Biodegradation of chlorinated aliphatic compounds

Dechlorination of dichloromethane by a biofilter enriched with electroactive bacteria: Performance, kinetics, and microbial community

Dichloromethane (DCM) is a recalcitrant volatile organic compound that exhibits biological toxicity and bioaccumulation. In this study, gaseous DCM was removed using an electroactive bacterial biofilter (EBB) with graphite rod as the anode and carbon felt as the cathode. The highest removal efficiency (97.09%) was achieved at a cathodic potential of -600 mV (vs. Ag/AgCl). The EBB had a maximum elimination capacity of 79.29 g m^-3 h^-1 when the inlet load was 96.48 g m^-3 h^-1. There was no substrate inhibition phenomenon observed in the EBB, and the Michaelis-Menten model was used to describe the kinetics of the EBB. High-throughput sequencing indicated that electroactive genera such as Rhodanobacter sp., Sphingomonas sp., Pseudomonas sp., Chryseobacterium sp., Pseudochrobactrum sp., and Mycobacterium sp. dominated the EBB. The microbial communities were stable and were slightly affected by the DCM inlet concentration. The results can be applied for the effective treatment of recalcitrant volatile organic compounds (VOCs).

Enzymatic assays for the assessment of toxic effects of halogenated organic contaminants in water and food. A review

Halogenated organic compounds are a particular group of contaminants consisting of a large number of substances, and of great concern due to their persistence in the environment, potential for bioaccumulation and toxicity. Some of these compounds have been classified as persistent organic pollutants (POPs) under The Stockholm Convention and many toxicity assessments have been conducted on them previously. In this work we provide an overview of enzymatic assays used in these studies to establish toxic effects and dose-response relationships. Studies in vivo and in vitro have been considered with a particular emphasis on the impact of halogenated compounds on the activity of relevant enzymes to the humans and the environment. Most information available in the literature focuses on chlorinated compounds, but brominated and fluorinated molecules are also the target of increasing numbers of studies. The enzymes identified can be classified as enzymes: i) the activities of which are affected by the presence of halogenated organic compounds, and ii) those involved in their metabolisation/detoxification resulting in increased activities. In both cases the halogen substituent seems to have an important role in the effects observed. Finally, the use of these enzymes in biosensing tools for monitoring of halogenated compounds is described.

Perspective on Diabatic Models of Chemical Reactivity as Illustrated by the Gas-Phase S(N)2 Reaction of Acetate Ion with 1,2-Dichloroethane

Diabatic models are widely employed for studying chemical reactivity in condensed phases and enzymes, but there has been little discussion of the pros and cons of various diabatic representations for this purpose. Here we discuss and contrast six different schemes for computing diabatic potentials for a charge rearrangement reaction. They include (i) the variational diabatic configurations (VDC) constructed by variationally optimizing individual valence bond structures and (ii) the consistent diabatic configurations (CDC) obtained by variationally optimizing the ground-state adiabatic energy, both in the nonorthogonal molecular orbital valence bond (MOVB) method, along with the orthogonalized (iii) VDC-MOVB and (iv) CDC-MOVB models. In addition, we consider (v) the fourfold way (based on diabatic molecular orbitals and configuration uniformity), and (vi) empirical valence bond (EVB) theory. To make the considerations concrete, we calculate diabatic electronic states and diabatic potential energies along the reaction path that connects the reactant and the product ion-molecule complexes of the gas-phase bimolecular nucleophilic substitution (S(N)2) reaction of 1,2-dichloethane (DCE) with acetate ion, which is a model reaction corresponding to the reaction catalyzed by haloalkane dehalogenase. We utilize ab initio block-localized molecular orbital theory to construct the MOVB diabatic states and ab initio multi-configuration quasidegenerate perturbation theory to construct the fourfold-way diabatic states; the latter are calculated at reaction path geometries obtained with the M06-2X density functional. The EVB diabatic states are computed with parameters taken from the literature. The MOVB and fourfold-way adiabatic and diabatic potential energy profiles along the reaction path are in qualitative but not quantitative agreement with each other. In order to validate that these wave-function-based diabatic states are qualitatively correct, we show that the reaction energy and barrier for the adiabatic ground state, obtained with these methods, agree reasonably well with the results of high-level calculations using the composite G3SX and G3SX(MP3) methods and the BMC-CCSD multi-coefficient correlation method. However, a comparison of the EVB gas-phase adiabatic ground-state reaction path with those obtained from MOVB and with the fourfold way reveals that the EVB reaction path geometries show a systematic shift towards the products region, and that the EVB lowest-energy path has a much lower barrier. The free energies of solvation and activation energy in water reported from dynamical calculations based on EVB also imply a low activation barrier in the gas phase. In addition, calculations of the free energy of solvation using the recently proposed SM8 continuum solvation model with CM4M partial atomic charges lead to an activation barrier in reasonable agreement with experiment only when the geometries and the gas-phase barrier are those obtained from electronic structure calculations, i.e., methods i-v. These comparisons show the danger of basing the diabatic states on molecular mechanics without the explicit calculation of electronic wave functions. Furthermore, comparison of schemes i-v with one another shows that significantly different quantitative results can be obtained by using different methods for extracting diabatic states from wave function calculations, and it is important for each user to justify the choice of diabatization method in the context of its intended use.

Biochemical interpretation of quantitative structure-activity relationships (QSAR) for biodegradation of N-heterocycles: a complementary approach to predict biodegradability

Prediction of the biodegradability of organic compounds is an ecologically desirable and economically feasible tool for estimating the environmental fate of chemicals. We combined quantitative structure-activity relationships (QSAR) with the systematic collection of biochemical knowledge to establish rules for the prediction of aerobic biodegradation of N-heterocycles. Validated biodegradation data of 194 N-heterocyclic compounds were analyzed using the MULTICASE-method which delivered two QSAR models based on 17 activating (OSAR 1) and on 16 inactivating molecular fragments (GSAR 2), which were statistically significantly linked to efficient or poor biodegradability, respectively. The percentages of correct classifications were over 99% for both models, and cross-validation resulted in 67.9% (GSAR 1) and 70.4% (OSAR 2) correct predictions. Biochemical interpretation of the activating and inactivating characteristics of the molecular fragments delivered plausible mechanistic interpretations and enabled us to establish the following biodegradation rules: (1) Target sites for amidohydrolases and for cytochrome P450 monooxygenases enhance biodegradation of nonaromatic N-heterocycles. (2) Target sites for molybdenum hydroxylases enhance biodegradation of aromatic N-heterocycles. (3) Target sites for hydratation by an urocanase-like mechanism enhance biodegradation of imidazoles. Our complementary approach represents a feasible strategy for generating concrete rules for the prediction of biodegradability of organic compounds.

Removal of methyl chloroform in a coastal salt marsh of eastern China

The atmospheric burden of methyl chloroform (CH(3)CCl(3)) is still considerable due to its long atmospheric lifetime, although CH(3)CCl(3) emissions have declined considerably since it was included into the Montreal Protocol. Moreover, CH(3)CCl(3) emissions are used to estimate hydroxyl radical (OH) levels, trends, and hemispheric distributions, and thus the mass balance of the trace gas in the atmosphere is critical for characterizing OH concentrations. Salt marshes may be a potential sink for CH(3)CCl(3) due to its anoxic environment and abundant organic matter in sediments. In this study, seasonal dynamics of CH(3)CCl(3) fluxes were measured using static flux chambers from April 2004 to January 2005, along an elevational gradient of a coastal salt marsh in eastern China. To estimate the contribution of higher plants to the gas flux, plant aboveground biomass was experimentally harvested and the flux difference between the treatment and the intact was examined. In addition, the flux was analyzed in relation to soil and weather conditions. Along the elevational gradient, the salt marsh generally acted as a net sink of CH(3)CCl(3) in the growing season (from April to October). The flux of CH(3)CCl(3) ranged between -3.38 and -32.03 nmol m(-2)d(-1) (positive for emission and negative for consumption), and the maximum negative rate occurred at the cordgrass marsh. However, the measurements made during inundation indicated that the mudflat was a net source of CH(3)CCl(3). In the non-growing season (from November to March), the vegetated marsh was a minor source of CH(3)CCl(3) when soil was frozen, the emission rate ranging from 3.43 to 7.77 nmol m(-2)d(-1). However, the mudflat was a minor sink of CH(3)CCl(3) whether it was frozen or not in the non-growing season. Overall, the coastal salt marsh in eastern China was a large sink for the gas, because the magnitude of consumption rate was lager than that of emission, and because the duration of the growing season was longer than that of the non-growing season. Plant aboveground biomass had a great effect on the flux. Comparative analysis showed that the direction and magnitude of the effect of higher plants on the flux of CH(3)CCl(3) depended on timing of sampling vegetation type. In the growing season the plant biomass decreased the gas flux and acted as a large sink of the gas, whereas it presented as a minor source in the non-growing season. However, the mechanism underlying plant uptake process is not clear. The CH(3)CCl(3) flux was positively related to the dissolved salt concentration and organic matter content in soil, as well as light intensity, but it was negatively related to soil temperature, sulfate concentrations, and initial ambient atmospheric concentrations of CH(3)CCl(3). Our observations have important implications for estimation of the tropospheric lifetime of CH(3)CCl(3) and global OH concentration from the global budget concentration of CH(3)CCl(3).

Removal of 1,3-dichloro2-propanol and 3-chloro1,2-propanediol by the whole cell system of pseudomonas putida DSM 437

The removal of 1,3-dichloro-2-propanol (1,3-DCP), 3-chloro-1,2-propanediol (3-CPD) and their mixtures at concentrations up to 1,000 mg . L(-1) by the whole cell system of Pseudomonas putida DSM 437 was investigated. The 1,3-DCP removal rates ranged from 2.36 to 10.55 mg . L(-1) . h(-1); 3-CPD exhibited approximately two times higher removal rates compared to 1,3-DCP for all concentrations tested. Removal of 1,3-DCP and 3-CPD followed first-order kinetics with rate constants of 0.0109 h(-1) and 0.0206 h(-1), respectively. When the whole cell system of P. putida DSM 437 was applied to mixtures of the two halohdrins, complete removal of 1,3-DCP was achieved at 144 h while removal of 3-CPD was completed at times ranging from 72 to 144 h. Time to achieve 50% removal of both halohydrins depends on the initial concentration of each in the mixture. For 1,3-DCP, it ranged from 40.55 h at 200 mg . L(-1) to 53.28 h at 500 mg . L(-1) while the respected values for 3-CPD were 33.39 and 68.91 h.

Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities

Bacterial dehalogenases catalyse the cleavage of carbon-halogen bonds, which is a key step in aerobic mineralization pathways of many halogenated compounds that occur as environmental pollutants. There is a broad range of dehalogenases, which can be classified in different protein superfamilies and have fundamentally different catalytic mechanisms. Identical dehalogenases have repeatedly been detected in organisms that were isolated at different geographical locations, indicating that only a restricted number of sequences are used for a certain dehalogenation reaction in organohalogen-utilizing organisms. At the same time, massive random sequencing of environmental DNA, and microbial genome sequencing projects have shown that there is a large diversity of dehalogenase sequences that is not employed by known catabolic pathways. The corresponding proteins may have novel functions and selectivities that could be valuable for biotransformations in the future. Apparently, traditional enrichment and metagenome approaches explore different segments of sequence space. This is also observed with alkane hydroxylases, a category of proteins that can be detected on basis of conserved sequence motifs and for which a large number of sequences has been found in isolated bacterial cultures and genomic databases. It is likely that ongoing genetic adaptation, with the recruitment of silent sequences into functional catabolic routes and evolution of substrate range by mutations in structural genes, will further enhance the catabolic potential of bacteria toward synthetic organohalogens and ultimately contribute to cleansing the environment of these toxic and recalcitrant chemicals.

Fungal Aerobic Reductive Dechlorination of Ethyl 2-Chloroacetoacetate by Saccharomyces cerevisiae: Mechanism of a Novel Type of Microbial Dehalogenation

Saccharomyces cerevisiae reduces the beta-keto ester ethyl 2-chloroacetoacetate to the respective chiral cis- and trans-beta-hydroxy esters. In the course of chiral reduction, competing dehalogenation of the xenobiotic substrate to ethyl acetoacetate occurs, in a reaction mediated by cytosolic glutathione (GSH). Mechanistically, the dechlorination is a novel type of glutathione-dependent dehalogenation catalysed by an as yet unidentified glutathione-dependent dehalogenase. The first step consists of a nucleophilic replacement of the chloride substituent by glutathione. In the subsequent enzyme-catalysed step, a second glutathione molecule liberates the dehalogenation product by thiolytic attack at the thioether bridge, resulting in a net transfer of two electrons to the substrate and in the formation of glutathione disulfide (GSSG). Being effective under aerobic conditions and catalysed by a fungus, this reductive dechlorination of an aliphatic substrate is an outstanding example of a novel, glutathione-mediated microbial dehalogenation.

Growth inhibition of Escherichia coli by dichloromethane in cells expressing dichloromethane dehalogenase/glutathione S-transferase

Dichloromethane (DCM) dehalogenase converts DCM to formaldehyde via the formation of glutathione metabolites and generates 2 mol HCl per mol DCM metabolized. Growth of Escherichia coli expressing DCM dehalogenase was immediately and severely inhibited during conversion of 0.3 mM DCM. Intracellular pH (pH(i)) rapidly decreased and chloride ions were steadily released into the medium. Bacterial growth resumed after completion of DCM conversion and cell viability was unaffected. At 0.6 mM DCM there was no recovery from growth inhibition in liquid culture due to the build-up of inhibitory concentrations of formaldehyde. DCM turnover stimulated potassium efflux from cells, which was suppressed by glucose. The potassium efflux, therefore, did not contribute to growth inhibition. It was concluded that initial growth inhibition results from lowering of the cytoplasmic pH, but severity of growth inhibition was greater than expected for the change in pH(i). Possible contributors to growth inhibition are discussed.

Dehalogenation of haloalkanes by Mycobacterium tuberculosis H37Rv and other mycobacteria

Haloalkane dehalogenases convert haloalkanes to their corresponding alcohols by a hydrolytic mechanism. To date, various haloalkane dehalogenases have been isolated from bacteria colonizing environments that are contaminated with halogenated compounds. A search of current databases with the sequences of these known haloalkane dehalogenases revealed the presence of three different genes encoding putative haloalkane dehalogenases in the genome of the human parasite Mycobacterium tuberculosis H37Rv. The ability of M. tuberculosis and several other mycobacterial strains to dehalogenate haloaliphatic compounds was therefore studied. Intact cells of M. tuberculosis H37Rv were found to dehalogenate 1-chlorobutane, 1-chlorodecane, 1-bromobutane, and 1,2-dibromoethane. Nine isolates of mycobacteria from clinical material and four strains from a collection of microorganisms were found to be capable of dehalogenating 1,2-dibromoethane. Crude extracts prepared from two of these strains, Mycobacterium avium MU1 and Mycobacterium smegmatis CCM 4622, showed broad substrate specificity toward a number of halogenated substrates. Dehalogenase activity in the absence of oxygen and the identification of primary alcohols as the products of the reaction suggest a hydrolytic dehalogenation mechanism. The presence of dehalogenases in bacterial isolates from clinical material, including the species colonizing both animal tissues and free environment, indicates a possible role of parasitic microorganisms in the distribution of degradation genes in the environment.

Metabolism of Dichloromethane by the Strict Anaerobe Dehalobacterium formicoaceticum

The metabolism of dichloromethane by Dehalobacterium formicoaceticum in cell suspensions and crude cell extracts was investigated. The organism is a strictly anaerobic gram-positive bacterium that utilizes exclusively dichloromethane as a growth substrate and ferments this compound to formate and acetate in a molar ratio of 2:1. When [C]dichloromethane was degraded by cell suspensions, formate, the methyl group of acetate, and minor amounts of methanol were labeled, but there was no nuclear magnetic resonance signal corresponding to the carboxyl group of acetate. This finding and previously established carbon and electron balances suggested that dichloromethane was converted to methylene tetrahydrofolate, of which two-thirds was oxidized to formate while one-third gave rise to acetate by incorporation of CO(2) from the medium in the acetyl coenzyme A synthase reaction. When crude desalted extracts were incubated in the presence of dichloromethane, tetrahydrofolate, ATP, methyl viologen, and molecular hydrogen, dichloromethane and tetrahydrofolate were consumed, with the concomitant formation of stoichiometric amounts of methylene tetrahydrofolate. The in vitro transfer of the methylene group of dichloromethane onto tetrahydrofolate required substoichiometric amounts of ATP. The reaction was inhibited in a light-reversible fashion by 20 muM propyl iodide, thus suggesting involvement of a Co(I) corrinoid in the anoxic dehalogenation of dichloromethane. D. formicoaceticum exhibited normal growth with 0.8 mM sodium in the medium, and crude extracts contained ATPase activity that was partially inhibited by N,N'-dicyclohexylcarbodiimide and azide. During growth with dichloromethane, the organism thus may conserve energy not only by substrate-level phosphorylation but also by a chemiosmotic mechanism involving a sodium-independent F(0)F(1)-type ATP synthase.

Non-enzymatic and enzymatic hydrolysis of alkyl halides: a haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction

The semiempirical PM3 method, calibrated against ab initio HF/6-31+G(d) theory, has been used to elucidate the reaction of 1, 2-dichloroethane (DCE) with the carboxylate of Asp-124 at the active site of haloalkane dehalogenase of Xanthobacter autothropicus. Asp-124 and 13 other amino acid side chains that make up the active site cavity (Glu-56, Trp-125, Phe-128, Phe-172, Trp-175, Leu-179, Val-219, Phe-222, Pro-223, Val-226, Leu-262, Leu-263, and His-289) were included in the calculations. The three most significant observations of the present study are that: (i) the DCE substrate and Asp-124 carboxylate, in the reactive ES complex, are present as an ion-molecule complex with a structure similar to that seen in the gas-phase reaction of AcO- with DCE; (ii) the structures of the transition states in the gas-phase and enzymatic reaction are much the same where the structure formed at the active site is somewhat exploded; and (iii) the enthalpies in going from ground states to transition states in the enzymatic and gas-phase reactions differ by only a couple kcal/mol. The dehalogenase derives its catalytic power from: (i) bringing the electrophile and nucleophile together in a low-dielectric environment in an orientation that allows the reaction to occur without much structural reorganization; (ii) desolvation; and (iii) stabilizing the leaving chloride anion by Trp-125 and Trp-175 through hydrogen bonding.

Nonenzymatic and enzymatic hydrolysis of alkyl halides: a theoretical study of the SN2 reactions of acetate and hydroxide ions with alkyl chlorides

The SN2 displacements of chloride ion from CH3Cl, C2H5Cl, and C2H4Cl2 by acetate and hydroxide ions have been investigated, using ab initio molecular orbital theory at the HF/6-31+G(d), MP2/6-31+G(d), and MP4/6-31+G(d) levels of theory. The central barriers (calculated from the initial ion-molecule complex) of the reactions, the differences of the overall reaction energies, and the geometries of the transition states are compared. Essential stereochemical changes before and after the displacement reactions are described for selected cases. The gas phase reactions of hydroxide with CH3Cl, C2H5Cl, and C2H4Cl2 have no overall barrier, but there is a small overall barrier for the reactions of acetate with CH3Cl, C2H5Cl, and C2H4Cl2. A self-consistent reaction field solvation model was used to examine the SN2 reactions between methyl chloride and hydroxide ion and between 1,2-dichloroethane and acetate in solution. As expected, the reactions in polar solvent have a large barrier. However, the transition state structures determined by ab initio calculations change only slightly in the presence of a highly polar solvent as compared with the gas phase. We also calibrated the PM3 method for future study of an enzymatic SN2 displacement of halogen.

Anaerobic dehalogenases

Several anaerobic bacteria are able to reductively dehalogenate chlorinated hydrocarbons and to couple this reaction to the synthesis of ATP via a chemiosmotic mechanism (dehalorespiration). A few reductive dehalogenases have recently been purified and characterized. Preliminary investigations have been performed to elucidate the mechanism of dehalorespiration.

Strategies for the aerobic co-metabolism of chlorinated solvents

Recent field and laboratory studies have evaluated the potential for aerobic co-metabolism of chlorinated solvents. Different co-metabolic substrates and different methods of application have been tried, including growing indigenous microbes in situ, and injecting into the soil subsurface strains grown in subsurface reactors for their co-metabolic potential. There is much potential for using co-metabolism for treating a broad range of chlorinated aliphatic hydrocarbons. Recirculation wells have potential for adding soluble co-metabolic substrates (i.e. phenol and toluene) into contaminated aquifers, while direct addition of gaseous substrates (i.e. methane and propane) into aquifers also holds promise. Aromatic substrates (phenol and toluene) are best used for treatment of chlorinated ethenes, whereas gaseous co-metabolic substrate (methane and propane) are better suited for the treatment of chlorinated methanes and ethanes. Many factors can enhance co-metabolic transformations, such as nutrients and available energy sources.