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Bulka O, Picott K, Mahadevan R, Edwards EA. From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium. Appl Environ Microbiol 2024; 90:e0073224. [PMID: 38819127 PMCID: PMC11218628 DOI: 10.1128/aem.00732-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the mec cassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase-named acdA-and a complete mec cassette were found to be encoded on a single contig belonging to Dehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a Dehalobacter capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the mec cassette. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of Dehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.
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Affiliation(s)
- Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
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2
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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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3
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Kucharzyk KH, Murdoch FK, Wilson J, Michalsen M, Löffler FE, Murdoch RW, Istok JD, Hatzinger PB, Mullins L, Hill A. Integrated Advanced Molecular Tools Predict In Situ cVOC Degradation Rates: Field Demonstration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:557-569. [PMID: 38109066 DOI: 10.1021/acs.est.3c06231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Chlorinated volatile organic compound (cVOC) degradation rate constants are crucial information for site management. Conventional approaches generate rate estimates from the monitoring and modeling of cVOC concentrations. This requires time series data collected along the flow path of the plume. The estimates of rate constants are often plagued by confounding issues, making predictions cumbersome and unreliable. Laboratory data suggest that targeted quantitative analysis of Dehalococcoides mccartyi (Dhc) biomarker genes (qPCR) and proteins (qProt) can be directly correlated with reductive dechlorination activity. To assess the potential of qPCR and qProt measurements to predict rates, we collected data from cVOC-contaminated aquifers. At the benchmark study site, the rate constant for degradation of cis-dichloroethene (cDCE) extracted from monitoring data was 11.0 ± 3.4 yr-1, and the rate constant predicted from the abundance of TceA peptides was 6.9 yr-1. The rate constant for degradation of vinyl chloride (VC) from monitoring data was 8.4 ± 5.7 yr-1, and the rate constant predicted from the abundance of TceA peptides was 5.2 yr-1. At the other study sites, the rate constants for cDCE degradation predicted from qPCR and qProt measurements agreed within a factor of 4. Under the right circumstances, qPCR and qProt measurements can be useful to rapidly predict rates of cDCE and VC biodegradation, providing a major advance in effective site management.
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Affiliation(s)
| | | | - John Wilson
- Scissortail Environmental Solutions, LLC, Ada, Oklahoma 74820, United States
| | - Mandy Michalsen
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, Mississippi 39180, United States
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, Department of Microbiology, Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert W Murdoch
- Battelle Memorial Institute, Columbus, Ohio 43220, United States
| | - Jack D Istok
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, Tennessee 37831, United States
| | - Paul B Hatzinger
- Aptim Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Larry Mullins
- Battelle Memorial Institute, Columbus, Ohio 43220, United States
| | - Amy Hill
- Battelle Memorial Institute, Columbus, Ohio 43220, United States
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4
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Klaes S, Madan S, Deobald D, Cooper M, Adrian L. GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry. Int J Mol Sci 2023; 24:15692. [PMID: 37958676 PMCID: PMC10649880 DOI: 10.3390/ijms242115692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Profiling bacterial populations in mixed communities is a common task in microbiology. Sequencing of 16S small subunit ribosomal-RNA (16S rRNA) gene amplicons is a widely accepted and functional approach but relies on amplification primers and cannot quantify isotope incorporation. Tandem mass spectrometry proteotyping is an effective alternative for taxonomically profiling microorganisms. We suggest that targeted proteotyping approaches can complement traditional population analyses. Therefore, we describe an approach to assess bacterial community compositions at the family level using the taxonomic marker protein GroEL, which is ubiquitously found in bacteria, except a few obligate intracellular species. We refer to our method as GroEL-proteotyping. GroEL-proteotyping is based on high-resolution tandem mass spectrometry of GroEL peptides and identification of GroEL-derived taxa via a Galaxy workflow and a subsequent Python-based analysis script. Its advantage is that it can be performed with a curated and extendable sample-independent database and that GroEL can be pre-separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to reduce sample complexity, improving GroEL identification while simultaneously decreasing the instrument time. GroEL-proteotyping was validated by employing it on a comprehensive raw dataset obtained through a metaproteome approach from synthetic microbial communities as well as real human gut samples. Our data show that GroEL-proteotyping enables fast and straightforward profiling of highly abundant taxa in bacterial communities at reasonable taxonomic resolution.
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Affiliation(s)
- Simon Klaes
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Shobhit Madan
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty of Engineering, Ansbach University of Applied Sciences, 91522 Ansbach, Germany
| | - Darja Deobald
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
| | - Myriel Cooper
- Faculty III Process Sciences, Institute of Environmental Technology, Chair of Environmental Microbiology, Technische Universität Berlin, 10587 Berlin, Germany
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research (UFZ), 04318 Leipzig, Germany; (S.K.); (D.D.)
- Faculty III Process Sciences, Institute of Biotechnology, Chair of Geobiotechnology, Technische Universität Berlin, 13355 Berlin, Germany
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5
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Wu Z, Man Q, Niu H, Lyu H, Song H, Li R, Ren G, Zhu F, Peng C, Li B, Ma X. Recent advances and trends of trichloroethylene biodegradation: A critical review. Front Microbiol 2022; 13:1053169. [PMID: 36620007 PMCID: PMC9813602 DOI: 10.3389/fmicb.2022.1053169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Trichloroethylene (TCE) is a ubiquitous chlorinated aliphatic hydrocarbon (CAH) in the environment, which is a Group 1 carcinogen with negative impacts on human health and ecosystems. Based on a series of recent advances, the environmental behavior and biodegradation process on TCE biodegradation need to be reviewed systematically. Four main biodegradation processes leading to TCE biodegradation by isolated bacteria and mixed cultures are anaerobic reductive dechlorination, anaerobic cometabolic reductive dichlorination, aerobic co-metabolism, and aerobic direct oxidation. More attention has been paid to the aerobic co-metabolism of TCE. Laboratory and field studies have demonstrated that bacterial isolates or mixed cultures containing Dehalococcoides or Dehalogenimonas can catalyze reductive dechlorination of TCE to ethene. The mechanisms, pathways, and enzymes of TCE biodegradation were reviewed, and the factors affecting the biodegradation process were discussed. Besides, the research progress on material-mediated enhanced biodegradation technologies of TCE through the combination of zero-valent iron (ZVI) or biochar with microorganisms was introduced. Furthermore, we reviewed the current research on TCE biodegradation in field applications, and finally provided the development prospects of TCE biodegradation based on the existing challenges. We hope that this review will provide guidance and specific recommendations for future studies on CAHs biodegradation in laboratory and field applications.
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Affiliation(s)
- Zhineng Wu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Quanli Man
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Hanyu Niu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Honghong Lyu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Haokun Song
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Rongji Li
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Gengbo Ren
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Fujie Zhu
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Chu Peng
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Benhang Li
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Xiaodong Ma
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China,*Correspondence: Xiaodong Ma,
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6
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Morson N, Molenda O, Picott KJ, Richardson RE, Edwards EA. Long-term survival of Dehalococcoides mccartyi strains in mixed cultures under electron acceptor and ammonium limitation. FEMS MICROBES 2022; 3:xtac021. [PMID: 37332513 PMCID: PMC10117805 DOI: 10.1093/femsmc/xtac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/11/2022] [Accepted: 07/06/2022] [Indexed: 11/06/2023] Open
Abstract
Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and, therefore, believed to participate in horizontal gene transfer (HGT). To try to induce HGT of the vcrA-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for HGT of the vcrA-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA, which may have influenced substrate specificity. We also identified two nitrogen-fixing D. mccartyi strains in the KB-1 culture. The presence of multiple strains of D. mccartyi with distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1), and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce HGT of the vcrA-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific subclades of Dehalococcoides.
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Affiliation(s)
- Nadia Morson
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, ON M5S 3G5, Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Katherine J Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, 220 Hollister Dr, Ithaca, NY, Ithaca, NY, United States
| | - Elizabeth A Edwards
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, ON M5S 3G5, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada
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7
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Wang Q, Guo S, Ali M, Song X, Tang Z, Zhang Z, Zhang M, Luo Y. Thermally enhanced bioremediation: A review of the fundamentals and applications in soil and groundwater remediation. JOURNAL OF HAZARDOUS MATERIALS 2022; 433:128749. [PMID: 35364527 DOI: 10.1016/j.jhazmat.2022.128749] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Thermally enhanced bioremediation (TEB), a new concept proposed in recent years, explores the combination of thermal treatment and bioremediation to address the challenges of the low efficiency and long duration of bioremediation. This study presented a comprehensive review regarding the fundamentals of TEB and its applications in soil and groundwater remediation. The temperature effects on the bioremediation of contaminants were systematically reviewed. The thermal effects on the physical, chemical and biological characteristics of soil, and the corresponding changes of contaminants bioavailability and microbial metabolic activities were summarized. Specifically, the increase in temperature within a suitable range can proliferate enzymes enrichment, extracellular polysaccharides and biosurfactants production, and further enhancing bioremediation. Furthermore, a systematic evaluation of TEB applications by utilizing traditional in situ heating technologies, as well as renewable energy (e.g., stored aquifer thermal energy and solar energy), was provided. Additionally, TEB has been applied as a biological polishing technology post thermal treatment, which can be a cost-effective method to address the contaminants rebounds in groundwater remediation. However, there are still various challenges to be addressed in TEB, and future research perspectives to further improve the basic understanding and applications of TEB for the remediation of contaminated soil and groundwater are presented.
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Affiliation(s)
- Qing Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Siwei Guo
- Zhejiang University, Hangzhou, China
| | - Mukhtiar Ali
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhiwen Tang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuanxia Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Dehalogenation of Chlorinated Ethenes to Ethene by a Novel Isolate, " Candidatus Dehalogenimonas etheniformans". Appl Environ Microbiol 2022; 88:e0044322. [PMID: 35674428 DOI: 10.1128/aem.00443-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Dehalococcoides mccartyi strains harboring vinyl chloride (VC) reductive dehalogenase (RDase) genes are keystone bacteria for VC detoxification in groundwater aquifers, and bioremediation monitoring regimens focus on D. mccartyi biomarkers. We isolated a novel anaerobic bacterium, "Candidatus Dehalogenimonas etheniformans" strain GP, capable of respiratory dechlorination of VC to ethene. This bacterium couples formate and hydrogen (H2) oxidation to the reduction of trichloro-ethene (TCE), all dichloroethene (DCE) isomers, and VC with acetate as the carbon source. Cultures that received formate and H2 consumed the two electron donors concomitantly at similar rates. A 16S rRNA gene-targeted quantitative PCR (qPCR) assay measured growth yields of (1.2 ± 0.2) × 108 and (1.9 ± 0.2) × 108 cells per μmol of VC dechlorinated in cultures with H2 or formate as electron donor, respectively. About 1.5-fold higher cell numbers were measured with qPCR targeting cerA, a single-copy gene encoding a putative VC RDase. A VC dechlorination rate of 215 ± 40 μmol L-1 day-1 was measured at 30°C, with about 25% of this activity occurring at 15°C. Increasing NaCl concentrations progressively impacted VC dechlorination rates, and dechlorination ceased at 15 g NaCl L-1. During growth with TCE, all DCE isomers were intermediates. Tetrachloroethene was not dechlorinated and inhibited dechlorination of other chlorinated ethenes. Carbon monoxide formed and accumulated as a metabolic by-product in dechlorinating cultures and impacted reductive dechlorination activity. The isolation of a new Dehalogenimonas species able to effectively dechlorinate toxic chlorinated ethenes to benign ethene expands our understanding of the reductive dechlorination process, with implications for bioremediation and environmental monitoring. IMPORTANCE Chlorinated ethenes are risk drivers at many contaminated sites, and current bioremediation efforts focus on organohalide-respiring Dehalococcoides mccartyi strains to achieve detoxification. We isolated and characterized the first non-Dehalococcoides bacterium, "Candidatus Dehalogenimonas etheniformans" strain GP, capable of metabolic reductive dechlorination of TCE, all DCE isomers, and VC to environmentally benign ethene. In addition to hydrogen, the new isolate utilizes formate as electron donor for reductive dechlorination, providing opportunities for more effective electron donor delivery to the contaminated subsurface. The discovery that a broader microbial diversity can achieve detoxification of toxic chlorinated ethenes in anoxic aquifers illustrates the potential of naturally occurring microbes for biotechnological applications.
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9
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Asai M, Yoshida N, Kusakabe T, Ismaeil M, Nishiuchi T, Katayama A. Dehalococcoides mccartyi NIT01, a novel isolate, dechlorinates high concentrations of chloroethenes by expressing at least six different reductive dehalogenases. ENVIRONMENTAL RESEARCH 2022; 207:112150. [PMID: 34619124 DOI: 10.1016/j.envres.2021.112150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
This study presents the isolation of a novel strain of Dehalococcoides mccartyi, NIT01, which can completely dechlorinate up to 4.0 mM of trichloroethene to ethene via 1,2-cis-dichroroethene and vinyl chloride within 25 days. Strain NIT01 dechlorinated chloroethenes (CEs) at a temperature range of 25-32 °C and pH range of 6.5-7.8. The activity of the strain was inhibited by salt at more than 1.3% and inactivated by 1 h exposure to 2.0% air or 0.5 ppm hypochlorous acid. The genome of NIT01 was highly similar to that of the Dehalococcoides strains DCMB5, GT, 11a5, CBDB1, and CG5, and all included identical 16S rRNA genes. Moreover, NIT01 had 19 rdhA genes including NIT01-rdhA7 and rdhA13, which are almost identical to vcrA and pceA that encode known dehalogenases for tetrachloroethene and vinyl chloride, respectively. We also extracted RdhAs from the membrane fraction of NIT01 using 0.5% n-dodecyl-β-d-maltoside and separated them by anion exchange chromatography to identify those involved in CE dechlorination. LC/MS identification of the LDS-PAGE bands and RdhA activities in the fractions indicated cellular expression of six RdhAs. NIT01-RdhA7 (VcrA) and NIT01-RdhA15 were highly detected and NIT01-RdhA6 was the third-most detected. Among these three RdhAs, NIT01-RdhA15 and NIT01-RdhA6 had no biochemically identified relatives and were suggested to be novel functional dehalogenases for CEs. The expression of multiple dehalogenases may support bacterial tolerance to high concentrations of CEs.
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Affiliation(s)
- Masaki Asai
- Department of Civil and Environmental Engineering, Nagoya Institute of Technology (Nitech), Gokiso-Cho, Showa-Ku, Nagoya, Aichi, Japan
| | - Naoko Yoshida
- Department of Civil and Environmental Engineering, Nagoya Institute of Technology (Nitech), Gokiso-Cho, Showa-Ku, Nagoya, Aichi, Japan.
| | - Toshiya Kusakabe
- Department of Civil and Environmental Engineering, Nagoya Institute of Technology (Nitech), Gokiso-Cho, Showa-Ku, Nagoya, Aichi, Japan
| | - Mohamed Ismaeil
- Department of Environmental Engineering and Architecture, Graduate School of Environmental Studies, Nagoya University, Nagoya, 464-8603, Japan; Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Takumi Nishiuchi
- Division of Integrated Omics Research, Kanazawa University, Ishikawa, Japan
| | - Arata Katayama
- Department of Environmental Engineering and Architecture, Graduate School of Environmental Studies, Nagoya University, Nagoya, 464-8603, Japan
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10
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Zhu X, Deng S, Fang Y, Yang S, Zhong Y, Li D, Wang H, Wu J, Peng P. Dehalococcoides-Containing Enrichment Cultures Transform Two Chlorinated Organophosphate Esters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1951-1962. [PMID: 35015551 DOI: 10.1021/acs.est.1c06686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although chlorinated organophosphate esters (Cl-OPEs) have been reported to be ubiquitously distributed in various anoxic environments, little information is available on their fate under anoxic conditions. In this study, we report two Dehalococcoides-containing enrichment cultures that transformed 3.88 ± 0.22 μmol tris(2-chloroethyl) phosphate (TCEP) and 2.61 ± 0.02 μmol tris(1-chloro-2-propyl) phosphate (TCPP) within 10 days. Based on the identification of the transformed products and deuteration experiments, we inferred that TCEP may be transformed to generate bis(2-chloroethyl) phosphate and ethene via one-electron transfer (radical mechanism), followed by C-O bond cleavage. Ethene was subsequently reduced to ethane. Similarly, TCPP was transformed to form bis(1-chloro-2-propyl) phosphate and propene. 16S rRNA gene amplicon sequencing and quantitative polymerase chain reaction analysis revealed that Dehalococcoides was the predominant contributor to the transformation of TCEP and TCPP. Two draft genomes of Dehalococcoides assembled from the metagenomes of the TCEP- and TCPP-transforming enrichment cultures contained 14 and 15 putative reductive dehalogenase (rdh) genes, respectively. Most of these rdh genes were actively transcribed, suggesting that they might contribute to the transformation of TCEP and TCPP. Taken together, this study provides insights into the role of Dehalococcoides during the transformation of representative Cl-OPEs.
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Affiliation(s)
- Xifen Zhu
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaofu Deng
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China
| | - Yun Fang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Sen Yang
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yin Zhong
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510640, China
| | - Dan Li
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heli Wang
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junhong Wu
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping'an Peng
- State Key Laboratory of Organic Geochemistry, Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Wushan, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510640, China
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11
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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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12
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Ultrastructure of organohalide-respiring Dehalococcoidia revealed by cryo-electron tomography. Appl Environ Microbiol 2021; 88:e0190621. [PMID: 34788060 DOI: 10.1128/aem.01906-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dehalococcoides mccartyi (Dhc) and Dehalogenimonas spp. (Dhgm) are members of the class Dehalococcoidia, phylum Chloroflexi, characterized by streamlined genomes and a strict requirement for organohalogens as electron acceptors. Here, we used cryo-electron tomography to reveal morphological and ultrastructural features of Dhc strain BAV1 and 'Candidatus Dehalogenimonas etheniformans' strain GP cells at unprecedented resolution. Dhc cells were irregularly shaped discs (890 ± 110 nm long, 630 ± 110 nm wide and 130 ± 15 nm thick) with curved and straight sides that intersected at acute angles, whereas Dhgm cells appeared as slightly flattened cocci (760 ± 85 nm). The cell envelopes were composed of a cytoplasmic membrane (CM), a paracrystalline surface layer (S-layer) with hexagonal symmetry and ∼22 nm spacing between repeating units, and a layer of unknown composition separating the CM and the S-layer. Cell surface appendages were only detected in Dhc cells, whereas both cell types had bundled cytoskeletal filaments. Repetitive globular structures, ∼5 nm in diameter and ∼9 nm apart, were observed associated with the outer leaflet of the CM. We hypothesized that those represent organohalide respiration (OHR) complexes and estimated ∼30,000 copies per cell. In Dhgm cultures, extracellular lipid vesicles (20 - 110 nm in diameter) decorated with putative OHR complexes but lacking an S-layer were observed. The new findings expand our understanding of the unique cellular ultrastructure and biology of organohalide-respiring Dehalococcoidia. Importance: Dehalococcoidia respire organohalogen compounds and play relevant roles in bioremediation of groundwater, sediments and soils impacted with toxic chlorinated pollutants. Using advanced imaging tools, we have obtained 3-dimensional images at macromolecular resolution of whole Dehalococcoidia cells revealing their unique structural components. Our data detail the overall cellular shape, cell envelope architecture, cytoskeletal filaments, the likely localization of enzymatic complexes involved in reductive dehalogenation, and the structure of extracellular vesicles. The new findings expand our understanding of the cell structure-function relationship in Dehalococcoidia with implications for Dehalococcoidia biology and bioremediation.
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13
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A Microcosm Treatability Study for Evaluating Wood Mulch-Based Amendments as Electron Donors for Trichloroethene (TCE) Reductive Dechlorination. WATER 2021. [DOI: 10.3390/w13141949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, wood mulch-based amendments were tested in a bench-scale microcosm experiment in order to assess the treatability of saturated soils and groundwater from an industrial site contaminated by chlorinated ethenes. Wood mulch was tested alone as the only electron donor in order to assess its potential for stimulating the biological reductive dechlorination. It was also tested in combination with millimetric iron filings in order to assess the ability of the additive to accelerate/improve the bioremediation process. The efficacy of the selected amendments was compared with that of unamended control microcosms. The results demonstrated that wood mulch is an effective natural and low-cost electron donor to stimulate the complete reductive dechlorination of chlorinated solvents to ethene. Being a side-product of the wood industry, mulch can be used in environmental remediation, an approach which perfectly fits the principles of circular economy and addresses the compelling needs of a sustainable and low environmental impact remediation. The efficacy of mulch was further improved by the co-presence of iron filings, which accelerated the conversion of vinyl chloride into the ethene by increasing the H2 availability rather than by catalyzing the direct abiotic dechlorination of contaminants. Chemical analyses were corroborated by biomolecular assays, which confirmed the stimulatory effect of the selected amendments on the abundance of Dehalococcoides mccartyi and related reductive dehalogenase genes. Overall, this paper further highlights the application potential and environmental sustainability of wood mulch-based amendments as low-cost electron donors for the biological treatment of chlorinated ethenes.
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14
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Fenner K, Elsner M, Lueders T, McLachlan MS, Wackett LP, Zimmermann M, Drewes JE. Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence? ACS ES&T WATER 2021; 1:1541-1554. [PMID: 34278380 PMCID: PMC8276273 DOI: 10.1021/acsestwater.1c00025] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 05/14/2023]
Abstract
Complex microbial communities in environmental systems play a key role in the detoxification of chemical contaminants by transforming them into less active metabolites or by complete mineralization. Biotransformation, i.e., transformation by microbes, is well understood for a number of priority pollutants, but a similar level of understanding is lacking for many emerging contaminants encountered at low concentrations and in complex mixtures across natural and engineered systems. Any advanced approaches aiming to reduce environmental exposure to such contaminants (e.g., novel engineered biological water treatment systems, design of readily degradable chemicals, or improved regulatory assessment strategies to determine contaminant persistence a priori) will depend on understanding the causal links among contaminant removal, the key driving agents of biotransformation at low concentrations (i.e., relevant microbes and their metabolic activities), and how their presence and activity depend on environmental conditions. In this Perspective, we present the current understanding and recent methodological advances that can help to identify such links, even in complex environmental microbiomes and for contaminants present at low concentrations in complex chemical mixtures. We discuss the ensuing insights into contaminant biotransformation across varying environments and conditions and ask how much closer we have come to designing improved approaches to reducing environmental exposure to contaminants.
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Affiliation(s)
- Kathrin Fenner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95448 Bayreuth, Germany
| | - Michael S McLachlan
- Department of Environmental Science (ACES), Stockholm University, 106 91 Stockholm, Sweden
| | - Lawrence P Wackett
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, 85748 Garching, Germany
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15
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Yoshikawa M, Zhang M, Kawabe Y, Katayama T. Effects of ferrous iron supplementation on reductive dechlorination of tetrachloroethene and on methanogenic microbial community. FEMS Microbiol Ecol 2021; 97:6274675. [PMID: 33979429 PMCID: PMC8139862 DOI: 10.1093/femsec/fiab069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/10/2021] [Indexed: 11/14/2022] Open
Abstract
Chloroethenes are common soil and groundwater pollutants. Their dechlorination is impacted by environmental factors, such as the presence of metal ions. We here investigated the effect of ferrous iron on bacterial reductive dechlorination of chloroethenes and on methanogen community. Reductive dechlorination of tetrachloroethene was assayed with a groundwater sample originally containing 6.3 × 103 copies mL−1 of Dehalococcoides 16S rRNA gene and 2 mg L−1 of iron. Supplementation with 28 mg L−1 of ferrous iron enhanced the reductive dechlorination of cis-dichloroethene (cis-DCE) and vinyl chloride in the presence of methanogens. The supplementation shortened the time required for complete dechlorination of 1 mg L−1 of tetrachloroethene to ethene and ethane from 84 to 49 d. Methanogens, such as Candidatus ‘Methanogranum’, Methanomethylovorans and Methanocorpusculum, were significantly more abundant in iron-supplemented cultures than in non-supplemented cultures (P < 0.01). Upon methanogen growth inhibition by 2-bromoethanesulfonate and in the absence of iron supplementation, cis-DCE was not dechlorinated. Further, iron supplementation induced 71.3% dechlorination of cis-DCE accompanied by an increase in Dehalococcoides 16S rRNA and dehalogenase vcrA gene copies but not dehalogenase tceA gene copies. These observations highlight the cooperative effect of iron and methanogens on the reductive dechlorination of chloroethenes by Dehalococcoides spp.
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Affiliation(s)
- Miho Yoshikawa
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Ming Zhang
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Yoshishige Kawabe
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Taiki Katayama
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
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16
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Lin WH, Chen CC, Sheu YT, Tsang DCW, Lo KH, Kao CM. Growth inhibition of sulfate-reducing bacteria for trichloroethylene dechlorination enhancement. ENVIRONMENTAL RESEARCH 2020; 187:109629. [PMID: 32460090 DOI: 10.1016/j.envres.2020.109629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/26/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Trichloroethylene (TCE) is a frequently found organic contaminant in polluted-groundwater. In this microcosm study, effects of hydrogen-producing bacteria [Clostridium butyricum (Clostridium sp.)] and inhibitor of sulfate-reducing bacteria (SRB) addition on the enhancement of TCE dechlorination were evaluated. Results indicate that Clostridium sp. supplement could effectively enhance TCE reductive dechlorination (97.4% of TCE removal) due to increased hydrogen concentration and Dehalococcoides (DHC) populations (increased to 1 × 104 gene copies/L). However, addition of Clostridium sp. also caused the increase in dsrA (dissimilatory sulfide reductase subunit A) (increased to 2 × 108 gene copies/L), and thus, part of the hydrogen was consumed by SRB, which would limit the effective application of hydrogen by DHC. Control of Clostridium sp. addition is a necessity to minimize the adverse impact of Clostridium sp. on DHC growth. Ferric citrate caused the slight raise of the oxidation-reduction state, which resulted in growth inhibition of SRB. Molybdate addition inhibited the growth of SRB, and thus, the dsrA concentrations (dropped from 4 × 107 to 9 × 105 gene copies/L) and sulfate reduction efficiency were decreased. Increased DHC populations (increased from 8 × 103 to 1 × 105 gene copies/L) were due to increased available hydrogen (increased from 0 to 2 mg/L), which enhanced TCE dechlorination (99.3% TCE removal). Metagenomic analyses show that a significant microbial diversity was detected in microcosms with different treatments. Clostridium sp., ferric citrate, and molybdate addition caused a decreased SRB communities and increased fatty acid production microbial communities (increased from 4.9% to 20.2%), which would be beneficial to the hydrogen production and TCE dechlorination processes.
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Affiliation(s)
- Wei-Han Lin
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Yih-Terng Sheu
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kai-Hung Lo
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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17
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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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18
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Li Y, Wen LL, Zhao HP, Zhu L. Addition of Shewanella oneidensis MR-1 to the Dehalococcoides-containing culture enhances the trichloroethene dechlorination. ENVIRONMENT INTERNATIONAL 2019; 133:105245. [PMID: 31683156 DOI: 10.1016/j.envint.2019.105245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/28/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Dehalococcoides is able to completely dehalogenate tetrachloroethene (PCE) and trichloroethene (TCE) to ethene (ETH). However, the dechlorination efficiency of Dehalococcoides is low and result in the accumulation of toxic intermediates. In this study, Shewanella oneidensis MR-1 (S. oneidensis MR-1) was added to the Dehalococcoides-containing culture and the complete TCE to ETH dechlorination was shortened from 24 days to 16 days. Dehalococcoides-targeted 16S rRNA gene and two model reductive dehalogenase (RDase) genes (tceA and vcrA), responsible for dechlorinating TCE to vinyl chloride (VC) and VC to ETH respectively, were characterized. Results showed that S. oneidensis MR-1 has no effect on the cell growth while the RDase genes expression was up-regulated and the RDase activity of Dehalococcoides was elevated. The mRNA abundance of vcrA increased approximately tenfold along with the increased concentration of vitamin B12 (cyanocobalamin). Interestingly, the addition of S. oneidensis MR-1 increased the concentration of vitamin B12 by affecting the microbial community structure. Therefore, the addition of S. oneidensis MR-1 might have a positive effect on regulating the activity of RDase of functional microorganisms and uptake of vitamin B12, and further provided a practical vision of chloroethene dechlorination by the Dehalococcoides-containing culture.
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Affiliation(s)
- Yaru Li
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Organic Pollution Process and Control, Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Li-Lian Wen
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; College of Resource and Environmental Science, Hubei University, Wuhan 430062, China
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Organic Pollution Process and Control, Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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19
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Heavner GLW, Mansfeldt CB, Wilkins MJ, Nicora CD, Debs GE, Edwards EA, Richardson RE. Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site. Front Microbiol 2019; 10:1433. [PMID: 31316484 PMCID: PMC6610324 DOI: 10.3389/fmicb.2019.01433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/06/2019] [Indexed: 12/17/2022] Open
Abstract
RNA-based biomarkers have been successfully detected at field sites undergoing in situ bioremediation, but the detection of expressed enzymes is a more direct way to prove activity for a particular biocatalytic process of interest since they provide evidence of potential in situ activity rather than simply confirming presence and abundance of genes in a given population by measurement of DNA copies using qPCR. Here we successfully applied shotgun proteomics to field samples from a trichloroethene (TCE)-contaminated industrial site in southern Ontario, Canada that had been bio-augmented with the commercially available KB-1TM microbial culture. The KB-1TM culture contains multiple strains of Dehalococcoides mccartyi (D. mccartyi) as well as an organohalide respiring Geobacter species. The relative abundances of specific enzymatic proteins were subsequently compared to corresponding qPCR-derived levels of DNA and RNA biomarkers in the same samples. Samples were obtained from two wells with high hydraulic connectivity to the KB-1TM-bioaugemented enhanced in situ bioremediation system, and two control wells that showed evidence of low levels of native organohalide respiring bacteria (OHRB), Dehalococcoides and Geobacter. Enzymes involved in organohalide respiration were detected in the metaproteomes of all four field samples, as were chaperonins of D. mccartyi, chemotaxis proteins, and ATPases. The most highly expressed RDase in the bioaugmentation culture (VcrA) was the most highly detected enzyme overall in the bioaugmented groundwater samples. In one background groundwater well, we found high expression of the Geobacter pceA RDase. The DNA and RNA biomarkers detected using qPCR-based assays were a set of orthologs of Dehalococcoides reductive dehalogenases (VcrA, TceA, BvcA, dehalogenase “DET1545”), and the Ni-Fe uptake hydrogenase, HupL. Within a sample, RNA levels for key enzymes correlated with relative protein abundance. These results indicate that laboratory observations of TCE-bioremediation biomarker protein expression are recapitulated in field environmental systems and that both RNA and protein biomarker monitoring hold promise for activity monitoring of in situ populations of OHRB.
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Affiliation(s)
- Gretchen L W Heavner
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Cresten B Mansfeldt
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Michael J Wilkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Garrett E Debs
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Ruth E Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States
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20
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Temme HR, Carlson A, Novak PJ. Presence, Diversity, and Enrichment of Respiratory Reductive Dehalogenase and Non-respiratory Hydrolytic and Oxidative Dehalogenase Genes in Terrestrial Environments. Front Microbiol 2019; 10:1258. [PMID: 31231342 PMCID: PMC6567934 DOI: 10.3389/fmicb.2019.01258] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/21/2019] [Indexed: 11/13/2022] Open
Abstract
Organohalide-respiring bacteria have been linked to the cycling and possible respiration of chlorinated natural organic matter (Cl-NOM) in uncontaminated soils and sediments. The importance of non-respiratory hydrolytic/oxidative dechlorination processes in the cycling of Cl-NOM in terrestrial soil and sediment, however, is still not understood. This research analyzes the dechlorination potential of terrestrial systems through analysis of the metagenomes of urban lake sediments and cultures enriched with Cl-NOM. Even with the variability in sample type and enrichment conditions, the potential to dechlorinate was universal, with reductive dehalogenase genes and hydrolytic or oxidative dehalogenase genes found in all samples analyzed. The reductive dehalogenase genes detected grouped taxonomically with those from organohalide-respiring bacteria with broad metabolic capabilities, as opposed to those that obligately respire organohalides. Furthermore, reductive dehalogenase genes and two haloacid dehalogenase genes increased in abundance when sediment was enriched with high concentrations of Cl-NOM. Our data suggests that both respiratory and non-respiratory dechlorination processes are important for Cl-NOM cycling, and that non-obligate organohalide-respiring bacteria are most likely involved in these processes.
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Affiliation(s)
- Hanna R Temme
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Aaron Carlson
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Paige J Novak
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota, Minneapolis, MN, United States
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21
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Heckel B, Phillips E, Edwards E, Sherwood Lollar B, Elsner M, Manefield MJ, Lee M. Reductive Dehalogenation of Trichloromethane by Two Different Dehalobacter restrictus Strains Reveal Opposing Dual Element Isotope Effects. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2332-2343. [PMID: 30726673 DOI: 10.1021/acs.est.8b03717] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Trichloromethane (TCM) is a frequently detected and persistent groundwater contaminant. Recent studies have reported that two closely related Dehalobacter strains (UNSWDHB and CF) transform TCM to dichloromethane, with inconsistent carbon isotope effects (ε13CUNSWDHB = -4.3 ± 0.45‰; ε13CCF = -27.5 ± 0.9‰). This study uses dual element compound specific isotope analysis (C; Cl) to explore the underlying differences. TCM transformation experiments using strain CF revealed pronounced normal carbon and chlorine isotope effects (ε13CCF = -27.9 ± 1.7‰; ε37ClCF = -4.2 ± 0.2‰). In contrast, small carbon and unprecedented inverse chlorine isotope effects were observed for strain UNSWDHB (ε13CUNSWDHB = -3.1 ± 0.5‰; ε37ClUNSWDHB = 2.5 ± 0.3‰) leading to opposing dual element isotope slopes (λCF = 6.64 ± 0.14 vs λUNSWDHB = -1.20 ± 0.18). Isotope effects of strain CF were identical to experiments with TCM and Vitamin B12 (ε13CVitamin B12 = -26.0 ± 0.9‰, ε37ClVitamin B12 = -4.0 ± 0.2‰, λVitamin B12 = 6.46 ± 0.20). Comparison to previously reported isotope effects suggests outer-sphere-single-electron transfer or SN2 as possible underlying mechanisms. Cell suspension and cell free extract experiments with strain UNSWDHB were both unable to unmask the intrinsic KIE of the reductive dehalogenase (TmrA) suggesting that enzyme binding and/or mass-transfer into the periplasm were rate-limiting. Nondirected intermolecular interactions of TCM with cellular material were ruled out as reason for the inverse isotope effect by gas/water and gas/hexadecane partitioning experiments indicating specific, yet uncharacterized interactions must be operating prior to catalysis.
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Affiliation(s)
- Benjamin Heckel
- Institute of Groundwater Ecology , Helmholtz Zentrum München , Ingolstädter Landstr. 1 , 85764 Neuherberg , Germany
- Chair of Analytical Chemistry and Water Chemistry , Technical University of Munich , Marchioninistrasse 17 , D-81377 Munich , Germany
| | - Elizabeth Phillips
- Department of Earth Sciences 22 Russell St , University of Toronto , Toronto Ontario M5S 3B1 , Canada
| | - Elizabeth Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Barbara Sherwood Lollar
- Department of Earth Sciences 22 Russell St , University of Toronto , Toronto Ontario M5S 3B1 , Canada
| | - Martin Elsner
- Institute of Groundwater Ecology , Helmholtz Zentrum München , Ingolstädter Landstr. 1 , 85764 Neuherberg , Germany
- Chair of Analytical Chemistry and Water Chemistry , Technical University of Munich , Marchioninistrasse 17 , D-81377 Munich , Germany
| | - Michael J Manefield
- School of Civil and Environmental Engineering, Water Research Centre (WRC) , University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Matthew Lee
- School of Civil and Environmental Engineering, Water Research Centre (WRC) , University of New South Wales , Sydney , New South Wales 2052 , Australia
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22
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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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23
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Yin Y, Yan J, Chen G, Murdoch FK, Pfisterer N, Löffler FE. Nitrous Oxide Is a Potent Inhibitor of Bacterial Reductive Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:692-701. [PMID: 30558413 PMCID: PMC6944068 DOI: 10.1021/acs.est.8b05871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Organohalide-respiring bacteria are key players for the turnover of organohalogens. At sites impacted with chlorinated ethenes, bioremediation promotes reductive dechlorination; however, stoichiometric conversion to environmentally benign ethene is not always achieved. We demonstrate that nitrous oxide (N2O), a compound commonly present in groundwater, inhibits organohalide respiration. N2O concentrations in the low micromolar range decreased dechlorination rates and resulted in incomplete dechlorination of tetrachloroethene (PCE) in Geobacter lovleyi strain SZ and of cis-1,2-dichloroethene ( cDCE) and vinyl chloride (VC) in Dehalococcoides mccartyi strain BAV1 axenic cultures. Presumably, N2O interferes with reductive dechlorination by reacting with super-reduced Co(I)-corrinoids of reductive dehalogenases, which is supported by the finding that N2O did not inhibit corrinoid-independent fumarate-to-succinate reduction in strain SZ. Kinetic analyses revealed a best fit to the noncompetitive Michaelis-Menten inhibition model and determined N2O inhibitory constants, KI, for PCE and cDCE dechlorination of 40.8 ± 3.8 and 21.2 ± 3.5 μM in strain SZ and strain BAV1, respectively. The lowest KI value of 9.6 ± 0.4 μM was determined for VC to ethene reductive dechlorination in strain BAV1, suggesting that this crucial dechlorination step for achieving detoxification is most susceptible to N2O inhibition. Groundwater N2O concentrations exceeding 100 μM are not uncommon, especially in watersheds impacted by nitrate runoff from agricultural sources. Thus, dissolved N2O measurements can inform about cDCE and VC stalls at sites impacted with chlorinated ethenes.
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Affiliation(s)
- Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Liaoning 110016, People’s Republic of China
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Fadime Kara Murdoch
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nina Pfisterer
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Frank E. Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Corresponding Author: Phone: (865) 974-4933.
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24
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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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25
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Clark K, Taggart DM, Baldwin BR, Ritalahti KM, Murdoch RW, Hatt JK, Löffler FE. Normalized Quantitative PCR Measurements as Predictors for Ethene Formation at Sites Impacted with Chlorinated Ethenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13410-13420. [PMID: 30365883 PMCID: PMC6945293 DOI: 10.1021/acs.est.8b04373] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Quantitative PCR (qPCR) targeting Dehalococcoides mccartyi ( Dhc) biomarker genes supports effective management at sites impacted with chlorinated ethenes. To establish correlations between Dhc biomarker gene abundances and ethene formation (i.e., detoxification), 859 groundwater samples representing 62 sites undergoing monitored natural attenuation or enhanced remediation were analyzed. Dhc 16S rRNA genes and the vinyl chloride (VC) reductive dehalogenase genes bvcA and vcrA were detected in 88% and 61% of samples, respectively, from wells with ethene. Dhc 16S rRNA, bvcA, vcrA, and tceA (implicated in cometabolic reductive VC dechlorination) gene abundances all positively correlated with ethene formation. Significantly greater ethene concentrations were observed when Dhc 16S rRNA gene and VC RDase gene abundances exceeded 107 and 106 copies L-1, respectively, and when Dhc 16S rRNA- and bvcA + vcrA-to-total bacterial 16S rRNA gene ratios exceeded 0.1%. Dhc 16S rRNA gene-to- vcrA/ bvcA ratios near unity also indicated elevated ethene; however, no increased ethene was observed in 19 wells where vcrA and/or bvcA gene copy numbers exceeded Dhc cell numbers 10- to 10 000-fold. Approximately one-third of samples with detectable ethene lacked bvcA, vcrA, and tceA, suggesting that comprehensive understanding of VC detoxification biomarkers has not been achieved. Although the current biomarker suite is incomplete, the data analysis corroborates the value of the available Dhc DNA biomarkers for prognostic and diagnostic groundwater monitoring at sites impacted with chlorinated ethenes.
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Affiliation(s)
- Katherine Clark
- Microbial Insights, Incorporated, 10515 Research Drive, Knoxville, Tennessee 37932, United States
| | - Dora M. Taggart
- Microbial Insights, Incorporated, 10515 Research Drive, Knoxville, Tennessee 37932, United States
| | - Brett R. Baldwin
- Microbial Insights, Incorporated, 10515 Research Drive, Knoxville, Tennessee 37932, United States
| | - Kirsti M. Ritalahti
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert W. Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Janet K. Hatt
- School of Civil and Environmental Engineering, Atlanta, Georgia 30332-0512
| | - Frank E. Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, 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
- Biosciences Division and Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge Tennessee 37831, United States
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26
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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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27
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Pérez-de-Mora A, Lacourt A, McMaster ML, Liang X, Dworatzek SM, Edwards EA. Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi ( D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments. Front Microbiol 2018; 9:812. [PMID: 29867784 PMCID: PMC5968391 DOI: 10.3389/fmicb.2018.00812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023] Open
Abstract
Dehalococcoides mccartyi (D. mccartyi) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed D. mccartyi-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 D. mccartyi rdhA genes and used to measure population diversity in 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to D. mccartyi 16S rRNA gene copies revealed the presence of multiple distinct D. mccartyi strains in each culture, many more than the two strains inferred from 16S rRNA analysis. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi strains and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant D. mccartyi strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative rdhA abundances revealed D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene. These shifts indicate a selective pressure of the most abundant chlorinated electron acceptor, as was also observed in lab cultures. These results also suggest that reductive dechlorination at contaminated sites is brought about by multiple strains of D. mccartyi whether or not the site is bioaugmented. Understanding the driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.
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Affiliation(s)
- Alfredo Pérez-de-Mora
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Research Unit Analytical Biogeochemistry, Department of Environmental Sciences, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anna Lacourt
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Xiaoming Liang
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Elizabeth A Edwards
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
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28
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Schubert T, Adrian L, Sawers RG, Diekert G. Organohalide respiratory chains: composition, topology and key enzymes. FEMS Microbiol Ecol 2018; 94:4923014. [DOI: 10.1093/femsec/fiy035] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
- Department of Geobiotechnology, Technische Universität Berlin, Ackerstraße 74, D-13355 Berlin, Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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29
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Yan J, Bi M, Bourdon AK, Farmer AT, Wang PH, Molenda O, Quaile AT, Jiang N, Yang Y, Yin Y, Şimşir B, Campagna SR, Edwards EA, Löffler FE. Purinyl-cobamide is a native prosthetic group of reductive dehalogenases. Nat Chem Biol 2017; 14:8-14. [PMID: 29106396 PMCID: PMC6081238 DOI: 10.1038/nchembio.2512] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/02/2017] [Indexed: 01/21/2023]
Abstract
Cobamides such as vitamin B12 are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite prosthetic groups for carbon-halogen bond-cleaving reductive dehalogenases. This study reports the biosynthesis of a new cobamide with unsubstituted purine as the lower base and assigns unsubstituted purine a biological function by demonstrating that Coα-purinyl-cobamide (purinyl-Cba) is the native prosthetic group in catalytically active tetrachloroethene reductive dehalogenases of Desulfitobacterium hafniense. Cobamides featuring different lower bases are not functionally equivalent, and purinyl-Cba elicits different physiological responses in corrinoid-auxotrophic, organohalide-respiring bacteria. Given that cobamide-dependent enzymes catalyze key steps in essential metabolic pathways, the discovery of a novel cobamide structure and the realization that lower bases can effectively modulate enzyme activities generate opportunities to manipulate functionalities of microbiomes.
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Affiliation(s)
- Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.,Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, P.R. China.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Meng Bi
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew T Quaile
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
| | - Yi Yang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Burcu Şimşir
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA.,Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
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30
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Munro JE, Kimyon Ö, Rich DJ, Koenig J, Tang S, Low A, Lee M, Manefield M, Coleman NV. Co-occurrence of genes for aerobic and anaerobic biodegradation of dichloroethane in organochlorine-contaminated groundwater. FEMS Microbiol Ecol 2017; 93:4494361. [DOI: 10.1093/femsec/fix133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
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31
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Yang Y, Cápiro NL, Yan J, Marcet TF, Pennell KD, Löffler FE. Resilience and recovery of Dehalococcoides mccartyi following low pH exposure. FEMS Microbiol Ecol 2017; 93:4411799. [DOI: 10.1093/femsec/fix130] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/05/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yi Yang
- Department of Civil and Environmental Engineering, University of Tennessee, 325 John D. Tickle Bldg, 851 Neyland Drive, Knoxville, TN 37996, USA
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996, USA
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Bldg 1520, Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Natalie L. Cápiro
- Department of Civil and Environmental Engineering, 200 College Avenue, Tufts University, Medford, MA 02155, USA
| | - Jun Yan
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996, USA
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Bldg 1520, Bethel Valley Road, Oak Ridge, TN 37831, USA
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- Department of Microbiology, University of Tennessee, M409 Walters Life Science Bldg, Knoxville, TN 37996, USA
| | - Tyler F. Marcet
- Department of Civil and Environmental Engineering, 200 College Avenue, Tufts University, Medford, MA 02155, USA
| | - Kurt D. Pennell
- Department of Civil and Environmental Engineering, 200 College Avenue, Tufts University, Medford, MA 02155, USA
| | - Frank E. Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, 325 John D. Tickle Bldg, 851 Neyland Drive, Knoxville, TN 37996, USA
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996, USA
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Bldg 1520, Bethel Valley Road, Oak Ridge, TN 37831, USA
- Department of Microbiology, University of Tennessee, M409 Walters Life Science Bldg, Knoxville, TN 37996, USA
- Department of Biosystems Engineering and Soil Science, University of Tennessee, 2506 E.J. Chapman Dr., Knoxville, TN 37996, USA
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32
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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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33
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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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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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Dolinová I, Štrojsová M, Černík M, Němeček J, Macháčková J, Ševců A. Microbial degradation of chloroethenes: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13262-13283. [PMID: 28378313 DOI: 10.1007/s11356-017-8867-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/17/2017] [Indexed: 05/28/2023]
Abstract
Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.
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Affiliation(s)
- Iva Dolinová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Martina Štrojsová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jan Němeček
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jiřina Macháčková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
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Liang Y, Cook LJ, Mattes TE. Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13760-13774. [PMID: 28401391 DOI: 10.1007/s11356-017-8948-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
Assessment and monitoring of microbial community dynamics is useful when tracking the progress of vinyl chloride (VC) bioremediation strategies, particularly in dilute plumes where apparent VC attenuation rates are low. In a long-term field study, the abundance and the activity of microbial VC degraders were tracked in three monitoring wells (MW05, MW25, and MW19) along a dilute VC plume at Naval Air Station (NAS) Oceana. High-throughput sequencing of partial 16S ribosomal RNA (rRNA) genes and transcripts revealed diverse groundwater microbial communities and showed that methanotrophs and anaerobic respirers (e.g., methanogens, sulfate reducers, and iron reducers) were among the most active and abundant guilds. Quantitative PCR analysis showed that among bacterial guilds with a potential to contribute to VC biodegradation, methanotrophs were the most abundant and active microbial group. Ethene-oxidizing bacterial populations were less abundant and relatively inactive compared to methanotrophs. In MW19, expression of functional genes associated with both aerobic VC oxidation and anaerobic VC reduction was observed. Overall, our results reveal that the groundwater community contains various active bacterial guilds previously associated with metabolic and cometabolic VC degradation processes either under aerobic and anaerobic conditions that might have contributed to the slowly decreasing VC concentrations at the NAS Oceana site over the 6-year study period.
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Affiliation(s)
- Yi Liang
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Laura J Cook
- CH2M 5701 Cleveland Street Suite 200, Virginia Beach, VA, 23462, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA.
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Alfán-Guzmán R, Ertan H, Manefield M, Lee M. Isolation and Characterization of Dehalobacter sp. Strain TeCB1 Including Identification of TcbA: A Novel Tetra- and Trichlorobenzene Reductive Dehalogenase. Front Microbiol 2017; 8:558. [PMID: 28421054 PMCID: PMC5379058 DOI: 10.3389/fmicb.2017.00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/16/2017] [Indexed: 11/13/2022] Open
Abstract
Dehalobacter sp. strain TeCB1 was isolated from groundwater near Sydney, Australia, that is polluted with a range of organochlorines. The isolated strain is able to grow by reductive dechlorination of 1,2,4,5-tetrachlorobenzene to 1,3- and 1,4-dichlorobenzene with 1,2,4-trichlorobenzene being the intermediate daughter product. Transient production of 1,2-dichlorobenzene was detected with subsequent conversion to monochlorobenzene. The dehalogenation capability of strain TeCB1 to respire 23 alternative organochlorines was examined and shown to be limited to the use of 1,2,4,5-tetrachlorobenzene and 1,2,4-trichlorobenzene. Growth on 1,2,4-trichlorobenzene resulted in the production of predominantly 1,3- and 1,4-dichlorobenzene. The inability of strain TeCB1 to grow on 1,2-dichlorobenzene indicated that the production of monochlorobenzene during growth on 1,2,4,5-tetarchlorobezene was cometabolic. The annotated genome of strain TeCB1 contained only one detectable 16S rRNA gene copy and genes for 23 full-length and one truncated Reductive Dehalogenase (RDase) homologs, five unique to strain TeCB1. Identification and functional characterization of the 1,2,4,5-tetrachlorobenzene and 1,2,4-trichlorobenzene RDase (TcbA) was achieved using native-PAGE coupled with liquid chromatography tandem mass spectrometry. Interestingly, TcbA showed higher amino acid identity with tetrachloroethene reductases PceA (95% identity) from Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense Y51 than with the only other chlorinated benzene reductase [i.e., CbrA (30% identity)] functionally characterized to date.
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Affiliation(s)
- Ricardo Alfán-Guzmán
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia.,Department of Molecular Biology and Genetics, Istanbul UniversityIstanbul, Turkey
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
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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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Mayer-Blackwell K, Fincker M, Molenda O, Callahan B, Sewell H, Holmes S, Edwards EA, Spormann AM. 1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12187-12196. [PMID: 27809491 DOI: 10.1021/acs.est.6b02957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Bioremediation of groundwater contaminated with chlorinated aliphatic hydrocarbons such as perchloroethene and trichloroethene can result in the accumulation of the undesirable intermediate vinyl chloride. Such accumulation can either be due to the absence of specific vinyl chloride respiring Dehalococcoides mccartyi or to the inhibition of such strains by the metabolism of other microorganisms. The fitness of vinyl chloride respiring Dehalococcoides mccartyi subpopulations is particularly uncertain in the presence of chloroethene/chloroethane cocontaminant mixtures, which are commonly found in contaminated groundwater. Therefore, we investigated the structure of Dehalococcoides populations in a continuously fed reactor system under changing chloroethene/ethane influent conditions. We observed that increasing the influent ratio of 1,2-dichloroethane to trichloroethene was associated with ecological selection of a tceA-containing Dehalococcoides population relative to a vcrA-containing Dehalococcoides population. Although both vinyl chloride and 1,2-dichloroethane could be simultaneously transformed to ethene, prolonged exposure to 1,2-dichloroethane diminished the vinyl chloride transforming capacity of the culture. Kinetic tests revealed that dechlorination of 1,2-dichloroethane by the consortium was strongly inhibited by cis-dichloroethene but not vinyl chloride. Native polyacrylamide gel electrophoresis and mass spectrometry revealed that a trichloroethene reductive dehalogenase (TceA) homologue was the most consistently expressed of four detectable reductive dehalogenases during 1,2-dichloroethane exposure, suggesting that it catalyzes the reductive dihaloelimination of 1,2-dichloroethane to ethene.
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Affiliation(s)
- Koshlan Mayer-Blackwell
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Maeva Fincker
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Olivia Molenda
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Benjamin Callahan
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Holly Sewell
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Susan Holmes
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A Edwards
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
| | - Alfred M Spormann
- Civil and Environmental Engineering, ‡Chemical Engineering, and §Department of Statistics, Stanford University , Stanford, California 94305, United States
- Chemical Engineering & Applied Chemistry, and ⊥Cell and Systems Biology, University of Toronto , Toronto, Ontario M5S 3E5, Canada
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Mansfeldt CB, Heavner GW, Rowe AR, Hayete B, Church BW, Richardson RE. Inferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins. PLoS One 2016; 11:e0166234. [PMID: 27829029 PMCID: PMC5102406 DOI: 10.1371/journal.pone.0166234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 10/25/2016] [Indexed: 12/17/2022] Open
Abstract
The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™) on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture. In total, 49 and 24 microarray datasets were included in the REFS™ analysis to generate an ensemble of 1,000 networks for the Dehalococcoides population in the Cornell D2 and KB-1® culture, respectively. Considering only linkages that appeared in the consensus network for each culture (exceeding the determined frequency cutoff of ≥ 60%), the resulting Cornell D2 and KB-1® consensus networks maintained 1,105 nodes (genes or conditions) with 974 edges and 1,714 nodes with 1,455 edges, respectively. These consensus networks captured multiple strong and biologically informative relationships. One of the main highlighted relationships shared between these two cultures was a direct edge between the transcript encoding for the major reductive dehalogenase (tceA (D2) or vcrA (KB-1®)) and the transcript for the putative S-layer cell wall protein (DET1407 (D2) or KB1_1396 (KB-1®)). Additionally, transcripts for two key oxidoreductases (a [Ni Fe] hydrogenase, Hup, and a protein with similarity to a formate dehydrogenase, “Fdh”) were strongly linked, generalizing a strong relationship noted previously for Dehalococcoides mccartyi strain 195 to multiple strains of Dehalococcoides. Notably, the pangenome array utilized when monitoring the KB-1® culture was capable of resolving signals from multiple strains, and the network inference engine was able to reconstruct gene networks in the distinct strain populations.
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Affiliation(s)
- Cresten B. Mansfeldt
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| | - Gretchen W. Heavner
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
| | - Annette R. Rowe
- Field of Microbiology, Cornell University, Ithaca, NY, United States of America
| | - Boris Hayete
- GNS Healthcare. Cambridge, MA, United States of America
| | | | - Ruth E. Richardson
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY, United States of America
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Dolinová I, Czinnerová M, Dvořák L, Stejskal V, Ševců A, Černík M. Dynamics of organohalide-respiring bacteria and their genes following in-situ chemical oxidation of chlorinated ethenes and biostimulation. CHEMOSPHERE 2016; 157:276-285. [PMID: 27236848 DOI: 10.1016/j.chemosphere.2016.05.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 04/11/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Application of Fenton's reagent and enhanced reductive dechlorination are currently the most common remediation strategies resulting in removal of chlorinated ethenes. In this study, the influence of such techniques on organohalide-respiring bacteria was assessed at a site contaminated by chlorinated ethenes using a wide spectrum of molecular genetic markers, including 16S rRNA gene of the organohalide-respiring bacteria Dehaloccocoides spp., Desulfitobacterium and Dehalobacter; reductive dehalogenase genes (vcrA, bvcA) responsible for dechlorination of vinyl chloride and sulphate-reducing and denitrifying bacteria. In-situ application of hydrogen peroxide to induce a Fenton-like reaction caused an instantaneous decline in all markers below detection limit. Two weeks after application, the bvcA gene and Desulfitobacterium relative abundance increased to levels significantly higher than those prior to application. No significant decrease in the concentration of a range of chlorinated ethenes was observed due to the low hydrogen peroxide dose used. A clear increase in marker levels was also observed following in-situ application of sodium lactate, which resulted in a seven-fold increase in Desulfitobacterium and a three-fold increase in Dehaloccocoides spp. after 70 days. An increase in the vcrA gene corresponded with increase in Dehaloccocoides spp. Analysis of selected markers clearly revealed a positive response of organohalide-respiring bacteria to biostimulation and unexpectedly fast recovery after the Fenton-like reaction.
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Affiliation(s)
- Iva Dolinová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| | - Marie Czinnerová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| | - Lukáš Dvořák
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| | - Vojtěch Stejskal
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
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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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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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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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Yan J, Şimşir B, Farmer AT, Bi M, Yang Y, Campagna SR, Löffler FE. The corrinoid cofactor of reductive dehalogenases affects dechlorination rates and extents in organohalide-respiring Dehalococcoides mccartyi. ISME JOURNAL 2015; 10:1092-101. [PMID: 26555247 DOI: 10.1038/ismej.2015.197] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/09/2015] [Accepted: 09/22/2015] [Indexed: 12/20/2022]
Abstract
Corrinoid auxotrophic organohalide-respiring Dehalococcoides mccartyi (Dhc) strains are keystone bacteria for reductive dechlorination of toxic and carcinogenic chloroorganic contaminants. We demonstrate that the lower base attached to the essential corrinoid cofactor of reductive dehalogenase (RDase) enzyme systems modulates dechlorination activity and affects the vinyl chloride (VC) RDases BvcA and VcrA differently. Amendment of 5,6-dimethylbenzimidazolyl-cobamide (DMB-Cba) to Dhc strain BAV1 and strain GT cultures supported cis-1,2-dichloroethene-to-ethene reductive dechlorination at rates of 107.0 (±12.0) μM and 67.4 (±1.4) μM Cl(-) released per day, respectively. Strain BAV1, expressing the BvcA RDase, reductively dechlorinated VC to ethene, although at up to fivefold lower rates in cultures amended with cobamides carrying 5-methylbenzimidazole (5-MeBza), 5-methoxybenzimidazole (5-OMeBza) or benzimidazole (Bza) as the lower base. In contrast, strain GT harboring the VcrA RDase failed to grow and dechlorinate VC to ethene in medium amended with 5-OMeBza-Cba or Bza-Cba. The amendment with DMB to inactive strain GT cultures restored the VC-to-ethene-dechlorinating phenotype and intracellular DMB-Cba was produced, demonstrating cobamide uptake and remodeling. The distinct responses of Dhc strains with BvcA versus VcrA RDases to different cobamides implicate that the lower base exerts control over Dhc reductive dechlorination rates and extents (that is, detoxification), and therefore the dynamics of Dhc strains with discrete reductive dechlorination capabilities. These findings emphasize that the role of the corrinoid/lower base synthesizing community must be understood to predict strain-specific Dhc activity and achieve efficacious contaminated site cleanup.
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Affiliation(s)
- Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Burcu Şimşir
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Abigail T Farmer
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Meng Bi
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Yi Yang
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
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Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans-Dichloroethene Reductive Dehalogenase, TdrA. Appl Environ Microbiol 2015; 82:40-50. [PMID: 26452554 DOI: 10.1128/aem.02017-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/06/2015] [Indexed: 02/04/2023] Open
Abstract
The Dehalogenimonas population in a dechlorinating enrichment culture referred to as WBC-2 was previously shown to be responsible for trans-dichloroethene (tDCE) hydrogenolysis to vinyl chloride (VC). In this study, blue native polyacrylamide gel electrophoresis (BN-PAGE) followed by enzymatic assays and protein identification using liquid chromatography coupled with mass spectrometry (LC-MS/MS) led to the functional characterization of a novel dehalogenase, TdrA. This new reductive dehalogenase (RDase) catalyzes the dechlorination of tDCE to VC. A metagenome of the WBC-2 culture was sequenced, and a complete Dehalogenimonas genome, only the second Dehalogenimonas genome to become publicly available, was closed. The tdrA dehalogenase found within the Dehalogenimonas genome appears to be on a genomic island similar to genomic islands found in Dehalococcoides. TdrA itself is most similar to TceA from Dehalococcoides sp. strain FL2 with 76.4% amino acid pairwise identity. It is likely that the horizontal transfer of rdhA genes is not only a feature of Dehalococcoides but also a feature of other Dehalococcoidia, including Dehalogenimonas. A set of primers was developed to track tdrA in WBC-2 subcultures maintained on different electron acceptors. This newest dehalogenase is an addition to the short list of functionally defined RDases sharing the usual characteristic motifs (including an AB operon, a TAT export sequence, two iron-sulfur clusters, and a corrinoid binding domain), substrate flexibility, and evidence for horizontal gene transfer within the Dehalococcoidia.
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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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Islam MA, Tchigvintsev A, Yim V, Savchenko A, Yakunin AF, Mahadevan R, Edwards EA. Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. Microb Biotechnol 2015; 9:47-60. [PMID: 26374290 PMCID: PMC4720418 DOI: 10.1111/1751-7915.12315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 07/12/2015] [Accepted: 08/07/2015] [Indexed: 11/28/2022] Open
Abstract
Gene sequences annotated as proteins of unknown or non‐specific function and hypothetical proteins account for a large fraction of most genomes. In the strictly anaerobic and organohalide respiring Dehalococcoides mccartyi, this lack of annotation plagues almost half the genome. Using a combination of bioinformatics analyses and genome‐wide metabolic modelling, new or more specific annotations were proposed for about 80 of these poorly annotated genes in previous investigations of D. mccartyi metabolism. Herein, we report the experimental validation of the proposed reannotations for two such genes (KB1_0495 and KB1_0553) from D. mccartyi strains in the KB‐1 community. KB1_0495 or DmIDH was originally annotated as an NAD+‐dependent isocitrate dehydrogenase, but biochemical assays revealed its activity primarily with NADP+ as a cofactor. KB1_0553, also denoted as DmPMI, was originally annotated as a hypothetical protein/sugar isomerase domain protein. We previously proposed that it was a bifunctional phosphoglucose isomerase/phosphomannose isomerase, but only phosphomannose isomerase activity was identified and confirmed experimentally. Further bioinformatics analyses of these two protein sequences suggest their affiliation to potentially novel enzyme families within their respective larger enzyme super families.
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Affiliation(s)
- M Ahsanul Islam
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Anatoli Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Veronica Yim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- 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
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