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Zhang Y, Overbeck TJ, Skebba VLP, Gandhi NN. Genomic and Phenotypic Safety Assessment of Probiotic Bacillus coagulans Strain JBI-YZ6.3. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10305-4. [PMID: 38896222 DOI: 10.1007/s12602-024-10305-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Spore-forming Bacillus coagulans has been widely recognized as an important probiotic, which is commonly used in products for human consumption and animal feeds. B. coagulans exhibits beneficial traits from both Bacillus and lactic acid-producing Lactobacillus. The present study evaluated the safety of the newly isolated B. coagulans strain JBI-YZ6.3, using combined genomic and phenotypic analysis approaches. The taxonomic classification based on genome sequence and biochemical tests identified strain JBI-YZ6.3 as B. coagulans. Comprehensive genome-based analyses established JBI-YZ6.3 as a novel strain of B. coagulans. Antibiotic susceptibility testing showed that the strain JBI-YZ6.3 was sensitive to a panel of fourteen antibiotics, and no genes related to antibiotic resistance were found in its genome. The spores of strain JBI-YZ6.3 exhibited tolerance to acid and bile salts, as well as stability at ambient and elevated conditions of temperature and relative humidity. There were no homologs of Bacillus toxin genes identified in the genome of JBI-YZ6.3, and the strain exhibited no cytotoxicity towards Vero cells and human peripheral blood mononuclear cells. In conclusion, findings from this study support the safety of B. coagulans strain JBI-YZ6.3, which can be developed into new probiotic products for preventive and therapeutic benefits in human and animal hosts.
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Le ST, Israpanich A, Phenrat T. Using sequential H 2O 2 addition to sustain 1,2-dichloroethane detoxification by a nanoscale zerovalent iron-induced Fenton's system at a natural pH. CHEMOSPHERE 2022; 305:135376. [PMID: 35716714 DOI: 10.1016/j.chemosphere.2022.135376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/25/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
1,2-dichloroethane (1,2-DCA) is a chlorinated hydrocarbon used for polyvinyl chloride plastic production. As such, 1,2-DCA is a common persistent contaminant in saturated zones. While nanoscale zerovalent iron (NZVI) is considered an effective reductant for removing a wide range of chlorinated hydrocarbons, 1,2-DCA is resistant to reduction by NZVI as well as by modified forms of NZVI (e.g., sulfidated-NZVI). Hydroxyl radicals produced in Fenton's reaction can effectively degrade 1,2-DCA, but Fenton's reaction requires the acidification of saturated zones to achieve a groundwater pH of 3 to facilitate the catalytic reaction. To overcome this problem, this study has developed a sequential treatment process using an NZVI-induced Fenton-like reaction that can effectively degrade 1,2-DCA at an initially neutral pH range. The experiments were conducted using a high 1,2-DCA concentration (2000 mg/L) to evaluate the feasibility of using the treatment process at source zones. The process degraded 99% of 1,2-DCA with a pseudo-first-order rate constant of 0.49 h-1. Unlike the single-stage treatment process, the sequential treatment can control the used H2O2 concentration in the system, thus sustaining the reaction and resulting in more efficient 1,2-DCA degradation. To mimic subsurface conditions, batch experiments were conducted to remove 1,2-DCA sorbed in contaminated soil. The results show that 99% removal of 1,2-DCA was obtained within 16 h. Additionally, this study suggests that the NZVI can be used for at least three consecutive 1,2-DCA degradation cycles while maintaining high removal efficiency.
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Affiliation(s)
- Song-Thao Le
- Research Unit for Integrated Natural Resources Remediation and Reclamation (IN3R), Department of Civil Engineering, Faculty of Engineering, Naresuan University, Phitsanulok, Thailand; Center of Excellence for Sustainability of Health, Environment and Industry (SHEI), Faculty of Engineering, Naresuan University, Phitsanulok, Thailand
| | - Atsada Israpanich
- Research Unit for Integrated Natural Resources Remediation and Reclamation (IN3R), Department of Civil Engineering, Faculty of Engineering, Naresuan University, Phitsanulok, Thailand; Center of Excellence for Sustainability of Health, Environment and Industry (SHEI), Faculty of Engineering, Naresuan University, Phitsanulok, Thailand
| | - Tanapon Phenrat
- Research Unit for Integrated Natural Resources Remediation and Reclamation (IN3R), Department of Civil Engineering, Faculty of Engineering, Naresuan University, Phitsanulok, Thailand; Center of Excellence for Sustainability of Health, Environment and Industry (SHEI), Faculty of Engineering, Naresuan University, Phitsanulok, Thailand.
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Fernández-Verdejo D, Cortés P, Guisasola A, Blánquez P, Marco-Urrea E. Bioelectrochemically-assisted degradation of chloroform by a co-culture of Dehalobacter and Dehalobacterium. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 12:100199. [PMID: 36157346 PMCID: PMC9500365 DOI: 10.1016/j.ese.2022.100199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 06/16/2023]
Abstract
Using bioelectrochemical systems (BESs) to provide electrochemically generated hydrogen is a promising technology to provide electron donors for reductive dechlorination by organohalide-respiring bacteria. In this study, we inoculated two syntrophic dechlorinating cultures containing Dehalobacter and Dehalobacterium to sequentially transform chloroform (CF) to acetate in a BES using a graphite fiber brush as the electrode. In this co-culture, Dehalobacter transformed CF to stoichiometric amounts of dichloromethane (DCM) via organohalide respiration, whereas the Dehalobacterium-containing culture converted DCM to acetate via fermentation. BES were initially inoculated with Dehalobacter, and sequential cathodic potentials of -0.6, -0.7, and -0.8 V were poised after consuming three CF doses (500 μM) per each potential during a time-span of 83 days. At the end of this period, the accumulated DCM was degraded in the following seven days after the inoculation of Dehalobacterium. At this point, four consecutive amendments of CF at increasing concentrations of 200, 400, 600, and 800 μM were sequentially transformed by the combined degradation activity of Dehalobacter and Dehalobacterium. The Dehalobacter 16S rRNA gene copies increased four orders of magnitude during the whole period. The coulombic efficiencies associated with the degradation of CF reached values > 60% at a cathodic potential of -0.8 V when the degradation rate of CF achieved the highest values. This study shows the advantages of combining syntrophic bacteria to fully detoxify chlorinated compounds in BESs and further expands the use of this technology for treating water bodies impacted with pollutants.
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Affiliation(s)
- David Fernández-Verdejo
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Facultat de BioCiències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Albert Guisasola
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Paqui Blánquez
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Ernest Marco-Urrea
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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Natural Magnetite Minerals Enhance 1,2-Dichloroethane Reductive Dechlorination. MINERALS 2022. [DOI: 10.3390/min12070816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Contamination of soil and groundwater by chlorinated solvents is an environmental issue of primary concern. Recently, electrically conductive iron particles have been proposed as a novel approach to accelerate anaerobic bioremediation processes. In fact, it was demonstrated that conductive particles facilitate the exchange of electrons between microorganisms via Direct Interspecies Electron Transfer (DIET) processes, thus enhancing the pollutant-degrading potential of the microbial community. However, the use of natural minerals in this context has not been reported so far. In this study, we applied, for the first time, natural magnetite and hematite to accelerate the reductive dechlorination of 1,2-dichloroethane by an enrichment culture in lab-scale anaerobic microcosms. After four feeding cycles, low magnetite-amended microcosms (13 mg/L) yielded the highest rate of 1,2-DCA reductive dechlorination and reduced methanogenic activity. By contrast, hematite did not display any apparent stimulatory effect. Surprisingly, in the presence of higher amounts of iron oxides, a weaker effect was obtained, probably because iron(III) present in the minerals competed for the electrons necessary for reductive dechlorination. For all microcosms, the concentration of the toxic byproduct vinyl chloride was negligible throughout the whole study. The SEM/EDS analysis confirmed the close interaction between the conductive iron oxide particles and the dechlorinating bacteria. This work opens the possibility of using natural conductive minerals for bioremediation applications as well as shedding light on the previously unrecognized role of such minerals in contaminated ecosystems.
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Heckel B, Elsner M. Exploring Mechanisms of Biotic Chlorinated Alkane Reduction: Evidence of Nucleophilic Substitution (S N2) with Vitamin B 12. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6325-6336. [PMID: 35467338 DOI: 10.1021/acs.est.1c06066] [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: 06/14/2023]
Abstract
Chlorinated alkanes are notorious groundwater contaminants. Their natural reductive dechlorination by microorganisms involves reductive dehalogenases (RDases) containing cobamide as a cofactor. However, underlying mechanisms of reductive dehalogenation have remained uncertain. Here, observed products, radical trap experiments, UV-vis, and mass spectra demonstrate that (i) reduction by cobalamin (vitamin B12) involved chloroalkyl-cobalamin complexes (ii) whose formation involved a second-order nucleophilic substitution (SN2). Dual element isotope analysis subsequently linked insights from our model system to microbial reductive dehalogenation. Identical observed isotope effects in reduction of trichloromethane by Dehalobacter CF and cobalamin (Dehalobacter CF, εC = -27.9 ± 1.7‰; εCl = -4.2 ± 0.‰; λ = 6.6 ± 0.1; cobalamin, εC = -26.0 ± 0.9‰; εCl = -4.0 ± 0.2‰; λ = 6.5 ± 0.2) indicated the same underlying mechanism, as did identical isotope effects in the reduction of 1,2-dichloroethane by Dehalococcoides and cobalamin (Dehalococcoides, εC = -33.0 ± 0.4‰; εCl = -5.1 ± 0.1‰; λ = 6.5 ± 0.2; cobalamin, εC = -32.8 ± 1.7‰; εCl = -5.1 ± 0.2‰; λ = 6.4 ± 0.2). In contrast, a different, non-SN2 reaction was evidenced by different isotope effects in reaction of 1,2-dichloroethane with Dehalogenimonas (εC = -23.0 ± 2.0‰; εCl = -12.0 ± 0.8‰; λ = 1.9 ± 0.02) illustrating a diversity of biochemical reaction mechanisms manifested even within the same class of enzymes (RDases). This study resolves open questions in our understanding of bacterial reductive dehalogenation and, thereby, provides important information on the biochemistry of bioremediation.
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Affiliation(s)
- Benjamin Heckel
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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Rahim F, Abdullah SRS, Hasan HA, Kurniawan SB, Mamat A, Yusof KA, Ambak KI. A feasibility study for the treatment of 1,2-dichloroethane-contaminated groundwater using reedbed system and assessment of its natural attenuation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152799. [PMID: 34982990 DOI: 10.1016/j.scitotenv.2021.152799] [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: 06/25/2021] [Revised: 11/30/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
A reedbed system planted with Phragmites australis was implemented to treat chlorinated hydrocarbon-contaminated groundwater in an industrial plant area. Reedbed commissioning was conducted from July 2016 to November 2016 to treat contaminated groundwater via a pump-and-treat mechanism. Combination of horizontal and vertical reedbed systems was applied to treat 1,2-dichloroethane (1,2 DCA) under four parallel installations. The 2-acre horizontal and vertical reedbed systems were designed to treat approximately 305 m3/day of pumped groundwater. Initial concentration of 1,2 DCA was observed at 0.362 mg/L to 4320 mg/L, and the reedbed system successfully reduced the concentration up to 67.9%. The average outlet concentration was measured to be 2.08 mg/L, which was lower than the site-specific target level of 156 mg/L. Natural attenuation analysis was conducted using first-order decay kinetics, showing an average natural attenuation rate of 0.00372/year. Natural attenuation of 1,2 DCA was observed in shallow monitoring wells, which was indicated by the reduction trend of 1,2 DCA concentration, thereby confirming that the reedbed system worked well to remove 1.2 DCA from contaminated groundwater at the shallow profile.
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Affiliation(s)
- Fazli Rahim
- Petroliam Nasional Berhad (PETRONAS), Tower 1, PETRONAS Twin Towers, Kuala Lumpur City Centre, 50088 Kuala Lumpur, Malaysia; Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia
| | - Siti Rozaimah Sheikh Abdullah
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia.
| | - Hassimi Abu Hasan
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia; Research Centre for Sustainable Process Technology CESPRO, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Setyo Budi Kurniawan
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia.
| | - Alias Mamat
- Petroliam Nasional Berhad (PETRONAS), Tower 1, PETRONAS Twin Towers, Kuala Lumpur City Centre, 50088 Kuala Lumpur, Malaysia
| | - Kamarul Arifin Yusof
- Petroliam Nasional Berhad (PETRONAS), Tower 1, PETRONAS Twin Towers, Kuala Lumpur City Centre, 50088 Kuala Lumpur, Malaysia
| | - Khairil Irwan Ambak
- Petroliam Nasional Berhad (PETRONAS), Tower 1, PETRONAS Twin Towers, Kuala Lumpur City Centre, 50088 Kuala Lumpur, Malaysia
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Illy VD, Cohen GJV, Verardo E, Höhener P, Guiserix N, Atteia O. Using 1,1,1-Trichloroethane degradation data to understand NAPL dissolution and solute transport at real sites. JOURNAL OF CONTAMINANT HYDROLOGY 2022; 245:103934. [PMID: 34922184 DOI: 10.1016/j.jconhyd.2021.103934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Analytical and numerical models describing the evolution of contaminant concentrations in the plume associated with the dissolution of NAPL source and degradation processes were presented in the literature. At real sites and particularly in complex aquifers like chalk, it is difficult to understand how the sources of contaminants evolve with time. 1,1,1-Trichloroethane (1,1,1-TCA) is one of the few compounds with a well-known hydrolysis constant, that can help to improve knowledge of the contaminant sources and transport rates of dissolved contaminants in groundwater by dating the spill. In this work, different scenarios that could explain the evolution of the concentrations of 1,1,1-TCA and its degradation product 1,1-Dichloroethene (1,1-DCE) at a real contaminated site were investigated by analytical and numerical modelling. The results show that (1) the peaks of concentration time series do not correspond to a single contamination event even in the case of a complex medium, (2) the multiphasic behavior of the concentration time series is dictated by the dissolution in a heterogeneous medium, and (3) the persistence of the concentrations can arise from a small residual organic phase or transport in dual domain medium.
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Affiliation(s)
- Valeureux D Illy
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France; Renault SAS, 1 Allée du Golf, Guyancourt 78 280, France.
| | - Gregory J V Cohen
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France
| | - Elicia Verardo
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France
| | - Patrick Höhener
- Laboratoire de Chimie Environnementale-UMR 7376, Aix-Marseille Université-CNRS, 3 place Victor Hugo - Case 29, 13331 Marseille Cedex 3, France
| | | | - Olivier Atteia
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France
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Giannari D, Ho CH, Mahadevan R. A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PLoS Comput Biol 2021; 17:e1009060. [PMID: 34723959 PMCID: PMC8584699 DOI: 10.1371/journal.pcbi.1009060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/11/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
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Affiliation(s)
- Dafni Giannari
- 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
- The Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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9
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1,2-DCA Natural Attenuation Evaluation in Groundwater: Insight by Dual Isotope 13C/37Cl and Molecular Analysis Approach. WATER 2021. [DOI: 10.3390/w13050728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Natural attenuation (NA) processes represent a valuable option in groundwater remediation. At a heavily 1,2-dichloroethane (1,2-DCA) contaminated site, Compound-Specific Isotope Analysis (CSIA) in combination with Biological Molecular Tools (BMTs) were implemented as a rigorous characterization approach to evaluate the occurrence of Natural Attenuation in the proximity of the source area. By the use of microcosm experiments, the potential for natural and enhanced biodegradation under anaerobic conditions was documented, following the dichloroelimination pathway. Enrichment factors of −9.1‰ and −11.3‰ were obtained for 13C while Geobacter spp. and reductive dehalogenase genes (rdhs) were identified as main site-specific biomarkers. At pilot scale, enrichments of 13.5‰ and 6.3‰ for δ13C and δ37Cl, respectively, high levels of reductive dehalogenase (rdh group VI) along with the dominance of Geobacter spp. indicated the occurrence of significant dichloroelimination processes in groundwater under anaerobic conditions. By using the site-specific enrichment factors, degradation extents over approximately 70–80% were estimated, highlighting the relevant potential of NA in 1,2-DCA degradation in the vicinity of the source area at the site. The proposed fine-tuned protocol, including CSIA and BMTs, is proven to be effective as a groundwater remediation strategy, properly assessing and monitoring NA at site scale.
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Li T, Li H, Li C. A review and perspective of recent research in biological treatment applied in removal of chlorinated volatile organic compounds from waste air. CHEMOSPHERE 2020; 250:126338. [PMID: 32126329 DOI: 10.1016/j.chemosphere.2020.126338] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Chlorinated volatile organic compounds (Cl-VOCs) waste air is a kind of typical recalcitrant organic compounds, which poses a great threat to the ecological environment and human health. At present, the biotechnology is considered as a potential strategy for the Cl-VOCs removal due to the advantages of low energy consumption and less possibility of secondary pollution. This work summarizes the recent researches on strains, bioreactors and technology integration. The dominant pure strains for biodegradation of Cl-VOCs are first outlined with a special focus on the co-metabolism of multi-components. It then summarizes two bioreactors (optimized airlift reactor (ALR) and two-phase partitioning bioreactor (TPPB)) and strategy (addition of surfactant) for improvement of biotrickling filter (BTF), which are benefit to achieve the mass transfer enhancement in the removal of hydrophobic Cl-VOCs from waste air. After that, the integration technologies, such as magnetic field (MF)-BTF, non-thermal plasma (NTP)/ultraviolet light (UV)-BTF, and microbial electrolytic cells (MEC), are elucidated, which provide opportunities for complete mineralization of Cl-VOCs in a more efficient, energy-saving and economical way. Finally, current challenges and a perspective of future research on biotechnology for Cl-VOCs removal are thoroughly discussed.
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Affiliation(s)
- Tong Li
- National-Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources Utilization, Tianjin Key Laboratory of Chemical Process Safety, School of Chemical Engineering and Technology, Hebei University of Technology, 8 Guangrong Road, Tianjin, 300000, China
| | - Hao Li
- National-Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources Utilization, Tianjin Key Laboratory of Chemical Process Safety, School of Chemical Engineering and Technology, Hebei University of Technology, 8 Guangrong Road, Tianjin, 300000, China.
| | - Chunli Li
- National-Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources Utilization, Tianjin Key Laboratory of Chemical Process Safety, School of Chemical Engineering and Technology, Hebei University of Technology, 8 Guangrong Road, Tianjin, 300000, China
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11
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Low A, Zhao S, Rogers MJ, Zemb O, Lee M, He J, Manefield M. Isolation, characterization and bioaugmentation of an acidotolerant 1,2-dichloroethane respiring Desulfitobacterium species from a low pH aquifer. FEMS Microbiol Ecol 2020; 95:5454739. [PMID: 30980656 DOI: 10.1093/femsec/fiz055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/11/2019] [Indexed: 01/14/2023] Open
Abstract
A Desulfitobacterium sp. strain AusDCA of the Peptococcaceae family capable of respiring 1,2-dichloroethane (1,2-DCA) to ethene anaerobically with ethanol or hydrogen as electron donor at pH 5.0 with optimal range between pH 6.5-7.5 was isolated from an acidic aquifer near Sydney, Australia. Strain AusDCA is distant (94% nucleotide identity) from its nearest phylogenetic neighbor, D. metallireducens, and could represent a new species. Reference gene-based quantification of growth indicated a doubling time of 2 days in cultures buffered at pH 7.2, and a yield of 7.66 (± 4.0) × 106 cells µmol-1 of 1,2-DCA. A putative 1,2-DCA reductive dehalogenase was translated from a dcaAB locus and had high amino acid identity (97.3% for DcaA and 100% for DcaB) to RdhA1B1 of the 1,2-DCA respiring Dehalobacter strain WL. Proteomic analysis confirmed DcaA expression in the pure culture. Dehalogenation of 1,2-DCA (1.6 mM) was observed in batch cultures established from groundwater at pH 5.5 collected 38 days after in situ bioaugmentation but not in cultures established with groundwater collected at the same time from wells not receiving bioaugmentation. Overall, strain AusDCA can tolerate lower pH than previously characterized organohalide respiring bacteria and remained viable in groundwater at pH 5.5.
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Affiliation(s)
- Adrian Low
- Genome Structural Biology, Temasek Lifesciences Laboratory, 1 Research Link, Singapore 117604, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Olivier Zemb
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Matthew Lee
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
| | - Mike Manefield
- School of Chemical Engineering, School of Civil and Environmental Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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12
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Kucharzyk KH, Meisel JE, Kara-Murdoch F, Murdoch RW, Higgins SA, Vainberg S, Bartling CM, Mullins L, Hatzinger PB, Löffler FE. Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9. J Proteome Res 2020; 19:1812-1823. [PMID: 32135063 DOI: 10.1021/acs.jproteome.0c00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.
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Affiliation(s)
| | - Jayda E Meisel
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Fadime Kara-Murdoch
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States.,Department of Biosystems Engineering and Soil Science University of Tennessee, 2506 E. J. Chapman Drive, Knoxville, Tennessee 37996, United States
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996, United States.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Steven A Higgins
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Simon Vainberg
- APTIM, Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Craig M Bartling
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Larry Mullins
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Paul B Hatzinger
- APTIM, Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States.,Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996, United States.,Department of Civil and Environmental Engineering, University of Tennessee, 851 Neyland Drive, Knoxville, Tennessee 37996, United States.,Department of Biosystems Engineering and Soil Science University of Tennessee, 2506 E. J. Chapman Drive, Knoxville, Tennessee 37996, United States.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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13
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Chen F, Liang B, Li ZL, Yang JQ, Huang C, Lyu M, Yuan Y, Nan J, Wang AJ. Bioelectrochemical assisted dechlorination of tetrachloroethylene and 1,2-dichloroethane by acclimation of anaerobic sludge. CHEMOSPHERE 2019; 227:514-521. [PMID: 31004818 DOI: 10.1016/j.chemosphere.2019.04.066] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Volatile chlorinated hydrocarbons (VCHs) are often found as a type of persistent and ubiquitous contaminant in groundwater. The feasibility, characteristics and microbial mechanism of acclimation of biodiversity-rich inoculation source for bioelectrochemical stimulated VCH dechlorination remain poorly understood. Here, the superior bioelectrochemical catalytic activities were observed for tetrachloroethylene (0.26 mM d-1) and 1,2-dichloroethane (2.20 mM d-1) dechlorination in anaerobic sludge-acclimated biocathodes with an optimal potential of -0.5 V, averaging 1.60-2.71 times higher than those reported in previous works on biocathodes. When the cathode was applied as the sole electron donor for dechlorination, columbic efficiencies reached the values greater than 80%. Tetrachloroethylene dechlorination showed a metabolic pathway with cis-1,2-dichloroethene as the main product, whereas 1,2-dichloroethane was dechlorinated entirely to the nontoxic ethene. The cathodic biofilms were highly abundant with the dechlorination and electro-active genera, while significant bacterial consortium variation was observed in response to the different VCH types and changes in cathodic potential. Bacillus, Pseudomonas and Lactococcus were mostly enriched for tetrachloroethylene dechlorination, and pceA, tceA and omcX were highly expressed. Geobacter was the most predominant during 1,2-dichloroethane dechlorination with rdhA, tceA and omcX highly expressed. In addition, although the impact of cathodic potentials was weaker than that of VCH types, the lower cathodic potentials, the more abundant of the electrode respiring populations and the higher expression of extracellular electron transfer related gene. This study demonstrated the great potential of acclimation of anaerobic sludge by electrical stimulation for accelerating VCH remediations and gave insights into its working molecular mechanisms.
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Affiliation(s)
- Fan Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Jia-Qi Yang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Miao Lyu
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ye Yuan
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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14
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Peng P, Schneidewind U, Haest PJ, Bosma TNP, Danko AS, Smidt H, Atashgahi S. Reductive dechlorination of 1,2-dichloroethane in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants. Appl Microbiol Biotechnol 2019; 103:6837-6849. [PMID: 31250061 PMCID: PMC6667407 DOI: 10.1007/s00253-019-09985-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022]
Abstract
1,2-Dichloroethane (1,2-DCA) is one of the most abundant manmade chlorinated organic contaminants in the world. Reductive dechlorination of 1,2-DCA by organohalide-respiring bacteria (OHRB) can be impacted by other chlorinated contaminants such as chloroethenes and chloropropanes that can co-exist with 1,2-DCA at contaminated sites. The aim of this study was to evaluate the effect of chloroethenes and 1,2-dichloropropane (1,2-DCP) on 1,2-DCA dechlorination using sediment cultures enriched with 1,2-DCA as the sole chlorinated compound (EA culture) or with 1,2-DCA and tetrachloroethene (PCE) (EB culture), and to model dechlorination kinetics. Both cultures contained Dehalococcoides as most predominated OHRB, and Dehalogenimonas and Geobacter as other known OHRB. In sediment-free enrichments obtained from the EA and EB cultures, dechlorination of 1,2-DCA was inhibited in the presence of the same concentrations of either PCE, vinyl chloride (VC), or 1,2-DCP; however, concurrent dechlorination of dual chlorinated compounds was achieved. In contrast, 1,2-DCA dechlorination completely ceased in the presence of cis-dichloroethene (cDCE) and only occurred after cDCE was fully dechlorinated. In turn, 1,2-DCA did not affect dechlorination of PCE, cDCE, VC, and 1,2-DCP. In sediment-free enrichments obtained from the EA culture, Dehalogenimonas 16S rRNA gene copy numbers decreased 1–3 orders of magnitude likely due to an inhibitory effect of chloroethenes. Dechlorination with and without competitive inhibition fit Michaelis-Menten kinetics and confirmed the inhibitory effect of chloroethenes and 1,2-DCP on 1,2-DCA dechlorination. This study reinforces that the type of chlorinated substrate drives the selection of specific OHRB, and indicates that removal of chloroethenes and in particular cDCE might be necessary before effective removal of 1,2-DCA at sites contaminated with mixed chlorinated solvents.
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Affiliation(s)
- Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Uwe Schneidewind
- Department of Civil and Environmental Engineering, Western University, London, ON, Canada
| | - Pieter Jan Haest
- Advanced Groundwater Techniques (AGT), Aartselaar, Belgium
- Division of Geology, Department of Earth and Environmental Sciences, KU Leuven, Heverlee, Belgium
| | - Tom N P Bosma
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Anthony S Danko
- Centre for Natural Resources and the Environment (CERENA), Department of Mining Engineering, University of Porto (FEUP), Porto, Portugal
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
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15
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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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16
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Chen F, Li Z, Yang J, Liang B, Huang C, Cai W, Nan J, Wang A. Electron Fluxes in Biocathode Bioelectrochemical Systems Performing Dechlorination of Chlorinated Aliphatic Hydrocarbons. Front Microbiol 2018; 9:2306. [PMID: 30323798 PMCID: PMC6173060 DOI: 10.3389/fmicb.2018.02306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Bioelectrochemical systems (BESs) are regarded as a promising approach for the enhanced dechlorination of chlorinated aliphatic hydrocarbons (CAHs). However, the electron distribution and transfer considering dechlorination, methanogenesis, and other bioprocesses in these systems are little understood. This study investigated the electron fluxes in biocathode BES performing dechlorination of three typical CAHs, 1,1,2,2-tetrachloroethene (PCE), 1,1,2-trichloroethene (TCE) and 1,2-dichloroethane (1,2-DCA). Anaerobic sludge was inoculated to cathode and biocathode was acclimated by the direct acclimation and selection. The constructed biocathode at −0.26 V had significantly higher dechlorination efficiency (E24h > 99.0%) than the opened circuit (E24h of 17.2–27.5%) and abiotic cathode (E24h of 5.5–10.8%), respectively. Cyclic voltammetry analysis demonstrated the enhanced cathodic current and the positive shift of onset potential in the cathodic biofilm. Under autotrophic conditions with electrons from the cathode as sole energy source (columbic efficiencies of 80.4–90.0%) and bicarbonate as sole carbon source, CAHs dechlorination efficiencies were still maintained at 85.0 ± 2.0%, 91.4 ± 1.8%, and 84.9 ± 3.1% for PCE, TCE, and 1,2-DCA, respectively. Cis-1,2-dichloroethene was the final product for PCE and TCE, while 1,2-DCA went through a different dechlorination pathway with the non-toxic ethene as the final metabolite. Methane was the main by-product of the heterotrophic biocathode, and methane production could be enhanced to some extent by electrochemical stimulation. The various electron fluxes originating from the cathode and oxidation of organic substrates might be responsible for the enhanced CAHs dechlorination, while methane generation and bacterial growth would probably reduce the fraction of electrons provided for CAH dechlorination. The study deals with the dechlorination and competitive bioprocesses in CAH-dechlorinating biocathodes with a focus on electron fluxes.
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Affiliation(s)
- Fan Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Jiaqi Yang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Weiwei Cai
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China.,Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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17
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Leitão P, Aulenta F, Rossetti S, Nouws HPA, Danko AS. Impact of magnetite nanoparticles on the syntrophic dechlorination of 1,2-dichloroethane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:17-23. [PMID: 29245034 DOI: 10.1016/j.scitotenv.2017.12.110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/30/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Patrícia Leitão
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km. 29.300, 00015 Monterotondo, RM, Italy; Department of Mining Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; REQUIMTE/LAQV, Institute of Engineering of Porto, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 431, 4200-072 Porto, Portugal
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km. 29.300, 00015 Monterotondo, RM, Italy.
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Via Salaria km. 29.300, 00015 Monterotondo, RM, Italy
| | - Henri P A Nouws
- REQUIMTE/LAQV, Institute of Engineering of Porto, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida, 431, 4200-072 Porto, Portugal
| | - Anthony S Danko
- Department of Mining Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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18
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Franke S, Lihl C, Renpenning J, Elsner M, Nijenhuis I. Triple-element compound-specific stable isotope analysis of 1,2-dichloroethane for characterization of the underlying dehalogenation reaction in two Dehalococcoides mccartyi strains. FEMS Microbiol Ecol 2017; 93:4561051. [DOI: 10.1093/femsec/fix137] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/17/2017] [Indexed: 11/12/2022] Open
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19
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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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20
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Palau J, Shouakar-Stash O, Hatijah Mortan S, Yu R, Rosell M, Marco-Urrea E, Freedman DL, Aravena R, Soler A, Hunkeler D. Hydrogen Isotope Fractionation during the Biodegradation of 1,2-Dichloroethane: Potential for Pathway Identification Using a Multi-element (C, Cl, and H) Isotope Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10526-10535. [PMID: 28810730 DOI: 10.1021/acs.est.7b02906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Even though multi-element isotope fractionation patterns provide crucial information with which to identify contaminant degradation pathways in the field, those involving hydrogen are still lacking for many halogenated groundwater contaminants and degradation pathways. This study investigates for the first time hydrogen isotope fractionation during both aerobic and anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) using five microbial cultures. Transformation-associated isotope fractionation values (εbulkH) were -115 ± 18‰ (aerobic C-H bond oxidation), -34 ± 4‰ and -38 ± 4‰ (aerobic C-Cl bond cleavage via hydrolytic dehalogenation), and -57 ± 3‰ and -77 ± 9‰ (anaerobic C-Cl bond cleavage via reductive dihaloelimination). The dual-element C-H isotope approach (ΛC-H = Δδ2H/Δδ13C ≈ εbulkH/εbulkC, where Δδ2H and Δδ13C are changes in isotope ratios during degradation) resulted in clearly different ΛC-H values: 28 ± 4 (oxidation), 0.7 ± 0.1 and 0.9 ± 0.1 (hydrolytic dehalogenation), and 1.76 ± 0.05 and 3.5 ± 0.1 (dihaloelimination). This result highlights the potential of this approach to identify 1,2-DCA degradation pathways in the field. In addition, distinct trends were also observed in a multi- (i.e., Δδ2H versus Δδ37Cl versus Δδ13C) isotope plot, which opens further possibilities for pathway identification in future field studies. This is crucial information to understand the mechanisms controlling natural attenuation of 1,2-DCA and to design appropriate strategies to enhance biodegradation.
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Affiliation(s)
- Jordi Palau
- Centre for Hydrogeology and Geothermics, University of Neuchâtel , 2000 Neuchâtel, Switzerland
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona , Martí i Franquès s/n, 08028 Barcelona, Spain
- Institute of Environmental Assessment and Water Research (IDAEA), CSIC, and Hydrogeology Group (UPC-CSIC) , Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Orfan Shouakar-Stash
- Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
- Isotope Tracer Technologies Inc. , Waterloo, Ontario N2 V 1Z5, Canada
| | - Siti Hatijah Mortan
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona , Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Rong Yu
- Department of Environmental Engineering and Earth Sciences, Clemson University , Clemson, South Carolina 29634, United States
| | - Monica Rosell
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona , Martí i Franquès s/n, 08028 Barcelona, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona , Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - David L Freedman
- Department of Environmental Engineering and Earth Sciences, Clemson University , Clemson, South Carolina 29634, United States
| | - Ramon Aravena
- Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Albert Soler
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona , Martí i Franquès s/n, 08028 Barcelona, Spain
| | - Daniel Hunkeler
- Centre for Hydrogeology and Geothermics, University of Neuchâtel , 2000 Neuchâtel, Switzerland
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21
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Kunze C, Diekert G, Schubert T. Subtle changes in the active site architecture untangled overlapping substrate ranges and mechanistic differences of two reductive dehalogenases. FEBS J 2017; 284:3520-3535. [DOI: 10.1111/febs.14258] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/20/2017] [Accepted: 08/30/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Cindy Kunze
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology; Institute of Microbiology; Friedrich Schiller University; Jena Germany
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22
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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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23
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Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture. Appl Microbiol Biotechnol 2017; 101:5481-5492. [DOI: 10.1007/s00253-017-8236-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
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24
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Palau J, Yu R, Hatijah Mortan S, Shouakar-Stash O, Rosell M, Freedman DL, Sbarbati C, Fiorenza S, Aravena R, Marco-Urrea E, Elsner M, Soler A, Hunkeler D. Distinct Dual C-Cl Isotope Fractionation Patterns during Anaerobic Biodegradation of 1,2-Dichloroethane: Potential To Characterize Microbial Degradation in the Field. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:2685-2694. [PMID: 28192987 DOI: 10.1021/acs.est.6b04998] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This study investigates, for the first time, dual C-Cl isotope fractionation during anaerobic biodegradation of 1,2-dichloroethane (1,2-DCA) via dihaloelimination by Dehalococcoides and Dehalogenimonas-containing enrichment cultures. Isotopic fractionation of 1,2-DCA (εbulkC and εbulkCl) for Dehalococcoides (-33.0 ± 0.4‰ and -5.1 ± 0.1‰) and Dehalogenimonas-containing microcosms (-23 ± 2‰ and -12.0 ± 0.8‰) resulted in distinctly different dual element C-Cl isotope correlations (Λ = Δδ13C/Δδ37Cl ≈ εbulkC/εbulkCl), 6.8 ± 0.2 and 1.89 ± 0.02, respectively. Determined isotope effects and detected products suggest that the difference on the obtained Λ values for biodihaloelimination could be associated with a different mode of concerted bond cleavage rather than two different reaction pathways (i.e., stepwise vs concerted). Λ values of 1,2-DCA were, for the first time, determined in two field sites under reducing conditions (2.1 ± 0.1 and 2.2 ± 2.9). They were similar to the one obtained for the Dehalogenimonas-containing microcosms (1.89 ± 0.02) and very different from those reported for aerobic degradation pathways in a previous laboratory study (7.6 ± 0.1 and 0.78 ± 0.03). Thus, this study illustrates the potential of a dual isotope analysis to differentiate between aerobic and anaerobic biodegradation pathways of 1,2-DCA in the field and suggests that this approach might also be used to characterize dihaloelimination of 1,2-DCA by different bacteria, which needs to be confirmed in future studies.
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Affiliation(s)
- J Palau
- Centre for Hydrogeology and Geothermics, University of Neuchâtel , 2000 Neuchâtel, Switzerland
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Geologia, Universitat de Barcelona , Martí i Franquès s/n, 08028 Barcelona, Spain
- Institute of Environmental Assessment and Water Research (IDAEA), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain; Associated Unit: Hydrogeology Group (UPC-CSIC), Barcelona, Spain
| | - R Yu
- Department of Environmental Engineering and Earth Sciences, Clemson University , Clemson, South Carolina United States
| | - S Hatijah Mortan
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona , Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - O Shouakar-Stash
- Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
- Isotope Tracer Technologies Inc., Waterloo, Ontario Canada N2 V 1Z5
| | - M Rosell
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Geologia, Universitat de Barcelona , Martí i Franquès s/n, 08028 Barcelona, Spain
| | - D L Freedman
- Department of Environmental Engineering and Earth Sciences, Clemson University , Clemson, South Carolina United States
| | - C Sbarbati
- Department of Earth Sciences, "Sapienza" University , P.le A. Moro 5, 00185 Rome, Italy
| | - S Fiorenza
- Remediation Engineering and Technology, BP America, Houston, Texas 77079, United States
| | - R Aravena
- Department of Earth and Environmental Sciences, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - E Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona , Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - M Elsner
- Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - A Soler
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Geologia, Universitat de Barcelona , Martí i Franquès s/n, 08028 Barcelona, Spain
| | - D Hunkeler
- Centre for Hydrogeology and Geothermics, University of Neuchâtel , 2000 Neuchâtel, Switzerland
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Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, Löffler FE. 'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Syst Appl Microbiol 2016; 40:150-159. [PMID: 28292625 DOI: 10.1016/j.syapm.2016.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
Abstract
Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160±3μmolL-1 d-1. The DCM degrader attained 5.25×107±1.0×107 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4±0.8μm long and 0.4±0.1μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, 'Candidatus Dichloromethanomonas elyunquensis'.
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Affiliation(s)
- Sara Kleindienst
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Steven A Higgins
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Despina Tsementzi
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, DE 19714, USA
| | - Frank E Löffler
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.
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26
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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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27
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Passeport E, Landis R, Lacrampe-Couloume G, Lutz EJ, Mack EE, West K, Morgan S, Sherwood Lollar B. Sediment Monitored Natural Recovery Evidenced by Compound Specific Isotope Analysis and High-Resolution Pore Water Sampling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12197-12204. [PMID: 27771950 DOI: 10.1021/acs.est.6b02961] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Monitoring natural recovery of contaminated sediments requires the use of techniques that can provide definitive evidence of in situ contaminant degradation. In this study, a passive diffusion sampler, called "peeper", was combined with Compound Specific Isotope Analysis to determine benzene and monochlorobenzene (MCB) stable carbon isotope values at a fine vertical resolution (3 cm) across the sediment water interface at a contaminated site. Results indicated significant decrease in concentrations of MCB from the bottom to the top layers of the sediment over 25 cm, and a 3.5 ‰ enrichment in δ13C values of MCB over that distance. Benzene was always at lower concentrations than MCB, with consistently more depleted δ13C values than MCB. The redox conditions were dominated by iron reduction along most of the sediment profile. These results provide multiple lines of evidence for in situ reductive dechlorination of MCB to benzene. Stable isotope analysis of contaminants in pore water is a valuable method to demonstrate in situ natural recovery of contaminated sediments. This novel high-resolution approach is critical to deciphering the combined effects of parent contaminant (e.g., MCB) degradation and both production and simultaneous degradation of daughter products, especially benzene.
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Affiliation(s)
- Elodie Passeport
- Department of Earth Sciences, University of Toronto , Toronto, Ontario, M5S 3B1, Canada
| | - Richard Landis
- DuPont Engineering and Technology, Wilmington, Delaware 19803, United States
| | | | - Edward J Lutz
- The Chemours Company, Corporate Remediation Group, Wilmington, Delaware 19899, United States
| | - E Erin Mack
- DuPont Corporate Remediation Group, Wilmington, Delaware 19803, United States
| | - Kathryn West
- AECOM, Deepwater, New Jersey 02907, United States
| | - Scott Morgan
- AECOM, Deepwater, New Jersey 02907, United States
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Stedtfeld RD, Stedtfeld TM, Samhan F, Kanitkar YH, Hatzinger PB, Cupples AM, Hashsham SA. Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater. J Microbiol Methods 2016; 131:61-67. [PMID: 27720723 DOI: 10.1016/j.mimet.2016.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022]
Abstract
Nucleic acid amplification of biomarkers is increasingly used to monitor microbial activity and assess remedial performance in contaminated aquifers. Previous studies described the use of filtration, elution, and direct isothermal amplification (i.e. no DNA extraction and purification) as a field-able means to quantify Dehalococcoides spp. in groundwater. This study expands previous work with direct loop mediated isothermal amplification (LAMP) for the detection and quantification of Dehalobacter spp. in groundwater. Experiments tested amplification of DNA with and without crude lysis and varying concentrations of humic acid. Three separate field-able methods of biomass concentration with eight aquifer samples were also tested, comparing direct LAMP with traditional DNA extraction and quantitative PCR (qPCR). A new technique was developed where filters were amplified directly within disposable Gene-Z chips. The direct filter amplification (DFA) method eliminated an elution step and provided a detection limit of 102Dehalobacter cells per 100mL. LAMP with crudely lysed Dehalobacter had a negligible effect on threshold time and sensitivity compared to lysed samples. The LAMP assay was more resilient than traditional qPCR to humic acid in sample, amplifying with up to 100mg per L of humic acid per reaction compared to 1mg per L for qPCR. Of the tested field-able concentrations methods, DFA had the lowest coefficient of variation among Dehalobacter spiked groundwater samples and lowest threshold time indicating high capture efficiency and low inhibition. While demonstrated with Dehalobacter, the DFA method can potentially be used for a number of applications requiring field-able, rapid (<60min) and highly sensitive quantification of microorganisms in environmental water samples.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Farag Samhan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Water Pollution Control, National Research Centre, 33 El-Bohouth, P.O. 12622, Ad-Doqi, Giza, Egypt
| | - Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | | | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
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29
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Munro JE, Liew EF, Ly MA, Coleman NV. A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site. Appl Environ Microbiol 2016; 82:5298-308. [PMID: 27342553 PMCID: PMC4988179 DOI: 10.1128/aem.01373-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED 1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1 Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination. IMPORTANCE Earlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes.
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Affiliation(s)
- Jacob E Munro
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Elissa F Liew
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Mai-Anh Ly
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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30
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Mondal PK, Lima G, Zhang D, Lomheim L, Tossell RW, Patel P, Sleep BE. Evaluation of peat and sawdust as permeable reactive barrier materials for stimulating in situ biodegradation of trichloroethene. JOURNAL OF HAZARDOUS MATERIALS 2016; 313:37-48. [PMID: 27054663 DOI: 10.1016/j.jhazmat.2016.03.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/29/2016] [Accepted: 03/19/2016] [Indexed: 06/05/2023]
Abstract
Two low cost solid organic materials, sawdust and peat, were tested in laboratory batch microcosm and flow-through column experiments to determine their suitability for application in permeable reactive barriers (PRBs) supporting biodegradation of trichloroethene (TCE). In microcosms with peat, TCE (∼30μM) was sequentially and completely degraded to cis-dichloroethene (cDCE), vinyl chloride, and ethene through reductive dechlorination. In microcosms with sawdust, reductive dechlorination of TCE stopped at cDCE and high methane production (up to 3000μM) was observed. 16S rRNA gene copy numbers of Dehalobacter and Archaea were higher (1000 and 10 times, respectively) in sawdust microcosms than those in peat microcosms. Dehalococcoides and vcrA gene copy numbers were 10 times higher in peat microcosms than in sawdust microcosms. These gene copy number differences are consistent with the extent of TCE degradation and production of methane in the microcosms. Flow-through column experiments showed that hydraulic conductivity reduction with time was consistently greater in the sawdust column compared to the peat column. The greater conductivity reduction was likely due to biofouling and methane gas bubble formation. The experimental observations indicate that peat has potential to be a better solid organic material than sawdust to support reductive dechlorination of TCE in PRB applications.
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Affiliation(s)
- Pulin K Mondal
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Glaucia Lima
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - David Zhang
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Line Lomheim
- BioZone, University of Toronto, 200 College Avenue, Toronto, Ontario M5S 3E5, Canada
| | - Robert W Tossell
- Pinchin Ltd., 2470 Milltower Court, Mississauga, Ontario L5 N 7W5, Canada
| | - Paresh Patel
- Pinchin Ltd., 2470 Milltower Court, Mississauga, Ontario L5 N 7W5, Canada
| | - Brent E Sleep
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada.
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31
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Kocur CMD, Lomheim L, Molenda O, Weber KP, Austrins LM, Sleep BE, Boparai HK, Edwards EA, O'Carroll DM. Long-Term Field Study of Microbial Community and Dechlorinating Activity Following Carboxymethyl Cellulose-Stabilized Nanoscale Zero-Valent Iron Injection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:7658-7670. [PMID: 27305345 DOI: 10.1021/acs.est.6b01745] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells. The entire microbial community was tracked using 16S rRNA gene amplicon pyrosequencing. Following nZVI-CMC injection, a clear shift in microbial community was observed, with most notable increases in the dechlorinating genera Dehalococcoides and Dehalogenimonas. This study suggests that coupled abiotic degradation (i.e., from reaction with nZVI) and biotic degradation fueled by CMC led to the long-term degradation of chlorinated ethenes at this field site. Furthermore, nZVI-CMC addition stimulated dehalogenator growth (e.g., Dehalococcoides) and biotic degradation of chlorinated ethenes.
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Affiliation(s)
- Chris M D Kocur
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
- CH2M HILL Canada Limited , 72 Victoria Street Kitchener, Ontario, Canada , N2G 4Y9
| | - Line Lomheim
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Olivia Molenda
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Kela P Weber
- Environmental Sciences Group, Chemistry and Chemical Engineering, Royal Military College of Canada , PO Box 17000, Station Forces, Kingston, Ontario, Canada , K7K 7B4
| | - Leanne M Austrins
- CH2M HILL Canada Limited , 72 Victoria Street Kitchener, Ontario, Canada , N2G 4Y9
| | - Brent E Sleep
- Civil Engineering, University of Toronto , 35 Saint George Street, Toronto, Ontario, Canada , M5S 1A4
| | - Hardiljeet K Boparai
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
| | - Elizabeth A Edwards
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Denis M O'Carroll
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
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32
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Zhang S, Hou Z, Du XM, Li DM, Lu XX. Assessment of biostimulation and bioaugmentation for removing chlorinated volatile organic compounds from groundwater at a former manufacture plant. Biodegradation 2016; 27:223-236. [PMID: 27351716 DOI: 10.1007/s10532-016-9768-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/13/2016] [Indexed: 12/01/2022]
Abstract
Site in a former chemical manufacture plant in China was found contaminated with high level of chlorinated volatile organic compounds (CVOCs). The major contaminants chloroform (CF), 1,2-dichloroethane (1,2-DCA) and vinyl chloride (VC) in groundwater were up to 4.49 × 104, 2.76 × 106 and 4.35 × 104 μg/L, respectively. Ethene and methane were at concentrations up to 2219.80 and 165.85 μg/L, respectively. To test the hypothesis that the CVOCs in groundwater at this site could be removed via biodegradation, biomarker analyses and microcosm studies were conducted. Dehalococcoides 16S rRNA gene and VC-reductase gene vcrA at densities up to 1.5 × 104 and 3.2 × 104 copies/L were detected in some of the groundwater samples, providing strong evidence that dechlorinating bacteria were present in the aquifer. Results from the microcosm studies showed that at moderate concentrations (CF about 4000 μg/L and 1,2-DCA about 100 μg/L), CF was recalcitrant under natural condition but was degraded under biostimulation and bioaugmentation, while 1,2-DCA was degraded under all the three conditions. At high concentration (CF about 1,000,000 μg/L and 1,2-DCA about 20,000 μg/L), CF was recalcitrant under all the three treatments and 1,2-DCA was only degraded under bioaugmentation, indicating that high concentrations of contaminants were inhibitory to the bacteria. Electron donors had influence on the degradation of contaminants. Of the four fatty acids (pyruvate, acetate, propionate and lactate) examined, all could stimulate the degradation of 1,2-DCA at both moderate and high concentrations, whereas only pyruvate and acetate could stimulate the degradation of CF at moderate concentration. In the microcosms, the observed first-order degradation rates of CF and 1,2-DCA were up to 0.12 and 0.11/day, respectively. Results from the present study provided scientific basis for remediating CVOCs contaminated groundwater at the site.
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Affiliation(s)
- Shu Zhang
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, 90095, United States.
| | - Zhen Hou
- Laboratory for Earth Surface Processes, Ministry of Education, College of Urban and Environmental Sciences, Peking University, 100871, Beijing, China
| | - Xiao-Ming Du
- Chinese Research Academy of Environmental Sciences, 100012, Beijing, China
| | | | - Xiao-Xia Lu
- Laboratory for Earth Surface Processes, Ministry of Education, College of Urban and Environmental Sciences, Peking University, 100871, Beijing, China.
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33
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Koenig JC, Boparai HK, Lee MJ, O'Carroll DM, Barnes RJ, Manefield MJ. Particles and enzymes: Combining nanoscale zero valent iron and organochlorine respiring bacteria for the detoxification of chloroethane mixtures. JOURNAL OF HAZARDOUS MATERIALS 2016; 308:106-112. [PMID: 26808236 DOI: 10.1016/j.jhazmat.2015.12.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/16/2015] [Accepted: 12/20/2015] [Indexed: 06/05/2023]
Abstract
Nanoscale zero valent iron (nZVI) and organochlorine respiring bacteria (ORB) are two technologies used to detoxify chlorinated aliphatic hydrocarbons (CAHs). nZVI can rapidly detoxify high CAH concentrations, but is quickly oxidised and unable to degrade certain CAHs (e.g., 1,2-dichlorothane). In contrast, ORB can dechlorinate CAHs resistant to nZVI (e.g., 1,2-dichlorothane) but are inhibited by other CAHs of concern degradable by nZVI (e.g., chloroform and carbon tetrachloride). Combining the two was proposed as a unique treatment train to overcome each technology's shortcomings. In this study, this combined remedy was investigated using a mixture of 1,2-dichloroethane, degradable by ORB but not nZVI, and 1,1,2-trichloroethane, susceptible to both. Results indicated that nZVI rapidly dechlorinated 1,1,2-trichloroethane when supplied above 0.5 g/L, however ORB were inhibited and unable to dechlorinate 1,2-dichloroethane. pH increase and ionic species associated with nZVI did not significantly impact ORB, pinpointing Fe(0) particles as responsible for ORB inhibition. Below 0.05 g/L nZVI, ORB activity was stimulated. Results suggest that combining ORB and nZVI at appropriate doses can potentially treat a wider range of CAHs than each individual remedy. At field sites where nZVI was applied, it is likely that in situ nZVI concentrations were below the threshold of negative consequences.
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Affiliation(s)
- Joanna C Koenig
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, Sydney, NSW 2052, Australia.
| | - Hardiljeet K Boparai
- Dept. of Civil and Environmental Engineering, The University of Western Ontario, London, Ontario N6A 5B9, Canada
| | - Matthew J Lee
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Denis M O'Carroll
- School of Civil and Environmental Engineering, The University of New South Wales, Manly Vale, Sydney, NSW 2093, Australia
| | - Robert J Barnes
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, Sydney, NSW 2052, Australia
| | - Michael J Manefield
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, Sydney, NSW 2052, Australia
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34
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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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35
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Wang SY, Kuo YC, Huang YZ, Huang CW, Kao CM. Bioremediation of 1,2-dichloroethane contaminated groundwater: Microcosm and microbial diversity studies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 203:97-106. [PMID: 25863886 DOI: 10.1016/j.envpol.2015.03.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 06/04/2023]
Abstract
In this study, the effectiveness of bioremediating 1,2-dichloroethane (DCA)-contaminated groundwater under different oxidation-reduction processes was evaluated. Microcosms were constructed using indigenous bacteria and activated sludge as the inocula and cane molasses and a slow polycolloid-releasing substrate (SPRS) as the primary substrates. Complete DCA removal was obtained within 30 days under aerobic and reductive dechlorinating conditions. In anaerobic microcosms with sludge and substrate addition, chloroethane, vinyl chloride, and ethene were produced. The microbial communities and DCA-degrading bacteria in microcosms were characterized by 16S rRNA-based denatured-gradient-gel electrophoresis profiling and nucleotide sequence analyses. Real-time polymerase chain reaction was applied to evaluate the variations in Dehalococcoides spp. and Desulfitobacterium spp. Increase in Desulfitobacterium spp. indicates that the growth of Desulfitobacterium might be induced by DCA. Results indicate that DCA could be used as the primary substrate under aerobic conditions. The increased ethene concentrations imply that dihaloelimination was the dominate mechanism for DCA biodegradation.
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Affiliation(s)
- S Y Wang
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Y C Kuo
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Y Z Huang
- Bioenvironmental Engineering Department, Chung Yuan University, Chung Li, Taiwan
| | - C W Huang
- Deaprtment of Biological Science, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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Diverse Reductive Dehalogenases Are Associated with Clostridiales-Enriched Microcosms Dechlorinating 1,2-Dichloroethane. BIOMED RESEARCH INTERNATIONAL 2015; 2015:242856. [PMID: 26273600 PMCID: PMC4529907 DOI: 10.1155/2015/242856] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 03/06/2015] [Indexed: 11/17/2022]
Abstract
The achievement of successful biostimulation of active microbiomes for the cleanup of a polluted site is strictly dependent on the knowledge of the key microorganisms equipped with the relevant catabolic genes responsible for the degradation process. In this work, we present the characterization of the bacterial community developed in anaerobic microcosms after biostimulation with the electron donor lactate of groundwater polluted with 1,2-dichloroethane (1,2-DCA). Through a multilevel analysis, we have assessed (i) the structural analysis of the bacterial community; (ii) the identification of putative dehalorespiring bacteria; (iii) the characterization of functional genes encoding for putative 1,2-DCA reductive dehalogenases (RDs). Following the biostimulation treatment, the structure of the bacterial community underwent a notable change of the main phylotypes, with the enrichment of representatives of the order Clostridiales. Through PCR targeting conserved regions within known RD genes, four novel variants of RDs previously associated with the reductive dechlorination of 1,2-DCA were identified in the metagenome of the Clostridiales-dominated bacterial community.
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Kocur CMD, Lomheim L, Boparai HK, Chowdhury AIA, Weber KP, Austrins LM, Edwards EA, Sleep BE, O'Carroll DM. Contributions of Abiotic and Biotic Dechlorination Following Carboxymethyl Cellulose Stabilized Nanoscale Zero Valent Iron Injection. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:8648-56. [PMID: 26090687 DOI: 10.1021/acs.est.5b00719] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A pilot scale injection of nanoscale zerovalent iron (nZVI) stabilized with carboxymethyl cellulose (CMC) was performed at an active field site contaminated with a range of chlorinated volatile organic compounds (cVOC). The cVOC concentrations and microbial populations were monitored at the site before and after nZVI injection. The remedial injection successfully reduced parent compound concentrations on site. A period of abiotic degradation was followed by a period of enhanced biotic degradation. Results suggest that the nZVI/CMC injection created conditions that stimulated the native populations of organohalide-respiring microorganisms. The abundance of Dehalococcoides spp. immediately following the nZVI/CMC injection increased by 1 order of magnitude throughout the nZVI/CMC affected area relative to preinjection abundance. Distinctly higher cVOC degradation occurred as a result of the nZVI/CMC injection over a 3 week evaluation period when compared to control wells. This suggests that both abiotic and biotic degradation occurred following injection.
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Affiliation(s)
- Chris M D Kocur
- ∥CH2M HILL Canada Limited, 72 Victoria Street, Kitchener, Ontario N2G 4Y9, Canada
| | | | | | | | - Kela P Weber
- §Environmental Sciences Group, Chemistry and Chemical Engineering, Royal Military College of Canada, P.O. Box 17000, Station Forces, Kingston, Ontario K7K 7B4, Canada
| | - Leanne M Austrins
- ∥CH2M HILL Canada Limited, 72 Victoria Street, Kitchener, Ontario N2G 4Y9, Canada
| | | | - Brent E Sleep
- ⊥Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
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Parthasarathy A, Stich TA, Lohner ST, Lesnefsky A, Britt RD, Spormann AM. Biochemical and EPR-spectroscopic investigation into heterologously expressed vinyl chloride reductive dehalogenase (VcrA) from Dehalococcoides mccartyi strain VS. J Am Chem Soc 2015; 137:3525-32. [PMID: 25686300 PMCID: PMC4516053 DOI: 10.1021/ja511653d] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reductive dehalogenases play a critical role in the microbial detoxification of aquifers contaminated with chloroethenes and chlorethanes by catalyzing the reductive elimination of a halogen. We report here the first heterologous production of vinyl chloride reductase VcrA from Dehalococcoides mccartyi strain VS. Heterologously expressed VcrA was reconstituted to its active form by addition of hydroxocobalamin/adenosylcobalamin, Fe(3+), and sulfide in the presence of mercaptoethanol. The kinetic properties of reconstituted VcrA catalyzing vinyl chloride reduction with Ti(III)-citrate as reductant and methyl viologen as mediator were similar to those obtained previously for VcrA as isolated from D. mccartyi strain VS. VcrA was also found to catalyze a novel reaction, the environmentally important dihaloelimination of 1,2-dichloroethane to ethene. Electron paramagnetic resonance (EPR) spectroscopic studies with reconstituted VcrA in the presence of mercaptoethanol revealed the presence of Cob(II)alamin. Addition of Ti(III)-citrate resulted in the appearance of a new signal characteristic of a reduced [4Fe-4S] cluster and the disappearance of the Cob(II)alamin signal. UV-vis absorption spectroscopy of Ti(III)citrate-treated samples revealed the formation of two new absorption maxima characteristic of Cob(I)alamin. No evidence for the presence of a [3Fe-4S] cluster was found. We postulate that during the reaction cycle of VcrA, a reduced [4Fe-4S] cluster reduces Co(II) to Co(I) of the enzyme-bound cobalamin. Vinyl chloride reduction to ethene would be initiated when Cob(I)alamin transfers an electron to the substrate, generating a vinyl radical as a potential reaction intermediate.
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Affiliation(s)
- Anutthaman Parthasarathy
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Svenja T. Lohner
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - Ann Lesnefsky
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Alfred M. Spormann
- Departments of Chemical Engineering and Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
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Zhang D, Zhang C, Xiao Z, Suzuki D, Katayama A. Humin as an electron donor for enhancement of multiple microbial reduction reactions with different redox potentials in a consortium. J Biosci Bioeng 2015; 119:188-94. [DOI: 10.1016/j.jbiosc.2014.07.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 06/26/2014] [Accepted: 07/24/2014] [Indexed: 11/24/2022]
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Primers That Target Functional Genes of Organohalide-Respiring Bacteria. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_75] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Stedtfeld RD, Stedtfeld TM, Kronlein M, Seyrig G, Steffan RJ, Cupples AM, Hashsham SA. DNA extraction-free quantification of Dehalococcoides spp. in groundwater using a hand-held device. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13855-63. [PMID: 25360694 DOI: 10.1021/es503472h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nucleic acid amplification of biomarkers is increasingly used to measure microbial activity and predict remedial performance in sites with trichloroethene (TCE) contamination. Field-based genetic quantification of microorganisms associated with bioremediation may help increase accuracy that is diminished through transport and processing of groundwater samples. Sterivex cartridges and a previously undescribed mechanism for eluting biomass was used to concentrate cells. DNA extraction-free loop mediated isothermal amplification (LAMP) was monitored in real-time with a point of use device (termed Gene-Z). A detection limit of 10(5) cells L(–1) was obtained, corresponding to sensitivity between 10 to 100 genomic copies per reaction for assays targeting the Dehalococcoides spp. specific 16S rRNA gene and vcrA gene, respectively. The quantity of Dehalococcoides spp. genomic copies measured from two TCE contaminated groundwater samples with conventional means of quantification including filtration, DNA extraction, purification, and qPCR was comparable to the field ready technique. Overall, this method of measuring Dehalococcoides spp. and vcrA genes in groundwater via direct amplification without intentional DNA extraction and purification is demonstrated, which may provide a more accurate mechanism of predicting remediation rates.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature 2014; 517:513-516. [PMID: 25327251 PMCID: PMC4968649 DOI: 10.1038/nature13901] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/30/2014] [Indexed: 11/08/2022]
Abstract
Organohalide chemistry underpins many industrial and agricultural processes, and a large proportion of environmental pollutants are organohalides. Nevertheless, organohalide chemistry is not exclusively of anthropogenic origin, with natural abiotic and biological processes contributing to the global halide cycle. Reductive dehalogenases are responsible for biological dehalogenation in organohalide respiring bacteria, with substrates including polychlorinated biphenyls or dioxins. Reductive dehalogenases form a distinct subfamily of cobalamin (B12)-dependent enzymes that are usually membrane associated and oxygen sensitive, hindering detailed studies. Here we report the characterization of a soluble, oxygen-tolerant reductive dehalogenase and, by combining structure determination with EPR (electron paramagnetic resonance) spectroscopy and simulation, show that a direct interaction between the cobalamin cobalt and the substrate halogen underpins catalysis. In contrast to the carbon-cobalt bond chemistry catalysed by the other cobalamin-dependent subfamilies, we propose that reductive dehalogenases achieve reduction of the organohalide substrate via halogen-cobalt bond formation. This presents a new model in both organohalide and cobalamin (bio)chemistry that will guide future exploitation of these enzymes in bioremediation or biocatalysis.
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Palau J, Cretnik S, Shouakar-Stash O, Höche M, Elsner M, Hunkeler D. C and Cl isotope fractionation of 1,2-dichloroethane displays unique δ¹³C/δ³⁷Cl patterns for pathway identification and reveals surprising C-Cl bond involvement in microbial oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9430-9437. [PMID: 25010210 DOI: 10.1021/es5031917] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This study investigates dual element isotope fractionation during aerobic biodegradation of 1,2-dichloroethane (1,2-DCA) via oxidative cleavage of a C-H bond (Pseudomonas sp. strain DCA1) versus C-Cl bond cleavage by S(N)2 reaction (Xanthobacter autotrophicus GJ10 and Ancylobacter aquaticus AD20). Compound-specific chlorine isotope analysis of 1,2-DCA was performed for the first time, and isotope fractionation (ε(bulk)(Cl)) was determined by measurements of the same samples in three different laboratories using two gas chromatography-isotope ratio mass spectrometry systems and one gas chromatography-quadrupole mass spectrometry system. Strongly pathway-dependent slopes (Δδ13C/Δδ37Cl), 0.78 ± 0.03 (oxidation) and 7.7 ± 0.2 (S(N)2), delineate the potential of the dual isotope approach to identify 1,2-DCA degradation pathways in the field. In contrast to different ε(bulk)(C) values [-3.5 ± 0.1‰ (oxidation) and -31.9 ± 0.7 and -32.0 ± 0.9‰ (S(N)2)], the obtained ε(bulk)(Cl) values were surprisingly similar for the two pathways: -3.8 ± 0.2‰ (oxidation) and -4.2 ± 0.1 and -4.4 ± 0.2‰ (S(N)2). Apparent kinetic isotope effects (AKIEs) of 1.0070 ± 0.0002 (13C-AKIE, oxidation), 1.068 ± 0.001 (13C-AKIE, S(N)2), and 1.0087 ± 0.0002 (37Cl-AKIE, S(N)2) fell within expected ranges. In contrast, an unexpectedly large secondary 37Cl-AKIE of 1.0038 ± 0.0002 reveals a hitherto unrecognized involvement of C-Cl bonds in microbial C-H bond oxidation. Our two-dimensional isotope fractionation patterns allow for the first time reliable 1,2-DCA degradation pathway identification in the field, which unlocks the full potential of isotope applications for this important groundwater contaminant.
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Affiliation(s)
- Jordi Palau
- Centre for Hydrogeology and Geothermics, University of Neuchâtel , 2000 Neuchâtel, Switzerland
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44
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Mayer-Blackwell K, Azizian MF, Machak C, Vitale E, Carpani G, de Ferra F, Semprini L, Spormann AM. Nanoliter qPCR platform for highly parallel, quantitative assessment of reductive dehalogenase genes and populations of dehalogenating microorganisms in complex environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9659-9667. [PMID: 25046033 DOI: 10.1021/es500918w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Idiosyncratic combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. Here we report the development of a nanoliter qPCR platform to identify organohalogen-respiring bacteria and populations by quantifying major orthologous reductive dehalogenase gene groups. The qPCR assays can be operated in parallel within a 5184-well nanoliter qPCR (nL-qPCR) chip at a single annealing temperature and buffer condition. We developed a robust bioinformatics approach to select from thousands of computationally proposed primer pairs those that are specific to individual rdh gene groups and compatible with a single amplification condition. We validated hundreds of the most selective qPCR assays and examined their performance in a trichloroethene-degrading bioreactor, revealing population structures as well as their unexpected shifts in abundance and community dynamics.
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Affiliation(s)
- Koshlan Mayer-Blackwell
- Civil and Environmental Engineering, §Geological and Environmental Sciences, and ⊥Chemical Engineering, Stanford University , Stanford, California 94305, United States
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45
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Yu HY, Wang YK, Chen PC, Li FB, Chen MJ, Hu M. The effect of ammonium chloride and urea application on soil bacterial communities closely related to the reductive transformation of pentachlorophenol. JOURNAL OF HAZARDOUS MATERIALS 2014; 272:10-19. [PMID: 24662270 DOI: 10.1016/j.jhazmat.2014.02.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 10/08/2013] [Accepted: 02/24/2014] [Indexed: 06/03/2023]
Abstract
Pentachlorophenol (PCP) is widely distributed in the soil, and nitrogen fertilizer is extensively used in agricultural production. However, studies on the fate of organic contaminants as affected by nitrogen fertilizer application have been rare and superficial. The present study aimed to examine the effect of ammonium chloride (NH4Cl) and urea (CO(NH2)2) application on the reductive transformation of PCP in a paddy soil. The study showed that the addition of low concentrations of NH4Cl/CO(NH2)2 enhanced the transformation of PCP, while the addition of high concentrations of NH4Cl/CO(NH2)2 had the opposite effect. The variations in the abundance of soil microbes in response to NH4Cl/CO(NH2)2 addition showed that both NH4Cl and CO(NH2)2 had inhibitory effects on the growth of dissimilatory iron-reducing bacteria (DIRB) of the genus Comamonas. In contrast, for the genus Shewanella, low concentrations of NH4Cl inhibited growth, and high concentrations of NH4Cl enhanced growth, whereas all concentrations of CO(NH2)2 showed enhancement effects. In addition, consistent patterns of variation were found between the abundances of dechlorinating bacteria in the genus Dehalobacter and PCP transformation rates under NH4Cl/CO(NH2)2 addition. In conclusion, nitrogen application produced variations in the structure of the soil microbial community, especially in the abundance of dissimilatory iron-reducing bacteria and dechlorinating bacteria, which, in turn, affected PCP dechlorination.
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Affiliation(s)
- Huan-Yun Yu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
| | - Yong-kui Wang
- Environmental Science and Engineering College, Hubei Polytechic University, Huangshi 435003, Hubei, PR China
| | - Peng-cheng Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
| | - Fang-bai Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China.
| | - Man-jia Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
| | - Min Hu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
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46
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Nelson JL, Jiang J, Zinder SH. Dehalogenation of chlorobenzenes, dichlorotoluenes, and tetrachloroethene by three Dehalobacter spp. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:3776-3782. [PMID: 24593835 DOI: 10.1021/es4044769] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Three enrichment cultures containing Dehalobacter spp. were developed that dehalogenate each of the dichlorobenzene (DCB) isomers to monochlorobenzene (MCB), and the strains using 1,2-DCB (12DCB1) or 1,3-DCB (13DCB1) are now considered isolated, whereas the strain using 1,4-DCB (14DCB1) is considered highly enriched. In this study, we examined the dehalogenation capability of each strain to use chlorobenzenes with three or more chlorines, tetrachloroethene (PCE), or dichlorotoluene (DCT) isomers. Strain 12DCB1 preferentially dehalogenated singly flanked chlorines, but not doubly flanked or unflanked chlorines. It dehalogenated pentachlorobenzene to MCB with little buildup of intermediates. Strain 13DCB1, which could use either 1,3-DCB or 1,2-DCB, demonstrated the widest dehalogenation spectrum of electron acceptors tested, and dehalogenated every chlorobenzene isomer except 1,4-DCB. Notably, strain 13DCB1 dehalogenated the recalcitrant 1,3,5-trichlorobenzene isomer to MCB, and qPCR of 16S rRNA genes indicated that strain 13DCB1 grew. Strain 14DCB1 exhibited the narrowest range of substrate utilization, but was the only strain to dehalogenate para-substituted chlorines. Strains 12DCB1 and 13DCB1 dehalogenated PCE to cis-dichloroethene, and all strains dehalogenated 3,4-DCT to monochlorotoluene. These findings show that Dehalobacter spp., like Dehalococcoides spp., are versatile dehalogenators and should be considered when determining the fate of chlorinated organics at contaminated sites.
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Affiliation(s)
- Jennifer L Nelson
- Department of Microbiology, 270 Wing Hall, Cornell University , Ithaca, New York 14853, United States
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Koenig JC, Groissmeier KD, Manefield MJ. Tolerance of anaerobic bacteria to chlorinated solvents. Microbes Environ 2014; 29:23-30. [PMID: 24441515 PMCID: PMC4041229 DOI: 10.1264/jsme2.me13113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 11/08/2013] [Indexed: 11/12/2022] Open
Abstract
The aim of this research was to evaluate the effects of four chlorinated aliphatic hydrocarbons (CAHs), perchloroethene (PCE), carbon tetrachloride (CT), chloroform (CF) and 1,2-dichloroethane (1,2-DCA), on the growth of eight anaerobic bacteria: four fermentative species (Escherichia coli, Klebsiella sp., Clostridium sp. and Paenibacillus sp.) and four respiring species (Pseudomonas aeruginosa, Geobacter sulfurreducens, Shewanella oneidensis and Desulfovibrio vulgaris). Effective concentrations of solvents which inhibited growth rates by 50% (EC50) were determined. The octanol-water partition coefficient or log Po/w of a CAH proved a generally satisfactory measure of its toxicity. Most species tolerated approximately 3-fold and 10-fold higher concentrations of the two relatively more polar CAHs CF and 1,2-DCA, respectively, than the two relatively less polar compounds PCE and CT. EC50 values correlated well with growth rates observed in solvent-free cultures, with fast-growing organisms displaying higher tolerance levels. Overall, fermentative bacteria were more tolerant to CAHs than respiring species, with iron- and sulfate-reducing bacteria in particular appearing highly sensitive to CAHs. These data extend the current understanding of the impact of CAHs on a range of anaerobic bacteria, which will benefit the field of bioremediation.
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Affiliation(s)
- Joanna C. Koenig
- Centre for Marine Bioinnovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Kathrin D. Groissmeier
- Helmholtz Institute of Groundwater Ecology, Ingolstaedter Landstrasse 1, D-85764, Neuherberg, Germany
| | - Mike J. Manefield
- Centre for Marine Bioinnovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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Hug LA, Edwards EA. Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens. Front Microbiol 2013; 4:341. [PMID: 24312087 PMCID: PMC3832961 DOI: 10.3389/fmicb.2013.00341] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/29/2013] [Indexed: 01/11/2023] Open
Abstract
Reductive dehalogenases are the critical enzymes for anaerobic organohalide respiration, a microbial metabolic process that has been harnessed for bioremediation efforts to resolve chlorinated solvent contamination in groundwater and is implicated in the global halogen cycle. Reductive dehalogenase sequence diversity is informative for the dechlorination potential of the site or enrichment culture. A suite of degenerate PCR primers targeting a comprehensive curated set of reductive dehalogenase genes was designed and applied to 12 DNA samples extracted from contaminated and pristine sites, as well as six enrichment cultures capable of reducing chlorinated compounds to non-toxic end-products. The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and the reductive dehalogenase complement of each sample determined. The results indicate that the diversity of the reductive dehalogenase gene family is much deeper than is currently accounted for: one-third of the translated proteins have less than 70% pairwise amino acid identity to database sequences. Approximately 60% of the sequenced reductive dehalogenase genes were broadly distributed, being identified in four or more samples, and often in previously sequenced genomes as well. In contrast, 17% of the sequenced reductive dehalogenases were unique, present in only a single sample and bearing less than 90% pairwise amino acid identity to any previously identified proteins. Many of the broadly distributed reductive dehalogenases are uncharacterized in terms of their substrate specificity, making these intriguing targets for further biochemical experimentation. Finally, comparison of samples from a contaminated site and an enrichment culture derived from the same site 8 years prior allowed examination of the effect of the enrichment process.
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Affiliation(s)
- Laura A Hug
- Department of Cell and Systems Biology, University of Toronto Toronto, ON, Canada
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Munro JE, Liew EF, Coleman NV. Adaptation of a membrane bioreactor to 1,2-dichloroethane revealed by 16S rDNA pyrosequencing and dhlA qPCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:13668-13676. [PMID: 24175727 DOI: 10.1021/es403292s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A pilot-scale membrane bioreactor (MBR) was tested for bioremediation of 1,2-dichloroethane (DCA) in groundwater. Pyrosequencing of 16S rDNA was used to study changes in the microbiology of the MBR over 137 days, including a 67 day initial adaptation phase of increasing DCA concentration. The bacterial community in the MBR was distinct from those in soil and groundwater at the same site, and was dominated by alpha- and beta- proteobacteria, including Rhodobacter, Methylibium, Rhodopseudomonas, Methyloversatilis, Caldilinea, Thiobacillus, Azoarcus, Hyphomicrobium, and Leptothrix. Biodegradation of DCA in the MBR began after 26 days, and was sustained for the remainder of the experiment. A quantitative PCR (qPCR) assay for the dehalogenase gene dhlA was developed to monitor DCA-degrading bacteria in the MBR, and a positive correlation was seen between dhlA gene abundance and the cumulative amount of DCA that had entered the MBR. Genera previously associated with aerobic DCA biodegradation (Xanthobacter, Ancylobacter, Azoarcus) were present in the MBR, and the abundance of Azoarcus correlated well with dhlA gene abundance. This study shows that MBRs can be an effective method for removal of DCA from groundwater, and that the dhlA qPCR is a rapid and sensitive method for detection of DCA-degrading bacteria.
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Affiliation(s)
- Jacob E Munro
- School of Molecular Bioscience, Building G08, University of Sydney , Darlington, New South Wales, 2006, Australia
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Isolation and characterization of a novel Dehalobacter species strain TCP1 that reductively dechlorinates 2,4,6-trichlorophenol. Biodegradation 2013; 25:313-23. [PMID: 23995979 DOI: 10.1007/s10532-013-9662-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
Chlorophenols are widely used as biocides, leading them to being prevalent environmental contaminants that pose toxic threats to ecosystems. In this study, a Dehalobacter species strain TCP1 was isolated from a digester sludge sample, which is able to dechlorinate 2,4,6-trichlorophenol (2,4,6-TCP) to 4-monochlorophenol (4-MCP) with H2 as the sole electron donor and acetate as the carbon source. Strain TCP1 also distinguishes itself from other Dehalobacter species with its capability to dechlorinate tetrachloroethene or trichloroethene (TCE) to both cis- and trans-dichloroethenes in a ratio of 5.6 (±0.2):1. The growth yields of strain TCP1 on TCE and 2,4,6-TCP were 4.14 × 10(13) and 5.77 × 10(13) cells mol(-1) of Cl(-) released, respectively. Strain TCP1 contains five unusually long 16S rRNA gene copies per genome, and the extra length is due to the ~110 bp insertion sequences at their 5'-ends. This suggests that strain TCP1 may represent a novel Dehalobacter species. A putative chlorophenol reductive dehalogenase gene-debcprA-was identified to catalyze the ortho-chlorine removal from 2,4,6-TCP. Both the culture-dependent and housekeeping rpoB gene-based approaches indicate the purity of the culture. Strain TCP1 can serve as a promising candidate for the bioremediation of 2,4,6-TCP contaminated sites, and its discovery expands our understanding of metabolic capabilities of Dehalobacter species.
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