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Ng TL, Silver PA. Sustainable B 12-Dependent Dehalogenation of Organohalides in E. coli. ACS Chem Biol 2024; 19:380-391. [PMID: 38254247 DOI: 10.1021/acschembio.3c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Microbial bioremediation can provide an environmentally friendly and scalable solution to treat contaminated soil and water. However, microbes have yet to optimize pathways for degrading persistent anthropogenic pollutants, in particular organohalides. In this work, we first expand our repertoire of enzymes useful for bioremediation. By screening a panel of cobalamin (B12)-dependent reductive dehalogenases, we identified previously unreported enzymes that dechlorinate perchloroethene and regioselectively deiodinate the thyroidal disruptor 2,4,6-triiodophenol. One deiodinase, encoded by the animal-associated anaerobe Clostridioides difficile, was demonstrated to dehalogenate the naturally occurring metabolites L-halotyrosines. In cells, several combinations of ferredoxin oxidoreductase and flavodoxin extract and transfer low-potential electrons from pyruvate to drive reductive dehalogenation without artificial reductants and mediators. This work provides new insights into a relatively understudied family of B12-dependent enzymes and sets the stage for engineering synthetic pathways for degrading unnatural small molecule pollutants.
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Affiliation(s)
- Tai L Ng
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute of Biologically-Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute of Biologically-Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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2
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Soder-Walz JM, Wasmund K, Deobald D, Vicent T, Adrian L, Marco-Urrea E. Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses. Environ Microbiol 2023; 25:2604-2620. [PMID: 37452527 DOI: 10.1111/1462-2920.16464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
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.
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Affiliation(s)
- Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Darja Deobald
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
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3
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Tucci M, Fernández-Verdejo D, Resitano M, Ciacia P, Guisasola A, Blánquez P, Marco-Urrea E, Cruz Viggi C, Matturro B, Crognale S, Aulenta F. Toluene-driven anaerobic biodegradation of chloroform in a continuous-flow bioelectrochemical reactor. CHEMOSPHERE 2023; 338:139467. [PMID: 37437617 DOI: 10.1016/j.chemosphere.2023.139467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/12/2023] [Accepted: 07/09/2023] [Indexed: 07/14/2023]
Abstract
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.
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Affiliation(s)
- Matteo Tucci
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - David Fernández-Verdejo
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Marco Resitano
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Pamela Ciacia
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Albert Guisasola
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Paqui Blánquez
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Ernest Marco-Urrea
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Carolina Cruz Viggi
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Simona Crognale
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km 29.300, 00015, Monterotondo, RM, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
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4
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Zhang X, Wang Z, Li Z, Shaik S, Wang B. [4Fe–4S]-Mediated Proton-Coupled Electron Transfer Enables the Efficient Degradation of Chloroalkenes by Reductive Dehalogenases. ACS Catal 2023. [DOI: 10.1021/acscatal.2c06306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xuan Zhang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zikuan Wang
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Zhen Li
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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5
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Phillips E, Bulka O, Picott K, Kümmel S, Edwards E, Nijenhuis I, Gehre M, Dworatzek S, Webb J, Lollar BS. Investigation of Active Site Amino Acid Influence on Carbon and Chlorine Isotope Fractionation during Reductive Dechlorination. FEMS Microbiol Ecol 2022; 98:6608266. [PMID: 35700008 DOI: 10.1093/femsec/fiac072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Reductive dehalogenases (RDases) are corrinoid-dependent enzymes that reductively dehalogenate organohalides in respiratory processes. By comparing isotope effects in biotically-catalyzed reactions to reference experiments with abiotic corrinoid-catalysts, compound-specific isotope analysis (CSIA) has been shown to yield valuable insights into enzyme mechanisms and kinetics, including RDases. Here, we report isotopic fractionation (ε) during biotransformation of chloroform (CF) for carbon (εC = -1.52 ± 0.34‰) and chlorine (εCl = -1.84 ± 0.19‰), corresponding to a ΛC/Cl value of 1.13 ± 0.35. These results are highly suppressed compared to isotope effects observed both during CF biotransformation by another organism with a highly similar RDase (> 95% sequence identity) at the amino acid level, and to those observed during abiotic dehalogenation of CF. Amino acid differences occur at four locations within the two different RDases' active sites, and this study examines whether these differences potentially affect the observed εC, εCl, and ΛC/Cl. Structural protein models approximating the locations of the residues elucidate possible controls on reaction mechanisms and/or substrate binding efficiency. These four locations are not conserved among other chloroalkane reducing RDases with high amino acid similarity (> 90%), suggesting that these locations may be important in determining isotope fractionation within this homologous group of RDases.
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Affiliation(s)
- Elizabeth Phillips
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, Toronto, Ontario M5S 3B1, Canada
| | - Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Elizabeth Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Matthias Gehre
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | | | | | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, Toronto, Ontario M5S 3B1, Canada
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6
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Soder-Walz JM, Torrentó C, Algora C, Wasmund K, Cortés P, Soler A, Vicent T, Rosell M, Marco-Urrea E. Trichloromethane dechlorination by a novel Dehalobacter sp. strain 8M reveals a third contrasting C and Cl isotope fractionation pattern within this genus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152659. [PMID: 34954170 DOI: 10.1016/j.scitotenv.2021.152659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
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 (εC = -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 (εCl = -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 ΛC/Cl = 2.8 ± 0.3). This ΛC/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.
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Affiliation(s)
- Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra, Spain
| | - Clara Torrentó
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), c/ Martí Franquès s/n, 08028 Barcelona, Spain
| | - Camelia Algora
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1010, Austria
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Facultat de BioCiències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Albert Soler
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), c/ Martí Franquès s/n, 08028 Barcelona, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra, Spain
| | - Mònica Rosell
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Institut de Recerca de l'Aigua (IdRA), Universitat de Barcelona (UB), c/ Martí Franquès s/n, 08028 Barcelona, Spain.
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra, Spain
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7
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Cimmino L, Schmid AW, Holliger C, Maillard J. Stoichiometry of the Gene Products From the Tetrachloroethene Reductive Dehalogenase Operon pceABCT. Front Microbiol 2022; 13:838026. [PMID: 35283847 PMCID: PMC8905343 DOI: 10.3389/fmicb.2022.838026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors. Our model organisms are Dehalobacter restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and Desulfitobacterium hafniense strain TCE1, a bacterium with a versatile metabolism. The key enzyme is the PCE reductive dehalogenase (PceA) that is encoded in the highly conserved gene cluster (pceABCT) in both above-mentioned strains, and in other Firmicutes OHRB. To date, the functions of PceA and PceT, a dedicated molecular chaperone for the maturation of PceA, are well defined. However, the role of PceB and PceC are still not elucidated. We present a multilevel study aiming at deciphering the stoichiometry of pceABCT individual gene products. The investigation was assessed at RNA level by reverse transcription and (quantitative) polymerase chain reaction, while at protein level, proteomic analyses based on parallel reaction monitoring were performed to quantify the Pce proteins in cell-free extracts as well as in soluble and membrane fractions of both strains using heavy-labeled reference peptides. At RNA level, our results confirmed the co-transcription of all pce genes, while the quantitative analysis revealed a relative stoichiometry of the gene transcripts of pceA, pceB, pceC, and pceT at ~ 1.0:3.0:0.1:0.1 in D. restrictus. This trend was not observed in D. hafniense strain TCE1, where no substantial difference was measured for the four genes. At proteomic level, an apparent 2:1 stoichiometry of PceA and PceB was obtained in the membrane fraction, and a low abundance of PceC in comparison to the other two proteins. In the soluble fraction, a 1:1 stoichiometry of PceA and PceT was identified. In summary, we show that the pce gene cluster is transcribed as an operon with, however, a level of transcription that differs for individual genes, an observation that could be explained by post-transcriptional events. Despite challenges in the quantification of integral membrane proteins such as PceB and PceC, the similar abundance of PceA and PceB invites to consider them as forming a membrane-bound PceA2B protein complex, which, in contrast to the proposed model, seems to be devoid of PceC.
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Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Adrien W Schmid
- Protein Core Facility, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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8
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6577122. [DOI: 10.1093/femsec/fiac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
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9
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Heterologous expression of active Dehalobacter spp. respiratory reductive dehalogenases in Escherichia coli. Appl Environ Microbiol 2021; 88:e0199321. [PMID: 34851719 DOI: 10.1128/aem.01993-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reductive dehalogenases (RDases) are a family of redox enzymes that are required for anaerobic organohalide respiration, a microbial process that is useful in bioremediation. Structural and mechanistic studies of these enzymes have been greatly impeded due to challenges in RDase heterologous expression, potentially because of their cobamide-dependence. There have been a few successful attempts at RDase production in unconventional heterologous hosts, but a robust method has yet to be developed. Here we outline a novel respiratory RDase expression system using Escherichia coli. The overexpression of E. coli's cobamide transport system, btu, and anaerobic expression conditions were found to be essential for production of active RDases from Dehalobacter - an obligate organohalide respiring bacterium. The expression system was validated on six enzymes with amino acid sequence identities as low as 28%. Dehalogenation activity was verified for each RDase by assaying cell-free extracts of small-scale expression cultures on various chlorinated substrates including chloroalkanes, chloroethenes, and hexachlorocyclohexanes. Two RDases, TmrA from Dehalobacter sp. UNSWDHB and HchA from Dehalobacter sp. HCH1, were purified by nickel affinity chromatography. Incorporation of the cobamide and iron-sulfur cluster cofactors was verified; though, the precise cobalamin incorporation could not be determined due to variance between methodologies, and the specific activity of TmrA was consistent with that of the native enzyme. The heterologous expression of respiratory RDases, particularly from obligate organohalide respiring bacteria, has been extremely challenging and unreliable. Here we present a relatively straightforward E. coli expression system that has performed well for a variety of Dehalobacter spp. RDases. IMPORTANCE Understanding microbial reductive dehalogenation is important to refine the global halogen cycle and to improve bioremediation of halogenated contaminants; however, studies of the family of enzymes responsible are limited. Characterization of reductive dehalogenase enzymes has largely eluded researchers due to the lack of a reliable and high-yielding production method. We are presenting an approach to express reductive dehalogenase enzymes from Dehalobacter, a key group of organisms used in bioremediation, in E. coli. This expression system will propel the study of reductive dehalogenases by facilitating their production and isolation, allowing researchers to pursue more in-depth questions about the activity and structure of these enzymes. This platform will also provide a starting point to improve the expression of reductive dehalogenases from many other organisms.
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10
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Ghezzi D, Filippini M, Cappelletti M, Firrincieli A, Zannoni D, Gargini A, Fedi S. Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23017-23035. [PMID: 33438126 DOI: 10.1007/s11356-020-12236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
- Laboratory of NanoBiotechnology, IRCSS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Maria Filippini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Alessandro Gargini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
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11
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Yan J, Wang J, Villalobos Solis MI, Jin H, Chourey K, Li X, Yang Y, Yin Y, Hettich RL, Löffler FE. Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing Dehalococcoides mccartyi. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4831-4841. [PMID: 33683880 DOI: 10.1021/acs.est.0c07354] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring Dehalococcoidia expressing vinyl chloride (VC) reductive dehalogenase (RDase). The tceA gene encoding the trichloroethene-dechlorinating RDase TceA is frequently detected in contaminated groundwater but not recognized as a biomarker for VC detoxification. We demonstrate that tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as an electron acceptor when sufficient vitamin B12 (B12) is provided. Strain FL2 cultures that received 50 μg L-1 B12 completely dechlorinated VC to ethene at rates of 14.80 ± 1.30 μM day-1 and attained 1.64 ± 0.11 × 108 cells per μmol of VC consumed. Strain 195 attained similar growth yields of 1.80 ± 1.00 × 108 cells per μmol of VC consumed, and both strains could be consecutively transferred with VC as the electron acceptor. Proteomic analysis demonstrated TceA expression in VC-grown strain FL2 cultures. Resequencing of the strain FL2 and strain 195 tceA genes identified non-synonymous substitutions, although their consequences for TceA function are currently unknown. The finding that Dhc strains expressing TceA respire VC can explain ethene formation at chlorinated solvent sites, where quantitative polymerase chain reaction analysis indicates that tceA dominates the RDase gene pool.
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Affiliation(s)
- Jun Yan
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jingjing Wang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Huijuan Jin
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Karuna Chourey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiuying Li
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yi Yang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
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12
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Yang MI, Previdsa M, Edwards EA, Sleep BE. Two distinct Dehalobacter strains sequentially dechlorinate 1,1,1-trichloroethane and 1,1-dichloroethane at a field site treated with granular zero valent iron and guar gum. WATER RESEARCH 2020; 186:116310. [PMID: 32858243 DOI: 10.1016/j.watres.2020.116310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Chlorinated ethanes are environmental pollutants found frequently at many contaminated industrial sites. 1,1,1-Trichloroethane (1,1,1-TCA) can be dechlorinated and detoxified via abiotic transformation or biologically by the action of dechlorinating microorganisms such as Dehalobacter (Dhb). At a field site, it is challenging to distinguish abiotic vs. biotic mechanisms as both processes share common transformation products. In this study, we evaluated using the Dhb 16S rRNA gene and specific reductive dehalogenase genes as biomarkers for 1,1,1-TCA and 1,1-dichloroethane (1,1-DCA) dechlorination. We analyzed samples from laboratory groundwater microcosms and from an industrial site where a mixture of granular zero valent iron (ZVI) and guar gum was injected for 1,1,1-TCA remediation. Abiotic and biotic transformation products were monitored and the changes in dechlorinating organisms were tracked using quantitative PCR (qPCR) with primers targeting the Dhb 16S rRNA gene and two functional genes cfrA and dcrA encoding enzymes that dechlorinate 1,1,1-TCA to 1,1-DCA and 1,1-DCA to chloroethane (CA), respectively. The abundance of the cfrA- and dcrA-like genes confirmed that the two dechlorination steps were carried out by two distinct Dhb populations at the site. The biomarkers used in this study proved useful for monitoring different Dhb populations responsible for step-wise dechlorination and tracking biodegradation of 1,1,1-TCA and 1,1-DCA where both abiotic (e.g., with ZVI) and biotic processes co-occur.
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Affiliation(s)
- M Ivy Yang
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada
| | - Michael Previdsa
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, M5S 3E5, Canada.
| | - Brent E Sleep
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada.
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13
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Metagenomic- and Cultivation-Based Exploration of Anaerobic Chloroform Biotransformation in Hypersaline Sediments as Natural Source of Chloromethanes. Microorganisms 2020; 8:microorganisms8050665. [PMID: 32370295 PMCID: PMC7284496 DOI: 10.3390/microorganisms8050665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/22/2020] [Accepted: 04/29/2020] [Indexed: 01/23/2023] Open
Abstract
Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. No CF removal was observed in abiotic control cultures without artificial electron donors, indicating biotic CF dechlorination in the enrichment cultures. Increasing vitamin B12 concentration from 0.04 to 4 µM in enrichment cultures enhanced CF removal and reduced DCM formation. In cultures amended with 4 µM vitamin B12 and 13C labelled CF, formation of 13CO2 was detected. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected using quantitative PCR nor metagenomic analysis of the enrichment cultures. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO2, were detected. Accordingly, metagenome-assembled genomes of Clostridiales encoded enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis, which are known to be involved in fortuitous and nonspecific CF transformation. This study indicates that hypersaline lake microbiomes may act as a filter to reduce CF emission to the atmosphere.
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14
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Molenda O, Puentes Jácome LA, Cao X, Nesbø CL, Tang S, Morson N, Patron J, Lomheim L, Wishart DS, Edwards EA. Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:663-678. [PMID: 32159535 DOI: 10.1039/c9em00605b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Organohalide respiring bacteria (OHRB) express reductive dehalogenases for energy conservation and growth. Some of these enzymes catalyze the reductive dehalogenation of chlorinated and brominated pollutants in anaerobic subsurface environments, providing a valuable ecosystem service. Dehalococcoides mccartyi strains have been most extensively studied owing to their ability to dechlorinate all chlorinated ethenes - most notably carcinogenic vinyl chloride - to ethene. The genomes of OHRB, particularly obligate OHRB, often harbour multiple putative reductive dehalogenase genes (rdhA), most of which have yet to be characterized. We recently sequenced and closed the genomes of eight new strains, increasing the number of available D. mccartyi genomes in NCBI from 16 to 24. From all available OHRB genomes, we classified predicted translations of reductive dehalogenase genes using a previously established 90% amino acid pairwise identity cut-off to identify Ortholog Groups (OGs). Interestingly, the majority of D. mccartyi dehalogenase gene sequences, once classified into OGs, exhibited a remarkable degree of synteny (gene order) in all genomes sequenced to date. This organization was not apparent without the classification. A high degree of synteny indicates that differences arose from rdhA gene loss rather than recombination. Phylogenetic analysis suggests that most rdhA genes have a long evolutionary history in the Dehalococcoidia with origin prior to speciation of Dehalococcoides and Dehalogenimonas. We also looked for evidence of synteny in the genomes of other species of OHRB. Unfortunately, there are too few closed Dehalogenimonas genomes to compare at this time. There is some partial evidence for synteny in the Dehalobacter restrictus genomes, but here too more closed genomes are needed for confirmation. Interestingly, we found that the rdhA genes that encode enzymes that catalyze dehalogenation of industrial pollutants are the only rdhA genes with strong evidence of recent lateral transfer - at least in the genomes examined herein. Given the utility of the RdhA sequence classification to comparative analyses, we are building a public web server () for the community to use, which allows users to add and classify new sequences, and download the entire curated database of reductive dehalogenases.
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Affiliation(s)
- Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.
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15
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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16
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Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME JOURNAL 2019; 13:1042-1055. [PMID: 30607026 DOI: 10.1038/s41396-018-0333-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
Abstract
Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate-pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.
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Affiliation(s)
- Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Han-Chen Ho
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
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17
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Abstract
Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy with the use of halogenated compounds as terminal electron acceptors. Genes involved in OHR are organized in reductive dehalogenase (rdh) gene clusters and can be found in relatively high copy numbers in the genomes of organohalide-respiring bacteria (OHRB). The minimal rdh gene set is composed by rdhA and rdhB, encoding the catalytic enzyme involved in reductive dehalogenation and its putative membrane anchor, respectively. In this chapter, we present the major findings concerning the regulatory strategies developed by OHRB to control the expression of the rdh gene clusters. The first section focuses on the description of regulation patterns obtained from targeted transcriptional analyses, and from transcriptomic and proteomic studies, while the second section offers a detailed overview of the biochemically characterized OHR regulatory proteins identified so far. Depending on OHRB, transcriptional regulators belonging to three different protein families are found in the direct vicinity of rdh gene clusters, suggesting that they activate the transcription of their cognate gene cluster. In this chapter, strong emphasis was laid on the family of CRP/FNR-type RdhK regulators which belong to members of the genera Dehalobacter and Desulfitobacterium. Whereas only chlorophenols have been identified as effectors for RdhK regulators, the protein sequence diversity suggests a broader organohalide spectrum. Thus, effector identification of new regulators offers a promising alternative to elucidate the substrates of yet uncharacterized reductive dehalogenases. Future work investigating the possible cross-talk between OHR regulators and their possible use as biosensors is discussed.
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18
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Rodríguez-Fernández D, Torrentó C, Palau J, Marchesi M, Soler A, Hunkeler D, Domènech C, Rosell M. Unravelling long-term source removal effects and chlorinated methanes natural attenuation processes by C and Cl stable isotopic patterns at a complex field site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:286-296. [PMID: 30029110 DOI: 10.1016/j.scitotenv.2018.07.130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 06/08/2023]
Abstract
The effects of contaminant sources removal in 2005 (i.e. barrels, tank, pit and wastewater pipe sources) on carbon tetrachloride (CT) and chloroform (CF) concentration in groundwater were assessed at several areas of a fractured multi-contaminant aquifer (Òdena, Spain) over a long-term period (2010-2014). Changes in redox conditions, in these chlorinated methanes (CMs) concentration and in their carbon isotopic compositions (δ13C) were monitored in multilevel wells. δ13C values from these wells were compared to those obtained from sources (barrels, tank and pit before their removal, 2002-2005) and to commercial solvents values in literature. Additionally, CMs natural attenuation processes were identified by C-Cl isotope slopes (Λ). Analyses revealed the downstream migration of the pollutant focus and an efficient removal of DNAPLs in the pit source's influence area. However, the removal of the contaminated soil from former tank and wastewater pipe was incomplete as leaching from unsaturated zone was proved, evidencing these areas are still active sources. Nevertheless, significant CMs degradation was detected close to all sources and Λ values pointed to different reactions. For CT in the tank area, Λ value fitted with hydrogenolysis pathway although other possible reduction processes were also uncovered. Near the wastewater pipe area, CT thiolytic reduction combined with hydrogenolysis was derived. The highest CT degradation extent accounted for these areas was 72 ± 11% and 84 ± 6%, respectively. For CF, the Λ value in the pit source's area was consistent with oxidation and/or with transport of CF affected by alkaline hydrolysis from upstream interception trenches. In contrast, isotope data evidenced CF reduction in the tank and wastewater pipe influence areas, although the observed Λ slightly deviates from the reference values, likely due to the continuous leaching of CF degraded in the non-saturated zone by a mechanism different from reduction.
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Affiliation(s)
- Diana Rodríguez-Fernández
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain.
| | - Clara Torrentó
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain; Centre for Hydrogeology and Geothermics, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Jordi Palau
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain; Centre for Hydrogeology and Geothermics, University of Neuchâtel, 2000 Neuchâtel, Switzerland; Institute of Environmental Assessment and Water Research (IDAEA), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Barcelona, Spain
| | - Massimo Marchesi
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain; Politecnico di Milano, Dept. of Civil and Environmental Engineering (DICA), Piazza L. Da Vinci, 32, 20133 Milano, Italy
| | - Albert Soler
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain
| | - Daniel Hunkeler
- Centre for Hydrogeology and Geothermics, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Cristina Domènech
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain
| | - Mònica Rosell
- Grup MAiMA, Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain
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19
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Wang S, Qiu L, Liu X, Xu G, Siegert M, Lu Q, Juneau P, Yu L, Liang D, He Z, Qiu R. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnol Adv 2018; 36:1194-1206. [DOI: 10.1016/j.biotechadv.2018.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/08/2023]
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20
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Rodríguez-Fernández D, Torrentó C, Guivernau M, Viñas M, Hunkeler D, Soler A, Domènech C, Rosell M. Vitamin B 12 effects on chlorinated methanes-degrading microcosms: Dual isotope and metabolically active microbial populations assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:1615-1625. [PMID: 29054650 DOI: 10.1016/j.scitotenv.2017.10.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/21/2017] [Accepted: 10/08/2017] [Indexed: 06/07/2023]
Abstract
Field-derived anoxic microcosms were used to characterize chloroform (CF) and carbon tetrachloride (CT) natural attenuation to compare it with biostimulation scenarios in which vitamin B12 was added (B12/pollutant ratio of 0.01 and 0.1) by means of by-products, carbon and chlorine compound-specific stable-isotope analysis, and the active microbial community through 16S rRNA MiSeq high-throughput sequencing. Autoclaved slurry controls discarded abiotic degradation processes. B12 catalyzed CF and CT biodegradation without the accumulation of dichloromethane, carbon disulphide, or CF. The carbon isotopic fractionation value of CF (ƐCCF) with B12 was -14±4‰, and the value for chlorine (ƐClCF) was -2.4±0.4‰. The carbon isotopic fractionation values of CT (ƐCCT) were -16±6 with B12, and -13±2‰ without B12; and the chlorine isotopic fractionation values of CT (ƐClCT) were -6±3 and -4±2‰, respectively. Acidovorax, Ancylobacter, and Pseudomonas were the most metabolically active genera, whereas Dehalobacter and Desulfitobacterium were below 0.1% of relative abundance. The dual C-Cl element isotope slope (Λ=Δδ13C/Δδ37Cl) for CF biodegradation (only detected with B12, 7±1) was similar to that reported for CF reduction by Fe(0) (8±2). Several reductive pathways might be competing in the tested CT scenarios, as evidenced by the lack of CF accumulation when B12 was added, which might be linked to a major activity of Pseudomonas stutzeri; by different chlorine apparent kinetic isotope effect values and Λ which was statistically different with and without B12 (5±1 vs 6.1±0.5), respectively. Thus, positive B12 effects such as CT and CF degradation catalyst were quantified for the first time in isotopic terms, and confirmed with the major activity of species potentially capable of their degradation. Moreover, the indirect benefits of B12 on the degradation of chlorinated ethenes were proved, creating a basis for remediation strategies in multi-contaminant polluted sites.
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Affiliation(s)
- Diana Rodríguez-Fernández
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain.
| | - Clara Torrentó
- Centre d'hydrogéologie et de géothermie, Université de Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Miriam Guivernau
- GIRO Joint Research Unit IRTA-UPC, IRTA, Torre Marimon, Caldes de Montbui E-08140, Spain
| | - Marc Viñas
- GIRO Joint Research Unit IRTA-UPC, IRTA, Torre Marimon, Caldes de Montbui E-08140, Spain
| | - Daniel Hunkeler
- Centre d'hydrogéologie et de géothermie, Université de Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Albert Soler
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain
| | - Cristina Domènech
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain
| | - Mònica Rosell
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain
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21
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Puentes Jácome LA, Edwards EA. A switch of chlorinated substrate causes emergence of a previously undetected native Dehalobacter population in an established Dehalococcoides-dominated chloroethene-dechlorinating enrichment culture. FEMS Microbiol Ecol 2018; 93:4569067. [PMID: 29088371 DOI: 10.1093/femsec/fix141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/26/2017] [Indexed: 01/08/2023] Open
Abstract
Chlorobenzenes are soil and groundwater pollutants of concern that can be reductively dehalogenated by organohalide-respiring bacteria from the genera Dehalococcoides and Dehalobacter. The bioaugmentation culture KB-1® harbours Dehalococcoides mccartyi spp. that reductively dehalogenate trichloroethene to ethene. It contains more than 30 reductive dehalogenase genes; some of them are highly similar to genes found in the chlorobenzene-respiring Dehalococcoides mccartyi strain CBDB1. We explored the chlorobenzene dehalogenation capability of the KB-1 enrichment culture using 1,2,4-trichlorobenzene (1,2,4-TCB). We achieved adaptation of KB-1 to 1,2,4-TCB that is dehalogenated to a mixture of dichlorobenzenes, and subsequently to monochlorobenzene and benzene. Surprisingly, a native Dehalobacter population, and not a Dehalococcoides population, couples the dechlorination of 1,2,4-TCB to growth achieving an average yield of 1.1 ± 0.6 × 1013 cells per mole of Cl- released. Interestingly, the dechlorination of 1,2,4-TCB occurs alongside the complete dechlorination of trichloroethene to ethene in cultures fed both electron acceptors. Dehalobacter was not previously identified as a major player in KB-1, but its ecological niche was favoured by the introduction of 1,2,4-TCB. Based on 16S rRNA phylogeny, Dehalobacter populations seem to cluster into specialised clades, and are likely undergoing substrate specialisation as a strategy to reduce competition for electron acceptors.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
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Pan Y, Chen J, Zhou H, Farzana S, Tam NFY. Vertical distribution of dehalogenating bacteria in mangrove sediment and their potential to remove polybrominated diphenyl ether contamination. MARINE POLLUTION BULLETIN 2017; 124:1055-1062. [PMID: 28034497 DOI: 10.1016/j.marpolbul.2016.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/09/2016] [Accepted: 12/11/2016] [Indexed: 06/06/2023]
Abstract
The removal and degradation of polybrominated diphenyl ethers (PBDEs) in sediments are not clear. The vertical distribution of total and dehalogenating bacteria in sediment cores collected from a typical mangrove swamp in South China and their intrinsic degradation potential were investigated. These bacterial groups had the highest abundances in surface sediments (0-5cm). A 5-months microcosm experiment also showed that surface sediments had the highest rate to remove BDE-47 than deeper sediments (5-30cm) under anaerobic condition. The deeper sediments, being more anaerobic, had lower population of dehalogenating bacteria leading to a weaker BDE-47 removal potential than surface sediments. Stepwise multiple regression analysis indicated that Dehalococcoides spp. were the most important dehalogenating bacteria affecting the anaerobic removal of BDE-47 in mangrove sediments. This is the first study reporting that mangrove sediments harbored diverse groups of dehalogenating bacteria and had intrinsic potential to remove PBDE contamination.
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Affiliation(s)
- Ying Pan
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road, Nanjing 210098, China
| | - Haichao Zhou
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; Futian-CityU Mangrove R&D Centre, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shazia Farzana
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Nora F Y Tam
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
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23
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Kunze C, Diekert G, Schubert T. Subtle changes in the active site architecture untangled overlapping substrate ranges and mechanistic differences of two reductive dehalogenases. FEBS J 2017; 284:3520-3535. [DOI: 10.1111/febs.14258] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/20/2017] [Accepted: 08/30/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Cindy Kunze
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
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24
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Yoshikawa M, Zhang M, Toyota K. Biodegradation of Volatile Organic Compounds and Their Effects on Biodegradability under Co-Existing Conditions. Microbes Environ 2017; 32:188-200. [PMID: 28904262 PMCID: PMC5606688 DOI: 10.1264/jsme2.me16188] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs. In order to investigate the potential of biodegrading multiple VOCs, we initially reviewed the biodegradation of individual VOCs. VOCs include chlorinated ethenes (tetrachloroethene, trichloroethene, dichloroethene, and vinyl chloride), BTEX (benzene, toluene, ethylbenzene, and xylene), and chlorinated methanes (carbon tetrachloride, chloroform, and dichloromethane). We also summarized essential information on the biodegradation of each kind of VOC under aerobic and anaerobic conditions, together with the microorganisms that are involved in VOC-degrading pathways. Interactions among multiple VOCs were then discussed based on concrete examples. Under conditions in which multiple VOCs co-exist, the biodegradation of a VOC may be constrained, enhanced, and/or unaffected by other compounds. Co-metabolism may enhance the degradation of other VOCs. In contrast, constraints are imposed by the toxicity of co-existing VOCs and their by-products, catabolite repression, or competition between VOC-degrading enzymes. This review provides fundamental, but systematic information for designing strategies for the bioremediation of multiple VOCs, as well as information on the role of key microorganisms that degrade VOCs.
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Affiliation(s)
- Miho Yoshikawa
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST).,Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
| | - Ming Zhang
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
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25
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Identification of Multiple Dehalogenase Genes Involved in Tetrachloroethene-to-Ethene Dechlorination in a Dehalococcoides-Dominated Enrichment Culture. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9191086. [PMID: 28894752 PMCID: PMC5574268 DOI: 10.1155/2017/9191086] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/03/2017] [Indexed: 11/17/2022]
Abstract
Chloroethenes (CEs) are widespread groundwater toxicants that are reductively dechlorinated to nontoxic ethene (ETH) by members of Dehalococcoides. This study established a Dehalococcoides-dominated enrichment culture (designated “YN3”) that dechlorinates tetrachloroethene (PCE) to ETH with high dechlorination activity, that is, complete dechlorination of 800 μM PCE to ETH within 14 days in the presence of Dehalococcoides species at 5.7 ± 1.9 × 107 copies of 16S rRNA gene/mL. The metagenome of YN3 harbored 18 rdhA genes (designated YN3rdhA1–18) encoding the catalytic subunit of reductive dehalogenase (RdhA), four of which were suggested to be involved in PCE-to-ETH dechlorination based on significant increases in their transcription in response to CE addition. The predicted proteins for two of these four genes, YN3RdhA8 and YN3RdhA16, showed 94% and 97% of amino acid similarity with PceA and VcrA, which are well known to dechlorinate PCE to trichloroethene (TCE) and TCE to ETH, respectively. The other two rdhAs, YN3rdhA6 and YN3rdhA12, which were never proved as rdhA for CEs, showed particularly high transcription upon addition of vinyl chloride (VC), with 75 ± 38 and 16 ± 8.6 mRNA copies per gene, respectively, suggesting their possible functions as novel VC-reductive dehalogenases. Moreover, metagenome data indicated the presence of three coexisting bacterial species, including novel species of the genus Bacteroides, which might promote CE dechlorination by Dehalococcoides.
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26
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Azizian MF, Semprini L. Simultaneous anaerobic transformation of carbon tetrachloride to carbon dioxide and tetrachloroethene to ethene in a continuous flow column. JOURNAL OF CONTAMINANT HYDROLOGY 2017; 203:93-103. [PMID: 28716488 DOI: 10.1016/j.jconhyd.2017.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/30/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
The simultaneous anaerobic transformation of tetrachloroethene (PCE) and carbon tetrachloride (CT) was evaluated in a continuous flow column. The column was packed with quartz sand and bioaugmented with the Evanite culture (EV) that is capable of transforming PCE to ethene. Azizian and Semprini (2016) reported that PCE and CT could be simultaneously transformed in the column, with PCE (0.1mM) transformed mainly to ethene and CT (0.015mM) to chloroform (CF) (20%) and an unknown transformation product, likely carbon dioxide (CO2). The fermentation of propionate, formed from lactate fermentation, was inhibited after the transformation of CT, likely from the exposure to CF. Reported here is the second phase of that study where a second bioaugmentation of the EV culture was made to reintroduce a lactate and propionate fermenting population to the column. Effective lactate and propionate fermentation were restored with a H2 concentration of ~25nM maintained in the column effluent. PCE (0.1mM) was effectively transformed to ethene (~98%) and vinyl chloride (VC) (~2%). Unlabeled CT (0.015 to 0.03mM) was completely transformed with a transient build-up of CF and chloromethane (CM), which were subsequently removed below their detection limits. A series of transient tests were initiated through the addition of carbon-13 labeled CT (13CT), with concentrations gradually increased from 0.03 to 0.10mM. GC-MS analysis of the column effluent showed that 13C labeled CO2 (13CO2) was formed, ranging from 82 to 93% of the 13CT transformed, with the transient increases in 13CO2 associated with the increased concentration of 13CT. A modified COD analysis indicated a lesser amount of 13CT (18%) was transformed to soluble products, while 13CO2 represented 82% the 13CT transformed. In a final transient test, the influent lactate concentration was decreased from 1.1 to 0.67mM. The transformation of both CT and PCE changed dramatically. Only 59% of the 13CT was transformed, primarily to CF. 13CO2 concentrations gradually decreased to background levels, indicating CO2 was no longer a transformation product. PCE transformation resulted in the following percentage of products formed: cDCE (60%), VC (36%), and ethene (4%). Incomplete propionate fermentation was also observed, consistent with the build-up of CF and the decrease in H2 concentrations to approximately 2nM. The results clearly demonstrate that high concentrations of CT were transformed to CO2, and effective PCE dehalogenation to ethene was maintained when excess lactate was fed and propionate was effectively fermented. However, when the lactate concentration was reduced, both PCE and CT transformation and propionate fermentation were negatively impacted.
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Affiliation(s)
- Mohammad F Azizian
- School of Chemical, Biological and Environmental Engineering, 116 Johnson Hall, Oregon State University, Corvallis, OR 97331, United States.
| | - Lewis Semprini
- School of Chemical, Biological and Environmental Engineering, 116 Johnson Hall, Oregon State University, Corvallis, OR 97331, United States
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Jugder BE, Bohl S, Lebhar H, Healey RD, Manefield M, Marquis CP, Lee M. A bacterial chloroform reductive dehalogenase: purification and biochemical characterization. Microb Biotechnol 2017. [PMID: 28631300 PMCID: PMC5658581 DOI: 10.1111/1751-7915.12745] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We report herein the purification of a chloroform (CF)-reducing enzyme, TmrA, from the membrane fraction of a strict anaerobe Dehalobacter sp. strain UNSWDHB to apparent homogeneity with an approximate 23-fold increase in relative purity compared to crude lysate. The membrane fraction obtained by ultracentrifugation was solubilized in Triton X-100 in the presence of glycerol, followed by purification by anion exchange chromatography. The molecular mass of the purified TmrA was determined to be 44.5 kDa by SDS-PAGE and MALDI-TOF/TOF. The purified dehalogenase reductively dechlorinated CF to dichloromethane in vitro with reduced methyl viologen as the electron donor at a specific activity of (1.27 ± 0.04) × 103 units mg protein-1 . The optimum temperature and pH for the activity were 45°C and 7.2, respectively. The UV-visible spectrometric analysis indicated the presence of a corrinoid and two [4Fe-4S] clusters, predicted from the amino acid sequence. This is the first report of the production, purification and biochemical characterization of a CF reductive dehalogenase.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Susanne Bohl
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,Department of Biotechnology, Mannheim University of Applied Sciences, 68163, Mannheim, Germany
| | - Helene Lebhar
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Robert D Healey
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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Affiliation(s)
- Maeva Fincker
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
| | - Alfred M. Spormann
- Department of Civil and Environmental Engineering and Department of Chemical Engineering, Stanford University, Stanford, California 94305;,
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29
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Torrentó C, Palau J, Rodríguez-Fernández D, Heckel B, Meyer A, Domènech C, Rosell M, Soler A, Elsner M, Hunkeler D. Carbon and Chlorine Isotope Fractionation Patterns Associated with Different Engineered Chloroform Transformation Reactions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:6174-6184. [PMID: 28482655 DOI: 10.1021/acs.est.7b00679] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To use compound-specific isotope analysis for confidently assessing organic contaminant attenuation in the environment, isotope fractionation patterns associated with different transformation mechanisms must first be explored in laboratory experiments. To deliver this information for the common groundwater contaminant chloroform (CF), this study investigated for the first time both carbon and chlorine isotope fractionation for three different engineered reactions: oxidative C-H bond cleavage using heat-activated persulfate, transformation under alkaline conditions (pH ∼ 12) and reductive C-Cl bond cleavage by cast zerovalent iron, Fe(0). Carbon and chlorine isotope fractionation values were -8 ± 1‰ and -0.44 ± 0.06‰ for oxidation, -57 ± 5‰ and -4.4 ± 0.4‰ for alkaline hydrolysis (pH 11.84 ± 0.03), and -33 ± 11‰ and -3 ± 1‰ for dechlorination, respectively. Carbon and chlorine apparent kinetic isotope effects (AKIEs) were in general agreement with expected mechanisms (C-H bond cleavage in oxidation by persulfate, C-Cl bond cleavage in Fe(0)-mediated reductive dechlorination and E1CB elimination mechanism during alkaline hydrolysis) where a secondary AKIECl (1.00045 ± 0.00004) was observed for oxidation. The different dual carbon-chlorine (Δδ13C vs Δδ37Cl) isotope patterns for oxidation by thermally activated persulfate and alkaline hydrolysis (17 ± 2 and 13.0 ± 0.8, respectively) vs reductive dechlorination by Fe(0) (8 ± 2) establish a base to identify and quantify these CF degradation mechanisms in the field.
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Affiliation(s)
- Clara Torrentó
- Centre for Hydrogeology and Geothermics, Université de Neuchâtel , 2000 Neuchâtel, Switzerland
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Martí Franques s/n, Universitat de Barcelona (UB) , 08028 Barcelona, Spain
| | - Jordi Palau
- Centre for Hydrogeology and Geothermics, Université de Neuchâtel , 2000 Neuchâtel, Switzerland
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Martí Franques s/n, Universitat de Barcelona (UB) , 08028 Barcelona, Spain
| | - Diana Rodríguez-Fernández
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Martí Franques s/n, Universitat de Barcelona (UB) , 08028 Barcelona, Spain
| | - Benjamin Heckel
- Institute of Groundwater Ecology, Helmholtz Zentrum München , 85764 Neuherberg, Germany
| | - Armin Meyer
- Institute of Groundwater Ecology, Helmholtz Zentrum München , 85764 Neuherberg, Germany
| | - Cristina Domènech
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Martí Franques s/n, Universitat de Barcelona (UB) , 08028 Barcelona, Spain
| | - Mònica Rosell
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Martí Franques s/n, Universitat de Barcelona (UB) , 08028 Barcelona, Spain
| | - Albert Soler
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Martí Franques s/n, Universitat de Barcelona (UB) , 08028 Barcelona, Spain
| | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München , 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich , Marchioninistrasse 17, D-81377 Munich, Germany
| | - Daniel Hunkeler
- Centre for Hydrogeology and Geothermics, Université de Neuchâtel , 2000 Neuchâtel, Switzerland
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30
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Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture. Appl Microbiol Biotechnol 2017; 101:5481-5492. [DOI: 10.1007/s00253-017-8236-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
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31
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Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, Löffler FE. 'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Syst Appl Microbiol 2016; 40:150-159. [PMID: 28292625 DOI: 10.1016/j.syapm.2016.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
Abstract
Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160±3μmolL-1 d-1. The DCM degrader attained 5.25×107±1.0×107 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4±0.8μm long and 0.4±0.1μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, 'Candidatus Dichloromethanomonas elyunquensis'.
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Affiliation(s)
- Sara Kleindienst
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Steven A Higgins
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Despina Tsementzi
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, DE 19714, USA
| | - Frank E Löffler
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.
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Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME JOURNAL 2016; 11:626-640. [PMID: 27898054 DOI: 10.1038/ismej.2016.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/25/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional. Using strain CF to experimentally verify annotations, we determined that the predicted defective serine biosynthesis pathway can be rescued with a promiscuous serine hydroxymethyltransferase. Strain CF grew without added thiamine although the thiamine biosynthesis pathway is predicted to be absent; intracellular thiamine diphosphate, the cofactor of carboxylases in central metabolism, was not detected in cell extracts. Thus, strain CF may use amino acids to replenish central metabolites, portending entangled metabolite exchanges in ACT-3. Consistent with annotation, strain CF possesses a functional corrinoid biosynthesis pathway, demonstrated by increasing corrinoid content during growth and guided cobalamin biosynthesis in corrinoid-free medium. Chloroform toxicity to corrinoid-producing methanogens and acetogens may drive the conservation of corrinoid autotrophy in Dehalobacter strains. Heme detection in strain CF cell extracts suggests the 'archaeal' heme biosynthesis pathway also functions in anaerobic Firmicutes. This study reinforces the importance of incorporating enzyme promiscuity and cofactor availability in genome-scale functional predictions and identifies essential nutrient interdependencies in anaerobic dechlorinating microbial communities.
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33
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Jugder BE, Ertan H, Wong YK, Braidy N, Manefield M, Marquis CP, Lee M. Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:814-824. [PMID: 27452500 DOI: 10.1111/1758-2229.12444] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Organohalide respiring bacteria (ORB) are capable of utilising organohalides as electron acceptors for the generation of cellular energy and consequently play an important role in the turnover of natural and anthropogenically-derived organohalides. In this study, the response of a Dehalobacter sp. strain UNSWDHB to the addition of trichloromethane (TCM) after a 50 h period of its absence (suffocation) was evaluated from a transcriptomic and proteomic perspective. The up-regulation of TCM reductive dehalogenase genes (tmrABC) and their gene products (TmrABC) was confirmed at both transcriptional and proteomic levels. Other findings include the upregulation of various hydrogenases (membrane-associated Ni-Fe hydrogenase complexes and soluble Fe-Fe hydrogenases), formate dehydrogenases, complex I and a pyrophosphate-energized proton pump. The elevated expression of enzymes associated with carbon metabolism, including complete Wood Ljungdahl pathway, during TCM respiration raises interesting questions on possible fates of intracellular formate and its potential role in the physiology of this bacterium. Overall, the findings presented here provide a broader view on the bioenergetics and general physiology of Dehalobacter UNSWDHB cells actively respiring with TCM.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
- Department of Molecular Biology and Genetics, Istanbul University, Turkey
| | - Yie Kuan Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Nady Braidy
- Faculty of Medicine, School of Psychiatry, Centre for Healthy Brain Ageing, University of New South Wales, Sydney, Australia
| | - Michael Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
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34
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Wong YK, Holland SI, Ertan H, Manefield M, Lee M. Isolation and characterization ofDehalobacter sp.strain UNSWDHB capable of chloroform and chlorinated ethane respiration. Environ Microbiol 2016; 18:3092-105. [DOI: 10.1111/1462-2920.13287] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Yie K. Wong
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Sophie I. Holland
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
- Department of Molecular Biology and Genetics; Istanbul University; Turkey
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
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35
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Nijenhuis I, Kuntze K. Anaerobic microbial dehalogenation of organohalides — state of the art and remediation strategies. Curr Opin Biotechnol 2016; 38:33-8. [DOI: 10.1016/j.copbio.2015.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/03/2015] [Indexed: 11/26/2022]
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Schiffmacher EN, Becker JG, Lorah MM, Voytek MA. The effects of co-contaminants and native wetland sediments on the activity and dominant transformation mechanisms of a 1,1,2,2-tetrachloroethane (TeCA)-degrading enrichment culture. CHEMOSPHERE 2016; 147:239-247. [PMID: 26766361 DOI: 10.1016/j.chemosphere.2015.12.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/03/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
Bioremediation strategies, including bioaugmentation with chlorinated ethene-degrading enrichment cultures, have been successfully applied in the cleanup of subsurface environments contaminated with tetrachloroethene (PCE) and/or trichloroethene (TCE). However, these compounds are frequently found in the environment as components of mixtures that may also contain chlorinated ethanes and methanes. Under these conditions, the implementation of bioremediation may be complicated by inhibition effects, particularly when multiple dehalorespirers are present. We investigated the ability of the 1,1,2,2-tetrachloroethane (TeCA)-dechlorinating culture WBC-2 to biotransform TeCA alone, or a mixture of TeCA plus PCE and carbon tetrachloride (CT), in microcosms. The microcosms contained electron donors provided to biostimulate the added culture and sediment collected from a wetland where numerous "hotspots" of contamination with chlorinated solvent mixtures exist. The dominant TeCA biodegradation mechanism mediated by the WBC-2 culture in the microcosms was different in the presence of these wetland sediments than in the sediment-free enrichment culture or in previous WBC-2 bioaugmented microcosms and column tests conducted with wetland sediment collected at nearby sites. The co-contaminants and their daughter products also inhibited TeCA biodegradation by WBC-2. These results highlight the need to conduct biodegradability assays at new sites, particularly when multiple contaminants and dehalorespiring populations are present.
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Affiliation(s)
- Emily N Schiffmacher
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Jennifer G Becker
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Michelle M Lorah
- United States Geological Survey, MD-DE-DC Water Science Center, 5522 Research Park Drive, Baltimore, MD 21228, USA.
| | - Mary A Voytek
- United States Geological Survey, 430 National Center, Reston, VA 20192, USA.
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Jugder BE, Ertan H, Bohl S, Lee M, Marquis CP, Manefield M. Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation. Front Microbiol 2016; 7:249. [PMID: 26973626 PMCID: PMC4771760 DOI: 10.3389/fmicb.2016.00249] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/15/2016] [Indexed: 01/31/2023] Open
Abstract
Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.
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Affiliation(s)
- Bat-Erdene Jugder
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia; Department of Molecular Biology and Genetics, Istanbul UniversityIstanbul, Turkey
| | - Susanne Bohl
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydney, NSW, Australia; Department of Biotechnology, Mannheim University of Applied SciencesMannheim, Germany
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Christopher P Marquis
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
| | - Michael Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales Sydney, NSW, Australia
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Kublik A, Deobald D, Hartwig S, Schiffmann CL, Andrades A, von Bergen M, Sawers RG, Adrian L. Identification of a multi-protein reductive dehalogenase complex inDehalococcoides mccartyistrain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement. Environ Microbiol 2016; 18:3044-56. [DOI: 10.1111/1462-2920.13200] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/03/2015] [Accepted: 12/23/2015] [Indexed: 02/01/2023]
Affiliation(s)
- Anja Kublik
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Darja Deobald
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Stefanie Hartwig
- Institute of Microbiology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle Germany
| | - Christian L. Schiffmann
- Department of Proteomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Adarelys Andrades
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
| | - Martin von Bergen
- Department of Proteomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
- Department of Metabolomics; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
- Centre for Microbial Communities; University of Aalborg; Fredrik Bajers Vej 7H 9220 Aalborg East Denmark
| | - R. Gary Sawers
- Institute of Microbiology; Martin-Luther University Halle-Wittenberg; Kurt-Mothes-Str. 3 06120 Halle Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Permoserstraße 15 04318 Leipzig Germany
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Tang S, Wang PH, Higgins SA, Löffler FE, Edwards EA. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates. Front Microbiol 2016; 7:100. [PMID: 26903979 PMCID: PMC4751268 DOI: 10.3389/fmicb.2016.00100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. This analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.
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Affiliation(s)
- Shuiquan Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Po Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Steven A Higgins
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Frank E Löffler
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA; Department of Civil and Environmental Engineering, University of TennesseeKnoxville, TN, USA
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
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Jugder BE, Ertan H, Lee M, Manefield M, Marquis CP. Reductive Dehalogenases Come of Age in Biological Destruction of Organohalides. Trends Biotechnol 2015; 33:595-610. [DOI: 10.1016/j.tibtech.2015.07.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
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Chen Y, Wen Y, Zhou J, Zhou Q, Vymazal J, Kuschk P. Transformation of chloroform in model treatment wetlands: from mass balance to microbial analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:6198-6205. [PMID: 25901522 DOI: 10.1021/es506357e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chloroform is one of the common disinfection byproducts, which is not susceptible to degradation and poses great health concern. In this study, the chloroform removal efficiencies and contributions of sorption, microbial degradation, plant uptake, and volatilization were evaluated in six model constructed wetlands (CWs). The highest chloroform removal efficiency was achieved in litter-added CWs (99%), followed by planted (46-54%) and unplanted CWs (39%). Mass balance study revealed that sorption (73.5-81.2%) and microbial degradation (17.6-26.2%) were the main chloroform removal processes in litter-added CWs, and that sorption (53.6-66.1%) and plant uptake (25.3-36.2%) were the primary contributors to chloroform removal in planted CWs. Around 60% of chloroform got accumulated in the roots after plant uptake, and both transpiration and gas-phase transport were expected to be the drivers for the plant uptake. Sulfate-reducing bacteria and methanogens were found to be the key microorganisms for chloroform biodegradation through cometabolic dechlorination, and positive correlations were observed between functional genes (dsrA, mcrA) and biodegradation rates. Overall, this study suggests that wetland is an efficient ecosystem for sustainable chloroform removal, and that plant and litter can enhance the removal performance through root uptake and microbial degradation stimulation, respectively.
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Affiliation(s)
- Yi Chen
- †Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, P.R. China
- ‡Department of Landscape Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Prague 16521, Czech Republic
- §Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research -UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Yue Wen
- †Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, P.R. China
| | - Junwei Zhou
- †Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, P.R. China
| | - Qi Zhou
- †Key Laboratory of Yangtze Water Environment of Ministry of the State Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, P.R. China
| | - Jan Vymazal
- ‡Department of Landscape Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Prague 16521, Czech Republic
| | - Peter Kuschk
- §Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research -UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes. Appl Environ Microbiol 2015; 81:4626-33. [PMID: 25934625 DOI: 10.1128/aem.00536-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/23/2015] [Indexed: 02/07/2023] Open
Abstract
Many reductive dehalogenases (RDases) have been identified in organohalide-respiring microorganisms, and yet their substrates, specific activities, and conditions for expression are not well understood. We tested whether RDase expression varied depending on the substrate-exposure history of reductive dechlorinating communities. For this purpose, we used the enrichment culture KB-1 maintained on trichloroethene (TCE), as well as subcultures maintained on the intermediates cis-dichloroethene (cDCE) and vinyl chloride (VC). KB-1 contains a TCE-to-cDCE dechlorinating Geobacter and several Dehalococcoides strains that together harbor many of the known chloroethene reductases. Expressed RDases were identified using blue native polyacrylamide gel electrophoresis, enzyme assays in gel slices, and peptide sequencing. As anticipated but never previously quantified, the RDase from Geobacter was only detected transiently at the beginning of TCE dechlorination. The Dehalococcoides RDase VcrA and smaller amounts of TceA were expressed in the parent KB-1 culture during complete dechlorination of TCE to ethene regardless of time point or amended substrate. The Dehalococcoides RDase BvcA was only detected in enrichments maintained on cDCE as growth substrates, in roughly equal abundance to VcrA. Only VcrA was detected in subcultures enriched on VC. Enzyme assays revealed that 1,1-DCE, a substrate not used for culture enrichment, afforded the highest specific activity. trans-DCE was substantially dechlorinated only by extracts from cDCE enrichments expressing BvcA. RDase gene distribution indicated enrichment of different strains of Dehalococcoides as a function of electron acceptor TCE, cDCE, or VC. Each chloroethene reductase has distinct substrate preferences leading to strain selection in mixed communities.
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Lee M, Wells E, Wong YK, Koenig J, Adrian L, Richnow HH, Manefield M. Relative contributions of Dehalobacter and zerovalent iron in the degradation of chlorinated methanes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4481-4489. [PMID: 25764054 DOI: 10.1021/es5052364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The role of bacteria and zerovalent iron (Fe(0)) in the degradation of chlorinated solvents in subsurface environments is of interest to researchers and remediation practitioners alike. Fe(0) used in reactive iron barriers for groundwater remediation positively interacted with enrichment cultures containing Dehalobacter strains in the transformation of halogenated methanes. Chloroform transformation and dichloromethane formation was up to 8-fold faster and 14 times higher, respectively, when a Dehalobacter-containing enrichment culture was combined with Fe(0) compared with Fe(0) alone. The dichloromethane-fermenting culture transformed dichloromethane up to three times faster with Fe(0) compared to without. Compound-specific isotope analysis was employed to compare abiotic and biotic chloroform and dichloromethane degradation. The isotope enrichment factor for the abiotic chloroform/Fe(0) reaction was large at -29.4 ± 2.1‰, while that for chloroform respiration by Dehalobacter was minimal at -4.3 ± 0.45‰. The combined abiotic/biotic dechlorination was -8.3 ± 0.7‰, confirming the predominance of biotic dechlorination. The enrichment factor for dichloromethane fermentation was -15.5 ± 1.5‰; however, in the presence of Fe(0) the factor increased to -23.5 ± 2.1‰, suggesting multiple mechanisms were contributing to dichloromethane degradation. Together the results show that chlorinated methane-metabolizing organisms introduced into reactive iron barriers can have a significant impact on trichloromethane and dichloromethane degradation and that compound-specific isotope analysis can be employed to distinguish between the biotic and abiotic reactions involved.
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Affiliation(s)
- Matthew Lee
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Eliza Wells
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Yie Kuan Wong
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Joanna Koenig
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Lorenz Adrian
- ‡Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoser Strasse 15, Leipzig 04318, Germany
| | - Hans H Richnow
- ‡Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoser Strasse 15, Leipzig 04318, Germany
| | - Mike Manefield
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
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Primers That Target Functional Genes of Organohalide-Respiring Bacteria. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_75] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Meta-analyses of Dehalococcoides mccartyi strain 195 transcriptomic profiles identify a respiration rate-related gene expression transition point and interoperon recruitment of a key oxidoreductase subunit. Appl Environ Microbiol 2014; 80:6062-72. [PMID: 25063656 DOI: 10.1128/aem.02130-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6±0.6 μM Cl-/h)- and fast (22.9±9.6 μM Cl-/h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n=53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112).
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Mukherjee K, Bowman KS, Rainey FA, Siddaramappa S, Challacombe JF, Moe WM. Dehalogenimonas lykanthroporepellensBL-DC-9Tsimultaneously transcribes manyrdhAgenes during organohalide respiration with 1,2-DCA, 1,2-DCP, and 1,2,3-TCP as electron acceptors. FEMS Microbiol Lett 2014; 354:111-8. [DOI: 10.1111/1574-6968.12434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/21/2014] [Accepted: 03/24/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Kalpataru Mukherjee
- Department of Biological Sciences; Louisiana State University; Baton Rouge LA USA
| | - Kimberly S. Bowman
- Department of Biological Sciences; Louisiana State University; Baton Rouge LA USA
- Department of Civil and Environmental Engineering; Louisiana State University; Baton Rouge LA USA
| | - Fred A. Rainey
- Department of Biological Sciences; Louisiana State University; Baton Rouge LA USA
- Department of Biological Sciences; University of Alaska Anchorage; Anchorage AK USA
| | - Shivakumara Siddaramappa
- Bioscience Division; Los Alamos National Laboratory; Los Alamos NM USA
- Institute of Bioinformatics and Applied Biotechnology; Bengaluru India
| | | | - William M. Moe
- Department of Civil and Environmental Engineering; Louisiana State University; Baton Rouge LA USA
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Nelson JL, Jiang J, Zinder SH. Dehalogenation of chlorobenzenes, dichlorotoluenes, and tetrachloroethene by three Dehalobacter spp. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:3776-3782. [PMID: 24593835 DOI: 10.1021/es4044769] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Three enrichment cultures containing Dehalobacter spp. were developed that dehalogenate each of the dichlorobenzene (DCB) isomers to monochlorobenzene (MCB), and the strains using 1,2-DCB (12DCB1) or 1,3-DCB (13DCB1) are now considered isolated, whereas the strain using 1,4-DCB (14DCB1) is considered highly enriched. In this study, we examined the dehalogenation capability of each strain to use chlorobenzenes with three or more chlorines, tetrachloroethene (PCE), or dichlorotoluene (DCT) isomers. Strain 12DCB1 preferentially dehalogenated singly flanked chlorines, but not doubly flanked or unflanked chlorines. It dehalogenated pentachlorobenzene to MCB with little buildup of intermediates. Strain 13DCB1, which could use either 1,3-DCB or 1,2-DCB, demonstrated the widest dehalogenation spectrum of electron acceptors tested, and dehalogenated every chlorobenzene isomer except 1,4-DCB. Notably, strain 13DCB1 dehalogenated the recalcitrant 1,3,5-trichlorobenzene isomer to MCB, and qPCR of 16S rRNA genes indicated that strain 13DCB1 grew. Strain 14DCB1 exhibited the narrowest range of substrate utilization, but was the only strain to dehalogenate para-substituted chlorines. Strains 12DCB1 and 13DCB1 dehalogenated PCE to cis-dichloroethene, and all strains dehalogenated 3,4-DCT to monochlorotoluene. These findings show that Dehalobacter spp., like Dehalococcoides spp., are versatile dehalogenators and should be considered when determining the fate of chlorinated organics at contaminated sites.
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Affiliation(s)
- Jennifer L Nelson
- Department of Microbiology, 270 Wing Hall, Cornell University , Ithaca, New York 14853, United States
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Kawai M, Futagami T, Toyoda A, Takaki Y, Nishi S, Hori S, Arai W, Tsubouchi T, Morono Y, Uchiyama I, Ito T, Fujiyama A, Inagaki F, Takami H. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. Front Microbiol 2014; 5:80. [PMID: 24624126 PMCID: PMC3939436 DOI: 10.3389/fmicb.2014.00080] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/13/2014] [Indexed: 02/01/2023] Open
Abstract
Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.
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Affiliation(s)
- Mikihiko Kawai
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Taiki Futagami
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Department of Bioscience and Biotechnology, Kyushu University Fukuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan
| | - Yoshihiro Takaki
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Shinro Nishi
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Sayaka Hori
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Wataru Arai
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Taishi Tsubouchi
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, National Institutes of Natural Sciences Okazaki, Japan ; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies Okazaki, Japan
| | - Takehiko Ito
- Department of Biological Sciences, Tokyo Institute of Technology Yokohama, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
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49
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Ding C, Zhao S, He J. A Desulfitobacterium sp. strain PR reductively dechlorinates both 1,1,1-trichloroethane and chloroform. Environ Microbiol 2014; 16:3387-97. [PMID: 24428759 DOI: 10.1111/1462-2920.12387] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 01/04/2014] [Indexed: 11/30/2022]
Abstract
1,1,1-Trichloroethane (TCA) and chloroform are two notorious groundwater pollutants. Here we report the isolation and characterization of Desulfitobacterium sp. strain PR that rapidly dechlorinates both compounds. In pyruvate-amended medium, strain PR reductively dechlorinates ∼ 1.0 mM TCA completely to monochloroethane within 15 days. Under the same conditions, strain PR dechlorinates ∼ 1.2 mM chloroform to predominantly dichloromethane (∼ 1.14 mM) and trace amount of monochloromethane (∼ 0.06 mM) within 10 days. Strain PR shares 96.7% 16S rRNA gene sequence similarity with its closest relative - Desulfitobacterium metallireducens strain 853-15; however, it distinguishes itself from known Desulfitobacterium strains by its inability of utilizing several of their commonly shared substrates such as lactate, thiosulfate and sulfite. A reductive dehalogenase gene (ctrA) in strain PR was identified to be responsible for dechlorination of both TCA and chloroform, showing a maximum expression level of 5.95 ∼ 6.25 copies of transcripts cell(-1) . CtrA shares 94% amino acid sequence identity with CfrA in Dehalobacter sp. strain CF50 and DcrA in Dehalobacter sp. strain DCA. Interestingly, strain PR could tolerate high aqueous concentrations (up to 0.45 mM) of trichloroethene, another groundwater pollutant that often coexists with TCA/chloroform. As the first chloroform-respiring and the second TCA-respiring isolate that has been identified, Desulfitobacterium sp. strain PR may prove useful in remediation of halogenated alkanes with trihalomethyl (-CX₃) groups.
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Affiliation(s)
- Chang Ding
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
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50
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Xu M, Gu X, Lu S, Qiu Z, Sui Q. Role of Reactive Oxygen Species for 1,1,1-Trichloroethane Degradation in a Thermally Activated Persulfate System. Ind Eng Chem Res 2014. [DOI: 10.1021/ie403689d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Minhui Xu
- State Environmental
Protection
Key Laboratory of Environmental Risk Assessment and Control on Chemical
Process, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaogang Gu
- State Environmental
Protection
Key Laboratory of Environmental Risk Assessment and Control on Chemical
Process, East China University of Science and Technology, Shanghai 200237, China
| | - Shuguang Lu
- State Environmental
Protection
Key Laboratory of Environmental Risk Assessment and Control on Chemical
Process, East China University of Science and Technology, Shanghai 200237, China
| | - Zhaofu Qiu
- State Environmental
Protection
Key Laboratory of Environmental Risk Assessment and Control on Chemical
Process, East China University of Science and Technology, Shanghai 200237, China
| | - Qian Sui
- State Environmental
Protection
Key Laboratory of Environmental Risk Assessment and Control on Chemical
Process, East China University of Science and Technology, Shanghai 200237, China
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