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The ISME Journal Jun 2021Dichloromethane (DCM; CHCl) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels. As a dense non-aqueous phase liquid, DCM...
Dichloromethane (DCM; CHCl) 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'.
Topics: Biodegradation, Environmental; Carbon; Carbon Isotopes; Methylene Chloride; Peptococcaceae
PubMed: 33452483
DOI: 10.1038/s41396-020-00881-y -
Infection 1980Current problems in the classification and identification of Peptococcaceae with special reference to clinically significant species are discussed briefly. Further...
Current problems in the classification and identification of Peptococcaceae with special reference to clinically significant species are discussed briefly. Further research is needed to clarify most of the existing discrepancies.
Topics: Peptococcaceae
PubMed: 7450858
DOI: 10.1007/BF01639880 -
Science (New York, N.Y.) Mar 2009We report here molecular mechanisms underlying a bacteria-archaeon symbiosis. We found that a fermentative bacterium used its flagellum for interaction with a specific...
We report here molecular mechanisms underlying a bacteria-archaeon symbiosis. We found that a fermentative bacterium used its flagellum for interaction with a specific methanogenic archaeon. The archaeon perceived a bacterial flagellum protein and activated its metabolism (methanogenesis). Transcriptome analyses showed that a substantial number of genes in the archaeon, including those involved in the methanogenesis pathway, were up-regulated after the contact with the flagellum protein. These findings suggest that the bacterium communicates with the archaeon by using its flagellum.
Topics: Archaeal Proteins; Bacterial Proteins; Flagella; Gene Expression Regulation, Archaeal; Hydrogen; Methane; Methanobacteriaceae; Peptococcaceae; Symbiosis; Up-Regulation
PubMed: 19299611
DOI: 10.1126/science.1170086 -
FEMS Microbiology Reviews Sep 2006Desulfitobacterium spp. are strictly anaerobic bacteria that were first isolated from environments contaminated by halogenated organic compounds. They are very versatile... (Review)
Review
Desulfitobacterium spp. are strictly anaerobic bacteria that were first isolated from environments contaminated by halogenated organic compounds. They are very versatile microorganisms that can use a wide variety of electron acceptors, such as nitrate, sulfite, metals, humic acids, and man-made or naturally occurring halogenated organic compounds. Most of the Desulfitobacterium strains can dehalogenate halogenated organic compounds by mechanisms of reductive dehalogenation, although the substrate spectrum of halogenated organic compounds varies substantially from one strain to another, even with strains belonging to the same species. A number of reductive dehalogenases and their corresponding gene loci have been isolated from these strains. Some of these loci are flanked by transposition sequences, suggesting that they can be transmitted by horizontal transfer via a catabolic transposon. Desulfitobacterium spp. can use H2 as electron donor below the threshold concentration that would allow sulfate reduction and methanogenesis. Furthermore, there is some evidence that syntrophic relationships occur between Desulfitobacterium spp. and sulfate-reducing bacteria, from which the Desulfitobacterium cells acquire their electrons by interspecies hydrogen transfer, and it is believed that this relationship also occurs in a methanogenic consortium. Because of their versatility, desulfitobacteria can be excellent candidates for the development of anaerobic bioremediation processes. The release of the complete genome of Desulfitobacterium hafniense strain Y51 and information from the partial genome sequence of D. hafniense strain DCB-2 will certainly help in predicting how desulfitobacteria interact with their environments and other microorganisms, and the mechanisms of actions related to reductive dehalogenation.
Topics: Biodegradation, Environmental; Chlorine; Desulfitobacterium; Genes, Bacterial; Genes, rRNA; Humic Substances; Hydrogen; Metals; Oxidation-Reduction; Phylogeny; Sulfites
PubMed: 16911041
DOI: 10.1111/j.1574-6976.2006.00029.x -
Environmental Science & Technology Aug 2018Dichloromethane (DCM) is a probable human carcinogen and frequent groundwater contaminant and contributes to stratospheric ozone layer depletion. DCM is degraded by...
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 (H), 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 and ε) of -42.4 ± 0.7‰ and -5.3 ± 0.1‰, respectively, were measured in D. formicoaceticum cultures. A similar ε of -5.2 ± 0.1‰, but a substantially lower ε of -18.3 ± 0.2‰, were determined for Ca. Dichloromethanomonas elyunquensis. The ε and ε values resulted in distinctly different dual element C-Cl isotope correlations (Λ = ΔδC/ΔδCl) of 7.89 ± 0.12 and 3.40 ± 0.03 for D. formicoaceticum and Ca. Dichloromethanomonas elyunquensis, respectively. The distinct Λ 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.
Topics: Anaerobiosis; Biodegradation, Environmental; Carbon; Carbon Isotopes; Chlorine; Methylene Chloride; Peptococcaceae
PubMed: 29975517
DOI: 10.1021/acs.est.8b01583 -
Philosophical Transactions of the Royal... Apr 2013In this report, a complete description of Desulfitobacterium hafniense strain PCP-1 is presented. The D. hafniense strain PCP-1 was isolated from a methanogenic... (Review)
Review
In this report, a complete description of Desulfitobacterium hafniense strain PCP-1 is presented. The D. hafniense strain PCP-1 was isolated from a methanogenic consortium for its capacity to dehalogenate pentachlorophenol (PCP) into 3-chlorophenol. This strain is also capable of dehalogenating several other chloroaromatic compounds and tetrachloroethene into trichloroethene. Four gene loci encoding putative chlorophenol-reductive dehalogenases (CprA2 to CprA5) were detected, and the products of two of these loci have been demonstrated to dechlorinate different chlorinated phenols. Strain PCP-1 was used in laboratory-scale bioprocesses to degrade PCP present in contaminated environments. Desulfitobacterium hafniense PCP-1 is an excellent candidate for the development of efficient bioprocesses to degrade organohalide compounds.
Topics: Biodegradation, Environmental; Chlorophenols; Desulfitobacterium; Gene Expression Regulation, Bacterial; Gene Transfer, Horizontal; Genes, Bacterial; Genetic Loci; Halogenation; Pentachlorophenol; Phylogeny; RNA, Ribosomal, 16S; Species Specificity; Transcription, Genetic
PubMed: 23479749
DOI: 10.1098/rstb.2012.0319 -
MBio Apr 2021Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed...
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising " Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated " Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An ()-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota. Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
Topics: Anaerobiosis; Bacteria, Anaerobic; Base Composition; Dichloroacetic Acid; Fermentation; Humans; Peptococcaceae; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33906923
DOI: 10.1128/mBio.00537-21 -
Current Opinion in Biotechnology Jun 2013In the last few years there has been a burst of genomes released for organohalide respiring bacteria (referred to as OHRB herein though the process is otherwise known as... (Review)
Review
In the last few years there has been a burst of genomes released for organohalide respiring bacteria (referred to as OHRB herein though the process is otherwise known as dehalorespiration, reductive dechlorination, or halorespiration). The microorganisms are employed in bioremediation of sites contaminated with chlorinated ethene, ethane, and methanes, as well as chlorinated aromatics. Of particular note are the releases of the first Dehalogenimonas genome (a Dehalococcoides-related Chloroflexi) and not one but seven Dehalobacter (meta)genomes. Collectively, genomes from these three genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) clearly support their niche as obligate OHRB, while other genera with sequenced genomes (Desulfitobacterium, Geobacter, and Anaeromyxobacter) maintain organohalide respiration (OHR) as one of many possible energy conserving respiration strategies. The obligate OHRB genomes consistently harbor 10-39 unique reductive dehalogenase (RDase) genes and they are flanked with not only transcriptional regulators but also transposition related genes. Active transposition likely plays a key role in the accumulation of such a broad and tightly regulated dehalogenase repertoire. Functional assays are now the bottleneck for genome-informed discovery of dehalogenase substrate ranges.
Topics: Biodegradation, Environmental; Chloroflexi; Desulfitobacterium; Gene Expression Regulation, Bacterial; Gene Transfer, Horizontal; Genome, Bacterial; Geobacter; Halogenation; Hydrolases; Peptococcaceae; Phylogeny
PubMed: 23490446
DOI: 10.1016/j.copbio.2013.02.014 -
Reviews of Infectious Diseases 1984Anaerobic bacteria are part of the normal flora of mucous membranes and outnumber aerobic bacteria in the oral cavity and gastrointestinal tract. Anaerobes can be... (Review)
Review
Anaerobic bacteria are part of the normal flora of mucous membranes and outnumber aerobic bacteria in the oral cavity and gastrointestinal tract. Anaerobes can be isolated from pediatric patients with various infections when appropriate techniques for transportation and cultivation of samples are employed. Frequently anaerobes are isolated in combination with other facultative or aerobic bacteria. The genera or groups of anaerobes most frequently isolated from pyogenic infections in children are (in order of decreasing frequency) OFFteroides, Clostridium, gram-positive cocci, Fusobacterium, gram-positive rods (Eubacterium, Lactobacillus, Propionibacterium, Actinomyces, and Bifidobacterium), and gram-negative cocci (Veillonella and Acidaminococcus). Clostridium perfringens causes bacteremia and wound infections. Clostridium botulinum can produce a paralytic toxin that causes a lethal illness in adults and a paralytic syndrome in infants. Clostridium difficile can cause antibiotic-associated colitis or diarrhea. Bacteroides fragilis is most frequently involved in intraabdominal infections, infections of the female genital tract, subcutaneous abscesses, and bacteremia. Bacteroides melaninogenicus and Bacteroides oralis are the predominent anaerobes in orofacial infections and aspiration pneumonia. Fusobacterium species are pathogens in aspiration pneumonia, brain abscesses, and orofacial infections. Anaerobic gram-positive cocci can be recovered from all types of infections but predominate in respiratory tract and intra-abdominal infections. Recognition of the pathogenic qualities of the various anaerobic organisms can assist in their prompt identification and in the initiation of appropriate therapy.
Topics: Actinomyces; Bacteria, Anaerobic; Bacterial Infections; Bacteroides; Bacteroides Infections; Child; Child, Preschool; Clostridium; Clostridium Infections; Fusobacterium; Gram-Negative Bacteria; Gram-Positive Bacteria; Humans; Peptococcaceae; Propionibacterium; Veillonella
PubMed: 6372028
DOI: 10.1093/clinids/6.supplement_1.s187 -
Bioscience, Biotechnology, and... Jul 2019The basic functions of a propionate-oxidizing bacterium flagellum, such as motility and chemotaxis, have not been studied. To investigate its motility, we compared with...
The basic functions of a propionate-oxidizing bacterium flagellum, such as motility and chemotaxis, have not been studied. To investigate its motility, we compared with that of , an aflagellar propionate-oxidizing bacterium, in soft agar medium. cells spread, while cells moved downward slightly, indicating flagellum-dependent motility in SI. The motility of was inhibited by the addition of carbonyl cyanide m-chlorophenyl hydrazone, a proton uncoupler, which is consistent with the fact that stator protein, MotB of , shared sequence homology with proton-type stators. In addition, 5-N-ethyl-N-isopropyl amiloride, an Na channel blocker, showed no inhibitory effect on the motility. Furthermore, of complemented the defective swimming ability of ∆. These results suggest that the motility of SI depends on the proton-type flagellar motor.
Topics: Deltaproteobacteria; Escherichia coli; Flagella; Peptococcaceae
PubMed: 30919743
DOI: 10.1080/09168451.2019.1597618