Dehalococcoides-Mediated B12-Dependent Reductive Dehalogenation of Aromatics Does Not Proceed through Outer-Sphere Electron Transfer

Organohalide respiration in Dehalococcoides strains represents a novel mode of proton motive force generation

Dehalococcoides strains grow obligately by respiration with hydrogen as an electron donor and halogenated compounds as terminal electron acceptors, catalysed by a single membrane-integrated protein supercomplex. Many insights have been gained into the respiratory complex based on physiological experiments, biochemical analyses, genome sequencing, and proteomics. Recent data acquired from activity tests with deuterated water and whole cells revealed the mode of energy conservation by this respiratory complex. The data shows that the proton required for periplasmic dehalogenation originates from inside the cell, suggesting an electrogenic protonation of the electron acceptor, while two protons are released into the periplasm by hydrogen oxidation. This surprisingly simple mechanism of pmf generation aligns with the subunit composition of the respiratory complex, the orientation of the subunits in the membrane, the absence of quinones as electron mediators, the rigidity of the cell membrane, as evidenced by its phospholipid fatty acid composition, and with proton channels formed by protonatable amino acid residues identified in the AlphaFold2-predicted structure of one of the membrane-spanning subunits. The respiration model is characterised by: (i) electrogenic protonation of the electron acceptor; (ii) reliance on a single protein complex for pmf generation without quinones; (iii) lack of transmembrane cytochromes; (iv) presence of both redox-active centres on the same side of the membrane, both facing the periplasm; and (v) restriction of the electron flow to periplasmic subunits of the respiratory complex. This type of respiration may represent an ancestral, quinone-free mechanism, offering inspiring new biotechnological applications.

Multi-element (2H, 13C, 37Cl) isotope analysis to characterize reductive transformation of α-, β-, γ-, and δ-HCH isomers by cobalamin and Fe0 nanoparticles

Hexachlorocyclohexane (HCH), a typical persistent organic pollutant, poses a serious threat to both human health and the environment. The degradability of HCH isomers (α, β, γ, and δ) varies significantly under anoxic aqueous conditions and the corresponding reductive transformation mechanisms remain elusive. This work employed multi-element (2H, 13C, 37Cl) stable isotope analysis to characterize the reductive dehalogenation mechanisms of HCH isomers using cobalamin (vitamin B₁₂) reduced with Ti3+ and Fe0 nanoparticles. The isotopic fractionation of HCH isomers varied from -2.8 ± 0.5 to -7.0 ± 0.7 ‰ for carbon (εC), from not significant to -62.4 ± 5.2 ‰ for hydrogen (εH), and from -1.4 ± 0.2 to -4.7 ± 0.5 ‰ for chlorine (εCl), respectively. Dual C-Cl isotopic fractionation values (ΛC/Cl) for α-, β-, γ- and δ-HCH during the transformation by B12 were determined to be 2.0 ± 0.2, 1.5 ± 0.2, 1.1 ± 0.1, and 1.9 ± 0.3, respectively. The ΛC/Cl values of β- and δ-HCH in the reaction with Fe0 nanoparticles were found to be similar (1.9 ± 0.3 and 1.9 ± 0.2). However, the apparent kinetic isotope effect AKIEC/AKIECl values suggested that the bond cleavage mechanism of δ-HCH may differ from that of other isomers. The comparison of the angles θ by multi-element isotope plot showed a distinct differentiation between the pathways of anaerobic transformation of HCH isomers and aerobic pathways reported in the literature. Therefore, multi-element isotope analysis could offer a new perspective for characterizing the fate of HCH isomers.

Unravelling the processes involved in biodegradation of chlorinated organic pollutant: From microbial community to isolated organohalide degraders

Hundreds of studies have demonstrated the bioremediation of chlorinated organic pollutants (COPs) in flooded environments. However, the role of specific functional strains in degrading COPs under complex media such as wetlands is still unclear. Here, we focused on the microbial characteristics of COP-polluted sediments, identified the bacteria responsible for degradation and conducted a genomic analysis of these bacteria. Four strains were obtained and identified as Petrimonas sulfuriphila PET, Robertmurraya sp. CYTO, Hungatella sp. CloS1 and Enterococcus avium PseS3, respectively. They were capable of degrading a typical COP, γ-hexachlorocyclohexane (γ-HCH). The residual γ-HCH concentrations were 58.8 % (PET), 45.6 % (CYTO), 60.2 % (CloS1), and 69.3 % (PseS3) of its initial value, respectively. Strain PET, CYTO and CloS1 could degrade γ-HCH to its dehalogenation product chlorobenzene. Each strain harbors genes annotated to the pathway of halogenated organic matter degradation (e.g. 2-haloacid dehalogenase) and cobalamin biosynthesis, which are involved in the degradation of COPs. Comparative genomic analysis of the four strains and other classical organohalide-respiring bacteria (e.g. Dehalococcoides mccartyi and Sulfurospirillum multivorans DSM 12446) showed that they share orthologous clusters related to the cobalamin biosynthetic process (GO:0009236). VB12 was also detected in the culture systems of the four strains, further highlighting the importance of cobalamin in COPs degradation. In the genome of the four strains, some genes were annotated to the halogenated organic matter degradation and cobalamin biosynthesis pathway within horizontal gene transfer (HGT) regions. This further indicated that microorganisms carrying these genes can adapt faster to pollution stress through HGT. Together, these findings revealed the co-evolution mechanism of functional strains and may provide novel insights into improved bioremediation strategies for COP-polluted complex media based on generalist organochlorine-degrading bacteria.

Anaerobic biotransformation of two novel brominated flame retardants: Kinetics, isotope fractionation and reaction mechanisms

1,2,5,6-tetrabromocyclooctane (TBCO) and 2,3-dibromopropyl-2,4,6-tribromophenyl ether (DPTE), as safer alternatives to traditional brominated flame retardants, have been extensively detected in various environmental media and pose emerging risks. However, much less is known about their fate in the environment. Anaerobic microbial transformation is a key pathway for the natural attenuation of contaminants. This study investigated, for the first time, the microbial transformation behaviors of β-TBCO and DPTE by Dehalococcoides mccartyi strain CG1. The results indicated that both β-TBCO and DPTE could be easily transformed by D. mccartyi CG1 with kobs values of 0.0218 ± 0.0015 h-1 and 0.0089 ± 0.0003 h-1, respectively. In particular, β-TBCO seemed to undergo dibromo-elimination and then epoxidation to form 4,5-dibromo-9-oxabicyclo[6.1.0]nonane, while DPTE experienced debromination at the benzene ring (ortho-bromine being removed prior to para-bromine) rather than at the carbon chain. Additionally, pronounced carbon and bromine isotope fractionations were observed during biotransformation of β-TBCO and DPTE, suggesting that C-Br bond breaking is the rate-limiting step of their biotransformation. Finally, coupled with identified products and isotope fractionation patterns, β-elimination (E2) and Sn2-nucleophilic substitution were considered the most likely microbial transformation mechanisms for β-TBCO and DPTE, respectively. This work provides important information for assessing the potential of natural attenuation and environmental risks of β-TBCO and DPTE.

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.

Recent advances and trends of trichloroethylene biodegradation: A critical review

Trichloroethylene (TCE) is a ubiquitous chlorinated aliphatic hydrocarbon (CAH) in the environment, which is a Group 1 carcinogen with negative impacts on human health and ecosystems. Based on a series of recent advances, the environmental behavior and biodegradation process on TCE biodegradation need to be reviewed systematically. Four main biodegradation processes leading to TCE biodegradation by isolated bacteria and mixed cultures are anaerobic reductive dechlorination, anaerobic cometabolic reductive dichlorination, aerobic co-metabolism, and aerobic direct oxidation. More attention has been paid to the aerobic co-metabolism of TCE. Laboratory and field studies have demonstrated that bacterial isolates or mixed cultures containing Dehalococcoides or Dehalogenimonas can catalyze reductive dechlorination of TCE to ethene. The mechanisms, pathways, and enzymes of TCE biodegradation were reviewed, and the factors affecting the biodegradation process were discussed. Besides, the research progress on material-mediated enhanced biodegradation technologies of TCE through the combination of zero-valent iron (ZVI) or biochar with microorganisms was introduced. Furthermore, we reviewed the current research on TCE biodegradation in field applications, and finally provided the development prospects of TCE biodegradation based on the existing challenges. We hope that this review will provide guidance and specific recommendations for future studies on CAHs biodegradation in laboratory and field applications.

Microbial reductive dechlorination of polychlorinated dibenzo-p-dioxins: Pathways and features unravelled via electron density

Microbial reductive dechlorination provides a promising approach for remediating sites contaminated with polychlorinated dibenzo-p-dioxins (PCDDs). Nonetheless, the overall dechlorination pathways and features remain elusive. Herein, we address these issues by quantum chemical calculations, considering the calibrations of reductive dechlorination of 15 PCDDs mediated by three Dehalococcoides strains. Chlorine substituents with lower electron density are prone to be microbially abstracted, which differentiates 72 microbe-active PCDDs from 3 nonactive analogues with a success rate of 100%. For all 256 transformation routes of 75 PCDDs, electron density differences of chlorines pinpoint 105 viable and 125 unviable pathways, corresponding a success rate of 90%. The feasibility of 26 reductive dechlorination pathways are uncertain because of the limited available experimental data. 98% (251/256) of microbial chlorine abstraction follows an order of Cl_O,Cl>Cl_Cl,Cl>Cl_H,O>Cl_H,Cl>Cl_H,H=0. PCDDs solely containing chlorines at C₁, C₄, C₆, and/or C₉ can be completely dechlorinated to non-chlorinated dioxin; while PCDDs housing chlorines at C₂, C₃, C₇, and/or C₈ can be dechlorinated to 2-MCDD or 2,7/8-DCDD as final products. These findings also support reductive dechlorination of PCDDs in mixed cultures and sediments (> 98% and 83%). These findings would promote the application of dechlorinating bacteria in targeted remediation and facilitate the respective studies on other POPs.

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.