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

Generalization of Classification of AlkB Family Alkane Monooxygenases from Rhodococcus (sensu lato) Group Based on Phylogenetic Analysis and Genomic Context Comparison

Alkane-oxidizing bacteria play a crucial role in the global carbon cycle. Rhodococcus species are well-known hydrocarbon degraders, distinguished by the harboring of multiple homologs of AlkB family alkane monooxygenases. Although different types of rhodococcal AlkBs have been described, the overall picture of their diversity remains unclear, leaving gaps in the current classification. We conducted a phylogenetic analysis of all AlkBs identified in Rhodococcus (sensu lato) and examined the genomic context of the corresponding genes. The sequence clustering was well aligned with genomic neighborhoods, allowing both features to be used as criteria for proposing AlkB types that form distinct phylogenetic groups and have characteristic genomic contexts. Our approach allowed us to revise the classification of previously described AlkBs, identifying eight types on their basis, and to propose three new ones. Alkane monooxygenases whose genes are co-localized with rubredoxin genes can be considered a generalized AlkBR type, the most common among all Rhodococcus. In the AlkB0 type, which is a paralog of AlkBR, violations of conservativity in known alkane monooxygenase signature motifs were found. Our findings provide a more consistent classification framework for rhodococcal AlkB that prevents the over-reporting of "novel" types and contributes to a deeper understanding of alkane monooxygenase diversity.

Simulation and prediction of sulfamethazine migration, transformation and risk diffusion during cross-media infiltration from surface water to groundwater driven by dynamic water level: Machine learning coupled HYDRUS-GMS model

Seasonal water level fluctuations in rivers significantly influenced the cross-media migration, transformation, and risk diffusion of antibiotics from the vadose zone into groundwater. This study developed a coupled model integrating machine learning (ML) with HYDRUS-3D and GMS to accurately predict sulfamethazine migration under dynamic water levels. The predictive accuracy (E≥0.98) of this ML-HYDRUS-GMS model was enhanced by accounting for seasonal water level fluctuations and biogeochemical variability. Significant seasonal differences presented with sulfamethazine diffusion in the vadose zone with the migration rate decreased from 0.06 m/d to 0.02 m/d with the transition from wet to dry seasons. After 6 years of infiltration, it reached groundwater, where lateral migration rates, influenced by seasonal flow variations, were 0.12 m/d in the wet season and decreased to 0.07 m/d in the dry season, with a diffusion range extending to 217 m over 100 years. This discrepant continuous filtration of sulfamethazine and the succession of metabolic pathways induced toxicity range to expand by 65.6 m and the risk to increase to warning level. Sulfamethazine underwent oxidative breakdown in aerobic vadose zone conditions, while anaerobic groundwater conditions led to hydrogenation and reduction, increasing its migration distance.

Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation

Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.

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.

From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium

Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the mec cassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase-named acdA-and a complete mec cassette were found to be encoded on a single contig belonging to Dehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a Dehalobacter capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the mec cassette.

IMPORTANCE

Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of Dehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.

Metabolite cross-feeding enables concomitant catabolism of chlorinated methanes and chlorinated ethenes in synthetic microbial assemblies

Isolate studies have been a cornerstone for unraveling metabolic pathways and phenotypical (functional) features. Biogeochemical processes in natural and engineered ecosystems are generally performed by more than a single microbe and often rely on mutualistic interactions. We demonstrate the rational bottom-up design of synthetic, interdependent co-cultures to achieve concomitant utilization of chlorinated methanes as electron donors and organohalogens as electron acceptors. Specialized anaerobes conserve energy from the catabolic conversion of chloromethane or dichloromethane to formate, H2, and acetate, compounds that the organohalide-respiring bacterium Dehalogenimonas etheniformans strain GP requires to utilize cis-1,2-dichloroethenene and vinyl chloride as electron acceptors. Organism-specific qPCR enumeration matched the growth of individual dechlorinators to the respective functional (i.e. dechlorination) traits. The metabolite cross-feeding in the synthetic (co-)cultures enables concomitant utilization of chlorinated methanes (i.e. chloromethane and dichloromethane) and chlorinated ethenes (i.e. cis-1,2-dichloroethenene and vinyl chloride) without the addition of an external electron donor (i.e. formate and H2). The findings illustrate that naturally occurring chlorinated C1 compounds can sustain anaerobic food webs, an observation with implications for the development of interdependent, mutualistic communities, the sustenance of microbial life in oligotrophic and energy-deprived environments, and the fate of chloromethane/dichloromethane and chlorinated electron acceptors (e.g. chlorinated ethenes) in pristine environments and commingled contaminant plumes.

Toluene-driven anaerobic biodegradation of chloroform in a continuous-flow bioelectrochemical reactor

Subsurface co-contamination by multiple pollutants can be challenging for the design of bioremediation strategies since it may require promoting different and often antagonistic degradation pathways. Here, we investigated the simultaneous degradation of toluene and chloroform (CF) in a continuous-flow anaerobic bioelectrochemical reactor. As a result, 47 μmol L-1 d-1 of toluene and 60 μmol L-1 d-1 of CF were concurrently removed, when the anode was polarized at +0.4 V vs. Standard Hydrogen Electrode (SHE). Analysis of the microbial community structure and key functional genes allowed to identify the involved degradation pathways. Interestingly, when acetate was supplied along with toluene, to simulate the impact of a readily biodegradable substrate on process performance, toluene degradation was adversely affected, likely due to competitive inhibition effects. Overall, this study proved the efficacy of the developed bioelectrochemical system in simultaneously treating multiple groundwater contaminants, paving the way for the application in real-world scenarios.

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.

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.

Catalytic ozonation of dichloromethane at low temperature and even room temperature on Mn-loaded catalysts

Five Mn-loaded catalysts were synthesized on γ-Al2O3, TiO2, ZrO2, nano γ-Al2O3 and nanoZrO2 supports. The catalytic ozonation of DCM (dichloromethane) was evaluated under industrial conditions (i.e., temperature, O3 input, H2O and SO2 content). According to results, >90% DCM conversion without O3 residue was achieved for all samples at 120 °C and an O3/DCM ratio of 6. At 20-120 °C, the highest Mn3+ content, abundant surface oxygen species and more weak acid sites led to the best performance of Mn/nanoAl2O3 (M/A-II). At 20 °C and 120 °C, 80% and 95% DCM can be degraded respectively on M/A-II at 20 °C with matched surface oxygen species and acidity. An O3/DCM ratio of 6 was optimal for performance and economy. For the effects of complex exhaust, both H2O and SO2 deactivated M/A-II. The H2O-induced deactivation was recoverable and also removed surface-deposited chlorine-containing species, enhancing the HCl selectivity. Finally, the Cl equilibrium of the reaction was comprehensively analyzed.