Molecular and carbon isotopic characterization of an anaerobic stable enrichment culture containing Dehalobacterium sp. during dichloromethane fermentation

The inflammatory immunity and gut microbiota are associated with fear response differences in laying hens

The fear response is a crucial adaptive mechanism for coping with environmental changes, and the individuals have different levels of fearfulness. The purpose of this study was to determine the status of the immune response and gut health in hens with different fear responses. A total of 80 healthy 75-wk-old native Lindian chickens were individually housed in conventional cages and categorized into high (TH) and low (TL) levels of fearfulness using the tonic immobility (TI) test. The immunological status and intestinal health of the laying hens were assessed, and the intestinal microbial community was sequenced using 16S rRNA testing. The results showed that the immune-related genes of interleukin (IL)-1β, IL-4, IL-6, and IgG were significantly upregulated in the spleen of TH hens compared with hens in the TL group (P < 0.01). The inflammatory immune-related genes Toll-like receptor (TLR)2, TLR4, nuclear factor (NF)-κB, inducible nitric oxide synthase (iNOS), cyclooxygenase (COX)-2, IL-10, and IgG were significantly increased in the intestinal tract, whereas IL-4, IgA, and the intestinal barrier gene claudin-4 were significantly decreased in TH hens (P < 0.05). In addition, serum concentrations of IL-1β, IL-6, IL-10, interferon (IFN)-α and IgG were significantly higher in TH hens (P < 0.01). A high fear response also led to changes in gut microbial diversity, with a higher Simpson's index and lower β-diversity similarity than hens with a low-fear response (P < 0.05). The TH group showed an increase in 8 genera, including Bacillaceae and Coprococcus, whereas the genus Anaerorhabdus decreased (P < 0.05). The gut microbiota has also been associated with gut barrier genes, and inflammatory cytokines. Bartonella stimulates IL-1β and IgG secretion, whereas Lactobacillus inhibits IL-6 secretion, and Coprococcus and Subdoligranulum are associated with the maintenance of intestinal barrier function. The results of this study suggest that laying hens with high fear response levels have a more sensitive immune response and a more enriched gut microbiota, which may have positive effects on adapting to a complex environment.

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.

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.

Combining nanoscale zero-valent iron and anaerobic dechlorinating bacteria to degrade chlorinated methanes and 1,2-dichloroethane

Nanoscale zero-valent iron (nZVI) has the potential to degrade a diversity of chlorinated compounds, and it is widely used for remediation of contaminated groundwaters. However, some frequently detected contaminants such as dichloromethane (DCM) and 1,2-dichloroethane (1,2-DCA) have shown nearly no reactivity with nZVI. Here, we tested the feasibility of combining anaerobic dechlorinating bacteria, Dehalobacterium and Dehalogenimonas, and nZVI as a treatment train to detoxify chlorinated methanes (i.e., chloroform-CF- and DCM), and 1,2-DCA. First, we showed that CF (500 μM) was fully degraded by 1 g/L nZVI to DCM as a major by-product, which was susceptible to fermentation by Dehalobacterium to innocuous products. Our results indicate that soluble compounds released by nZVI might cause an inhibitory impact on Dehalobacterium activity, avoiding DCM depletion. The DCM dechlorination activity was recovered when transferred to a fresh medium without nZVI. The increase in H2 production and pH was discarded as potential inhibitors. Similarly, a Dehalogenimonas-containing culture was unable to dichloroeliminate 1,2-DCA when exposed to 1 g/L nZVI, but dechlorinating activity was also recovered when transferred to nZVI-free media. The recovery of the dechlorinating activity of Dehalobacterium and Dehalogenimonas suggests that combination of nZVI and bioremediation techniques can be feasible under field conditions where dilution processes can alleviate the impact of the potential inhibitory soluble compounds.

Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons

This review presents a comprehensive summary of the latest research in the field of bioremediation with filamentous fungi. The main focus is on the issue of recent progress in remediation of pharmaceutical compounds, heavy metal treatment and oil hydrocarbons mycoremediation that are usually insufficiently represented in other reviews. It encompasses a variety of cellular mechanisms involved in bioremediation used by filamentous fungi, including bio-adsorption, bio-surfactant production, bio-mineralization, bio-precipitation, as well as extracellular and intracellular enzymatic processes. Processes for wastewater treatment accomplished through physical, biological, and chemical processes are briefly described. The species diversity of filamentous fungi used in pollutant removal, including widely studied species of Aspergillus, Penicillium, Fusarium, Verticillium, Phanerochaete and other species of Basidiomycota and Zygomycota are summarized. The removal efficiency of filamentous fungi and time of elimination of a wide variety of pollutant compounds and their easy handling make them excellent tools for the bioremediation of emerging contaminants. Various types of beneficial byproducts made by filamentous fungi, such as raw material for feed and food production, chitosan, ethanol, lignocellulolytic enzymes, organic acids, as well as nanoparticles, are discussed. Finally, challenges faced, future prospects, and how innovative technologies can be used to further exploit and enhance the abilities of fungi in wastewater remediation, are mentioned.

Bioelectrochemically-assisted degradation of chloroform by a co-culture of Dehalobacter and Dehalobacterium

Using bioelectrochemical systems (BESs) to provide electrochemically generated hydrogen is a promising technology to provide electron donors for reductive dechlorination by organohalide-respiring bacteria. In this study, we inoculated two syntrophic dechlorinating cultures containing Dehalobacter and Dehalobacterium to sequentially transform chloroform (CF) to acetate in a BES using a graphite fiber brush as the electrode. In this co-culture, Dehalobacter transformed CF to stoichiometric amounts of dichloromethane (DCM) via organohalide respiration, whereas the Dehalobacterium-containing culture converted DCM to acetate via fermentation. BES were initially inoculated with Dehalobacter, and sequential cathodic potentials of -0.6, -0.7, and -0.8 V were poised after consuming three CF doses (500 μM) per each potential during a time-span of 83 days. At the end of this period, the accumulated DCM was degraded in the following seven days after the inoculation of Dehalobacterium. At this point, four consecutive amendments of CF at increasing concentrations of 200, 400, 600, and 800 μM were sequentially transformed by the combined degradation activity of Dehalobacter and Dehalobacterium. The Dehalobacter 16S rRNA gene copies increased four orders of magnitude during the whole period. The coulombic efficiencies associated with the degradation of CF reached values > 60% at a cathodic potential of -0.8 V when the degradation rate of CF achieved the highest values. This study shows the advantages of combining syntrophic bacteria to fully detoxify chlorinated compounds in BESs and further expands the use of this technology for treating water bodies impacted with pollutants.

Trichloromethane dechlorination by a novel Dehalobacter sp. strain 8M reveals a third contrasting C and Cl isotope fractionation pattern within this genus

Trichloromethane (TCM) is a pollutant frequently detected in contaminated aquifers, and only four bacterial strains are known to respire it. Here, we obtained a novel Dehalobacter strain capable of transforming TCM to dichloromethane, which was denominated Dehalobacter sp. strain 8M. Besides TCM, strain 8M also completely transformed 1,1,2-trichloroethane to vinyl chloride and 1,2-dichloroethane. Quantitative PCR analysis for the 16S rRNA genes confirmed growth of Dehalobacter with TCM and 1,1,2-trichloroethane as electron acceptors. Carbon and chlorine isotope fractionation during TCM transformation was studied in cultured cells and in enzymatic assays with cell suspensions and crude protein extracts. TCM transformation in the three studied systems resulted in small but significant carbon (ε_C = -2.7 ± 0.1‰ for respiring cells, -3.1 ± 0.1‰ for cell suspensions, and - 4.1 ± 0.5‰ for crude protein extracts) and chlorine (ε_Cl = -0.9 ± 0.1‰, -1.1 ± 0.1‰, and - 1.2 ± 0.2‰, respectively) isotope fractionation. A characteristic and consistent dual CCl isotope fractionation pattern was observed for the three systems (combined Λ^C/Cl = 2.8 ± 0.3). This Λ^C/Cl differed significantly from previously reported values for anaerobic dechlorination of TCM by the corrinoid cofactor vitamin B12 and other Dehalobacter strains. These findings widen our knowledge on the existence of different enzyme binding mechanisms underlying TCM-dechlorination within the genus Dehalobacter and demonstrates that dual isotope analysis could be a feasible tool to differentiate TCM degraders at field studies.

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.

Enhanced dechlorination of 1,2-dichloropropane to propene in a bioelectrochemical system mediated by Dehalogenimonas

Bioelectrochemical systems (BES) are promising technologies to enhance the growth of organohalide-respiring bacteria and to treat chlorinated aliphatic hydrocarbons. In this study, two carbon-based cathodic electrode materials, a graphite brush and a carbon cloth, were used as hydrogen suppliers to couple growth of Dehalogenimonas and dechlorination of 1,2-DCP to nontoxic propene in the cathode vessel. The BES with graphite brush electrode consumed ~4000 µM 1,2-DCP during 110 days and exhibited a degradation rate 5.6-fold higher than the maximum value obtained with the carbon cloth electrode, with a cathode potential set at -0.7 V. Quantitative PCR confirmed that Dehalogenimonas gene copies increased by two orders of magnitude in the graphite brush BES, with an average yield of 1.2·10⁸±5·10⁷ cells per µmol of 1,2-DCP degraded. The use of a pulsed voltage operation (cathode potential set at -0.6 V for 16 h and -1.1 V for 8 h) increased the coulombic efficiency and degradation of 1,2-DCP when compared with a continuous voltage operation of -1.1 V. Bacterial cell aggregates were observed in the surface of the graphite brush electrodes by electron scanning microscopy, suggesting biofilm formation. This study expands the range of chlorinated compounds degradable and organohalide-respiring bacteria capable of growing in BES.

Novel dichloromethane-fermenting bacteria in the Peptococcaceae family

Dichloromethane (DCM; CH2Cl2) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels. As a dense non-aqueous phase liquid, DCM migrates vertically through groundwater to low redox zones, yet information on anaerobic microbial DCM transformation remains scarce due to a lack of cultured organisms. We report here the characterisation of DCMF, the dominant organism in an anaerobic enrichment culture (DFE) capable of fermenting DCM to the environmentally benign product acetate. Stable carbon isotope experiments demonstrated that the organism assimilated carbon from DCM and bicarbonate via the Wood-Ljungdahl pathway. DCMF is the first anaerobic DCM-degrading population also shown to metabolise non-chlorinated substrates. It appears to be a methylotroph utilising the Wood-Ljungdahl pathway for metabolism of methyl groups from methanol, choline, and glycine betaine. The flux of these substrates from subsurface environments may either directly (DCM, methanol) or indirectly (choline, glycine betaine) affect the climate. Community profiling and cultivation of cohabiting taxa in culture DFE without DCMF suggest that DCMF is the sole organism in this culture responsible for substrate metabolism, while the cohabitants persist via necromass recycling. Genomic and physiological evidence support placement of DCMF in a novel genus within the Peptococcaceae family, 'Candidatus Formimonas warabiya'.

Interspecies interaction and effect of co-contaminants in an anaerobic dichloromethane-degrading culture

An anaerobic stable mixed culture dominated by bacteria belonging to the genera Dehalobacterium, Acetobacterium, Desulfovibrio, and Wolinella was used as a model to study the microbial interactions during DCM degradation. Physiological studies indicated that DCM was degraded in this mixed culture at least in a three-step process: i) fermentation of DCM to acetate and formate, ii) formate oxidation to CO₂ and H₂, and iii) H₂/CO₂ reductive acetogenesis. The 16S rRNA gene sequencing of cultures enriched with formate or H₂ showed that Desulfovibrio was the dominant population followed by Acetobacterium, but sequences representing Dehalobacterium were only present in cultures amended with DCM. Nuclear magnetic resonance analyses confirmed that acetate produced from ¹³C-labelled DCM was marked at the methyl ([2-¹³C]acetate), carboxyl ([1-¹³C]acetate), and both ([1,2-¹³C]acetate) positions, which is in accordance to acetate formed by both direct DCM fermentation and H₂/CO₂ acetogenesis. The inhibitory effect of ten different co-contaminants frequently detected in groundwaters on DCM degradation was also investigated. Complete inhibition of DCM degradation was observed when chloroform, perfluorooctanesulfonic acid, and diuron were added at 838, 400, and 107 μM, respectively. However, the inhibited cultures recovered the DCM degradation capability when transferred to fresh medium without co-contaminants. Findings derived from this work are of significant relevance to provide a better understanding of the synergistic interactions among bacteria to accomplish DCM degradation as well as to predict the effect of co-contaminants during anaerobic DCM bioremediation in groundwater.

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.

Accelerated microbial reductive dechlorination of 2,4,6-trichlorophenol by weak electrical stimulation

Microbial reductive dechlorination of chlorinated aromatics frequently suffers from the long dechlorination period and the generation of toxic metabolites. Biocathode bioelectrochemical systems were verified to be effective in the degradation of various refractory pollutants. However, the electrochemical and microbial related working mechanisms for bio-dechlorination by electro-stimulation remain poorly understood. In this study, we reported the significantly improved 2,4,6-trichlorophenol dechlorination activity through the weak electro-stimulation (cathode potential of -0.36 V vs. SHE), as evidenced by the 3.1 times higher dechlorination rate and the complete dechlorination ability with phenol as the end dechlorination product. The high reductive dechlorination rate (20.8 μM/d) could be maintained by utilizing electrode as an effective electron donor (coulombic efficiency of 82.3 ± 4.8%). Cyclic voltammetry analysis of the cathodic biofilm gave the direct evidences of the cathodic respiration with the improved and positive-shifted reduction peaks of 2,4,6-TCP, 2,4-DCP and 4-CP. The optimal 2,4,6-TCP reductive dechlorination rate (24.2 μM/d) was obtained when a small amount of lactate (2 mM) was added, and the generation of H₂ and CH₄ were accompanied due to the biological fermentation and methanogenesis. The electrical stimulation significantly altered the cathodic biofilm structure and composition with some potential dechlorinators (like Acetobacterium) predominated. The microbial interactions in the ecological network of cathodic biofilm were more simplified than the planktonic community. However, some potential dechlorinators (Acetobacterium, Desulfovibrio, etc.) shared more positive interactions. The co-existence and possible cooperative relationships between potential dechlorinators and fermenters (Sedimentibacter, etc.) were revealed. Meanwhile, the competitive interrelations between potential dechlorinators and methanogens (Methanomassiliicoccus) were found. In the network of plankton, the fermenters and methanogens possessed the more positive interrelations. Electro-stimulation at the cathodic potential of -0.36 V selectively enhanced the dechlorination function, while it showed little influence on either fermentation or methanogenesis process. The study gave suggestions for the enhanced bioremediation of chlorinated aromatics, in views of the electro-stimulation capacity, efficiency and microbial interrelations related microbial mechanism.

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.

Dichloromethane biodegradation in multi-contaminated groundwater: Insights from biomolecular and compound-specific isotope analyses

Dichloromethane (DCM) is a widespread and toxic industrial solvent which often co-occurs with chlorinated ethenes at polluted sites. Biodegradation of DCM occurs under both oxic and anoxic conditions in soils and aquifers. Here we investigated in situ and ex situ biodegradation of DCM in groundwater sampled from the industrial site of Themeroil (France), where DCM occurs as a major co-contaminant of chloroethenes. Carbon isotopic fractionation (ε_C) for DCM ranging from -46 to -22‰ were obtained under oxic or denitrifying conditions, in mineral medium or contaminated groundwater, and for laboratory cultures of Hyphomicrobium sp. strain GJ21 and two new DCM-degrading strains isolated from the contaminated groundwater. The extent of DCM biodegradation (B%) in the aquifer, as evaluated by compound-specific isotope analysis (δ¹³C), ranged from 1% to 85% applying DCM-specific ε_C derived from reference strains and those determined in this study. Laboratory groundwater microcosms under oxic conditions showed DCM biodegradation rates of up to 0.1 mM·day^-1, with concomitant chloride release. Dehalogenase genes dcmA and dhlA involved in DCM biodegradation ranged from below 4 × 10² (boundary) to 1 × 10⁷ (source zone) copies L^-1 across the contamination plume. High-throughput sequencing on the 16S rrnA gene in groundwater samples showed that both contaminant level and terminal electron acceptor processes (TEAPs) influenced the distribution of genus-level taxa associated with DCM biodegradation. Taken together, our results demonstrate the potential of DCM biodegradation in multi-contaminated groundwater. This integrative approach may be applied to contaminated aquifers in the future, in order to identify microbial taxa and pathways associated with DCM biodegradation in relation to redox conditions and co-contamination levels.

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

Dichloromethane (DCM) is a probable human carcinogen and frequent groundwater contaminant and contributes to stratospheric ozone layer depletion. DCM is degraded by aerobes harboring glutathione-dependent DCM dehalogenases; however, DCM contamination occurs in oxygen-deprived environments, and much less is known about anaerobic DCM metabolism. Some members of the Peptococcaceae family convert DCM to environmentally benign products including acetate, formate, hydrogen (H₂), and inorganic chloride under strictly anoxic conditions. The current study applied stable carbon and chlorine isotope fractionation measurements to the axenic culture Dehalobacterium formicoaceticum and to the consortium RM comprising DCM degrader Candidatus Dichloromethanomonas elyunquensis. Degradation-associated carbon and chlorine isotope enrichment factors (ε_C and ε_Cl) of -42.4 ± 0.7‰ and -5.3 ± 0.1‰, respectively, were measured in D. formicoaceticum cultures. A similar ε_Cl of -5.2 ± 0.1‰, but a substantially lower ε_C of -18.3 ± 0.2‰, were determined for Ca. Dichloromethanomonas elyunquensis. The ε_C and ε_Cl values resulted in distinctly different dual element C-Cl isotope correlations (Λ^C/Cl = Δδ¹³C/Δδ³⁷Cl) of 7.89 ± 0.12 and 3.40 ± 0.03 for D. formicoaceticum and Ca. Dichloromethanomonas elyunquensis, respectively. The distinct Λ^C/Cl values obtained for the two cultures imply mechanistically distinct C-Cl bond cleavage reactions, suggesting that members of Peptococcaceae employ different pathways to metabolize DCM. These findings emphasize the utility of dual carbon-chlorine isotope analysis to pinpoint DCM degradation mechanisms and to provide an additional line of evidence that detoxification is occurring at DCM-contaminated sites.

Can white-rot fungi be a real wastewater treatment alternative for organic micropollutants removal? A review

Micropollutants are a diverse group of compounds that are detected at trace concentrations and may have a negative effect on the environment and/or human health. Most of them are unregulated contaminants, although they have raised a concern in the scientific and global community and future regulation might be written in the near future. Several approaches have been tested to remove micropollutants from wastewater streams. In this manuscript, a focus is placed in reactor biological treatments that use white-rot fungi. A critical review of white-rot fungal-based technologies for micropollutant removal from wastewater has been conducted, several capabilities and limitations of such approaches have been identified and a range of solutions to overcome most of the limitations have been reviewed and/or proposed. Overall, this review argues that white-rot fungal reactors could be an efficient technology to remove micropollutants from specific wastewater streams.

Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21

The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples of environments contaminated with halogenated pollutants and capable of using dichloromethane as its sole carbon and energy source, was determined.