatic N increasing nucleophilic substitution of Cl atom. This study suggests considering the potential influences of phylogenetic diversity of bacterial isolates and evolution of enzymes on the applications of CSIA method in future study.

Stable isotope fractionation associated with the synthesis of hexachlorocyclohexane isomers for characterizing sources

The stable isotope fingerprints of hexachlorocyclohexane (HCH) isomers have potential for identifying sources as they are related to the synthesis processes and isotopic compositions of raw materials. However, the isotopic fractionation associated with the synthesis processes has not been investigated. Therefore, photochemical synthesis experiments using benzene and chlorine gas were conducted to characterize the associated isotopic fractionation under different conditions. Different patterns of isotopic fractionation factors (α_C, α_Cl, and α_H) were observed in each experiment. The large variability of α_H is related to the accumulating secondary hydrogen isotope effects or the rearrangement of C-H bonds at the cyclohexane ring. An increase of δ¹³C and δ³⁷Cl values of HCH isomers was observed during synthesis, which is related to the C-Cl bond formation in the radical dichlorination forming HCH and the subsequent chlorine substitution forming heptachlorocyclohexanes. The large variability of δ²H values is related to the secondary and primary hydrogen isotope effects. Different δ¹³C, δ³⁷Cl and δ²H values among HCH isomers were observed, indicating that conformational complexity of HCH caused by arrangement of C-Cl bonds in planar and axial positions also influence the isotope values. The understanding of isotopic fractionation during HCH synthesis can be indicative for source identification in the field.

Stable Carbon Isotope Analysis of Hexachlorocyclohexanes by Liquid–Liquid Extraction Gas Chromatography Isotope Ratio Mass Spectrometry: Method Evaluation and Applications

Compound specific isotope analysis (CSIA) and enantiomer specific isotope analysis (ESIA) are powerful tools for assessing the fate of hexachlorocyclohexanes (HCHs) in the environment. However, there is no systematic study on the CSIA and ESIA analysis test methods of the carbon isotopes of HCHs in water and soil environments, in particular the isotope fractionation in the pre-concentration process. We endeavored to test the compatibility of CSIA and ESIA with the liquid–liquid extraction method of HCHs in water. The results showed that there were negligible changes in the δ13C of HCHs after extraction, indicating that liquid–liquid extraction can be used as a pre-concentration method for the determination of δ13C of HCHs in water. The optimized method was validated and then applied to differentiate three HCHs from different manufacturers, to identify in situ degradation of HCHs of groundwater from a contaminated site and to resolve the carbon isotope fractionation occurring in the α-HCH oxidation by CaO2/Fe(II) Fenton system. The results showed that the same reagents from different manufacturers have different carbon isotope compositions, and different isomers from the same manufacturer also have different isotope compositions, showing useful evidence in identifying the source of HCHs. The more enriched δ13C in the down-gradient wells indicated that HCHs have undergone biodegradation or/and chemical reactions in the groundwater system of the site. Carbon isotopic enrichment factors (εC) of −1.90 ± 0.10‰ were obtained in the oxidation process. Hence, the method validated in this study has great potential as a method for identifying the degradation of HCHs in a water environment.

Dehalogenation of α-hexachlorocyclohexane by iron sulfide nanoparticles: Study of reaction mechanism with stable carbon isotopes and pH variations

The biodegradation of hexachlorocyclohexanes (HCHs) is known to be accompanied by isotope fractionation of carbon (¹³C/¹²C), but no systematic studies were performed on abiotic degradation of HCH isomers by iron (II) minerals. In this study, we explored the carbon isotope fractionation of α-HCH during dechlorination by FeS nanoparticles at different pH values. The results of three different experiments showed that the apparent rate constants during dehalogenation of α-HCH by FeS increased with pH. The lowest apparent rate constant value α-HCH during dehalogenation by FeS was 0.009 d^-1 at pH value of 2.4, while the highest was 1.098 d^-1 at pH 11.8. α-HCH was completely dechlorinated by FeS only at pH values 9.9 and 11.8, while the corresponding apparent rate constants were 0.253 d^-1 and 1.098 d^-1, respectively. Regardless of the pH used, the 1,2,4-trichlorobenzene (1,2,4-TCB), 1,2-dichlorobenzene (1,2-DCB), and benzene were the dominant degradation products of α-HCH. An enrichment factor (ε_C) of -4.7 ± 1.3‰ was obtained for α-HCH using Rayleigh model, which is equivalent to an apparent kinetic isotope effect (AKIE_C) value of 1.029 ± 0.008 for dehydrohalogenation, and of 1.014 ± 0.004 for dihaloelimination, respectively. The magnitude of isotope fractionation from this study suggests that abiotic isotope fractionation by FeS must be taken into account in anoxic sediments and aquifers contaminated with HCH isomers, when high concentrations of FeS are present in the above-mentioned anoxic environments.

Lake Superior Has Lost over 90% of Its Pesticide HCH Load since 1986

The time trend of α- and γ-hexachlorocyclohexane (HCH) isomers in Lake Superior water was followed from 1986 to 2016, the longest record for any persistent organic pollutant (POP) in Great Lakes water. Dissipation of α-HCH and γ-HCHs was first order, with halving times (t1/2) of 5.7 and 8.5 y, respectively. Loss rates were not significantly different starting a decade later (1996-2016). Concentrations of β-HCH were followed from 1996-2016 and dissipated more slowly (t1/2 = 16 y). In 1986, the lake contained an estimated 98.8 tonnes of α-HCH and 13.2 tonnes of γ-HCH; by 2016, only 2.7% and 7.9% of 1986 quantities remained. Halving times of both isomers in water were longer than those reported in air, and for γ-HCH, they were longer in water than those reported in lake trout. Microbial degradation was evident by enantioselective depletion of (+)α-HCH, which increased from 1996 to 2011. Volatilization was the main removal process for both isomers, followed by degradation (hydrolytic and microbial) and outflow through the St. Mary's River. Sedimentation was minor. Major uncertainties in quantifying removal processes were in the two-film model for predicting volatilization and in microbial degradation rates. The study highlights the value of long-term monitoring of chemicals in water to interpreting removal processes and trends in biota.

Potential Role of Methanogens in Microbial Reductive Dechlorination of Organic Chlorinated Pollutants In Situ

Previous studies often attribute microbial reductive dechlorination to organohalide-respiring bacteria (OHRB) or cometabolic dechlorination bacteria (CORB). Even though methanogenesis frequently occurs during dechlorination of organic chlorinated pollutants (OCPs) in situ, the underestimated effect of methanogens and their interactions with dechlorinators remains unknown. We investigated the association between dechlorination and methanogenesis, as well as the performance of methanogens involved in reductive dechlorination, through the use of meta-analysis, incubation experiment, untargeted metabolomic analysis, and thermodynamic modeling approaches. The meta-analysis indicated that methanogenesis is largely synchronously associated with OCP dechlorination, that OHRB are not the sole degradation engineers that maintain OCP bioremediation, and that methanogens are fundamentally needed to sustain microenvironment functional balance. Laboratory results further confirmed that Methanosarcina barkeri (M. barkeri) promotes the dechlorination of γ-hexachlorocyclohexane (γ-HCH). Untargeted metabolomic analysis revealed that the application of γ-HCH upregulated the metabolic functioning of chlorocyclohexane and chlorobenzene degradation in M. barkeri, further confirming that M. barkeri potentially possesses an auxiliary dechlorination function. Finally, quantum analysis based on density functional theory (DFT) indicated that the methanogenic coenzyme F430 significantly reduces the activation barrier to dechlorination. Collectively, this work suggests that methanogens are highly involved in microbial reductive dechlorination at OCP-contaminated sites and may even directly favor OCP degradation.

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.

Characterizing the biotransformation of hexachlorocyclohexanes in wheat using compound-specific stable isotope analysis and enantiomer fraction analysis

Hexachlorocyclohexane isomers (HCHs) are persistent organic pollutants being responsible for environmental contamination worldwide. In order to characterize transformation of HCHs in different plant compartments during uptake, a hydroponic experimental setup was designed using wheat as the test plant. The extent of transformation was determined by using compound-specific isotope analysis (CSIA) and enantiomer fraction (EF) analysis. In nutrient solutions, no change of carbon (δ¹³C) and chlorine isotope ratios (δ³⁷Cl) of α-HCH and β-HCH was detected throughout the experiment indicating no transformation there. In wheat leaves, stems and roots, however, transformation of α-HCH due to a C‒Cl bond cleavage was indicated by increasing δ¹³C and δ³⁷Cl compared to the nutrient solution. In addition, 1,3,4,5,6-pentachlorocyclohexene (PCCH) was identified as the major metabolite of α-HCH transformation. For β-HCH, in contrast, no transformation was detected. The evaluation of enantiomer fraction analysis revealed no change of the EF(-) in the nutrient solution or on root surface but a decrease in the wheat compartments, providing an evidence for the preferential biological transformation of (-)α-HCH in wheat. The current study provides the first experimental evidence for biotransformation of α-HCH in wheat using CSIA and EF and provides a concept to evaluate processes during phytoremediation.

Quantification of Lambda (Λ) in multi-elemental compound-specific isotope analysis

In multi-elemental compound-specific isotope analysis the lambda (Λ) value expresses the isotope shift of one element versus the isotope shift of a second element. In dual-isotope plots, the slope of the regression lines typical reveals the footprint of the underlying isotope effects allowing to distinguish degradation pathways of an organic contaminant molecule in the environment. While different conventions and fitting procedures are used in the literature to determine Λ, it remains unclear how they affect the magnitude of Λ. Here we generate synthetic data for benzene δ²H and δ¹³C with two enrichment factors ε_H and ε_C using the Rayleigh equation to examine how different conventions and linear fitting procedures yield distinct Λ. Fitting an error-free data set in a graph plotting the δ²H versus δ¹³C overestimates Λ by 0.225%⋅ε_H/ε_C, meaning that if ε_H/ε_Cis larger than 22, Λ is overestimated by more than 5%. The correct fitting of Λ requires a natural logarithmic transformation of δ²H versus δ¹³C data. Using this transformation, the ordinary linear regression (OLR), the reduced major-axis (RMA) and the York methods find the correct Λ, even for large ε_H/ε_C. Fitting a dataset with synthetic data with typical random errors let to the same conclusion and positioned the suitability of each regression method. We conclude that fitting of non-transformed δ values should be discontinued. The validity of most previous Λ values is not compromised, although previously obtained Λ values for large ε_H/ε_C could be corrected using our error estimation to improve comparison.

Seeking the Source of Catalytic Efficiency of Lindane Dehydrochlorinase, LinA

Herein we present the results of an in-depth simulation study of LinA and its two variants. In our analysis, we combined the exploration of protein conformational dynamics with and without bound substrates (hexachlorocyclohexane (HCH) isomers) performed using molecular dynamics simulation followed by the extraction of the most frequently visited conformations and their characteristics with a detailed description of the interactions taking place in the active site between the respective HCH molecule and the first shell residues by using symmetry-adapted perturbation theory (SAPT) calculations. A detailed investigation of the conformational space of LinA substates has been accompanied by description of enzymatic catalytic steps carried out using a hybrid quantum mechanics/molecular mechanics (QM/MM) potential along with the computation of the potential of mean force (PMF) to estimate the free energy barriers for the studied transformations: dehydrochlorination of γ-, (-)-α-, and (+)-α-HCH by LinA-type I and -type II variants. The applied combination of computational techniques allowed us not only to characterize two LinA types but also to point to the most important differences between them and link their features to catalytic efficiency each of them possesses toward the respective ligand. More importantly it has been demonstrated that type I protein is more mobile, its active site has a larger volume, and the dehydrochlorination products are stabilized more strongly than in the case of type II enzyme, due to differences in the residues present in the active sites. Additionally, interaction energy calculations revealed very interesting patterns not predicted before but having the potential to be utilized in any attempts of improving LinA catalytic efficiency. On the basis of all these observations, LinA-type I protein seems to be more preorganized for the dehydrochlorination reaction it catalyzes than the type II variant.

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.

Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene

Intensive historical and worldwide use of pesticide formulations containing hexachlorocyclohexane (HCH) has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates, inferred from production rates of the dechlorinated products, MCB and benzene, increased progressively from <3 to ∼12 μM/day over 2 years. The molar ratio of benzene to MCB produced was a function of the substrate isomer and ranged from β (0.77 ± 0.15), α (0.55 ± 0.09), γ (0.13 ± 0.02), to δ (0.06 ± 0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundances of Pelobacter and Dehalobacter, most notably in the α-HCH and δ-HCH cultures. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step toward better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.

Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?

Hexachlorocyclohexane (HCH) isomers constitute a group of persistent organic pollutants. Their mass production and treatment have led to a global environmental problem that continues to this day. The characterization of modes of degradation of HCH by isotope fractionation is a current challenge. Multi isotope fractionation analysis provides a concept to characterize the nature of enzymatic and chemical transformation reactions. The understanding of the kinetic isotope effects (KIE) on bond cleavage reaction contributes to analyses of the mechanism of chemical and enzymatic reactions. Herein, carbon, chlorine, and hydrogen kinetic isotope effects are measured and predicted for the dehydrochlorination reaction of γ-HCH promoted by the hydroxyl ion in aqueous solution. Quantum mechanical (QM) microsolvation with an implicit solvation model and path integral formalism in combination with free-energy perturbation and umbrella sampling (PI-FEP/UM) and quantum mechanical/molecular mechanical QM/MM potentials for including solvent effects as well as calculating isotope effects are used and analyzed with respect to their performance in reproducing measured values. Reaction characterization is discussed based on the magnitudes of obtained isotope effects. The comparative analysis between the chemical dehydrochlorination of γ-HCH in aqueous media and catalyzed reaction by dehydrochlorinase, LinA is presented and discussed. Based on the values of isotope effects, these two processes seem to occur via the same net mechanism.

Enantiomer and Carbon Isotope Fractionation of α-Hexachlorocyclohexane by Sphingobium indicum Strain B90A and the Corresponding Enzymes

Chiral organic contaminants, like α-hexachlorocyclohexane (α-HCH), showed isotope fractionation and enantiomer fractionation during biodegradation. This study aims to understand the correlation between these two processes. Initial tests of α-HCH degradation by six Sphingobium strains (with different LinA variants) were conducted. Results showed variable enantiomer selectivity over the time course. In contrast, constant enantiomer selectivity was observed in experiments employing (i) cell suspensions, (ii) crude extracts, or (iii) LinA1 and LinA2 enzymes of strain B90A for α-HCH degradation in enzyme activity assay buffer. The average value of enantioselectivity (ES) were -0.45 ± 0.03 (cell suspensions), -0.60 ± 0.05 (crude extracts), and 1 (LinA1) or -1 (LinA2). The average carbon isotope enrichment factors (ε_c) of (+)α- and (-)α-HCH were increased from cells suspensions (-6.3 ± 0.1‰ and -2.3 ± 0.03‰) over crude extracts (-7.7 ± 0.4‰ and -3.4 ± 0.02‰) to purified enzymes (-11.1 ± 0.3‰ and -3.8 ± 0.2‰). The variability of ES and the ε_c were discussed based on the effect of mass transport and degradation rates. Our study demonstrates that enantiomer and isotope fractionation of α-HCH are two independent processes and both are affected by underlying reactions of individual enzymes and mass transport to a different extent.

Assessing Aerobic Biotransformation of Hexachlorocyclohexane Isomers by Compound-Specific Isotope Analysis

Contamination of soils and sediments with the highly persistent hexachlorocyclohexanes (HCHs) continues to be a threat for humans and the environment. Despite the existence of bacteria capable of biodegradation and cometabolic transformation of HCH isomers, such processes occur over time scales of decades and are thus challenging to assess. Here, we explored the use of compound-specific isotope analysis (CSIA) to track the aerobic biodegradation and biotransformation pathways of the most prominent isomers, namely, (-)-α-, (+)-α-, β-, γ-, and δ-HCH, through changes of their C and H isotope composition in assays of LinA2 and LinB enzymes. Dehydrochlorination of (+)-α-, γ-, and δ-HCH catalyzed by LinA2 was subject to substantial C and H isotope fraction with apparent ¹³C- and ²H-kinetic isotope effects (AKIEs) of up to 1.029 ± 0.001 and 6.7 ± 2.9, respectively, which are indicative of bimolecular eliminations. Hydrolytic dechlorination of δ-HCH by LinB exhibited even larger C but substantially smaller H isotope fractionation with ¹³C- and ²H-AKIEs of 1.073 ± 0.006 and 1.41 ± 0.04, respectively, which are typical for nucleophilic substitutions. The systematic evaluation of isomer-specific phenomena showed that, in addition to contaminant uptake limitations, diffusion-limited turnover ((-)-α-HCH), substrate dissolution (β-HCH), and potentially competing reactions catalyzed by constitutively expressed enzymes might bias the assessment of HCH biodegradation by CSIA at contaminated sites.