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Niu S, Li C, Gao S, Tian J, Zhang C, Li L, Huang Y, Lyu H. Biochar, microbes, and biochar-microbe synergistic treatment of chlorinated hydrocarbons in groundwater: a review. Front Microbiol 2024; 15:1443682. [PMID: 39091302 PMCID: PMC11291464 DOI: 10.3389/fmicb.2024.1443682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
Dehalogenating bacteria are still deficient when targeted to deal with chlorinated hydrocarbons (CHCs) contamination: e.g., slow metabolic rates, limited substrate range, formation of toxic intermediates. To enhance its dechlorination capacity, biochar and its composites with appropriate surface activity and biocompatibility are selected for coupled dechlorination. Because of its special surface physical and chemical properties, it promotes biofilm formation by dehalogenating bacteria on its surface and improves the living environment for dehalogenating bacteria. Next, biochar and its composites provide active sites for the removal of CHCs through adsorption, activation and catalysis. These sites can be specific metal centers, functional groups or structural defects. Under microbial mediation, these sites can undergo activation and catalytic cycles, thereby increasing dechlorination efficiency. However, there is a lack of systematic understanding of the mechanisms of dechlorination in biogenic and abiogenic systems based on biochar. Therefore, this article comprehensively summarizes the recent research progress of biochar and its composites as a "Taiwan balm" for the degradation of CHCs in terms of adsorption, catalysis, improvement of microbial community structure and promotion of degradation and metabolism of CHCs. The removal efficiency, influencing factors and reaction mechanism of the degraded CHCs were also discussed. The following conclusions were drawn, in the pure biochar system, the CHCs are fixed to its surface by adsorption through chemical bonds on its surface; the biochar composite material relies on persistent free radicals and electron shuttle mechanisms to react with CHCs, disrupting their molecular structure and reducing them; biochar-coupled microorganisms reduce CHCs primarily by forming an "electron shuttle bridge" between biological and non-biological organisms. Finally, the experimental directions to be carried out in the future are suggested to explore the optimal solution to improve the treatment efficiency of CHCs in water.
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Affiliation(s)
- Shixin Niu
- Shandong Provincial Geo-mineral Engineering Exploration Institute, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan, China
- Shandong Engineering Research Center for Environmental Protection and Remediation on Groundwater, Jinan, China
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Changsuo Li
- Shandong Provincial Geo-mineral Engineering Exploration Institute, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan, China
- Shandong Engineering Research Center for Environmental Protection and Remediation on Groundwater, Jinan, China
| | - Shuai Gao
- Shandong Provincial Geo-mineral Engineering Exploration Institute, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan, China
- Shandong Engineering Research Center for Environmental Protection and Remediation on Groundwater, Jinan, China
| | - Jingya Tian
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
| | - Chao Zhang
- Shandong Provincial Geo-mineral Engineering Exploration Institute, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan, China
- Shandong Engineering Research Center for Environmental Protection and Remediation on Groundwater, Jinan, China
| | - Lixia Li
- Shandong Provincial Geo-mineral Engineering Exploration Institute, Shandong Provincial Bureau of Geology & Mineral Resources, Jinan, China
- Shandong Engineering Research Center for Environmental Protection and Remediation on Groundwater, Jinan, China
| | - Yao Huang
- Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Academy of Sciences, Guangzhou, China
| | - Honghong Lyu
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin, China
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Guío J, Fillat MF, Peleato ML, Sevilla E. Responses of Anabaena sp. PCC7120 to lindane: Physiological effects and differential expression of potential lin genes. Microbiologyopen 2023; 12:e1355. [PMID: 37379427 PMCID: PMC10134481 DOI: 10.1002/mbo3.1355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 06/30/2023] Open
Abstract
Lindane (γ-HCH) is an organochlorine pesticide that causes huge environmental concerns worldwide due to its recalcitrance and toxicity. The use of the cyanobacterium Anabaena sp. PCC 7120 in aquatic lindane bioremediation has been suggested but information relative to this process is scarce. In the present work, data relative to the growth, pigment composition, photosynthetic/respiration rate, and oxidative stress response of Anabaena sp. PCC 7120 in the presence of lindane at its solubility limit in water are shown. In addition, lindane degradation experiments revealed almost a total disappearance of lindane in the supernatants of Anabaena sp. PCC 7120 culture after 6 days of incubation. The diminishing in lindane concentration was in concordance with an increase in the levels of trichlorobenzene inside the cells. Furthermore, to identify potential orthologs of the linA, linB, linC, linD, linE, and linR genes from Sphingomonas paucimobilis B90A in Anabaena sp. PCC 7120, a whole genome screening was performed allowing the identification of five putative lin orthologs (all1353 and all0193 putative orthologs of linB, all3836 putative orthologs of linC, and all0352 and alr0353 putative orthologs of linE and linR, respectively) which could be involved in the lindane degradation pathway. Differential expression analysis of these genes in the presence of lindane revealed strong upregulation of one of the potential lin genes of Anabaena sp. PCC 7120.
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Affiliation(s)
- Jorge Guío
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex SystemsUniversidad de ZaragozaZaragozaSpain
| | - Maria F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex SystemsUniversidad de ZaragozaZaragozaSpain
| | - Maria L. Peleato
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex SystemsUniversidad de ZaragozaZaragozaSpain
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular and Institute for Biocomputation and Physics of Complex SystemsUniversidad de ZaragozaZaragozaSpain
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3
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Yin X, Hua H, Dyer J, Landis R, Fennell D, Axe L. Degradation of chlorinated solvents with reactive iron minerals in subsurface sediments from redox transition zones. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130470. [PMID: 36493644 DOI: 10.1016/j.jhazmat.2022.130470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Reactive iron (Fe) mineral coatings found in subsurface reduction-oxidation transition zones (RTZs) contribute to the attenuation of contaminants. An 18.3-m anoxic core was collected from the site, where constituents of concern (COCs) in groundwater included chlorinated solvents. Reactive Fe mineral coatings were found to be abundant in the RTZs. This research focused on evaluating reaction kinetics with anoxic sediments bearing ferrous mineral nano-coatings spiked with either tetrachloroethylene (PCE), trichloroethylene (TCE), or 1,4-dichlorobenzene (1,4-DCB). Reaction kinetics with RTZ sediments followed pseudo-first-order reactions for the three contaminants with 90% degradation achieved in less than 39 days. The second-order rate constants for the three COCs ranged from 6.20 × 10-4 to 1.73 × 10-3 Lg-1h-1 with pyrite (FeS2), 4.97 × 10-5 to 1.24 × 10-3 Lg-1h-1with mackinawite (FeS), 1.25 × 10-4 to 1.89 × 10-4 Lg-1h-1 with siderite (FeCO3), and 1.79 × 10-4 to 1.10 × 10-3 Lg-1h-1 with magnetite (Fe3O4). For these three chlorinated solvents, the trend for the rate constants followed: Fe(II) sulfide minerals > magnetite > siderite. The high reactivity of Fe mineral coatings is hypothesized to be due to the large surface areas of the nano-mineral coatings. As a result, these surfaces are expected to play an important role in the attenuation of chlorinated solvents in contaminated subsurface environments.
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Affiliation(s)
- Xin Yin
- Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07032, USA
| | - Han Hua
- Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07032, USA; Department of Civil, Construction & Environmental Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - James Dyer
- Savannah River National Laboratory, Aiken, SC 29808, USA
| | | | - Donna Fennell
- Rutgers University, Department of Environmental Sciences, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Lisa Axe
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technzhaology, Newark, NJ 07032, USA.
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4
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Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
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Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
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De Vera J, Chen W, Phillips E, Gilevska T, Morgan SA, Norcross S, West K, Mack EE, Lollar BS. Compound-specific isotope analysis (CSIA) evaluation of degradation of chlorinated benzenes (CBs) and benzene in a contaminated aquifer. JOURNAL OF CONTAMINANT HYDROLOGY 2022; 250:104051. [PMID: 35901656 DOI: 10.1016/j.jconhyd.2022.104051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/18/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Compound-specific isotope analysis (CSIA) has become a valuable tool in understanding the fate of organic contaminants at field sites. However, its application to chlorinated benzenes (CBs), a group of toxic and persistent groundwater contaminants, has received less attention. This study employed CSIA to investigate the occurrence of natural degradation of various CBs and benzene in a contaminated aquifer. Despite the complexity of the study area (e.g., installation of a sheet pile barrier and the presence of a complex set of contaminants), the substantial enrichments in δ13C values (i.e., >2‰) for all CBs and benzene across the sampling wells indicate in situ degradation of these compounds. In particular, the 13C enrichments for 1,2,4-trichlorobenzene (1,2,4-TCB) and 1,2-dichlorobenzene (1,2-DCB) display good correlations with decreasing groundwater concentrations, consistent with the effects of in situ biodegradation. Using the Rayleigh model, the extent of degradation (EoD) is estimated to be 47-99% for 1,2-DCB, and 21-73% for 1,2,4-TCB. The enrichments observed for the other CBs (1,4-DCB and chlorobenzene (MCB)) and benzene at the site are also suggestive of in situ biodegradation. Due to simultaneous degradation and production of 1,4-DCB (a major 1,2,4-TCB degradation product), MCB (from DCB degradation), and benzene (from MCB degradation), the estimation of EoD for these intermediate compounds is more complex but a modelling simulation supports in situ biodegradation of these daughter products. In particular, the fact that the δ13C values of MCB and benzene (i.e., daughter products of 1,2,4-TCB) are more enriched than the original δ13C value of their parent 1,2,4-TCB provides definitive evidence for the occurrence of in situ biodegradation of the MCB and benzene.
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Affiliation(s)
- Joan De Vera
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | - Weibin Chen
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | - Elizabeth Phillips
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | - Tetyana Gilevska
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | | | | | - Kathryn West
- AECOM, 1 Canal Rd, Pennsville, NJ 08023, United States
| | - E Erin Mack
- Corteva Agriscience, 974 Centre Road, Wilmington, DE 19805, United States
| | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada.
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Li X, Yang Y, Wang J, Jin H, Zhang Y, Cui Y, Song Y, Yan J. Organohalide Respiration with Diclofenac by Dehalogenimonas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11266-11276. [PMID: 35921385 DOI: 10.1021/acs.est.1c08824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Diclofenac (DCF) is a pharmaceutically active contaminant frequently found in aquatic ecosystems. The transformation pathways and microbiology involved in the biodegradation of DCF, particularly under anoxic conditions, remain poorly understood. Here, we demonstrated microbially mediated reductive dechlorination of DCF in anaerobic enrichment culture derived from contaminated river sediment. Over 90% of the initial 76.7 ± 3.6 μM DCF was dechlorinated at a maximum rate of 1.8 ± 0.3 μM day-1 during a 160 days' incubation. Mass spectrometric analysis confirmed that 2-(2-((2-chlorophenyl)amino)phenyl)acetic acid (2-CPA) and 2-anilinophenylacetic acid (2-APA) were formed as the monochlorinated and nonchlorinated DCF transformation products, respectively. A survey of microbial composition and Sanger sequencing revealed the enrichment and dominance of a new Dehalogenimonas population, designated as Dehalogenimonas sp. strain DCF, in the DCF-dechlorinating community. Following the stoichiometric conversion of DCF to 2-CPA (76.0 ± 2.1 μM) and 2-APA (3.7 ± 0.8 μM), strain DCF cell densities increased by 24.4 ± 4.4-fold with a growth yield of 9.0 ± 0.1 × 108 cells per μmol chloride released. Our findings expand the metabolic capability in the genus Dehalogenimonas and highlight the relevant roles of organohalide-respiring bacteria for the natural attenuation of halogenated contaminants of emerging concerns (e.g., DCF).
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Affiliation(s)
- Xiuying Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Yi Yang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Jingjing Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Huijuan Jin
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaozhi Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiru Cui
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yufang Song
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
| | - Jun Yan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Room 512 South Building, 72 Wenhua Road, Shenyang, Liaoning 110016, China
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Hudari MSB, Richnow H, Vogt C, Nijenhuis I. Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review. FEMS Microbiol Ecol 2022; 98:6638985. [PMID: 35810002 DOI: 10.1093/femsec/fiac081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.
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Affiliation(s)
- Mohammad Sufian Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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8
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Chen T, Zou C, Chen F, Yuan Y, Pan J, Zhao Q, Wang M, Qiao L, Cheng H, Ding C, Wang A. Response of 2,4,6-trichlorophenol-reducing biocathode to burial depth in constructed wetland sediments. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128066. [PMID: 34915250 DOI: 10.1016/j.jhazmat.2021.128066] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Biocathode systems could be used for in-situ bioremediation of chlorophenols (CPs) in constructed wetland (CW) sediments. However, little is known regarding whether or how cathode burial depths affect the dechlorination of CPs in sediments. Here, 2,4,6-trichlorophenol (2,4,6-TCP)-dechlorinating biocathode systems were constructed under a cathode potential of - 0.7 V (vs. a saturated calomel electrode, SCE) at three different cathode burial depths (5, 10, and 15 cm). The 2,4,6-TCP removal efficiency and average transformation rate with the biocathode increased by 21.46-36.86% and 14.63-34.88% compared to those in the non-electrode groups. Deeper cathode burial depths enhanced the 2,4,6-TCP dechlorination performance. Furthermore, the oxidation-reduction potential (ORP) of the sediment decreased with sediment depth and the applied potential created a more favorable redox environment for the enrichment of functional bacteria. Deeper cathode burial depths also promoted the selective enrichment of electro-active and dechlorinating bacteria (e.g., Bacillus and Dehalobacter, respectively). The biocathode thus served as the carrier, electron source, and regulator of functional bacteria to accelerate the transformation of 2,4,6-TCP (2,4,6-TCP → 2,4-dichlorophenol → 4-chlorophenol → phenol) in sediments. These results offer insights into the effects of cathode burial depth on 2,4,6-TCP dechlorination in sediments from a redox environment and microbial community structure standpoint.
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Affiliation(s)
- Tianming Chen
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Province Engineering Research Center of Intelligent Environmental Protection Equipment, Yancheng Institute of Technology, Yancheng 224051, China
| | - Chao Zou
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Fan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Ye Yuan
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; Jiangsu Province Engineering Research Center of Intelligent Environmental Protection Equipment, Yancheng Institute of Technology, Yancheng 224051, China.
| | - Jingjing Pan
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Qi Zhao
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Mansi Wang
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China
| | - Liang Qiao
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Province Engineering Research Center of Intelligent Environmental Protection Equipment, Yancheng Institute of Technology, Yancheng 224051, China
| | - Haoyi Cheng
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng Ding
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Jiangsu Province Engineering Research Center of Intelligent Environmental Protection Equipment, Yancheng Institute of Technology, Yancheng 224051, China
| | - Aijie Wang
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; Jiangsu Province Engineering Research Center of Intelligent Environmental Protection Equipment, Yancheng Institute of Technology, Yancheng 224051, China.
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9
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Gilevska T, Sullivan Ojeda A, Kümmel S, Gehre M, Seger E, West K, Morgan SA, Mack EE, Sherwood Lollar B. Multi-element isotopic evidence for monochlorobenzene and benzene degradation under anaerobic conditions in contaminated sediments. WATER RESEARCH 2021; 207:117809. [PMID: 34741903 DOI: 10.1016/j.watres.2021.117809] [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: 03/24/2021] [Revised: 08/10/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Industrial chemicals are frequently detected in sediments due to a legacy of chemical spills. Globally, site remedies for groundwater and sediment decontamination include natural attenuation by in situ abiotic and biotic processes. Compound-specific isotope analysis (CSIA) is a diagnostic tool to identify, quantify, and characterize degradation processes in situ, and in some cases can differentiate between abiotic degradation and biodegradation. This study reports high-resolution carbon, chlorine, and hydrogen stable isotope profiles for monochlorobenzene (MCB), and carbon and hydrogen stable isotope profiles for benzene, coupled with measurements of pore water concentrations in contaminated sediments. Multi-element isotopic analysis of δ13C and δ37Cl for MCB were used to generate dual-isotope plots, which for 2 locations at the study site resulted in ΛC/Cl(130) values of 1.42 ± 0.19 and ΛC/Cl(131) values of 1.70 ± 0.15, consistent with theoretical calculations for carbon-chlorine bond cleavage (ΛT = 1.80 ± 0.31) via microbial reductive dechlorination. For benzene, significant δ2H (122‰) and δ13C (6‰) depletion trends, followed by enrichment trends in δ13C (1.6‰) in the upper part of the sediment, were observed at the same location, indicating not only production of benzene due to biodegradation of MCB, but subsequent biotransformation of benzene itself to nontoxic end-products. Degradation rate constants calculated independently using chlorine isotopic data and carbon isotopic data, respectively, agreed within uncertainty thus providing multiple lines of evidence for in situ contaminant degradation via reductive dechlorination and providing the foundation for a novel approach to determine site-specific in situ rate estimates essential for the prediction of remediation outcomes and timelines.
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Affiliation(s)
- Tetyana Gilevska
- Department of Earth Sciences, University of Toronto, Toronto, ON M5S 3B1, Canada; CNRS/EOST, ITES UMR 7063, Earth and Environment Institute of Strasbourg (ITES), University of Strasbourg, Strasbourg, 67084, France
| | - Ann Sullivan Ojeda
- Department of Earth Sciences, University of Toronto, Toronto, ON M5S 3B1, Canada; Department of Geosciences, Auburn University, Auburn, AL 36849, United States
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, UFZ, Leipzig, 04318, Germany
| | - Matthias Gehre
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, UFZ, Leipzig, 04318, Germany
| | - Edward Seger
- The Chemours Company, Wilmington, DE 19810, United States
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Puentes Jácome LA, Lomheim L, Gaspard S, Edwards EA. Biodegradation of Lindane (γ-Hexachlorocyclohexane) To Nontoxic End Products by Sequential Treatment with Three Mixed Anaerobic Microbial Cultures. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2968-2979. [PMID: 33557520 DOI: 10.1021/acs.est.0c07221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The γ isomer of hexachlorocyclohexane (HCH), also known as lindane, is a carcinogenic persistent organic pollutant. Lindane was used worldwide as an agricultural insecticide. Legacy soil and groundwater contamination with lindane and other HCH isomers is still a big concern. The biotic reductive dechlorination of HCH to nondesirable and toxic lower chlorinated compounds such as monochlorobenzene (MCB) and benzene, among others, has been broadly documented. Here, we demonstrate that complete biodegradation of lindane to nontoxic end products is attainable using a sequential treatment approach with three mixed anaerobic microbial cultures referred to as culture I, II, and III. Biaugmentation with culture I achieved dechlorination of lindane to MCB and benzene. Culture II was able to dechlorinate MCB to benzene, and finally, culture III carried out methanogenic benzene degradation. Distinct Dehalobacter populations, corresponding to different 16S rRNA amplicon sequence variants in culture I and culture II, were responsible for lindane and MCB dechlorination, respectively. This study continues to highlight key roles of Dehalobacter as chlorobenzene- and HCH -respiring bacteria and demonstrates that sequential treatment with specialized anaerobic cultures may be explored at field sites in order to address legacy soil and groundwater contamination with HCH.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Sarra Gaspard
- Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre, Guadeloupe, French West-Indies 97157, France
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3E5, Canada
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11
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Zhao S, Rogers MJ, He J. Abundance of organohalide respiring bacteria and their role in dehalogenating antimicrobials in wastewater treatment plants. WATER RESEARCH 2020; 181:115893. [PMID: 32502751 DOI: 10.1016/j.watres.2020.115893] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/25/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic organohalide contaminants present in wastewater treatment plants (WWTPs) often remain untreated and can be discharged into the environment. Although organohalide respiring bacteria (OHRB) contribute to the elimination of anthropogenic organohalides in natural anaerobic environments, reductive dehalogenation by OHRB in mainstream WWTPs remains poorly understood. In this study, we quantified OHRB during a long-term operation of a municipal WWTP with short hydraulic and sludge retention times (3 h and 1.5-5 days, respectively). The obligate OHRB were detected at high levels (averaging 2.56 ± 1.73 × 107 and 3.11 ± 1.16 × 107 16S rRNA gene copies/ml MLSS sludge in anoxic and aerobic zones, respectively) over the entire sampling period and throughout the wastewater treatment train. Microcosms derived from mainstream activated sludge contained an unidentified member of the Dehalococcoides genus that metabolically dechlorinated triclosan, used as a representative emerging organohalide antimicrobial, to diclosan, suggesting the potential of anaerobic degradation of emerging contaminants in WWTPs. To further understand the mechanisms for such antimicrobials' removal, an investigation of dechlorination of triclosan by Dehalococcoides strains was conducted. Dechlorination of environmentally relevant concentrations of triclosan to diclosan was observed in Dehalococcoides mccartyi strain CG1, yielding 4.59 ± 0.34 × 108 cells/μmole Cl- removed at a rate of 0.062 μM/day and a minimal inhibitory concentration of 0.5 mg/L. Notably, both the tolerance of strain CG1 to triclosan and the rate of triclosan dechlorination increased when CG1 was cultured in the presence of both triclosan and tetrachloroethene. Taken together, our results suggest that anaerobic degradation of organohalide antimicrobials might be more prevalent in mainstream WWTPs than previously speculated, though the low growth yields that are supported by triclosan dechlorination seem to indicate that other organohalide substrates could be necessary to sustain OHRB populations in these systems.
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Affiliation(s)
- Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore.
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12
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Chow SJ, Lorah MM, Wadhawan AR, Durant ND, Bouwer EJ. Sequential biodegradation of 1,2,4-trichlorobenzene at oxic-anoxic groundwater interfaces in model laboratory columns. JOURNAL OF CONTAMINANT HYDROLOGY 2020; 231:103639. [PMID: 32283437 DOI: 10.7281/t1/i3ilxo] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 05/24/2023]
Abstract
Halogenated organic solvents such as chlorobenzenes (CBs) are frequent groundwater contaminants due to legacy spills. When contaminated anaerobic groundwater discharges into surface water through wetlands and other transition zones, aeration can occur from various physical and biological processes at shallow depths, resulting in oxic-anoxic interfaces (OAIs). This study investigated the potential for 1,2,4-trichlorobenzene (1,2,4-TCB) biodegradation at OAIs. A novel upflow column system was developed to create stable anaerobic and aerobic zones, simulating a natural groundwater OAI. Two columns containing (1) sand and (2) a mixture of wetland sediment and sand were operated continuously for 295 days with varied doses of 0.14-1.4 mM sodium lactate (NaLac) as a model electron donor. Both column matrices supported anaerobic reductive dechlorination and aerobic degradation of 1,2,4-TCB spatially separated between anaerobic and aerobic zones. Reductive dechlorination produced a mixture of di- and monochlorobenzene daughter products, with estimated zero-order dechlorination rates up to 31.3 μM/h. Aerobic CB degradation, limited by available dissolved oxygen, occurred for 1,2,4-TCB and all dechlorinated daughter products. Initial reductive dechlorination did not enhance the overall observed extent or rate of subsequent aerobic CB degradation. Increasing NaLac dose increased the extent of reductive dechlorination, but suppressed aerobic CB degradation at 1.4 mM NaLac due to increased oxygen demand. 16S-rRNA sequencing of biofilm microbial communities revealed strong stratification of functional anaerobic and aerobic organisms between redox zones including the sole putative reductive dechlorinator detected in the columns, Dehalobacter. The sediment mixture column supported enhanced reductive dechlorination compared to the sand column at all tested NaLac doses and growth of Dehalobacter populations up to 4.1 × 108 copies/g (51% relative abundance), highlighting the potential benefit of sediments in reductive dechlorination processes. Results from these model systems suggest both substantial anaerobic and aerobic CB degradation can co-occur along the OAI at contaminated sites where bioavailable electron donors and oxygen are both present.
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Affiliation(s)
- Steven J Chow
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Michelle M Lorah
- U.S. Geological Survey, MD-DE-DC Water Science Center, Address: 5522 Research Park Drive, Baltimore, MD 21228, United States.
| | - Amar R Wadhawan
- Arcadis U.S. Inc., Address: 7550 Teague Road Suite 210, Hanover, MD 21076, United States
| | - Neal D Durant
- Geosyntec Consultants, Address: 10211 Wincopin Cir Floor 4, Columbia, MD 21044, United States
| | - Edward J Bouwer
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
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13
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Chow SJ, Lorah MM, Wadhawan AR, Durant ND, Bouwer EJ. Sequential biodegradation of 1,2,4-trichlorobenzene at oxic-anoxic groundwater interfaces in model laboratory columns. JOURNAL OF CONTAMINANT HYDROLOGY 2020; 231:103639. [PMID: 32283437 PMCID: PMC7217665 DOI: 10.1016/j.jconhyd.2020.103639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 05/09/2023]
Abstract
Halogenated organic solvents such as chlorobenzenes (CBs) are frequent groundwater contaminants due to legacy spills. When contaminated anaerobic groundwater discharges into surface water through wetlands and other transition zones, aeration can occur from various physical and biological processes at shallow depths, resulting in oxic-anoxic interfaces (OAIs). This study investigated the potential for 1,2,4-trichlorobenzene (1,2,4-TCB) biodegradation at OAIs. A novel upflow column system was developed to create stable anaerobic and aerobic zones, simulating a natural groundwater OAI. Two columns containing (1) sand and (2) a mixture of wetland sediment and sand were operated continuously for 295 days with varied doses of 0.14-1.4 mM sodium lactate (NaLac) as a model electron donor. Both column matrices supported anaerobic reductive dechlorination and aerobic degradation of 1,2,4-TCB spatially separated between anaerobic and aerobic zones. Reductive dechlorination produced a mixture of di- and monochlorobenzene daughter products, with estimated zero-order dechlorination rates up to 31.3 μM/h. Aerobic CB degradation, limited by available dissolved oxygen, occurred for 1,2,4-TCB and all dechlorinated daughter products. Initial reductive dechlorination did not enhance the overall observed extent or rate of subsequent aerobic CB degradation. Increasing NaLac dose increased the extent of reductive dechlorination, but suppressed aerobic CB degradation at 1.4 mM NaLac due to increased oxygen demand. 16S-rRNA sequencing of biofilm microbial communities revealed strong stratification of functional anaerobic and aerobic organisms between redox zones including the sole putative reductive dechlorinator detected in the columns, Dehalobacter. The sediment mixture column supported enhanced reductive dechlorination compared to the sand column at all tested NaLac doses and growth of Dehalobacter populations up to 4.1 × 108 copies/g (51% relative abundance), highlighting the potential benefit of sediments in reductive dechlorination processes. Results from these model systems suggest both substantial anaerobic and aerobic CB degradation can co-occur along the OAI at contaminated sites where bioavailable electron donors and oxygen are both present.
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Affiliation(s)
- Steven J Chow
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Michelle M Lorah
- U.S. Geological Survey, MD-DE-DC Water Science Center, Address: 5522 Research Park Drive, Baltimore, MD 21228, United States.
| | - Amar R Wadhawan
- Arcadis U.S. Inc., Address: 7550 Teague Road Suite 210, Hanover, MD 21076, United States
| | - Neal D Durant
- Geosyntec Consultants, Address: 10211 Wincopin Cir Floor 4, Columbia, MD 21044, United States
| | - Edward J Bouwer
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
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14
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Molenda O, Puentes Jácome LA, Cao X, Nesbø CL, Tang S, Morson N, Patron J, Lomheim L, Wishart DS, Edwards EA. Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:663-678. [PMID: 32159535 DOI: 10.1039/c9em00605b] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Organohalide respiring bacteria (OHRB) express reductive dehalogenases for energy conservation and growth. Some of these enzymes catalyze the reductive dehalogenation of chlorinated and brominated pollutants in anaerobic subsurface environments, providing a valuable ecosystem service. Dehalococcoides mccartyi strains have been most extensively studied owing to their ability to dechlorinate all chlorinated ethenes - most notably carcinogenic vinyl chloride - to ethene. The genomes of OHRB, particularly obligate OHRB, often harbour multiple putative reductive dehalogenase genes (rdhA), most of which have yet to be characterized. We recently sequenced and closed the genomes of eight new strains, increasing the number of available D. mccartyi genomes in NCBI from 16 to 24. From all available OHRB genomes, we classified predicted translations of reductive dehalogenase genes using a previously established 90% amino acid pairwise identity cut-off to identify Ortholog Groups (OGs). Interestingly, the majority of D. mccartyi dehalogenase gene sequences, once classified into OGs, exhibited a remarkable degree of synteny (gene order) in all genomes sequenced to date. This organization was not apparent without the classification. A high degree of synteny indicates that differences arose from rdhA gene loss rather than recombination. Phylogenetic analysis suggests that most rdhA genes have a long evolutionary history in the Dehalococcoidia with origin prior to speciation of Dehalococcoides and Dehalogenimonas. We also looked for evidence of synteny in the genomes of other species of OHRB. Unfortunately, there are too few closed Dehalogenimonas genomes to compare at this time. There is some partial evidence for synteny in the Dehalobacter restrictus genomes, but here too more closed genomes are needed for confirmation. Interestingly, we found that the rdhA genes that encode enzymes that catalyze dehalogenation of industrial pollutants are the only rdhA genes with strong evidence of recent lateral transfer - at least in the genomes examined herein. Given the utility of the RdhA sequence classification to comparative analyses, we are building a public web server () for the community to use, which allows users to add and classify new sequences, and download the entire curated database of reductive dehalogenases.
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Affiliation(s)
- Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.
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15
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Zhang D, Dang H, Li Z, Zhang C. Redox characteristics of humins and their coupling with potential PCB dechlorinators in southern Yellow Sea sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:296-304. [PMID: 31158658 DOI: 10.1016/j.envpol.2019.05.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Natural attenuation of polychlorinated biphenyls (PCBs) by indigenous bacteria is an effective remediation strategy for polluted marine sediments. This study investigated the relationships between PCB concentrations in sediment pore water, humin electron transfer capacity, and potential PCB dechlorinators at eight sediment sampling sites in the southern Yellow Sea, China, with differential PCB contamination. Station A2 showed the highest PCB concentration (453.16 ng L-1 for seven indicator PCBs), especially of less chlorinated PCB congeners (≤5 Cl atoms), humin redox activity, and Dehalococcoides abundance (p < 0.05). Statistical analyses revealed a highly positive correlation between Dehalococcoides abundance and PCB concentration (r = 0.836, p < 0.05) and the electron shuttling ability of humins (r = 0.952, p < 0.01), whereas this was not observed for total bacteria and other potential PCB dechlorinators, e.g., Dehalobacter and Dehalogenimonas. Based on these results, Dehalococcoides might play an important role in the in situ reductive dechlorination of PCBs involving humins in marine sediments, and the natural microbial PCB attenuation capacity at station A2 was high. Chemical characterizations, electrochemical properties, and Fourier transform infrared analysis suggested that humins at station A2 had the highest electron transfer capacity. Furthermore, quinones are likely to be the functional groups that shuttle electrons during PCB dechlorination. Overall, this study provides a useful foundation for evaluating the natural microbial attenuation potential and fates of PCBs in marine sediments and for determining the role of humins as redox mediators in in situ PCB dechlorination by putative indigenous dechlorinators.
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Affiliation(s)
- Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, Fujian, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, Heilongjiang, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China; The Guangxi Key Laboratory of Theory and Technology for Environmental Pollution Control, Guilin, 541006, Guangxi, China.
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16
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Gilevska T, Passeport E, Shayan M, Seger E, Lutz EJ, West KA, Morgan SA, Mack EE, Sherwood Lollar B. Determination of in situ biodegradation rates via a novel high resolution isotopic approach in contaminated sediments. WATER RESEARCH 2019; 149:632-639. [PMID: 30583106 DOI: 10.1016/j.watres.2018.11.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/06/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
A key challenge in conceptual models for contaminated sites is identification of the multiplicity of processes controlling contaminant concentrations and distribution as well as quantification of the rates at which such processes occur. Conventional protocol for calculating biodegradation rates can lead to overestimation by attributing concentration decreases to degradation alone. This study reports a novel approach of assessing in situ biodegradation rates of monochlorobenzene (MCB) and benzene in contaminated sediments. Passive diffusion samplers allowing cm-scale vertical resolution across the sediment-water interface were coupled with measurements of concentrations and stable carbon isotope signatures to identify zones of active biodegradation of both compounds. Large isotopic enrichment trends in 13C were observed for MCB (1.9-5.7‰), with correlated isotopic depletion in 13C for benzene (1.0-7.0‰), consistent with expected isotope signatures for substrate and daughter product produced by in situ biodegradation. Importantly in the uppermost sediments, benzene too showed a pronounced 13C enrichment trend of up to 2.2‰, providing definitive evidence for simultaneous degradation as well as production of benzene. The hydrogeological concept of representative elementary volume was applied to CSIA data for the first time and identified a critical zone of 10-15 cm with highest biodegradation potential in the sediments. Using both stable isotope-derived rate calculations and numerical modeling, we show that MCB degraded at a slower rate (0.1-1.4 yr-1 and 0.2-3.2 yr-1, respectively) than benzene (3.3-84.0 yr-1) within the most biologically active zone of the sediment, contributing to detoxification.
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Affiliation(s)
- Tetyana Gilevska
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, M5S 3B1, Canada
| | - Elodie Passeport
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, M5S 1A4, Canada; Department of Chemical Engineering and Applied Chemistry, Toronto, Ontario, M5S 3E5, Canada
| | - Mahsa Shayan
- Department of Earth Sciences, University of Toronto, Toronto, Ontario, M5S 3B1, Canada
| | - Edward Seger
- The Chemours Company, Wilmington, DE, 19810, USA
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17
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Zhang S, Ying Z, You J, Ye J, Cheng Z, Chen D, Chen J. Superior performance and mechanism of chlorobenzene degradation by a novel bacterium. RSC Adv 2019; 9:15004-15012. [PMID: 35516324 PMCID: PMC9064227 DOI: 10.1039/c9ra01229j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/05/2019] [Indexed: 01/08/2023] Open
Abstract
A newly isolated strain was identified as Ochrobactrum sp. by 16S rRNA sequence analysis and named as ZJUTCB-1.
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Affiliation(s)
- Shihan Zhang
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Zanyun Ying
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
| | - Juping You
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
| | - Jiexu Ye
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Zhuowei Cheng
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Dongzhi Chen
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Jianmeng Chen
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
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18
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Qiao W, Luo F, Lomheim L, Mack EE, Ye S, Wu J, Edwards EA. A Dehalogenimonas Population Respires 1,2,4-Trichlorobenzene and Dichlorobenzenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13391-13398. [PMID: 30371071 DOI: 10.1021/acs.est.8b04239] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chlorobenzenes are ubiquitous contaminants in groundwater and soil at many industrial sites. Previously, we demonstrated the natural attenuation of chlorobenzenes and benzene at a contaminated site inferred from a 5 year site investigation and parallel laboratory microcosm studies. To identify the microbes responsible for the observed dechlorination of chlorobenzenes, the microbial community was surveyed using 16S rRNA gene amplicon sequencing. Members of the Dehalobacter and Dehalococcoides are reported to respire chlorobenzenes; however, neither were abundant in our sediment microcosms. Instead, we observed a significant increase in the relative abundance of Dehalogenimonas from <1% to 16-30% during dechlorination of 1,2,4-trichlorobenzene (TCB), 1,2-dichlorobenzene (DCB), and 1,3-DCB over 19 months. Quantitative PCR (qPCR) confirmed that Dehalogenimonas gene copies increased by 2 orders of magnitude with an average yield of 3.6 ± 2.3 g cells per mol Cl- released ( N = 12). In transfer cultures derived from sediment microcosms, dechlorination of 1,4-DCB and monochlorobenzene (MCB) was carried out by Dehalobacter spp. with a growth yield of 3.0 ± 2.1 g cells per mol Cl- released ( N = 5). Here we show that a Dehalogenimonas population respire 1,2,4-TCB and 1,2-/1,3-DCB isomers. This finding emphasizes the need to monitor a broader spectrum of organohalide-respiring bacteria, including Dehalogenimonas, at sites contaminated with halogenated organic compounds.
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Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - E Erin Mack
- DuPont Corporate Remediation Group , Wilmington , Delaware 19805 , United States
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
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19
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Capozzi SL, Rodenburg LA, Krumins V, Fennell DE, Mack EE. Using positive matrix factorization to investigate microbial dehalogenation of chlorinated benzenes in groundwater at a historically contaminated site. CHEMOSPHERE 2018; 211:515-523. [PMID: 30086528 DOI: 10.1016/j.chemosphere.2018.07.180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/26/2018] [Accepted: 07/29/2018] [Indexed: 06/08/2023]
Abstract
Chlorinated benzenes are common groundwater contaminants in the United States, so demonstrating whether they undergo degradation in the subsurface is important in determining the best remedy for this contamination. The purpose of this work was to use a new data mining approach to investigate chlorinated benzene degradation pathways in the subsurface. Positive Matrix Factorization (PMF) was used to analyze long-term measurements of chlorinated benzene concentrations in groundwater at a contaminated site in New Jersey. A dataset containing 597 groundwater samples and 5 chlorinated benzenes and benzene collected from 144 wells over 20 years was investigated using PMF2 software. Despite the heterogeneity of this dataset, PMF analysis revealed patterns indicative of microbial dechlorination in the groundwater and provided insight about where dechlorination is occurring, to what extent, and under which geochemical conditions. PMF resolved a factor indicative of a source of 1,2,4-trichlorobenzene and 1,2-dichlorobenzene and two factors representing stages of dechlorination, one more advanced than the other. The PMF results indicated that virtually all of the 1,2-dichlorobenzene at the site arises from its use onsite, not from the dechlorination of trichlorobenzenes. Factors were further interpreted using ancillary data such as geochemical indicators and field parameters also measured in the samples. Analysis suggested that the partial and advanced dechlorination signals occur under different subsurface physical conditions. The results provided field validation of the current understanding of anaerobic dechlorination of chlorinated benzenes in the subsurface developed from laboratory studies. PMF is thereby shown to be a useful tool for investigating chlorinated benzene dechlorination.
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Affiliation(s)
- Staci L Capozzi
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, United States.
| | - Lisa A Rodenburg
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Donna E Fennell
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, United States
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Wilmington, DE, 19805, United States
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20
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Puentes Jácome LA, Edwards EA. A switch of chlorinated substrate causes emergence of a previously undetected native Dehalobacter population in an established Dehalococcoides-dominated chloroethene-dechlorinating enrichment culture. FEMS Microbiol Ecol 2018; 93:4569067. [PMID: 29088371 DOI: 10.1093/femsec/fix141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/26/2017] [Indexed: 01/08/2023] Open
Abstract
Chlorobenzenes are soil and groundwater pollutants of concern that can be reductively dehalogenated by organohalide-respiring bacteria from the genera Dehalococcoides and Dehalobacter. The bioaugmentation culture KB-1® harbours Dehalococcoides mccartyi spp. that reductively dehalogenate trichloroethene to ethene. It contains more than 30 reductive dehalogenase genes; some of them are highly similar to genes found in the chlorobenzene-respiring Dehalococcoides mccartyi strain CBDB1. We explored the chlorobenzene dehalogenation capability of the KB-1 enrichment culture using 1,2,4-trichlorobenzene (1,2,4-TCB). We achieved adaptation of KB-1 to 1,2,4-TCB that is dehalogenated to a mixture of dichlorobenzenes, and subsequently to monochlorobenzene and benzene. Surprisingly, a native Dehalobacter population, and not a Dehalococcoides population, couples the dechlorination of 1,2,4-TCB to growth achieving an average yield of 1.1 ± 0.6 × 1013 cells per mole of Cl- released. Interestingly, the dechlorination of 1,2,4-TCB occurs alongside the complete dechlorination of trichloroethene to ethene in cultures fed both electron acceptors. Dehalobacter was not previously identified as a major player in KB-1, but its ecological niche was favoured by the introduction of 1,2,4-TCB. Based on 16S rRNA phylogeny, Dehalobacter populations seem to cluster into specialised clades, and are likely undergoing substrate specialisation as a strategy to reduce competition for electron acceptors.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
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21
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Qiao W, Luo F, Lomheim L, Mack EE, Ye S, Wu J, Edwards EA. Natural Attenuation and Anaerobic Benzene Detoxification Processes at a Chlorobenzene-Contaminated Industrial Site Inferred from Field Investigations and Microcosm Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:22-31. [PMID: 29178800 DOI: 10.1021/acs.est.7b04145] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A five-year site investigation was conducted at a former chemical plant in Nanjing, China. The main contaminants were 1,2,4-trichlorobenzene (TCB) reaching concentrations up to 7300 μg/L, dichlorobenzene (DCB) isomers, monochlorobenzene (MCB), and benzene. Over time, these contaminants naturally attenuated to below regulatory levels under anaerobic conditions. To confirm the transformation processes and to explore the mechanisms, a corresponding laboratory microcosm study was completed demonstrating that 1,2,4-TCB was dechlorinated to 1,2-DCB, 1,3-DCB, and 1,4-DCB in approximately 2%/10%/88% molar proportions. The DCB isomers were dechlorinated via MCB to benzene, and, finally, benzene was degraded under prevailing sulfate-reducing conditions. Dechlorination could not be attributed to known dechlorinators Dehalobacter or Dehalococcoides, while anaerobic benzene degradation was mediated by microbes affiliated to a Deltaproteobacterium ORM2, previously associated with this activity. Unidentified organic compounds, possibly aromatic compounds related to past on-site production processes, were fueling the dechlorination reactions in situ. The microcosm study confirmed transformation processes inferred from field data and provided needed assurance for natural attenuation. Activity-based microcosm studies are often omitted from site characterization in favor of rapid and less expensive molecular surveys. However, the value of microcosm studies for confirming transformation processes, establishing electron balances, assessing cocontaminant inhibition, and validating appropriate monitoring tools is clear. At complex sites impacted by multiple compounds with poorly characterized transformation mechanisms, activity assays provide valuable data to incorporate into the conceptual site model to most effectively inform remediation alternatives.
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Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Elizabeth Erin Mack
- DuPont Corporate Remediation Group , Wilmington, Delaware 19805, United States
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
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Chen J, Wang PF, Wang C, Liu JJ, Gao H, Wang X. Spatial distribution and diversity of organohalide-respiring bacteria and their relationships with polybrominated diphenyl ether concentration in Taihu Lake sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 232:200-211. [PMID: 28943350 DOI: 10.1016/j.envpol.2017.08.124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 07/31/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
It is acknowledged that organohalide-respiring bacteria (OHRB) can degrade polybrominated diphenyl ethers (PBDEs); however, very little is known about the distribution of OHRB or their response to PBDE contamination in natural sediments. We collected sediments from 28 sampling sites in Taihu Lake, China, and investigated the spatial distribution and diversity of OHRB, and the relationships between the PBDE contamination levels and the PBDE removal potential. The abundances of five typical OHRB genera, namely Dehalobacter, Dehalococcoides, Dehalogenimonas, Desulfitobacterium, and Geobacter, ranged from 0.34 × 104 to 19.4 × 107 gene copies g-1 dry sediment, and varied significantly among different areas of Taihu Lake. OHRB were more abundant in sediments from Meiliang and Zhushan Bay, where the PBDE concentrations were higher, and the phylotype diversity of the OHRB belonging to the family Dehalococcoidaceae was lower, than reported for other areas. While the sulfate concentrations explained much of the spatial distribution of OHRB, PBDE concentrations were also a strong influence on the abundance and diversity of OHRB in the sediments. For Dehalococcoides, Dehalogenimonas and Geobacter, the abundance of each genus was positively related to its own potential to remove PBDEs. The dominant OHRB genus, Dehalogenimonas, may contribute most to in situ bioremediation of PBDEs in Taihu Lake.
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Affiliation(s)
- Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; The State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Pei-Fang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Jia-Jia Liu
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
| | - Xun Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, Hohai University, 1 Xikang Road, Nanjing 210098, PR China; College of Environment, Hohai University, 1 Xikang Road, Nanjing 210098, PR China
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Şimşir B, Yan J, Im J, Graves D, Löffler FE. Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:4821-4830. [PMID: 28328216 PMCID: PMC6944067 DOI: 10.1021/acs.est.6b05554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Contaminant discharge from fractured bedrock formations remains a remediation challenge. We applied an integrated approach to assess the natural attenuation potential of sediment that forms the transition zone between upwelling groundwater from a chlorinated solvent-contaminated fractured bedrock aquifer and the receiving surface water. In situ measurements demonstrated that reductive dechlorination in the sediment attenuated chlorinated compounds before reaching the water column. Microcosms established with creek sediment or in situ incubated Bio-Sep beads degraded C1-C3 chlorinated solvents to less-chlorinated or innocuous products. Quantitative PCR and 16S rRNA gene amplicon sequencing revealed the abundance and spatial distribution of known dechlorinator biomarker genes within the creek sediment and demonstrated that multiple dechlorinator populations degrading chlorinated C1-C3 alkanes and alkenes co-inhabit the sediment. Phylogenetic classification of bacterial and archaeal sequences indicated a relatively uniform distribution over spatial (300 m horizontally) scale, but Dehalococcoides and Dehalobacter were more abundant in deeper sediment, where 5.7 ± 0.4 × 105 and 5.4 ± 0.9 × 106 16S rRNA gene copies per g of sediment, respectively, were measured. The microbiological and hydrogeological characterization demonstrated that microbial processes at the fractured bedrock-sediment interface were crucial for preventing contaminants reaching the water column, emphasizing the relevance of this critical zone environment for contaminant attenuation.
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Affiliation(s)
- Burcu Şimşir
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jun Yan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Jeongdae Im
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01002, United States
| | - Duane Graves
- Geosyntec Consultants, Knoxville, Tennessee 37922, United States
| | - Frank E. Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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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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25
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Alfán-Guzmán R, Ertan H, Manefield M, Lee M. Isolation and Characterization of Dehalobacter sp. Strain TeCB1 Including Identification of TcbA: A Novel Tetra- and Trichlorobenzene Reductive Dehalogenase. Front Microbiol 2017; 8:558. [PMID: 28421054 PMCID: PMC5379058 DOI: 10.3389/fmicb.2017.00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/16/2017] [Indexed: 11/13/2022] Open
Abstract
Dehalobacter sp. strain TeCB1 was isolated from groundwater near Sydney, Australia, that is polluted with a range of organochlorines. The isolated strain is able to grow by reductive dechlorination of 1,2,4,5-tetrachlorobenzene to 1,3- and 1,4-dichlorobenzene with 1,2,4-trichlorobenzene being the intermediate daughter product. Transient production of 1,2-dichlorobenzene was detected with subsequent conversion to monochlorobenzene. The dehalogenation capability of strain TeCB1 to respire 23 alternative organochlorines was examined and shown to be limited to the use of 1,2,4,5-tetrachlorobenzene and 1,2,4-trichlorobenzene. Growth on 1,2,4-trichlorobenzene resulted in the production of predominantly 1,3- and 1,4-dichlorobenzene. The inability of strain TeCB1 to grow on 1,2-dichlorobenzene indicated that the production of monochlorobenzene during growth on 1,2,4,5-tetarchlorobezene was cometabolic. The annotated genome of strain TeCB1 contained only one detectable 16S rRNA gene copy and genes for 23 full-length and one truncated Reductive Dehalogenase (RDase) homologs, five unique to strain TeCB1. Identification and functional characterization of the 1,2,4,5-tetrachlorobenzene and 1,2,4-trichlorobenzene RDase (TcbA) was achieved using native-PAGE coupled with liquid chromatography tandem mass spectrometry. Interestingly, TcbA showed higher amino acid identity with tetrachloroethene reductases PceA (95% identity) from Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense Y51 than with the only other chlorinated benzene reductase [i.e., CbrA (30% identity)] functionally characterized to date.
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Affiliation(s)
- Ricardo Alfán-Guzmán
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia.,Department of Molecular Biology and Genetics, Istanbul UniversityIstanbul, Turkey
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
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26
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Lu Y, Ramiro-Garcia J, Vandermeeren P, Herrmann S, Cichocka D, Springael D, Atashgahi S, Smidt H. Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions. Appl Microbiol Biotechnol 2017; 101:2589-2601. [PMID: 27909745 PMCID: PMC5320011 DOI: 10.1007/s00253-016-8004-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/27/2023]
Abstract
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms.
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Affiliation(s)
- Yue Lu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | | | - Steffi Herrmann
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Danuta Cichocka
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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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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28
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Chen M, Tong H, Liu C, Chen D, Li F, Qiao J. A humic substance analogue AQDS stimulates Geobacter sp. abundance and enhances pentachlorophenol transformation in a paddy soil. CHEMOSPHERE 2016; 160:141-148. [PMID: 27372263 DOI: 10.1016/j.chemosphere.2016.06.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 06/07/2016] [Accepted: 06/14/2016] [Indexed: 06/06/2023]
Abstract
Soil humic substances can be used as redox mediators in accelerating the biotransformation of organic pollutants, and humus-respiring bacteria are widely distributed in soils. However, the impact of humic substances on the soil microbial community during the biotransformation of organic pollutants is expected to be crucial while remains to be unclear. In this study, the biostimulation of indigenous microbial communities and the consequent effects on anaerobic transformation of pentachlorophenol (PCP) by a model humic substance, anthraquinone-2,6-disulfonate (AQDS), were systematically investigated in a paddy soil. The addition of AQDS was observed to increase the production of HCl-extractable Fe(II) and enhance the PCP transformation rates consequently. The pseudo-first-order rate constants of the PCP transformation showed a positive exponential relationship with the AQDS dosage. The terminal restriction fragment length polymorphism (T-RFLP) results indicated the substantial effect of added AQDS on soil microbial community. The enhanced abundance of Geobacter sp. was disclosed to be most critical for accelerated PCP transformation when with AQDS, in which Geobacter sp. functioned for promoting the generation of active Fe(II) and consequently enhancing the PCP transformation rates. The transformation rates of PCP were exponentially correlated with the abundance of Geobacter sp. positively. The findings are expected to improve the understanding of diversity and ubiquity of microorganisms in humic substances-rich soils for accelerating the transformations of soil chlorinated pollutants.
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Affiliation(s)
- Manjia Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Hui Tong
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550009, China
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550009, China.
| | - Dandan Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China.
| | - Jiangtao Qiao
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
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29
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Xu X, Shao J, Li M, Gao K, Jin J, Zhu L. Reductive Transformation of p-chloronitrobenzene in the upflow anaerobic sludge blanket reactor coupled with microbial electrolysis cell: performance and microbial community. BIORESOURCE TECHNOLOGY 2016; 218:1037-1045. [PMID: 27455127 DOI: 10.1016/j.biortech.2016.07.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/02/2016] [Accepted: 07/09/2016] [Indexed: 06/06/2023]
Abstract
A microbial electrolysis cell (MEC) combined with an upflow anaerobic sludge blanket (UASB) reactor was operated to degrade p-chloronitrobenzenes (p-ClNB) effectively. The results indicated that p-ClNB was transformed to p-chloroaniline (p-ClAn) and then reduced via dechlorination pathways. In the MEC-UASB coupled system, p-ClNB, p-ClAn removal efficiency and dechlorination efficiency reached 99.63±0.37%, 40.39±9.26% and 32.16±8.12%, respectively, which was significantly improved in comparison with the control UASB system. In addition, the coupled system could maintain appropriate pH and promote anaerobic sludge granulation to exert a positive effect on reductive transformation of p-ClNB. PCR-DGGE experiment and 454 pyrophosphate sequencing analysis indicated that applied voltage would significantly influence the succession of microbial community and promote oriented enrichment of the functional bacteria, which could be the underlying reasons for the improved performance. This study demonstrated that MEC-UASB coupled system had a promising application prospect to remove the recalcitrant pollutants effectively.
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Affiliation(s)
- Xiangyang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China
| | - Junjie Shao
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology University, NJ 07102, United States
| | - Kaituo Gao
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; Equipment Engineering Company, China United Engineering Corporation, Hangzhou 310052, China
| | - Jie Jin
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Liang Zhu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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30
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Chen M, Liu C, Chen P, Tong H, Li F, Qiao J, Lan Q. Dynamics of the microbial community and Fe(III)-reducing and dechlorinating microorganisms in response to pentachlorophenol transformation in paddy soil. JOURNAL OF HAZARDOUS MATERIALS 2016; 312:97-105. [PMID: 27017395 DOI: 10.1016/j.jhazmat.2016.03.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 03/01/2016] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
Soil microorganisms play crucial roles in the fates of pollutants, and understanding the behaviour of these microorganisms is critical for the bioremediation of PCP-contaminated soil. However, shifts remain unclear in the community structure and Fe(III)-reducing and dechlorinating microorganisms during PCP transformation processes, especially during the stages from the lag to the dechlorination phase and from the dechlorination to the stationary phase. Here, a set of lab-scale experiments was performed to investigate the microbial community dynamics accompanying PCP transformation in paddy soil. 19μM of PCP was biotransformed completely in 10days for all treatments. T-RFLP analysis of the microbial community confirmed that Veillonellaceae and Clostridium sensu stricto were the dominant groups during PCP transformation, and the structures of the microbial communities changed due to the degree of biotransformation and the addition of lactate and AQDS. However, similar temporal dynamics of the microbial communities were obtained among all treatments. Furthermore, as revealed by quantitative PCR, the dynamics of Fe(III)-reducing and dechlorinating microorganisms, including Geobacter sp., Shewanella sp., and Dehalobacter sp., were consistent with the transformation kinetics of PCP, suggesting the critical roles played by these microorganisms in PCP transformation. These findings are valuable for making predictions of and proposing methods for the microbial detoxification of residual organochlorine pesticides in paddy soil.
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Affiliation(s)
- Manjia Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Chengshuai Liu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550009, China.
| | - Pengcheng Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Hui Tong
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550009, China
| | - Fangbai Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China.
| | - Jiangtao Qiao
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Qing Lan
- Guangdong Polytechnic of Environmental Protection Engineering, Foshan, Guangdong 528216, China
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31
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Nijenhuis I, Kuntze K. Anaerobic microbial dehalogenation of organohalides — state of the art and remediation strategies. Curr Opin Biotechnol 2016; 38:33-8. [DOI: 10.1016/j.copbio.2015.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/03/2015] [Indexed: 11/26/2022]
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32
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Tang S, Wang PH, Higgins SA, Löffler FE, Edwards EA. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates. Front Microbiol 2016; 7:100. [PMID: 26903979 PMCID: PMC4751268 DOI: 10.3389/fmicb.2016.00100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. This analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.
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Affiliation(s)
- Shuiquan Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Po Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Steven A Higgins
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Frank E Löffler
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA; Department of Civil and Environmental Engineering, University of TennesseeKnoxville, TN, USA
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
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Sun W, Li Y, McGuinness LR, Luo S, Huang W, Kerkhof LJ, Mack EE, Häggblom MM, Fennell DE. Identification of Anaerobic Aniline-Degrading Bacteria at a Contaminated Industrial Site. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11079-11088. [PMID: 26280684 DOI: 10.1021/acs.est.5b02166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Anaerobic aniline biodegradation was investigated under different electron-accepting conditions using contaminated canal and groundwater aquifer sediments from an industrial site. Aniline loss was observed in nitrate- and sulfate-amended microcosms and in microcosms established to promote methanogenic conditions. Lag times of 37 days (sulfate amended) to more than 100 days (methanogenic) were observed prior to activity. Time-series DNA-stable isotope probing (SIP) was used to identify bacteria that incorporated (13)C-labeled aniline in the microcosms established to promote methanogenic conditions. In microcosms from heavily contaminated aquifer sediments, a phylotype with 92.7% sequence similarity to Ignavibacterium album was identified as a dominant aniline degrader as indicated by incorporation of (13)C-aniline into its DNA. In microcosms from contaminated canal sediments, a bacterial phylotype within the family Anaerolineaceae, but without a match to any known genus, demonstrated the assimilation of (13)C-aniline. Acidovorax spp. were also identified as putative aniline degraders in both of these two treatments, indicating that these species were present and active in both the canal and aquifer sediments. There were multiple bacterial phylotypes associated with anaerobic degradation of aniline at this complex industrial site, which suggests that anaerobic transformation of aniline is an important process at the site. Furthermore, the aniline degrading phylotypes identified in the current study are not related to any known aniline-degrading bacteria. The identification of novel putative aniline degraders expands current knowledge regarding the potential fate of aniline under anaerobic conditions.
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Affiliation(s)
- Weimin Sun
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Yun Li
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | | | - Shuai Luo
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | | | - E Erin Mack
- DuPont, Corporate Remediation Group, Wilmington, Delaware 19714, United States
| | | | - Donna E Fennell
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
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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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Zhou X, Zhang C, Zhang D, Awata T, Xiao Z, Yang Q, Katayama A. Polyphasic characterization of an anaerobic hexachlorobenzene-dechlorinating microbial consortium with a wide dechlorination spectrum for chlorobenzenes. J Biosci Bioeng 2015; 120:62-8. [PMID: 25795569 DOI: 10.1016/j.jbiosc.2014.11.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/23/2014] [Accepted: 11/28/2014] [Indexed: 10/23/2022]
Abstract
An anaerobic consortium that was capable of reductively dechlorinating hexachlorobenzene (HCB) to benzene was enriched from contaminated sediment. The consortium was capable of dechlorinating all chlorobenzene isomers except 1,4-dichlorobenzene. Singly and doubly flanked chlorines, as well as unflanked meta-substituted chlorines, were dechlorinated, although doubly flanked chlorines were preferred. Formate, acetate and lactate (but not ethanol) could be utilized as optimum electron donors for reductive dechlorination. Alternative electron acceptors, including nitrate and sulfate, completely inhibited HCB degradation, whereas amorphous iron oxide (FeOOH) did not suppress dechlorination activity. No degradation was found in chloramphenicol-treated consortium; however, vancomycin, molybdate, and 2-bromoethanesulfonate did not inhibit HCB dechlorination. The results of inhibitory treatments suggested that the dechlorinators were non-sulfate-reducing gram-negative or vancomycin resistant gram-positive bacteria. In addition to physiological characterization, analyses of 16S rRNA gene library of the consortium and quantitative PCR of 16S rRNA genes suggested that Dehalococcoides sp. was involved in the reductive dechlorination of HCB, and Geobacter sp. may serve as a dechlorinating candidate.
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Affiliation(s)
- Xue Zhou
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8603, Japan
| | - Chunfang Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Hangzhou 310058, China; EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Dongdong Zhang
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Takanori Awata
- EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan; Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Zhixing Xiao
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Qi Yang
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Arata Katayama
- Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8603, Japan; EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan; Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
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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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Sun G, Zhang X, Hu Q, Zhang H, Zhang D, Li G. Biodegradation of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs) with plant and nutrients and their effects on the microbial ecological kinetics. MICROBIAL ECOLOGY 2015; 69:281-92. [PMID: 25213654 DOI: 10.1007/s00248-014-0489-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/29/2014] [Indexed: 05/17/2023]
Abstract
Four pilot-scale test mesocosms were conducted for the remediation of organochlorine pesticides (OCPs)-contaminated aged soil. The results indicate that the effects on degradation of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) were in the following order: nutrients/plant bioaugmentation (81.18 % for HCHs; 85.4 % for DDTs) > nutrients bioaugmentation > plant bioaugmentation > only adding water > control, and nutrients/plant bioaugmentation greatly enhanced the degradation of HCHs (81.18 %) and DDTs (85.4 %). The bacterial community structure, diversity and composition were assessed by 454-pyrosequencing of 16S recombinant RNA (rRNA), whereas the abundance of linA gene was determined by quantitative polymerase chain reaction. Distinct differences in bacterial community composition, structure, and diversity were a function of remediation procedure. Predictability of HCH/DDT degradation in soils was also investigated. A positive correlation between linA gene abundance and the removal ratio of HCHs was indicated by correlation analyses. A similar relationship was also confirmed between the degradation of HCHs/DDTs and the abundance of some assemblages (Gammaproteobacteria and Flavobacteria). Our results offer microbial ecological insight into the degradation of HCHs and DDTs in aged contaminated soil, which is helpful for the intensification of bioremediation through modifying plant-microbe patterns, and cessation of costly and time-consuming assays.
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Affiliation(s)
- Guangdong Sun
- State Key Laboratory of Environmental Simulation and Pollution Control, School of Environmental Science, Tsinghua University, 100084, Beijing, China,
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Diversity of dechlorination pathways and organohalide respiring bacteria in chlorobenzene dechlorinating enrichment cultures originating from river sludge. Biodegradation 2014; 25:757-76. [DOI: 10.1007/s10532-014-9697-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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Zhang D, Zhang C, Li Z, Suzuki D, Komatsu DD, Tsunogai U, Katayama A. Electrochemical stimulation of microbial reductive dechlorination of pentachlorophenol using solid-state redox mediator (humin) immobilization. BIORESOURCE TECHNOLOGY 2014; 164:232-240. [PMID: 24859215 DOI: 10.1016/j.biortech.2014.04.071] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/13/2014] [Accepted: 04/21/2014] [Indexed: 06/03/2023]
Abstract
Immobilized solid-phase humin on a graphite electrode set at -500 mV (vs. standard hydrogen electrode) significantly enhanced the microbial reductive dechlorination of pentachlorophenol as a stable solid-phase redox mediator in bioelectrochemical systems (BESs). Compared with the suspended system, the immobilized system dechlorinated PCP at a much higher efficiency, achieving 116 μmol Cl(-)g(-1) humin d(-1). Fluorescence microscopy showed a conspicuous growth of bacteria on the negatively poised immobilized humin. Electron balance analyses suggested that the electrons required for microbial dechlorination were supplied primarily from the humin-immobilized electrode. Microbial community analyses based on 16S rRNA genes showed that Dehalobacter and Desulfovibrio grew on the immobilized humin as potential dechlorinators. These findings extend the potential of BESs using immobilized solid-phase humin as the redox mediator for in situ bioremediation, given the wide distribution of humin and its efficiency and stability as a mediator.
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Affiliation(s)
- Dongdong Zhang
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Chunfang Zhang
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Zhiling Li
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Daisuke Suzuki
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Daisuke D Komatsu
- Graduate School of Environmental Studies, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Urumu Tsunogai
- Graduate School of Environmental Studies, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Arata Katayama
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan; EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan.
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Zhang C, Zhang D, Li Z, Akatsuka T, Yang S, Suzuki D, Katayama A. Insoluble Fe-humic acid complex as a solid-phase electron mediator for microbial reductive dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6318-25. [PMID: 24758743 DOI: 10.1021/es501056n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report that the insoluble Fe-HA complex, which was synthesized with both commercial Aldrich humic acid (HA) and natural HA, functions as a solid-phase electron mediator (EM) for the anaerobic microbial dechlorination of pentachlorophenol. Spectroscopic characterizations and sequential Fe extraction demonstrated that the Fe-HA complex was predominated with Na4P2O7-labile Fe (represented as the organically bound Fe fraction) and poorly ordered Fe fraction (the fraction left in the residue after the sequential extraction), which were associated with different possible binding processes with carboxylate and phenolic groups. The change in the electron-mediating activity caused by Fe extraction indicated that the electron-mediating function of the Fe-HA complex is attributable to the Na4P2O7-labile Fe fraction. The Fe-HA complex also accelerated the microbial reduction of Fe(III) oxide, which suggested the presence of multiple electron-mediating functions in the complex. The electron shuttle assay showed that the Fe-HA complex had an electron-accepting capacity of 0.82 mequiv g(-1) dry Fe-HA complex. The presence of redox-active moieties in the Fe-HA complex was verified by cyclic voltammetry analysis of the sample after electrical reduction, with a redox potential estimated at 0.02 V (vs a standard hydrogen electrode).
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Affiliation(s)
- Chunfang Zhang
- Graduate School of Engineering, Nagoya University , Chikusa, Nagoya, Aichi 464-8603, Japan
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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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Liang X, Mundle SOC, Nelson JL, Passeport E, Chan CCH, Lacrampe-Couloume G, Zinder SH, Sherwood Lollar B. Distinct carbon isotope fractionation during anaerobic degradation of dichlorobenzene isomers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:4844-4851. [PMID: 24758692 DOI: 10.1021/es4054384] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Chlorinated benzenes are ubiquitous organic contaminants found in groundwater and soils. Compound specific isotope analysis (CSIA) has been increasingly used to assess natural attenuation of chlorinated contaminants, in which anaerobic reductive dechlorination plays an essential role. In this work, carbon isotope fractionation of the three dichlorobenzene (DCB) isomers was investigated during anaerobic reductive dehalogenation in methanogenic laboratory microcosms. Large isotope fractionation of 1,3-DCB and 1,4-DCB was observed while only a small isotope effect occurred for 1,2-DCB. Bulk enrichment factors (εbulk) were determined from a Rayleigh model: -0.8 ± 0.1 ‰ for 1,2-DCB, -5.4 ± 0.4 ‰ for 1,3-DCB, and -6.3 ± 0.2 ‰ for 1,4-DCB. εbulk values were converted to apparent kinetic isotope effects for carbon (AKIE) in order to characterize the carbon isotope effect at the reactive positions for the DCB isomers. AKIE values are 1.005 ± 0.001, 1.034 ± 0.003, and 1.039 ± 0.001 for 1,2-DCB, 1,3-DCB, and 1,4-DCB, respectively. The large difference in AKIE values between 1,2-DCB and 1,3-DCB (or 1,4-DCB) suggests distinct reaction pathways may be involved for different DCB isomers during microbial reductive dechlorination by the methanogenic cultures.
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Affiliation(s)
- Xiaoming Liang
- Department of Earth Sciences, University of Toronto , Toronto, Ontario M5S 3B1, Canada
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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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Involvement of Dehalobacter strains in the anaerobic dechlorination of 2,4,6-trichlorophenol. J Biosci Bioeng 2013; 116:602-9. [DOI: 10.1016/j.jbiosc.2013.05.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/28/2013] [Accepted: 05/07/2013] [Indexed: 11/19/2022]
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Fullerton H, Crawford M, Bakenne A, Freedman DL, Zinder SH. Anaerobic oxidation of ethene coupled to sulfate reduction in microcosms and enrichment cultures. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:12374-12381. [PMID: 24033278 DOI: 10.1021/es4029765] [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
Ethene is considered recalcitrant under anaerobic conditions, but biological reduction to ethane and oxidation to CO2 have been reported; however, little is known about these processes or the organisms carrying them out. In this report we describe sulfate dependent ethene consumption in microcosms prepared with sediments from a freshwater canal. A first dose of 0.6 mmol/L ethene was consumed within 77 days, and a second dose was largely consumed twelve days later. Material from this microcosm was transferred into growth medium with ethene as the only electron donor (except for trace amounts of vitamins) and sulfate as the electron acceptor. Four doses of ethene were consumed at increasing rates, and the cultures have been transferred at least eight times in this medium. Conversion of [(14)C]ethene primarily to (14)CO2 was demonstrated in fifth and sixth generation cultures, as well as production of sulfide in other cultures, confirming the ethene/sulfate couple. Ovoid cells 1-2 μm in diameter were found in cultures containing ethene and sulfate, and quantitative PCR showed large increases in bacterial 16S rRNA gene copy number. Over half of a 16S rRNA gene clone library from a sixth-generation culture was a phylotype with a sequence ca. 90% identical with a clade of Deltaproteobacteria that includes Desulfovirga adipica and several Syntrophobacter spp. These studies have solidified the concept that deficits in mass balances for chloroethene fate in sulfate reducing zones of contaminated groundwater sites may be due to ethene oxidation, and suggest a unique phylotype is involved in this process.
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Affiliation(s)
- Heather Fullerton
- Department of Microbiology, Cornell University , Ithaca, New York 14853, United States
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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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Zhang C, Li Z, Suzuki D, Ye L, Yoshida N, Katayama A. A humin-dependent Dehalobacter species is involved in reductive debromination of tetrabromobisphenol A. CHEMOSPHERE 2013; 92:1343-1348. [PMID: 23769323 DOI: 10.1016/j.chemosphere.2013.05.051] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/19/2013] [Accepted: 05/20/2013] [Indexed: 06/02/2023]
Abstract
Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant on the market. It has been detected in various environmental samples, and a growing body of evidence has demonstrated its toxic effects on living organisms. In this study, we report the enrichment and phylogenetic identification of bacteria that debrominate TBBPA to bisphenol A in the presence of humin. Incubation experiments indicated that humin was required for this debromination activity. Of the five compounds examined for inclusion in the TBBPA-debrominating culture, formate was the optimal electron donor. A 16S rRNA gene library showed that the culture was dominated by three known dehalogenator genera: Dehalobacter, Geobacter, and Sulfurospirillum. Further investigation indicated that Dehalobacter was responsible for the debromination of TBBPA. PCR-denaturing gradient gel electrophoresis analysis showed that Dehalobacter grew in the culture by utilizing TBBPA. Moreover, the copy number of the Dehalobacter 16S rRNA genes increased by about two orders of magnitude in the cultures without the addition of TBBPA, whereas it increased by approximately four orders of magnitude when TBBPA was present. The incubation experiments showed that Dehalobacter was reliant on humin for its debromination activity, indicating a new type of metabolism in Dehalobacter that is linked to humin respiration.
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Affiliation(s)
- Chunfang Zhang
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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48
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Richardson RE. Genomic insights into organohalide respiration. Curr Opin Biotechnol 2013; 24:498-505. [DOI: 10.1016/j.copbio.2013.02.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 12/14/2022]
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49
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Tang S, Edwards EA. Identification of Dehalobacter reductive dehalogenases that catalyse dechlorination of chloroform, 1,1,1-trichloroethane and 1,1-dichloroethane. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120318. [PMID: 23479748 DOI: 10.1098/rstb.2012.0318] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two novel reductive dehalogenases (RDases) that are highly similar to each other but catalyse distinct dechlorination reactions were identified from Dehalobacter-containing mixed cultures. These two RDases were partially purified from crude protein extracts of anaerobic dechlorinating enrichment cultures using blue native polyacrylamide gel electrophoresis. Gel slices were assayed for dechlorinating activity, and associated proteins were identified using liquid chromatography tandem mass spectrometry with the metagenome of the parent culture as the reference database. The two RDases identified, annotated as CfrA and DcrA, share an amino acid identity of 95.2 per cent, but use different substrates: CfrA dechlorinates chloroform (CF) and 1,1,1-trichloroethane (1,1,1-TCA), but not 1,1-dichloroethane; DcrA dechlorinates 1,1-dichloroethane, but not CF or 1,1,1-TCA. These two novel RDases share no more than 40 per cent amino acid identity to any other known or putative RDases, but both have a twin-arginine motif and two iron-sulfur binding motifs conserved in most RDases. Peptides specific to two putative membrane anchor proteins, annotated as CfrB and DcrB, were also detected in gel slices.
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Affiliation(s)
- Shuiquan Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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50
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Rupakula A, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J. The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120325. [PMID: 23479754 DOI: 10.1098/rstb.2012.0325] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Dehalobacter restrictus strain PER-K23 is an obligate organohalide respiring bacterium, which displays extremely narrow metabolic capabilities. It grows only via coupling energy conservation to anaerobic respiration of tetra- and trichloroethene with hydrogen as sole electron donor. Dehalobacter restrictus represents the paradigmatic member of the genus Dehalobacter, which in recent years has turned out to be a major player in the bioremediation of an increasing number of organohalides, both in situ and in laboratory studies. The recent elucidation of the D. restrictus genome revealed a rather elaborate genome with predicted pathways that were not suspected from its restricted metabolism, such as a complete corrinoid biosynthetic pathway, the Wood-Ljungdahl (WL) pathway for CO2 fixation, abundant transcriptional regulators and several types of hydrogenases. However, one important feature of the genome is the presence of 25 reductive dehalogenase genes, from which so far only one, pceA, has been characterized on genetic and biochemical levels. This study describes a multi-level functional genomics approach on D. restrictus across three different growth phases. A global proteomic analysis allowed consideration of general metabolic pathways relevant to organohalide respiration, whereas the dedicated genomic and transcriptomic analysis focused on the diversity, composition and expression of genes associated with reductive dehalogenases.
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Affiliation(s)
- Aamani Rupakula
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, 1015 Lausanne, Switzerland
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