Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure

Complete 2,4,6-trichlorophenol degradation by anaerobic sludge acclimated with 4-chlorophenol: Synergetic effect of nZVI@BMPC and sodium lactate as an external nutrient

Ball-milled plastic char supported nano zero-valent iron (nZVI@BMPC) and their application combined with anaerobic sludge for microbial dechlorination of 2,4,6-trichlorophenol (2,4,6-TCP) were investigated. The XRD and FTIR analysis proved composition of zero valent states of iron, and the BET and SEM analysis showed that nZVI was uniformly distributed on the surface of BMPC. Successive addition of 1000 mg/L sodium lactate and nZVI@BMPC enhanced the acclamation of anaerobic sludge and resulted in the degradation of 4-CP within 80 days. The acclimated consortium with nZVI@BMPC completely degraded 2,4,6-TCP into CH4 and CO2, and the key dechlorination route was through 4-CP dechlorinaion and mineralization. The degradation rate of 2,4,6-TCP with nZVI@BMPC was 0.22/d, greater than that without nZVI@BMPC. The dechlorination efficiency was enhanced in the Fe2+/Fe3+ system controlled by nZVI@BMPC and iron-reducing bacteria. Metagenomic analysis result showed that the dominant de-chlorinators were Chloroflexi sp., Desulfovibrio, and Pseudomonas, which could directly degrade 2,4,6-TCP to 4-CP, especially, Chloroflexi bacterium could concurrently be used to mineralize 4-CP. The relative abundance of the functional genes cprA, acoA, acoB, and tfdB increased significantly in the presence of the nZVI@BMPC. This study provides a new strategy can be a good alternative for possible application in groundwater remediation.

Microbiome resistance mediates stimulation of reduced graphene oxide to simultaneous abatement of 2,2',4,4',5-pentabromodiphenyl ether and 3,4-dichloroaniline in paddy soils

Paddy soils near electrical and electronic waste recycling sites generally suffer from co-pollution of polybrominated diphenyl ethers and 3,4-dichloroaniline (3,4-DCA). This study tested the feasibility of reduced graphene oxide (rGO) to stimulate the simultaneous abatement of 2,2',4,4',5-pentabromodiphenyl ether (BDE99) and 3,4-DCA in percogenic paddy soil (PPS) and hydromorphic paddy soil (HPS). rGO improved the debromination extent of BDE99 and the transformation rate of 3,4-DCA in PPS, but did not affect their abatement in HPS. The inhibition of specific fermenters, acetogens, and methanogens after rGO addition contributed to BDE99 debromination by obligate organohalide-respiring bacteria (OHRB) in PPS, but relevant soil microbiomes (e.g., fermenters, acetogens, methanogens, and obligate OHRB) responded little to rGO in HPS. For 3,4-DCA, the enhanced activities of nitrogen-metabolic chloroaniline degraders by rGO increased its transformation rate in PPS, but was compensated by the decreased biotransformation from 3,4-DCA to 3,4-dichloroacetanilide after the addition of rGO to HPS. The discrepant stimulation of rGO between PPS and HPS was mediated by soil microbiome resistance. rGO has the application potential to stimulate the simultaneous abatement of polybrominated diphenyl ethers and chloroanilines in paddy soils with relatively low microbiome resistance.

Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses

Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.

Marine Dehalogenator and Its Chaperones: Microbial Duties and Responses in 2,4,6-Trichlorophenol Dechlorination

Marine environments contain diverse halogenated organic compounds (HOCs), both anthropogenic and natural, nourishing a group of versatile organohalide-respiring bacteria (OHRB). Here, we identified a novel OHRB (Peptococcaceae DCH) with conserved motifs but phylogenetically diverse reductive dehalogenase catalytic subunit (RdhAs) from marine enrichment culture. Further analyses clearly demonstrate the horizontal gene transfer of rdhAs among marine OHRB. Moreover, 2,4,6-trichlorophenol (TCP) was dechlorinated to 2,4-dichlorophenol and terminated at 4-chlorophenol in culture. Dendrosporobacter and Methanosarcina were the two dominant genera, and the constructed and verified metabolic pathways clearly demonstrated that the former provided various substrates for other microbes, while the latter drew nutrients, but might provide little benefit to microbial dehalogenation. Furthermore, Dendrosporobacter could readily adapt to TCP, and sporulation-related proteins of Dendrosporobacter were significantly upregulated in TCP-free controls, whereas other microbes (e.g., Methanosarcina and Aminivibrio) became more active, providing insights into how HOCs shape microbial communities. Additionally, sulfate could affect the dechlorination of Peptococcaceae DCH, but not debromination. Considering their electron accessibility and energy generation, the results clearly demonstrate that bromophenols are more suitable than chlorophenols for the enrichment of OHRB in marine environments. This study will greatly enhance our understanding of marine OHRB (rdhAs), auxiliary microbes, and microbial HOC adaptive mechanisms.

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.

Naturally Occurring Organohalogen Compounds-A Comprehensive Review

The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.

Mechanistic insight into co-metabolic dechlorination of hexachloro-1,3-butadiene in Dehalococcoides

Hexachloro-1,3-butadiene (HCBD) as one of emerging persistent organic pollutants (POPs) poses potential risk to human health and ecosystems. Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation represents a promising strategy to remediate HCBD-contaminated sites. Nonetheless, information on the HCBD-dechlorinating OHRB and their dechlorination pathways remain unknown. In this study, both in vivo and in vitro experiments, as well as quantum chemical calculation, were employed to successfully identify and characterize the reductive dechlorination of HCBD by Dehalococcoides. Results showed that some Dehalococcoides extensively dechlorinated HCBD to (E)-1,2,3-tri-CBD via (E)-1,1,2,3,4-penta-CBD and (Z,E)-1,2,3,4-tetra-CBD in a co-metabolic way. Both qPCR and 16S rRNA gene amplicon sequencing analyses suggested that the HCBD-dechlorinating Dehalococcoides coupled their cell growth with dechlorination of perchloroethene (PCE), rather than HCBD. The in vivo and in vitro ATPase assays indicated ≥78.89% decrease in ATPase activity upon HCBD addition, which suggested HCBD inhibition on ATPase-mediated energy harvest and provided rationality on the Dehalococcoides-mediated co-metabolic dechlorination of HCBD. Interestingly, dehalogenation screening of organohalides with the HCBD-dechlorinating enrichment cultures showed that debromination of bromodichloromethane (BDCM) was active in the in vitro RDase assays but non-active in the in vivo experiments. Further in vitro assays of hydrogenase activity suggested that significant inhibition of BDCM on the hydrogenase activity could block electron derivation from H₂ for consequent reduction of organohalides in the in vivo experiments. Therefore, our results provided unprecedented insight into metabolic, co-metabolic and RDase-active-only dehalogenation of varied organohalides by specific OHRB, which could guide future screening of OHRB for remediation of sites contaminated by HCBD and other POPs.

Occurrence and transformation of unknown organochlorines in the wastewater treatment plant using specific Fragment-Based method with LC Q-TOF MS

Wastewater treatment plants (WWTPs) are important point sources of organochlorines in surface waters. However, comprehensive molecular-level understanding of the occurrence and transformation of organochlorines in WWTPs remains elusive. In this study, a specific fragment-based screening method with SWATH of LC Q-TOF MS was established to better understand the molecular composition of organochlorines. This method effectively excludes the non-chlorinated signals and provides multi-dimensional information (e.g., retention time, precursor ion mass, product ions, and molecular formula) with one injection to identify the possible structures of organochlorines. Eighty-seven organochlorines were successfully screened in practical wastewater samples, where 8 chlorinated sulfonic acids, 4 chlorophenols, 4 chlorinated benzenediols, and 6 chlorinated benzoic acids were further (tentatively) identified. Relative abundance of organochlorines showed that their occurrence was associated with the treatment units. In particular, anaerobic biological and NaClO treatment units contributed to the formation of chlorinated by-products. Most chlorinated by-products were substituted with more chlorine atoms than organochlorines from the influent. Furthermore, the relative abundance indicated that the fate of organochlorines were related to their structures. Chlorinated benzene sulfonic acids would be removed by adsorption on activated sludge. Most chlorinated benzoic acids were refractory, but some were likely to be chlorinated during the anaerobic process. Chlorophenols and chlorinated benzenediols might undergo chlorination, dealkylation/C-O bond breakage, and bromination. Our study offers a new tool to gain molecular information on organochlorines in complex environmental samples and highlights the importance of molecular structures when evaluating the fate of organochlorines and managing effluent discharge to surrounding waters.

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.

Biodegradation of aromatic pollutants meets synthetic biology

Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.

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

Several anaerobic bacteria can couple the reduction of aromatic halides to energy conservation. This organohalide respiration is catalyzed by enzymes containing cob(I)alamin, an activated supernucleophilic form of the coenzyme vitamin B₁₂. However, the mechanism underlying the electron transfer (inner-sphere vs outer-sphere ET) still remains elusive. To clarify this issue, we selected 36 fluoro-, chloro-, and bromobenzenes as representative substrates and calculated their free-energy barriers at the quantum chemical density functional theory level, considering a wide range of theoretically possible outer-sphere ET mechanisms. Across all 336 reaction routes addressed, 334 routes involve free-energy barriers larger than 20 kcal/mol. For two reaction routes with highly brominated benzenes, free-energy barriers below 20 kcal/mol imply abiotic reduction as observed in experiments. Thus, microbial B₁₂-dependent aromatic reductive dehalogenation does not proceed through an outer-sphere ET mechanism. Instead, the present study strongly suggests that microbe-catalyzed reductive dehalogenation of aromatic halides is governed by inner-sphere ET.

A peroxidase coordinating to Zn (II) preventing heme bleaching and resistant to the interference of H2 O2

Dehaloperoxidase (DHP) catalyzes detoxifying halophenols. It is a heme-containing enzyme using H₂ O₂ as the oxidant. Heme bleaching from the active site is of great concern. In addition, the interference of DHP by H₂ O₂ leads to the inactivation of the enzyme. To solve these two problems, DHP is coordinated to Zn (II) in PBS buffer to form a biomineralized composite (DHP&Zn-CP). DHP&Zn-CP was characterized by measuring SEM and confocal images, as well as energy dispersive X-ray spectrometry mapping. Fluorescence spectra demonstrated that DHP&Zn-CP can prevent heme bleaching. Two-dimensional FTIR spectra were measured, dynamically providing insight into the structural change of DHP along the coordination process. Raman spectra were performed to analyze the structural change. The optical spectra confirmed that the forming of DHP&Zn-CP had a little effect on the structures of DHP. For the dehalogenation of 2,4,6-trichlorophenol, DHP&Zn-CP can tolerate the presence of H₂ O₂ and is resistant to the interference by H₂ O₂ . The catalytic efficiency of DHP&Zn-CP is much higher than that of free DHP.

Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation

Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.

Reductive Debromination of Polybrominated Diphenyl Ethers - Microbes, Processes and Dehalogenases

Extensive utilization of polybrominated diphenyl ethers (PBDEs) as flame retardants since the 1960s in a variety of commercial products has resulted in ubiquitous environmental distribution of commercial PBDE mixtures. Dangers posed to biological populations became apparent after the discovery of elevated levels of PBDEs in biota, most notably in human breast milk and tissues. Environmental persistence of PBDEs results in significant transboundary displacement, threatening fragile ecosystems globally. Despite efforts to curtail usage of PBDEs, public concern remains about the effects of legacy PBDEs contamination and continued discharge of PBDEs in regions lacking restrictions on usage and manufacture. Among available technologies for remediation of PBDEs such as ex-situ soil washing, electrokinetic degradation, and biodegradation, this review focuses on bioremediation by microbes under anaerobic conditions. Bioremediation is generally preferred as it is less disruptive to contaminated ecosystems, is cost-effective, and can be implemented at sites that may be inaccessible to more traditional ex-situ methods. The aims of this review are to (1) summarize current knowledge of anaerobic microbes that debrominate PBDEs and their associated synergistic partnerships with non-dehalogenating microbes; (2) explore current understandings of the metabolic reductive debromination of PBDE congeners; (3) discuss recent discoveries on dehalogenase genes involved in debromination of PBDEs.

Interaction Mode and Regioselectivity in Vitamin B12-Dependent Dehalogenation of Aryl Halides by Dehalococcoides mccartyi Strain CBDB1

The bacterium Dehalococcoides, strain CBDB1, transforms aromatic halides through reductive dehalogenation. So far, however, the structures of its vitamin B₁₂-containing dehalogenases are unknown, hampering clarification of the catalytic mechanism and substrate specificity as basis for targeted remediation strategies. This study employs a quantum chemical donor-acceptor approach for the Co(I)-substrate electron transfer. Computational characterization of the substrate electron affinity at carbon-halogen bonds enables discriminating aromatic halides ready for dehalogenation by strain CBDB1 (active substrates) from nondehalogenated (inactive) counterparts with 92% accuracy, covering 86 of 93 bromobenzenes, chlorobenzenes, chlorophenols, chloroanilines, polychlorinated biphenyls, and dibenzo-p-dioxins. Moreover, experimental regioselectivity is predicted with 78% accuracy by a site-specific parameter encoding the overlap potential between the Co(I) HOMO (highest occupied molecular orbital) and the lowest-energy unoccupied sigma-symmetry substrate MO (σ*), and the observed dehalogenation pathways are rationalized with a success rate of 81%. Molecular orbital analysis reveals that the most reactive unoccupied sigma-symmetry orbital of carbon-attached halogen X (σ_C-X^*) mediates its reductive cleavage. The discussion includes predictions for untested substrates, thus providing opportunities for targeted experimental investigations. Overall, the presently introduced orbital interaction model supports the view that with bacterial strain CBDB1, an inner-sphere electron transfer from the supernucleophile B₁₂ Co(I) to the halogen substituent of the aromatic halide is likely to represent the rate-determining step of the reductive dehalogenation.

Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer

The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors. Their reaction mechanism is under debate. Here we report on substrate–enzyme interactions in a tetrachloroethene RDase (PceA) that also converts aryl halides. The shape of PceA’s highly apolar active site directs binding of bromophenols at some distance from the cobalt and with the hydroxyl substituent towards the metal. A close cobalt–substrate interaction is not observed by electron paramagnetic resonance spectroscopy. Nonetheless, a halogen substituent para to the hydroxyl group is reductively eliminated and the path of the leaving halide is traced in the structure. Based on these findings, an enzymatic mechanism relying on a long-range electron transfer is concluded, which is without parallel in vitamin B₁₂-dependent biochemistry and represents an effective mode of RDase catalysis.

Cobalamin-containing reductive dehalogenases from organohalide-respiring bacteria play a key role in the degradation of halogenated organic compounds. Here the authors proposed a catalytic mechanism for dehalogenation that relies on a long-range electron transfer from the cobalt in the centre of the enzyme’s cofactor to the substrate.