Dual Carbon-Chlorine Isotope Analysis Indicates Distinct Anaerobic Dichloromethane Degradation Pathways in Two Members of Peptococcaceae

Insight into natural attenuation of tributyl phosphate by indigenous anaerobic microbes in soils: Implication by stable carbon isotope fractionation and microbial community structures

Organophosphate esters (OPEs) are widespread in the environment, with high persistence and toxicity. However, the underlying mechanisms of anaerobic microbial degradation of OPEs remain elusive in the field environment. In this study, the natural attenuation mechanisms of tributyl phosphate (TnBP) by indigenous anaerobic microorganisms in soils were investigated by using compound-specific stable isotope analysis (CSIA) and characterization of microbial communities. The results indicated that dibutyl phosphate (DnBP) was the major degradation product of TnBP. Significant carbon isotope fractionation was observed for TnBP during the anaerobic microbial degradation, and the carbon isotope enrichment factor (εC) was determined to be -2.71 ± 0.13‰. Unlike aerobic degradation with P-O bond cleavage, C-O bond cleavage was verified as the mode to removal a butyl side chain for TnBP to generate DnBP during the anaerobic microbial degradation. Microbial community analysis indicated that Sphingomonans, Nocardioides and Streptomyces were the important contributors to microbial degradation of TnBP in anoxic soils. TnBP altered microbial metabolic functions in anoxic soils, mainly enhancing the biosynthesis of ansamycins, ketone bodies and amino acids, and flagellar assembly, which promoted microbial degradation of TnBP. This study provided a better method to characterize the chemical bond cleavage mode and effect of OPEs on microbial communities, which was a prerequisite for the bioremediation of OPE pollution in soils.

MecE, MecB, and MecC proteins orchestrate methyl group transfer during dichloromethane fermentation

Dichloromethane (DCM), a common hazardous industrial chemical, is anaerobically metabolized by four bacterial genera: Dehalobacter, Dehalobacterium, Ca. Dichloromethanomonas, and Ca. Formimonas. However, the pivotal methyltransferases responsible for DCM transformation have remained elusive. In this study, we investigated the DCM catabolism of Dehalobacterium formicoaceticum strain EZ94, contained in an enriched culture, using a combination of biochemical approaches. Initially, enzymatic assays were conducted with cell-free protein extracts, after protein separation by blue native polyacrylamide gel electrophoresis. In the slices with the highest DCM transformation activity, a high absolute abundance of the methyltransferase MecC was revealed by mass spectrometry. Enzymatic activity assays with heterologously expressed MecB, MecC, and MecE from strain EZ94 showed complete DCM transformation only when all three enzymes were present. Our experimental results, coupled with the computational analysis of MecB, MecC, and MecE sequences, enabled us to assign specific roles in DCM transformation to each of the proteins. Our findings reveal that both MecE and MecC are zinc-dependent methyltransferases responsible for DCM demethylation and re-methylation of a product, respectively. MecB functions as a cobalamin-dependent shuttle protein transferring the methyl group between MecE and MecC. This study provides the first biochemical evidence of the enzymes involved in the anaerobic metabolism of DCM.IMPORTANCEDichloromethane (DCM) is a priority regulated pollutant frequently detected in groundwater. In this work, we identify the proteins responsible for the transformation of DCM fermentation in Dehalobacterium formicoaceticum strain EZ94 using a combination of biochemical approaches, heterologous expression of proteins, and computational analysis. These findings provide the basis to apply these proteins as biological markers to monitor bioremediation processes in the field.

Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation

Nitrogen is a limiting nutrient for degraders function in hydrocarbon-contaminated environments. Biological nitrogen fixation by diazotrophs is a natural solution for supplying bioavailable nitrogen. Here, we determined whether the diazotroph Azotobacter chroococcum HN can provide nitrogen to the polycyclic aromatic hydrocarbon-degrading bacterium Paracoccus aminovorans HPD-2 and further explored the synergistic interactions that facilitate pyrene degradation in nitrogen-deprived environments. We found that A. chroococcum HN and P. aminovorans HPD-2 grew and degraded pyrene more quickly in co-culture than in monoculture. Surface-enhanced Raman spectroscopy combined with 15N stable isotope probing (SERS - 15N SIP) demonstrated that A. chroococcum HN provided nitrogen to P. aminovorans HPD-2. Metabolite analysis and feeding experiments confirmed that cross-feeding occurred between A. chroococcum HN and P. aminovorans HPD-2 during pyrene degradation. Transcriptomic and metabolomic analyses further revealed that co-culture significantly upregulated key pathways such as nitrogen fixation, aromatic compound degradation, protein export, and the TCA cycle in A. chroococcum HN and quorum sensing, aromatic compound degradation and ABC transporters in P. aminovorans HPD-2. Phenotypic and fluorescence in situ hybridization (FISH) assays demonstrated that A. chroococcum HN produced large amounts of biofilm and was located at the bottom of the biofilm in co-culture, whereas P. aminovorans HPD-2 attached to the surface layer and formed a bridge-like structure with A. chroococcum HN. This study demonstrates that distinct syntrophic interactions occur between A. chroococcum HN and P. aminovorans HPD-2 and provides support for their combined use in organic pollutant degradation in nitrogen-deprived environments.

Novel Insights into Uptake, Translocation, and Transformation Mechanisms of 2,2',4,4'-Tetra Brominated Diphenyl Ether (BDE-47) in Wheat (Triticum aestivum L.): Implication by Compound-Specific Stable Isotope and Transcriptome Analysis

The uptake, translocation, and transformation of 2,2',4,4'-tetra brominated diphenyl ether (BDE-47) in wheat (Triticum aestivum L.) were comprehensively investigated by hydroponic experiments using compound-specific stable isotope analysis (CSIA) and transcriptome analysis. The results indicated that BDE-47 was quickly adsorbed on epidermis of wheat roots and then absorbed in roots via water and anion channels as well as an active process dependent on energy. A small fraction of BDE-47 in roots was subjected to translocation acropetally, and an increase of δ13C values in shoots than roots implied that BDE-47 in roots had to cross at least one lipid bilayer to enter the vascular bundle via transporters. In addition, accompanied by the decreasing concentrations, δ13C values of BDE-47 showed the increasing trend with time in shoots, indicating occurrence of BDE-47 transformation. OH-PBDEs were detected as transformation products, and the hydroxyl group preferentially substituted at the ortho-positions of BDE-47. Based on transcriptome analysis, genes encoding polybrominated diphenyl ether (PBDE)-metabolizing enzymes, including cytochrome P450 enzymes, nitrate reductases, and glutathione S-transferases, were significantly upregulated after exposure to BDE-47 in shoots, further evidencing BDE-47 transformation. This study first reported the stable carbon isotope fractionation of PBDEs during translocation and transformation in plants, and application of CSIA and transcriptome analysis allowed systematically characterize the environmental behaviors of pollutants in plants.

Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation

Dichloromethane (DCM, methylene chloride) is a toxic, high-volume industrial pollutant of long-standing. Anaerobic biodegradation is crucial for its removal from contaminated environments, yet prevailing mechanisms remain unresolved, especially concerning dehalogenation. In this study, we obtained an assembled genome of a novel DCM-degrading strain, Dehalobacterium formicoaceticum strain EZ94, from a stable DCM-degrading consortium, and we analyzed its proteome during degradation of DCM. A gene cluster recently predicted to play a major role in anaerobic DCM catabolism (the mec cassette) was found. Methyltransferases and other proteins encoded by the mec cassette were among the most abundant proteins produced, suggesting their involvement in DCM catabolism. Reductive dehalogenases were not detected. Genes and corresponding proteins for a complete Wood-Ljungdahl pathway, which could enable further metabolism of DCM carbon, were also found. Unlike for the anaerobic DCM degrader "Ca. F. warabiya," no genes for metabolism of the quaternary amines choline and glycine betaine were identified. This work provides independent and supporting evidence that mec-associated methyltransferases are key to anaerobic DCM metabolism.

A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia

Dehalobacterium formicoaceticum is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic representative of its class, the Dehalobacteriia, according to the Genome Taxonomy Database. However, substantial additional diversity has been revealed in this lineage through culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation appears to be a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as carbon and energy sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes and the presence of S-layers. The ability of D. formicoaceticum to grow on serine without DCM was experimentally confirmed and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We suggest that members of the Dehalobacteriia are low-abundance fermentative scavengers in anoxic habitats.

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.

Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by 'Candidatus Formimonas warabiya' strain DCMF

Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.

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

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

Identification and widespread environmental distribution of a gene cassette implicated in anaerobic dichloromethane degradation

Anthropogenic activities and natural processes release dichloromethane (DCM, methylene chloride), a toxic chemical with substantial ozone-depleting capacity. Specialized anaerobic bacteria metabolize DCM; however, the genetic basis for this process has remained elusive. Comparative genomics of the three known anaerobic DCM-degrading bacterial species revealed a homologous gene cluster, designated the methylene chloride catabolism (mec) gene cassette, comprising 8-10 genes encoding proteins with 79.6%-99.7% amino acid identities. Functional annotation identified genes encoding a corrinoid-dependent methyltransferase system, and shotgun proteomics applied to two DCM-catabolizing cultures revealed high expression of proteins encoded on the mec gene cluster during anaerobic growth with DCM. In a DCM-contaminated groundwater plume, the abundance of mec genes strongly correlated with DCM concentrations (R²  = 0.71-0.85) indicating their potential value as process-specific bioremediation biomarkers. mec gene clusters were identified in metagenomes representing peat bogs, the deep subsurface, and marine ecosystems including oxygen minimum zones (OMZs), suggesting a capacity for DCM degradation in diverse habitats. The broad distribution of anaerobic DCM catabolic potential infers a role for DCM as an energy source in various environmental systems, and implies that the global DCM flux (i.e., the rate of formation minus the rate of consumption) might be greater than emission measurements suggest.

Anaerobic biodegradation of chloroform and dichloromethane with a Dehalobacter enrichment culture

Chloroform (CF) and dichloromethane (DCM) are among the more commonly identified chlorinated aliphatic compounds found in contaminated soil and groundwater. Complete dechlorination of CF has been reported under anaerobic conditions by microbes that respire CF to DCM and others that biodegrade DCM. The objectives of this study were to ascertain if a commercially available bioaugmentation enrichment culture (KB-1® Plus CF) uses an oxidative or fermentative pathway for biodegradation of DCM; and to determine if the products from DCM biodegradation can support organohalide respiration of CF to DCM in the absence of an exogenous electron donor. In various treatments with the KB-1^® Plus CF culture to which ¹⁴C-CF was added, the predominant product was ¹⁴CO₂, indicating that oxidation is the predominant pathway for DCM. Recovery of ¹⁴C-DCM when biodegradation was still in progress confirmed that CF first undergoes reductive dechlorination to DCM. ¹⁴C-labeled organic acids, including acetate and propionate, were also recovered, suggesting that synthesis of organic acids provides a sink for the electron equivalents from oxidation of DCM. When the biomass was washed to remove organic acids from prior additions of exogenous electron donor and only CF and DCM were added, the culture completely dechlorinated CF. The total amount of DCM added was not sufficient to provide the electron equivalents needed to reduce CF to DCM. Thus, the additional reducing power came via the DCM generated from CF reduction. Nevertheless, the rate of CF consumption was considerably slower in comparison to treatments that received an exogenous electron donor. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are among the more commonly identified chlorinated aliphatic compounds found in contaminated soil and groundwater. One way to address this problem is to add microbes to the subsurface that can biodegrade these compounds. While microbes are known that can accomplish this task, less is known about the pathways used under anaerobic conditions. Some use an oxidative pathway, resulting mainly in carbon dioxide. Others use a fermentative pathway, resulting in formation of organic acids. In this study, a commercially available bioaugmentation enrichment culture (KB-1^® Plus CF) was evaluated using carbon-14 labelled chloroform. The main product formed was carbon dioxide, indicating the use of an oxidative pathway. The reducing power gained from oxidation was shown to support reductive dechlorination of CF to DCM. The results demonstrate the potential to achieve full dechlorination of CF and DCM to nonhazardous products that are difficult to identify in the field.

Water table fluctuations affect dichloromethane biodegradation in lab-scale aquifers contaminated with organohalides

Dichloromethane (DCM) is a toxic industrial solvent frequently detected in multi-contaminated aquifers. It can be degraded biotically or abiotically, and under oxic or anoxic conditions. The extent and pathways of DCM degradation in aquifers may thus depend on water table fluctuations and microbial responses to hydrochemical variations. Here, we examined the effect of water table fluctuations on DCM biodegradation in two laboratory aquifers fed with O₂-depleted DCM-spiked groundwater from a well-characterized former industrial site. Hydrochemistry, stable isotopes of DCM (δ¹³C and δ³⁷Cl), and bacterial community composition were examined to determine DCM mass removal and degradation pathways under steady-state (static water table) and transient (fluctuating water table) conditions. DCM mass removal was more pronounced under transient (95%) than under steady-state conditions (42%). C and Cl isotopic fractionation values were larger under steady-state (ε_bulk^C = -23.6 ± 3.2‰, and ε_bulk^Cl= -8.7 ± 1.6‰) than under transient conditions (ε_bulk^C = -11.8 ± 2.0‰, and ε_bulk^Cl = -3.1 ± 0.6‰). Dual C-Cl isotope analysis suggested the prevalence of distinct anaerobic DCM degradation pathways, with Λ^C/Cl values of 1.92 ± 0.30 and 3.58 ± 0.42 under steady-state and transient conditions, respectively. Water table fluctuations caused changes in redox conditions and oxygen levels, resulting in a higher relative abundance of Desulfosporosinus (Peptococcaceae family). Taken together, our results show that water table fluctuations enhanced DCM biodegradation, and correlated with bacterial taxa associated with anaerobic DCM degradation. Our integrative approach allows to evaluate anaerobic DCM degradation under dynamic hydrogeological conditions, and may help improving bioremediation strategies at DCM contaminated sites.

Competitive microbial degradation among PBDE congeners in anaerobic wetland sediments: Implication by multiple-line evidences including compound-specific stable isotope analysis

Polybrominated diphenyl ethers (PBDEs) are widespread contaminants in the environment. Microbial reductive debromination is one of the important attenuation processes for PBDEs in the anaerobic sediments. This study first investigated the interaction between BDE-47 and BDE-153 during the microbial degradation in wetland sediments by the multiple-line approaches including biodegradation kinetics, microbial community structures and stable isotope composition. BDE-47 and BDE-153 biodegradation fitted pseudo-zero-order kinetics, with the higher degradation rates in single than combined exposure, indicating the mutual inhibition in co-exposure condition. BDE-47 and BDE-153 shared the common dehalogenators (genus Dehalococcoides and Acinetobacter) with enrichment in combined exposure, indicating the potential competition in dehalogenating bacteria during biodegradation. Microbial degradation could lead to the isotopic fractionation of BDE-47 and BDE-153, with the smaller changes in δ¹³C in combined than single exposure. The apparent kinetic isotope effect of carbon (AKIE_C) was different between BDE-47 and BDE-153 in single exposure, whilst identical in combined exposure, indicating the similar degradation mechanism for BDE-47 and BDE-153 in co-exposure condition. These results revealed that the competition on microbial degradation occurred among PBDEs in co-exposure condition, which was important for the comprehensive risk assessment of simultaneous exposure to multiple PBDE congeners in the environment.

Multi-elemental C-Br-Cl isotope analysis for characterizing biotic and abiotic transformations of 1-bromo-2-chloroethane (BCE)

Multi-elemental C-Br-Cl compound-specific isotope analysis was applied for characterizing abiotic and biotic degradation of the environmental pollutant 1-bromo-2-chloroethane (BCE). Isotope effects were determined in the model processes following hydrolytic dehalogenation and dihaloelimination pathways as well as in a microcosm experiment by the microbial culture from the contaminated site. Hydrolytic dehalogenation of BCE under alkaline conditions and by DhaA enzyme resulted in similar dual isotope slopes (Ʌ_C/Br 21.9 ± 4.7 and 19.4 ± 1.8, respectively, and Ʌ_C/Cl ~ ∞). BCE transformation by cyanocobalamin (B12) and by Sulfurospirillum multivorans followed dihaloelimination and was accompanied by identical, within the uncertainty range, dual isotope slopes (Ʌ_C/Br 8.4 ± 1.7 and 7.9 ± 4.2, respectively, and Ʌ_C/Cl 2.4 ± 0.3 and 1.5 ± 0.6, respectively). Changes over time in the isotope composition of BCE from the contaminated groundwater showed only a slight variation in δ¹³C values and were not sufficient for the elucidation of the BCE degradation pathway in situ. However, an anaerobic microcosm experiment with the enrichment cultures from the contaminated groundwater presented dual isotope slopes similar to the hydrolytic pathway, suggesting that the potential for BCE degradation in situ by the hydrolytic dehalogenation pathway exists in the contaminated site.

Assessing microbial degradation degree and bioavailability of BDE-153 in natural wetland soils: Implication by compound-specific stable isotope analysis

Microbial degradation is an important pathway for the attenuation of polybrominated diphenyl ethers (PBDEs) in natural soils. In this study, the compound-specific stable isotope analysis (CSIA) was applied to characterize microbial degradation of BDE-153, one of the prevailing and toxic PBDE congeners, in natural wetland soils. During the 45-day incubation, the residual percentages of BDE-153 decreased to 67.9% and 73.6% in non-sterilized soils spiked with 1.0 and 5.0 μg/g, respectively, which were both much lower than those in sterilized soils (96.0% and 97.2%). This result indicated that microbial degradation could accelerate BDE-153 elimination in wetland soils. Meanwhile, the significant carbon isotope fractionation was observed in non-sterilized soils, with δ¹³C of BDE-153 shifting from -29.4‰ to -26.7‰ for 1.0 μg/g and to -27.2‰ for 5.0 μg/g, respectively, whilst not in sterilized soils. This phenomenon indicated microbial degradation could induce stable carbon isotope fractionation of BDE-153. The carbon isotope enrichment factor (ε_c) for BDE-153 microbial degradation was first determined as -7.58‰, which could be used to assess the microbial degradation and bioavailability of BDE-153 in wetland soils. Based on δ¹³C and ε_c, the new methods were developed to dynamically and quantitatively estimate degradation degree and bioavailability of BDE-153 during degradation process, respectively, which could exclude interference of physical processes. This work revealed that CSIA was a promising method to investigate in situ microbial degradation of PBDEs in field studies.

Multi-element (C, H, Cl, Br) stable isotope fractionation as a tool to investigate transformation processes for halogenated hydrocarbons

Compound-specific isotope analysis (CSIA) is a powerful tool to evaluate transformation processes of halogenated compounds. Many halogenated hydrocarbons allow for multiple stable isotopic systems (C, H, Cl, Br) to be measured for a single compound. This has led to a large body of literature describing abiotic and biotic transformation pathways and reaction mechanisms for contaminants such as chlorinated alkenes and alkanes as well as brominated hydrocarbons. Here, the current literature is reviewed and a new compilation of Λ values for multi-isotopic systems for halogenated hydrocarbons is presented. Case studies of each compound class are discussed and thereby the current strengths of multi-element isotope analysis, continuing challenges, and gaps in our current knowledge are identified for practitioners of multi-element CSIA to address in the near future.

Mineralization versus fermentation: evidence for two distinct anaerobic bacterial degradation pathways for dichloromethane

Dichloromethane (DCM) is an anthropogenic pollutant with ozone destruction potential that is also formed naturally. Under anoxic conditions, fermentation of DCM to acetate and formate has been reported in axenic culture Dehalobacterium formicoaceticum, and to acetate, H₂ and CO₂ in mixed culture RM, which harbors the DCM degrader 'Candidatus Dichloromethanomonas elyunquensis'. RM cultures produced 28.1 ± 2.3 μmol of acetate from 155.6 ± 9.3 μmol DCM, far less than the one third (i.e., about 51.9 µmol) predicted based on the assumed fermentation model, and observed in cultures of Dehalobacterium formicoaceticum. Temporal metabolite analyses using gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy revealed that no ¹³C-labeled acetate was formed in ¹³C-DCM-grown RM cultures, indicating acetate was not a direct product of DCM metabolism. The data were reconciled with DCM mineralization and H₂ consumption via CO₂ reduction to acetate and methane by homoacetogenic and methanogenic partner populations, respectively. In contrast, Dehalobacterium formicoaceticum produced ¹³C-labeled acetate and formate from ¹³C-DCM, consistent with a fermentation pathway. Free energy change calculations predicted that organisms with the mineralization pathway are the dominant DCM consumers in environments with H₂ <100 ppmv. These findings have implications for carbon and electron flow in environments where DCM is introduced through natural production processes or anthropogenic activities.

Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture

Bacteria capable of dechlorinating the toxic environmental contaminant dichloromethane (DCM, CH2Cl2) are of great interest for potential bioremediation applications. A novel, strictly anaerobic, DCM-fermenting bacterium, "DCMF", was enriched from organochlorine-contaminated groundwater near Botany Bay, Australia. The enrichment culture was maintained in minimal, mineral salt medium amended with dichloromethane as the sole energy source. PacBio whole genome SMRTTM sequencing of DCMF allowed de novo, gap-free assembly despite the presence of cohabiting organisms in the culture. Illumina sequencing reads were utilised to correct minor indels. The single, circularised 6.44 Mb chromosome was annotated with the IMG pipeline and contains 5,773 predicted protein-coding genes. Based on 16S rRNA gene and predicted proteome phylogeny, the organism appears to be a novel member of the Peptococcaceae family. The DCMF genome is large in comparison to known DCM-fermenting bacteria. It includes an abundance of methyltransferases, which may provide clues to the basis of its DCM metabolism, as well as potential to metabolise additional methylated substrates such as quaternary amines. Full annotation has been provided in a custom genome browser and search tool, in addition to multiple sequence alignments and phylogenetic trees for every predicted protein, http://www.slimsuite.unsw.edu.au/research/dcmf/.

Proteogenomics Reveals Novel Reductive Dehalogenases and Methyltransferases Expressed during Anaerobic Dichloromethane Metabolism

Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 nonredundant proteins, 521 of which could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/cofactor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM's genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of Dehalococcoides mccartyi strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of Dehalobacter sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.IMPORTANCE Naturally produced and anthropogenically released DCM can reside in anoxic environments, yet little is known about the diversity of organisms, enzymes, and mechanisms involved in carbon-chlorine bond cleavage in the absence of oxygen. A proteogenomic approach identified two RDases and four corrinoid-dependent methyltransferases expressed by the DCM degrader "Candidatus Dichloromethanomonas elyunquensis" strain RM, suggesting that reductive dechlorination and methyl group transfer play roles in anaerobic DCM degradation. These findings suggest that the characterized DCM-degrading bacterium Dehalobacterium formicoaceticum and "Candidatus Dichloromethanomonas elyunquensis" strain RM utilize distinct strategies for carbon-chlorine bond cleavage, indicating that multiple pathways evolved for anaerobic DCM metabolism. The specific proteins (e.g., RDases and methyltransferases) identified in strain RM may have value as biomarkers for monitoring anaerobic DCM degradation in natural and contaminated environments.