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Xu Y, Teng Y, Wang X, Wang H, Li Y, Ren W, Zhao L, Wei M, Luo Y. Biohydrogen utilization in legume-rhizobium symbiosis reveals a novel mechanism of accelerated tetrachlorobiphenyl transformation. BIORESOURCE TECHNOLOGY 2024; 404:130918. [PMID: 38823562 DOI: 10.1016/j.biortech.2024.130918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/03/2024]
Abstract
Symbiosis between Glycine max and Bradyrhizobium diazoefficiens were used as a model system to investigate whether biohydrogen utilization promotes the transformation of the tetrachlorobiphenyl PCB77. Both a H2 uptake-positive (Hup+) strain (wild type) and a Hup- strain (a hupL deletion mutant) were inoculated into soybean nodules. Compared with Hup- nodules, Hup+ nodules increased dechlorination significantly by 61.1 % and reduced the accumulation of PCB77 in nodules by 37.7 % (p < 0.05). After exposure to nickel, an enhancer of uptake hydrogenase, dechlorination increased significantly by 2.2-fold, and the accumulation of PCB77 in nodules decreased by 54.4 % (p < 0.05). Furthermore, the tetrachlorobiphenyl transformation in the soybean root nodules was mainly testified to be mediated by nitrate reductase (encoded by the gene NR) for tetrachlorobiphenyl dechlorination and biphenyl-2,3-diol 1,2-dioxygenase (bphC) for biphenyl degradation. This study demonstrates for the first time that biohydrogen utilization has a beneficial effect on tetrachlorobiphenyl biotransformation in a legume-rhizobium symbiosis.
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Affiliation(s)
- Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongzhe Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanning Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Li Q, Cui Y, Wang Z, Li Y, Yang H. Toxicity assessment of dioxins and their transformation by-products from inferred degradation pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 937:173416. [PMID: 38795989 DOI: 10.1016/j.scitotenv.2024.173416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024]
Abstract
Due to the significant POPs characteristics, dioxins caused concern in public health and environmental protection. Evaluating the toxicity risk of dioxin degradation pathways is critical. OCDD, 1,2,3,4,6,7,8-HpCDD, and 1,2,3,4,6,7,8-HpCDF, which are highly abundant in the environment and have strong biodegradation capabilities, were selected as precursor molecules in this study. Firstly, their transformation pathways were deduced during the metabolism of biometabolism, microbial aerobic, microbial anaerobic, and photodegradation pathways, and density function theory (DFT) was used to calculate the Gibbs free energy to infer the possibility of the occurrence of the transformation pathway. Secondly, the carcinogenic potential of the precursors and their degradation products was evaluated using the TOPKAT modeling method. With the help of the positive indicator (0-1) normalization method and heat map analysis, a significant increase in the toxic effect of some of the transformation products was found, and it was inferred that it was related to the structure of the transformation products. Meanwhile, the strength of the endocrine disrupting effect of dioxin transformation products was quantitatively assessed using molecular docking and subjective assignment methods, and it was found that dioxin transformation products with a higher content of chlorine atoms and molecules similar to those of thyroid hormones exhibited a higher risk of endocrine disruption. Finally, the environmental health risks caused by each degradation pathway were comprehensively assessed with the help of the negative indicator (1-2) standardization method, which provides a theoretical basis for avoiding the toxicity risks caused by dioxin degradation transformation. In addition, the 3D-QSAR model was used to verify the necessity and rationality of this study. This paper provides theoretical support and reference significance for the toxicity assessment of dioxin degradation by-products from inferred degradation pathways.
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Affiliation(s)
- Qing Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
| | - Yuhan Cui
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
| | - Zhonghe Wang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Hao Yang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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3
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Li Q, Yang H, Hao N, Du M, Zhao Y, Li Y, Li X. Biodegradability analysis of Dioxins through in silico methods: Model construction and mechanism analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118898. [PMID: 37657295 DOI: 10.1016/j.jenvman.2023.118898] [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: 06/04/2023] [Revised: 08/18/2023] [Accepted: 08/27/2023] [Indexed: 09/03/2023]
Abstract
The biodegradation treatment of dioxins has long been of interest due to its good ecological and economic effects. In this study, the biodegradability of polychlorinated dibenzo-p-dioxins (PCDDs) were investigated by constructing machine learning and multiple linear regression models. The maximum chlorine atomic charge (qHirshfeldCl+), which characterizes the biodegradation ability of PCDDs, was used as the response value. The random forest model was used to rank the importance on the 1471 descriptors of PCDDs, and the BCUTp-1 h, QXZ, JGI4, ATSC8c, VE3_Dt, topoShape, and maxwHBa were screened as the important descriptors by Pearson's correlation coefficient method. A quantitative structure-activity relationship (QSAR) model was constructed to predict the biodegradability of PCDDs. In addition, the extreme gradient boosting (XGBoost) and random forest model were also constructed and proved the good predictability of QSAR model. The biodegradability of polychlorinated dibenzofurans (PCDFs) can also be predicted by the constructed three models from a certain level after adjusting some model parameters, which further proved the versatility of the models. Besides, the sensitivity analysis of the QSAR model and a 3D-QSAR model was developed to investigate the biodegradability mechanisms of PCDDs. Results showed that the descriptors BCUTp-1 h, JGI4, and maxwHBa were the key descriptors in the biodegradability effect by the sensitivity analysis of the QSAR model. Coupled with the results of PCDDs biodegradability 3D-QSAR model, BCUTp-1 h, JGI4, and maxwHBa were confirmed as the main descriptors that affect the biodegradability of dioxins. This study provides a novel theoretical perspective for the research of the biodegradation of both PCDDs and PCDFs dioxins.
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Affiliation(s)
- Qing Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Hao Yang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Ning Hao
- College of New Energy and Environment, Jilin University, Changchun, 130012, China.
| | - Meijn Du
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Yuanyuan Zhao
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Xixi Li
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
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Kumar M, Saggu SK, Pratibha P, Singh SK, Kumar S. Exploring the role of microbes for the management of persistent organic pollutants. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118492. [PMID: 37384989 DOI: 10.1016/j.jenvman.2023.118492] [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: 02/16/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Persistent organic pollutants (POPs) are chemicals which have been persisting in the environment for many years due to their longer half-lives. POPs have gained attention over the last few decades due to the unsustainable management of chemicals which led to their widespread and massive contamination of biota from different strata and environments. Due to the widespread distribution, bio-accumulation and toxic behavior, POPs have become a risk for organisms and environment. Therefore, a focus is required to eliminate these chemicals from the environment or transform into non-toxic forms. Among the available techniques for the removal of POPs, most of them are inefficient or incur high operational costs. As an alternative to this, microbial bioremediation of POPs such as pesticides, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, pharmaceuticals and personal care products is much more efficient and cost-effective. Additionally, bacteria play a vital role in the biotransformation and solubilization of POPs, which reduces their toxicity. This review specifies the Stockholm Convention that evaluates the risk profile for the management of existing as well as emerging POPs. The sources, types and persistence of POPs along with the comparison of conventional elimination and bioremediation methods of POPs are discussed comprehensively. This study demonstrates the existing bioremediation techniques of POPs and summaries the potential of microbes which serve as enhanced, cost-effective, and eco-friendly approach for POPs elimination.
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Affiliation(s)
- Manoj Kumar
- School of Allied and Healthcare Sciences, GNA University, Phagwara, Punjab, 144401, India
| | - Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, 144004, India
| | - Pritu Pratibha
- Center for Excellence in Molecular Plant Science, Plant Stress Center, CAS, Shanghai, 201602, China
| | - Sunil Kumar Singh
- Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, 211002, India.
| | - Shiv Kumar
- Department of Microbiology, Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab, 151203, India.
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Li T, Lu Y, Liu L, He Y, Huang J, Peng X. Efficient degradation of hexabromocyclododecane using montmorillonite supported nano-zero-valent iron and Citrobacter sp. Y3. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131739. [PMID: 37269562 DOI: 10.1016/j.jhazmat.2023.131739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/05/2023]
Abstract
The coupling of modified nanoscale zero-valent iron (nZVI) with organohalide-degrading bacteria provides a promising solution for the remediation of hexabromocyclododecane (HBCD)-contaminated environments. However, the interactions between modified nZVI and dehalogenase bacteria are intricate, and the mechanisms of synergistic action and electron transfer are not clear, and requires further specific investigation. In this study, HBCD was used as a model pollutant, and stable isotope analysis revealed that organic montmorillonite (OMt)-supported nZVI coupled with the degrading bacterial strain Citrobacter sp. Y3 (nZVI/OMt-Y3) can use [13C]HBCD as the sole carbon source and degrade or even mineralise it into 13CO2 with a maximum conversion rate of 100% within approximately 5 days. Analysis of the intermediates showed that the degradation of HBCD mainly involves three different pathways: dehydrobromination, hydroxylation, and debromination. The proteomics results showed that nZVI introduction promoted the transport of electrons and debromination. Combining the results from XPS, FTIR, and Raman spectroscopy with the analysis results of proteinomics and biodegradation products, we verified the process of electron transport and proposed a metabolic mechanism of HBCD degradation by the nZVI/OMt-Y3. Moreover, this study provides insightful avenues and models for the further remediation of HBCD and other similar pollutants in the environment.
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Affiliation(s)
- Tianyu Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingyuan Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Lei Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuzhe He
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingfei Huang
- College of Plant Protection, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China.
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China.
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Dutta N, Usman M, Ashraf MA, Luo G, Zhang S. A critical review of recent advances in the bio-remediation of chlorinated substances by microbial dechlorinators. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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7
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Aravind Kumar J, Krithiga T, Sathish S, Renita AA, Prabu D, Lokesh S, Geetha R, Namasivayam SKR, Sillanpaa M. Persistent organic pollutants in water resources: Fate, occurrence, characterization and risk analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154808. [PMID: 35341870 DOI: 10.1016/j.scitotenv.2022.154808] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Persistent organic pollutants (POPs) are organic chemicals that can persist in the environment for a longer period due to their non-biodegradability. The pervasive and bio-accumulative behavior of POPs makes them highly toxic to the environmental species including plants, animals, and humans. The present review specifies the POP along with their fate, persistence, occurrence, and risk analysis towards humans. The different biological POPs degradation methods, especially the microbial degradation using bacteria, fungi, algae, and actinomycetes, and their mechanisms were described. Moreover, the source, transport of POPs to the environmental sources, and the toxic nature of POPs were discussed in detail. Agricultural and industrial activities are distinguished as the primary source of these toxic compounds, which are delivered to air, soil, and water, affecting on the social and economic advancement of society at a worldwide scale. This review also demonstrated the microbial degradation of POPs and outlines the potential for an eco-accommodating and cost-effective approach for the biological remediation of POPs using microbes. The direction for future research in eliminating POPs from the environmental sources through various microbial processes was emphasized.
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Affiliation(s)
- J Aravind Kumar
- Department of Biomass and Energy Conversion, Saveetha School of Engineering, SIMATS, Chennai, 602105, India.
| | - T Krithiga
- Department of Chemistry, Sathyabama Institute of Science and Technology, Chennai - 600119, India
| | - S Sathish
- Department of Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai - 600119, India
| | - A Annam Renita
- Department of Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai - 600119, India.
| | - D Prabu
- Department of Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai - 600119, India
| | - S Lokesh
- Department of Biomass and Energy Conversion, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - R Geetha
- Department of Instrumentation and Control Engineering, Saveetha School of Engineering, SIMATS, Chennai, India
| | - S Karthick Raja Namasivayam
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - Mika Sillanpaa
- Department of Chemical Engineering, School of Mining, Metallurgy and Chemical Engineering, University of Johannesburg, P. O. Box 17011, Doornfontein 2028, South Africa; Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; International Research Centre of Nanotechnology for Himalayan Sustainability (IRCNHS), Shoolini University, Solan, 173212, Himachal Pradesh, India
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8
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Underwood JC, Akob DM, Lorah MM, Imbrigiotta TE, Harvey RW, Tiedeman CR. Microbial Community Response to a Bioaugmentation Test to Degrade Trichloroethylene in a Fractured Rock Aquifer, Trenton, N.J. FEMS Microbiol Ecol 2022; 98:6617591. [PMID: 35749571 DOI: 10.1093/femsec/fiac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/12/2022] [Accepted: 06/22/2022] [Indexed: 11/12/2022] Open
Abstract
Bioaugmentation is a promising strategy for enhancing trichloroethylene (TCE) degradation in fractured rock. However, slow or incomplete biodegradation can lead to stalling at degradation byproducts such as 1,2-dichloroethene (cis-DCE) and vinyl chloride (VC). Over the course of 7 years, we examined the response of groundwater microbial populations in a bioaugmentation test where an emulsified vegetable oil solution (EOS®) and a dechlorinating consortium (KB-1®), containing the established dechlorinator Dehalococcoides, were injected into a TCE-contaminated fractured rock aquifer. Indigenous microbial communities responded within 2 days to added substrate and outcompeted KB-1®, and over the years of monitoring, several other notable turnover events were observed. Concentrations of ethene, the end product in reductive dechlorination, had the strongest correlations (p< 0.05) with members of Candidatus Colwellbacteria but their involvement in reductive dechlorination is unknown and warrants further investigation. Dehalococcoides never exceeded 0.6% relative abundance of groundwater microbial communities, despite its previously presumed importance at the site. Increased concentrations of carbon dioxide, acetic acid, and methane were positively correlated with increasing ethene concentrations; however, concentrations of cis-DCE and VC remained high by the end of the monitoring period suggesting preferential enrichment of indigenous partial dechlorinators over bioaugmented complete dechlorinators. This study highlights the importance of characterizing in situ microbial populations to understand how they can potentially enhance or inhibit augmented TCE degradation.
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Affiliation(s)
- J C Underwood
- U.S. Geological Survey, Water Mission Area, Boulder CO 80303USA
| | - D M Akob
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, 12201 Sunrise Valley Drive, Mailstop 954, Reston, VA 20192USA
| | - M M Lorah
- U.S. Geological Survey, MD-DE-DC Water Science Center, 5522 Research Park Drive, Baltimore, MD 21228USA
| | - T E Imbrigiotta
- U.S. Geological Survey, New Jersey Water Science Center, 3450 Princeton Pike, Suite 110, Lawrenceville, NJ 08648USA
| | - R W Harvey
- U.S. Geological Survey, Water Mission Area, Boulder CO 80303USA
| | - C R Tiedeman
- U.S. Geological Survey, Water Mission Area, Menlo Park, CA 94025USA
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Lee M, Liang G, Holland SI, O'Farrell C, Osborne K, Manefield MJ. Dehalobium species implicated in 2,3,7,8-tetrachlorodibenzo-p-dioxin dechlorination in the contaminated sediments of Sydney Harbour Estuary. MARINE POLLUTION BULLETIN 2022; 179:113690. [PMID: 35504213 DOI: 10.1016/j.marpolbul.2022.113690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Polychlorinated dibenzo-p-dioxins and furans (PCDD/F) are some of the most environmentally recalcitrant and toxic compounds. They occur naturally and as by-products of anthropogenic activity. Sydney Harbour Estuary (Sydney, Australia), is heavily contaminated with PCDD/F. Analysis of sediment cores revealed that the contamination source area in Homebush Bay continues to have one of the highest levels of PCDD/F contamination in the world (5207 pg WHO-TEQ g-1) with >50% of the toxicity attributed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), the most toxic PCDD/F congener. Comparison of congener profiles at the contamination source area with surrounding bays and historical data provided evidence for the attenuation of 2,3,7,8-TCDD and other congeners at the source area. This finding was supported by the detection of di-, mono- and unchlorinated dibenzo-p-dioxin. Microbial community analysis of sediments by 16S rRNA amplicon sequencing revealed an abundance of lineages from the class Dehalococcoidia (up to 15% of the community), including the genus Dehalobium (up to 0.5%). Anaerobic seawater enrichment cultures using perchloroethene as more biologically available growth substrate enriched the Dehalobium population by more than six-fold. The enrichment culture then proved capable of reductively dechlorinating 2,3,7,8-TCDD to 2,3,7-TriCDD and octachlorodibenzo-p-dibenzodioxin (OCDD) to hepta and hexa congeners. This work is the first to show microbial reductive dehalogenation of 2,3,7,8-TCDD with a bacterium from outside the Dehalococcoides genus, and one of only a few that demonstrates PCDD/F dechlorination in a marine environment.
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Affiliation(s)
- Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia.
| | - Gan Liang
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Sophie I Holland
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | | | - Keith Osborne
- New South Wales Department of Planning and Environment, Lidcombe, NSW 2141, Australia
| | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
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A Review of Soil Contaminated with Dioxins and Biodegradation Technologies: Current Status and Future Prospects. TOXICS 2022; 10:toxics10060278. [PMID: 35736887 PMCID: PMC9227754 DOI: 10.3390/toxics10060278] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022]
Abstract
This article provides a comprehensive assessment of dioxins contaminating the soil and evaluates the bioremediation technology currently being widely used, and also offers recommendations for future prospects. Soil pollution containing dioxins is extremely toxic and hazardous to human health and the environment. Dioxin concentrations in soils around the world are caused by a variety of sources and outcomes, but the main sources are from the consequences of war and human activities. Bioremediation technology (bioaugmentation, biostimulation, and phytoremediation) is considered an optimal and environmentally friendly technology, with the goal of applying native microbial communities and using plant species with a high biomass to treat contaminated dioxins in soil. The powerful bioremediation system is the growth of microorganisms that contribute to the increased mutualistic and competitive relationships between different strains of microorganisms. Although biological treatment technology can thoroughly treat contaminated dioxins in soil with high efficiency, the amount of gas generated and Cl radicals dispersed after the treatment process remains high. Further research on the subject is required to provide stricter control over the outputs noted in this study.
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11
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Zhang S, Li Y, Wang S. Microbial reductive dechlorination of polychlorinated dibenzo-p-dioxins: Pathways and features unravelled via electron density. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127673. [PMID: 34776298 DOI: 10.1016/j.jhazmat.2021.127673] [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: 09/12/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Microbial reductive dechlorination provides a promising approach for remediating sites contaminated with polychlorinated dibenzo-p-dioxins (PCDDs). Nonetheless, the overall dechlorination pathways and features remain elusive. Herein, we address these issues by quantum chemical calculations, considering the calibrations of reductive dechlorination of 15 PCDDs mediated by three Dehalococcoides strains. Chlorine substituents with lower electron density are prone to be microbially abstracted, which differentiates 72 microbe-active PCDDs from 3 nonactive analogues with a success rate of 100%. For all 256 transformation routes of 75 PCDDs, electron density differences of chlorines pinpoint 105 viable and 125 unviable pathways, corresponding a success rate of 90%. The feasibility of 26 reductive dechlorination pathways are uncertain because of the limited available experimental data. 98% (251/256) of microbial chlorine abstraction follows an order of ClO,Cl>ClCl,Cl>ClH,O>ClH,Cl>ClH,H=0. PCDDs solely containing chlorines at C1, C4, C6, and/or C9 can be completely dechlorinated to non-chlorinated dioxin; while PCDDs housing chlorines at C2, C3, C7, and/or C8 can be dechlorinated to 2-MCDD or 2,7/8-DCDD as final products. These findings also support reductive dechlorination of PCDDs in mixed cultures and sediments (> 98% and 83%). These findings would promote the application of dechlorinating bacteria in targeted remediation and facilitate the respective studies on other POPs.
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Affiliation(s)
- Shangwei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Yiyang Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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12
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Differentiating closely affiliated Dehalococcoides lineages by a novel genetic marker identified via computational pangenome analysis. Appl Environ Microbiol 2021; 88:e0218121. [PMID: 34910572 DOI: 10.1128/aem.02181-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a group, Dehalococcoides dehalogenate a wide range of organohalide pollutants but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among the Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences (in silico) and 10 different Dehalococcoides isolates (in vitro). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. Importance The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria. Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides, an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.
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Identification of Reductive Dehalogenases That Mediate Complete Debromination of Penta- and Tetrabrominated Diphenyl Ethers in Dehalococcoides spp. Appl Environ Microbiol 2021; 87:e0060221. [PMID: 34160266 DOI: 10.1128/aem.00602-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polybrominated diphenyl ethers (PBDEs) are persistent, highly toxic, and widely distributed environmental pollutants. The microbial populations and functional reductive dehalogenases (RDases) responsible for PBDE debromination in anoxic systems remain poorly understood, which confounds bioremediation of PBDE-contaminated sites. Here, we report a PBDE-debrominating enrichment culture dominated by a previously undescribed Dehalococcoides mccartyi population. A D. mccartyi strain, designated TZ50, whose genome contains 25 putative RDase-encoding genes, was isolated from the debrominating enrichment culture. Strain TZ50 dehalogenated a mixture of pentabrominated diphenyl ether (penta-BDE) and tetra-BDE congeners (total BDEs, 1.48 μM) to diphenyl ether within 2 weeks (0.58 μM Br-/day) via ortho- and meta-bromine elimination; strain TZ50 also dechlorinated tetrachloroethene (PCE) to vinyl chloride and ethene (260.2 μM Cl-/day). Results of native PAGE, proteomic profiling, and in vitro enzymatic activity assays implicated the involvement of three RDases in PBDE and PCE dehalogenation. TZ50_0172 (PteATZ50) and TZ50_1083 (TceATZ50) were responsible for the debromination of penta- and tetra-BDEs to di-BDE. TZ50_0172 and TZ50_1083 were also implicated in the dechlorination of PCE to trichloroethene (TCE) and of TCE to vinyl chloride/ethene, respectively. The other expressed RDase, TZ50_0090 (designated BdeA), was associated with the debromination of di-BDE to diphenyl ether, but its role in PCE dechlorination was unclear. Comparatively few RDases are known to be involved in PBDE debromination, and the identification of PteATZ50, TceATZ50, and BdeA provides additional information for evaluating debromination potential at contaminated sites. Moreover, the ability of PteATZ50 and TceATZ50 to dehalogenate both PBDEs and PCE makes strain TZ50 a suitable candidate for the remediation of cocontaminated sites. IMPORTANCE The ubiquity, toxicity, and persistence of polybrominated diphenyl ethers (PBDEs) in the environment have drawn significant public and scientific interest to the need for the remediation of PBDE-contaminated ecosystems. However, the low bioavailability of PBDEs in environmental compartments typically limits bioremediation of PBDEs and has long impeded the study of anaerobic microbial PBDE removal. In the current study, a novel Dehalococcoides mccartyi strain, dubbed strain TZ50, that expresses RDases that mediate organohalide respiration of both PBDEs and chloroethenes was isolated and characterized. Strain TZ50 could potentially be used to remediate multiple cooccurring organohalides in contaminated systems.
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Peng X, Lu Y, Wang Q, Yu L, Jia X, Wong PK, Qiu R. Kinetics, pathways and toxicity of hexabromocyclododecane biodegradation: Isolation of the novel bacterium Citrobacter sp. Y3. CHEMOSPHERE 2021; 274:129929. [PMID: 33979932 DOI: 10.1016/j.chemosphere.2021.129929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 01/18/2021] [Accepted: 02/06/2021] [Indexed: 06/12/2023]
Abstract
This research investigated the biodegradation kinetics, pathways and ecological risk of hexabromocyclododecane (HBCD) by a novel bacterium Citrobacter sp. Y3. Results showed the biodegradation followed a first-order model. The specific degradation rate constant of HBCD were obviously higher in batch experiments with combined carbon sources (k: 0.156-0.290 d-1) than those using HBCD as the sole carbon source (k: 0.055 d-1). Correspondingly, the degradation half-life became much shorter (T1/2: 2.39-4.44 d vs T1/2: 13.7 d). HBCD could be degraded through dehydrobromination and dehalohydroxylation, of which six possible degradation products were detected. To evaluate the ecological risk of HBCD biodegradation products, acute toxicity tests were assessed for the first time. The acute toxicity decreased slowly during treatment for 3-5 d and then decreased sharply. In general, treatment by Strain Y3 is not only a biodegradation process but also a detoxification process, thus it shows potential for bioremediation of HBCD contaminated sites.
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Affiliation(s)
- Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Yingyuan Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qi Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lan Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoshan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Po Keung Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China
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Qiu L, Zhang W, Gong A, Li J. Isolation and identification of a 2,3,7,8-Tetrachlorodibenzo-P-dioxin degrading strain and its biochemical degradation pathway. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2021; 19:541-551. [PMID: 34150257 PMCID: PMC8172717 DOI: 10.1007/s40201-021-00626-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
This study aims to find a high-efficiency degradation strain which can biodegrade the 2,3,7,8-Tetrachlorodibenzo-P-dioxin (2,3,7,8-TCDD). In this paper, a new fungus strain was isolated from activated sludge of Dagu Drainage River in Tianjin which was able to degrade 2,3,7,8-TCDD in the medium. Based on its morphology and phylogenetic analysis of its 18S rDNA sequence, the strain was identified as Penicillium sp. QI-1. Response surface methodology using central composite rotatable design of cultural conditions was successfully employed for optimization resulting in 87.9 % degradation of 2,3,7,8-TCDD (1 µg/mL) within 6 days. The optimum condition for degrading 2,3,7,8-TCDD was at 31℃ and pH 7.4. The biodegradation process was fitted to a first-order kinetic model. The kinetic equation was Ct=0.939e- 0.133t and its half-life was 5.21d. The fungus strain degraded 2,3,7,8-TCDD to form intermediates, they were 4,5-Dichloro-1,2-benzoquinone, 4,5-Dichlorocatechol, 2-Hydrooxy-1,4-benzoquinone, 1,2,4-Trihydroxybenzene and β-ketoadipic acid. A novel degradation pathway for 2,3,7,8-TCDD was proposed based on analysis of these metabolites. The results suggest that Penicillium sp. QI-1 may be an ideal microorganism for biodegradation of the 2,3,7,8-TCDD-contaminated environments.
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Affiliation(s)
- Lina Qiu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083 People’s Republic of China
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, University of Science and Technology Beijing, 100083 Beijing, China
| | - Weiwei Zhang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, University of Science and Technology Beijing, 100083 Beijing, China
- Basic Experimental Center for Natural Science, University of Science and Technology Beijing, Beijing, 100083 China
| | - Aijun Gong
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083 People’s Republic of China
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, University of Science and Technology Beijing, 100083 Beijing, China
| | - Jiandi Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083 People’s Republic of China
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Liang S, Xu S, Wang C, Ling J, Xian Z, Wu H, Tian H, Zhou S, Gu C. Enhanced alteration of poly(vinyl chloride) microplastics by hydrated electrons derived from indole-3-acetic acid assisted by a common cationic surfactant. WATER RESEARCH 2021; 191:116797. [PMID: 33422976 DOI: 10.1016/j.watres.2020.116797] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
In this study, a new photo-irradiated reductive dechlorination pathway and the underlying transformation mechanism are described for poly(vinyl chloride) microplastics (PVC-MPs). PVC-MPs underwent photo-reductive dechlorination process with the release of chloride ions. This reaction could be facilitated in the presence of indole-3-acetic acid (IAA) and hexadecyltrimethylammonium bromide (CTAB) under neutral pH and simulated sunlight irradiation conditions. Electrostatic interaction between IAA and CTAB produced neutral IAA/CTAB complex, which might account for the enhanced adsorption of IAA on PVC powders. Upon photo-irradiation, the adsorbed IAA was excited to generate hydrated electrons (eaq-), which could pass through a shorter distance to PVC-MP surface than that derived from homogeneous IAA molecules in aqueous solution. Transient spectra of laser flash photolysis provided direct evidence for the generation of eaq-, which supported the proposed dechlorination mechanism. Based on the results of attenuated total reflectance/Fourier transform infrared (ATR/FTIR) and Raman spectra, C-Cl bond cleavage and polyene formation were involved in the structural transformation of PVC-MPs. Due to the hydrophobic effects and π-π interactions between aromatic rings and polyene structures in PVC-MP surface, the PVC-MP powders irradiated in the presence of IAA/CTAB showed an enhanced sorption for both hydrophobic and hydrophilic aromatic chemicals.
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Affiliation(s)
- Sijia Liang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Shuxia Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Chao Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China.
| | - Jingyi Ling
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Zeyu Xian
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Hao Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
| | - Haoting Tian
- Shandong Provincial Key Laboratory of Water and Soil Conservation and Environmental Protection, College of Resource and Environment, Linyi University, Linyi 276005, PR China
| | - Shaoda Zhou
- Nanjing Kaver Scientific Instruments, Institute of Forestry Chemical Industry, China Academy of Forestry, Nanjing 210042, PR China
| | - Cheng Gu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, PR China
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Li Y, Wu S, Wang S, Zhao S, Zhuang X. Anaerobic degradation of xenobiotic organic contaminants (XOCs): The role of electron flow and potential enhancing strategies. J Environ Sci (China) 2021; 101:397-412. [PMID: 33334534 DOI: 10.1016/j.jes.2020.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 06/12/2023]
Abstract
In groundwater, deep soil layer, sediment, the widespread of xenobiotic organic contaminants (XOCs) have been leading to the concern of human health and eco-environment safety, which calls for a better understanding on the fate and remediation of XOCs in anoxic matrices. In the absence of oxygen, bacteria utilize various oxidized substances, e.g. nitrate, sulphate, metallic (hydr)oxides, humic substance, as terminal electron acceptors (TEAs) to fuel anaerobic XOCs degradation. Although there have been increasing anaerobic biodegradation studies focusing on species identification, degrading pathways, community dynamics, systematic reviews on the underlying mechanism of anaerobic contaminants removal from the perspective of electron flow are limited. In this review, we provide the insight on anaerobic biodegradation from electrons aspect - electron production, transport, and consumption. The mechanism of the coupling between TEAs reduction and pollutants degradation is deconstructed in the level of community, pure culture, and cellular biochemistry. Hereby, relevant strategies to promote anaerobic biodegradation are proposed for guiding to an efficient XOCs bioremediation.
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Affiliation(s)
- Yijing Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Sino-Danish Center, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Zhao
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Changes of the Proteome and Acetylome during Transition into the Stationary Phase in the Organohalide-Respiring Dehalococcoides mccartyi Strain CBDB1. Microorganisms 2021; 9:microorganisms9020365. [PMID: 33673241 PMCID: PMC7918482 DOI: 10.3390/microorganisms9020365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 11/17/2022] Open
Abstract
The strictly anaerobic bactGIerium Dehalococcoides mccartyi obligatorily depends on organohalide respiration for energy conservation and growth. The bacterium also plays an important role in bioremediation. Since there is no guarantee of a continuous supply of halogenated substrates in its natural environment, the question arises of how D. mccartyi maintains the synthesis and activity of dehalogenating enzymes under these conditions. Acetylation is a means by which energy-restricted microorganisms can modulate and maintain protein levels and their functionality. Here, we analyzed the proteome and Nε-lysine acetylome of D. mccartyi strain CBDB1 during growth with 1,2,3-trichlorobenzene as an electron acceptor. The high abundance of the membrane-localized organohalide respiration complex, consisting of the reductive dehalogenases CbrA and CbdbA80, the uptake hydrogenase HupLS, and the organohalide respiration-associated molybdoenzyme OmeA, was shown throughout growth. In addition, the number of acetylated proteins increased from 5% to 11% during the transition from the exponential to the stationary phase. Acetylation of the key proteins of central acetate metabolism and of CbrA, CbdbA80, and TatA, a component of the twin-arginine translocation machinery, suggests that acetylation might contribute to maintenance of the organohalide-respiring capacity of the bacterium during the stationary phase, thus providing a means of ensuring membrane protein integrity and a proton gradient.
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Min Y, Zhou X, Chen JJ, Chen W, Zhou F, Wang Z, Yang J, Xiong C, Wang Y, Li F, Yu HQ, Wu Y. Integrating single-cobalt-site and electric field of boron nitride in dechlorination electrocatalysts by bioinspired design. Nat Commun 2021; 12:303. [PMID: 33436610 PMCID: PMC7803959 DOI: 10.1038/s41467-020-20619-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/07/2020] [Indexed: 12/18/2022] Open
Abstract
The construction of enzyme-inspired artificial catalysts with enzyme-like active sites and microenvironment remains a great challenge. Herein, we report a single-atomic-site Co catalyst supported by carbon doped boron nitride (BCN) with locally polarized B-N bonds (Co SAs/BCN) to simulate the reductive dehalogenases. Density functional theory analysis suggests that the BCN supports, featured with ionic characteristics, provide additional electric field effect compared with graphitic carbon or N-doped carbon (CN), which could facilitate the adsorption of polarized organochlorides. Consistent with the theoretical results, the Co SAs/BCN catalyst delivers a high activity with nearly complete dechlorination (~98%) at a potential of -0.9 V versus Ag/AgCl for chloramphenicol (CAP), showing that the rate constant (k) contributed by unit mass of metal (k/ratio) is 4 and 19 times more active than those of the Co SAs/CN and state-of-the-art Pd/C catalyst, respectively. We show that Co single atoms coupled with BCN host exhibit high stability and selectivity in CAP dechlorination and suppress the competing hydrogen evolution reaction, endowing the Co SAs/BCN as a candidate for sustainable conversion of organic chloride.
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Affiliation(s)
- Yuan Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China
| | - Xiao Zhou
- Department of Applied Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China. .,College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, 200092, Shanghai, China.
| | - Jie-Jie Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China.
| | - Wenxing Chen
- Beijing Key Laboratory of Construction Tailorable Advanced Functional Materials and Green Applications, School of Materials Science and Engineering, Beijing Institute of Technology, 100081, Beijing, China
| | - Fangyao Zhou
- Department of Applied Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China
| | - Zhiyuan Wang
- Department of Applied Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China
| | - Jia Yang
- Department of Applied Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China
| | - Can Xiong
- Department of Applied Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China
| | - Ying Wang
- College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, 200092, Shanghai, China
| | - Fengting Li
- College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, 200092, Shanghai, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, 230026, Hefei, China
| | - Yuen Wu
- Department of Applied Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, 230026, Hefei, China.
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Nguyen BAT, Hsieh JL, Lo SC, Wang SY, Hung CH, Huang E, Hung SH, Chin WC, Huang CC. Biodegradation of dioxins by Burkholderia cenocepacia strain 869T2: Role of 2-haloacid dehalogenase. JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123347. [PMID: 33113713 DOI: 10.1016/j.jhazmat.2020.123347] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/10/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Dioxin compounds are persistent carcinogenic byproducts of anthropogenic activities such as waste combustion and other industrial activities. The ubiquitous distribution of dioxins is global concerns these days. Among of recent techniques, bioremediation, an eco-friendly and cost-effective technology, uses bacteria or fungi to detoxify in dioxins; however, not many bacteria can degrade the most toxic dioxin congener 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (TCDD). In this study, the endophytic bacterium Burkholderia cenocapacia 869T2 was capable of TCDD degradation by nearly 95 % after one-week of an aerobic incubation. Through transcriptomic analysis of the strain 869T2 at 6 -h and 12 -h TCDD exposure, a number of catabolic genes involved in dioxin metabolism were detected with high gene expressions in the presence of TCDD. The transcriptome data also indicated that B. cenocepacia strain 869T2 metabolized the dioxin compounds from an early phase (at 6 h) of the incubation, and the initial outline for a general dioxin degradation pathway were proposed. One of the catabolic genes, l-2-haloacid dehalogenase (2-HAD) was cloned to investigate its contribution in dioxin dehalogenation. By detecting the increasing concentration of chloride ions released from TCDD, our results indicated that the dehalogenase played a crucial role in dehalogenation of dioxin in the aerobic condition.
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Affiliation(s)
- Bao-Anh Thi Nguyen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ju-Liang Hsieh
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Shou-Chen Lo
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Sui-Yuan Wang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Chun-Hsiung Hung
- Department of Environmental Engineering, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Eugene Huang
- College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Shih-Hsun Hung
- Department of Horticulture, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Wei-Chih Chin
- General Research Service Center, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China; Department of Biological Sciences and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan, Republic of China.
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China.
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Mahfouz S, Mansour G, Murphy DJ, Hanano A. Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00347-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AbstractDioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.
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Yue Y, Chen J, Bao L, Wang J, Li Y, Zhang Q. Fluoroacetate dehalogenase catalyzed dehalogenation of halogenated carboxylic acids: A QM/MM approach. CHEMOSPHERE 2020; 254:126803. [PMID: 32361540 DOI: 10.1016/j.chemosphere.2020.126803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/11/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
Dehalogenation is one of the most important reactions in environmental pollution control, for instance, the degradation of persistent organic pollutants (POPs). Recently, fluoroacetate dehalogenase (FAcD) has been reported to catalyze the dehalogenation reactions, which shows great potential in treating halogenated pollutants. Here the dehalogenation mechanism catalyzed by FAcD was fully deciphered with the aid of quantum mechanics/molecular mechanics method. The results show that FAcD catalyzed dehalogenation efficiency follows the order of defluorination > dechlorination > debromination. The corresponding Boltzmann-weighted average barriers are 10.1, 19.7, and 20.9 kcal mol-1. Positive/negative correlations between activation barriers and structural parameters (e.g. distance and angle) for FAcD catalyzed dechlorination and debromination were established. Based on the structure-energy relationship, we propose that mutation of the binding pocket amino acids (e.g. His155, Trp156, Tyr219) to smaller proton donor amino acids (e.g. Serine, Threonine, Cysteine, Asparagine) may increase the efficiency for dechlorination and debromination. The results may of practical value for the efficient degradation of chlorined and bromined pollutants by harnessing FAcD.
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Affiliation(s)
- Yue Yue
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Jinfeng Chen
- School of Life Sciences, Westlake University, Hangzhou, 310000, PR China
| | - Lei Bao
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Junjie Wang
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Jinan, 250100, PR China.
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan, 250100, PR China
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23
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Hou D, Bolan NS, Tsang DCW, Kirkham MB, O'Connor D. Sustainable soil use and management: An interdisciplinary and systematic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138961. [PMID: 32353725 PMCID: PMC7182530 DOI: 10.1016/j.scitotenv.2020.138961] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 05/06/2023]
Abstract
Soil is a key component of Earth's critical zone. It provides essential services for agricultural production, plant growth, animal habitation, biodiversity, carbon sequestration and environmental quality, which are crucial for achieving the United Nations' Sustainable Development Goals (SDGs). However, soil degradation has occurred in many places throughout the world due to factors such as soil pollution, erosion, salinization, and acidification. In order to achieve the SDGs by the target date of 2030, soils may need to be used and managed in a manner that is more sustainable than is currently practiced. Here we show that research in the field of sustainable soil use and management should prioritize the multifunctional value of soil health and address interdisciplinary linkages with major issues such as biodiversity and climate change. As soil is the largest terrestrial carbon pool, as well as a significant contributor of greenhouse gases, much progress can be made toward curtailing the climate crisis by sustainable soil management practices. One identified option is to increase soil organic carbon levels, especially with recalcitrant forms of carbon (e.g., biochar application). In general, soil health is primarily determined by the actions of the farming community. Therefore, information management and knowledge sharing are necessary to improve the sustainable behavior of practitioners and end-users. Scientists and policy makers are important actors in this social learning process, not only to disseminate evidence-based scientific knowledge, but also in generating new knowledge in close collaboration with farmers. While governmental funding for soil data collection has been generally decreasing, newly available 5G telecommunications, big data and machine learning based data collection and analytical tools are maturing. Interdisciplinary studies that incorporate such advances may lead to the formation of innovative sustainable soil use and management strategies that are aimed toward optimizing soil health and achieving the SDGs.
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Affiliation(s)
- Deyi Hou
- School of Environment, Tsinghua University, Beijing 100084, China.
| | - Nanthi S Bolan
- Global Centre for Environmental Remediation, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Mary B Kirkham
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, United States
| | - David O'Connor
- School of Environment, Tsinghua University, Beijing 100084, China
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24
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Waseem H, Ali J, Syed JH, Jones KC. Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114676. [PMID: 33618452 DOI: 10.1016/j.envpol.2020.114676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.
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Affiliation(s)
- Hassan Waseem
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA; Department of Biotechnology, University of Sialkot, Sialkot, Punjab 51310, Pakistan
| | - Jafar Ali
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS University, Tarlai Kalan Park Road, Islamabad, 45550, Pakistan.
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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25
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Dean RK, Schneider CR, Almnehlawi HS, Dawson KS, Fennell DE. 2,3,7,8-Tetrachlorodibenzo- p-dioxin Dechlorination is Differentially Enhanced by Dichlorobenzene Amendment in Passaic River, NJ Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8380-8389. [PMID: 32432863 DOI: 10.1021/acs.est.0c00876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Polychlorinated dibenzo-p-dioxins (PCDDs) are a class of toxic organic compounds released by a number of industrial processes. Sediments of the Passaic River in New Jersey are contaminated by these compounds. To explore the ability of native organohalide respiring bacteria to dechlorinate PCDDs, we first enriched bacteria from sediments of the Passaic River on two organohalides, trichloroethene (TCE) and 1,2-dichlorobenzene (DCB). We then used these enriched sediment cultures and original, unamended sediment as the inocula in a secondary experiment with 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TeCDD), 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD), and 2,7-dichlorodibenzo-p-dioxin (2,7-DiCDD) as target organohalides. We observed dechlorination of 1,2,3,4-TeCDD by all inocula, although to different extents. We observed progressive dechlorination of 2,3,7,8-TeCDD only in bottles inoculated with the DCB enrichment culture, and dechlorination of 2,7-DiCDD almost exclusively in bottles inoculated with the original, unamended river sediment. Dechlorination of 1,2,3,4-TeCDD was more rapid than that of the other amended congeners. Phylotypes within the class Dehalococcoidia associated with organohalide dechlorination were differentially enriched in DCB versus TCE enrichment cultures, indicating that they may play a role in dechlorination of the PCDDs.
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Affiliation(s)
- Rachel K Dean
- Department of Environmental Sciences, Rutgers University, 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Cassidy R Schneider
- Department of Environmental Sciences, Rutgers University, 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Haider S Almnehlawi
- Department of Environmental Sciences, Rutgers University, 14 College Farm Road, New Brunswick, New Jersey 08901, United States
- College of Science, Al-Muthanna University, Samawah, AL-Muthanna 66001 Iraq
| | - Katherine S Dawson
- Department of Environmental Sciences, Rutgers University, 14 College Farm Road, New Brunswick, New Jersey 08901, 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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26
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Catlin DS, Yang X, Bennett B, Holz RC, Liu D. Structural basis for the hydrolytic dehalogenation of the fungicide chlorothalonil. J Biol Chem 2020; 295:8668-8677. [PMID: 32358058 DOI: 10.1074/jbc.ra120.013150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/29/2020] [Indexed: 11/06/2022] Open
Abstract
Cleavage of aromatic carbon-chlorine bonds is critical for the degradation of toxic industrial compounds. Here, we solved the X-ray crystal structure of chlorothalonil dehalogenase (Chd) from Pseudomonas sp. CTN-3, with 15 of its N-terminal residues truncated (ChdT), using single-wavelength anomalous dispersion refined to 1.96 Å resolution. Chd has low sequence identity (<15%) compared with all other proteins whose structures are currently available, and to the best of our knowledge, we present the first structure of a Zn(II)-dependent aromatic dehalogenase that does not require a coenzyme. ChdT forms a "head-to-tail" homodimer, formed between two α-helices from each monomer, with three Zn(II)-binding sites, two of which occupy the active sites, whereas the third anchors a structural site at the homodimer interface. The catalytic Zn(II) ions are solvent-accessible via a large hydrophobic (8.5 × 17.8 Å) opening to bulk solvent and two hydrophilic branched channels. Each active-site Zn(II) ion resides in a distorted trigonal bipyramid geometry with His117, His257, Asp116, Asn216, and a water/hydroxide as ligands. A conserved His residue, His114, is hydrogen-bonded to the Zn(II)-bound water/hydroxide and likely functions as the general acid-base. We examined substrate binding by docking chlorothalonil (2,4,5,6-tetrachloroisophtalonitrile, TPN) into the hydrophobic channel and observed that the most energetically favorable pose includes a TPN orientation that coordinates to the active-site Zn(II) ions via a CN and that maximizes a π-π interaction with Trp227 On the basis of these results, along with previously reported kinetics data, we propose a refined catalytic mechanism for Chd-mediated TPN dehalogenation.
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Affiliation(s)
- Daniel S Catlin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA
| | - Xinhang Yang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin, USA
| | - Richard C Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin, USA; Department of Chemistry, Colorado School of Mines, Golden, Colorado, USA.
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.
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27
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Saibu S, Adebusoye SA, Oyetibo GO. Aerobic bacterial transformation and biodegradation of dioxins: a review. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0294-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractWaste generation tends to surge in quantum as the population and living conditions grow. A group of structurally related chemicals of dibenzofurans and dibenzo-p-dioxins including their chlorinated congeners collectively known as dioxins are among the most lethal environmental pollutants formed during different anthropogenic activities. Removal of dioxins from the environment is challenging due to their persistence, recalcitrance to biodegradation, and prevalent nature. Dioxin elimination through the biological approach is considered both economically and environmentally as a better substitute to physicochemical conventional approaches. Bacterial aerobic degradation of these compounds is through two major catabolic routes: lateral and angular dioxygenation pathways. Information on the diversity of bacteria with aerobic dioxin degradation capability has accumulated over the years and efforts have been made to harness this fundamental knowledge to cleanup dioxin-polluted soils. This paper covers the previous decades and recent developments on bacterial diversity and aerobic bacterial transformation, degradation, and bioremediation of dioxins in contaminated systems.
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28
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Pimviriyakul P, Wongnate T, Tinikul R, Chaiyen P. Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions. Microb Biotechnol 2020; 13:67-86. [PMID: 31565852 PMCID: PMC6922536 DOI: 10.1111/1751-7915.13488] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.
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Affiliation(s)
- Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn UniversityNakhon Pathom73000Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme TechnologyFaculty of ScienceMahidol UniversityBangkok10400Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)Wangchan ValleyRayong21210Thailand
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29
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Dam HT, Sun W, McGuinness L, Kerkhof LJ, Häggblom MM. Identification of a Chlorodibenzo- p-dioxin Dechlorinating Dehalococcoides mccartyi by Stable Isotope Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14409-14419. [PMID: 31765134 DOI: 10.1021/acs.est.9b05395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Polychlorinated dibenzo-p-dioxins (PCDDs) are released into the environment from a variety of both anthropogenic and natural sources. While highly chlorinated dibenzo-p-dioxins are persistent under oxic conditions, in anoxic environments, these organohalogens can be reductively dechlorinated to less chlorinated compounds that are then more amenable to subsequent aerobic degradation. Identifying the microorganisms responsible for dechlorination is an important step in developing bioremediation approaches. In this study, we demonstrated the use of a DNA-stable isotope probing (SIP) approach to identify the bacteria active in dechlorination of PCDDs in river sediments, with 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) as a model. In addition, pyrosequencing of reverse transcribed 16S rRNA of TeCDD dechlorinating enrichment cultures was used to reveal active members of the bacterial community. A set of operational taxonomic units (OTUs) responded positively to the addition of 1,2,3,4-TeCDD in SIP microcosms assimilating 13C-acetate as the carbon source. Analysis of bacterial community profiles of the 13C labeled heavy DNA fraction revealed that an OTU corresponding to Dehalococcoides mccartyi accounted for a significantly greater abundance in cultures amended with 1,2,3,4-TeCDD than in cultures without 1,2,3,4-TeCDD. This implies the involvement of this Dehalococcoides mccartyi strain in the reductive dechlorination of 1,2,3,4-TeCDD and suggests the applicability of SIP for a robust assessment of the bioremediation potential of organohalogen contaminated sites.
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Affiliation(s)
- Hang T Dam
- Department of Biochemistry and Microbiology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
- Institute for Biological Interfaces 5 (IBG 5) , Karlsruhe Institute of Technology (KIT) , Eggenstein-Leopoldshafen 76344 , Germany
| | - Weimin Sun
- Department of Biochemistry and Microbiology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management , Guangdong Institute of Eco-Environmental Science & Technology , Guangzhou 510650 , China
| | - Lora McGuinness
- Department of Marine and Coastal Sciences, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers , The State University of New Jersey , New Brunswick , New Jersey 08901 , United States
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30
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Wang R, Lin CY, Chen SH, Lo KJ, Liu CT, Chou TH, Shih YH. Using high-throughput transcriptome sequencing to investigate the biotransformation mechanism of hexabromocyclododecane with Rhodopseudomonas palustris in water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:249-258. [PMID: 31349166 DOI: 10.1016/j.scitotenv.2019.07.140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
We discovered one purple photosynthetic bacterium, Rhodopseudomonas palustris YSC3, which has a specific ability to degrade 1, 2, 5, 6, 9, 10-hexabromocyclododecane (HBCD). The whole transcriptome of R. palustris YSC3 was analyzed using the RNA-based sequencing technology in illumina and was compared as well as discussed through Multi-Omics onLine Analysis System (MOLAS, http://molas.iis.sinica.edu.tw/NTUIOBYSC3/) platform we built. By using genome based mapping approach, we can align the trimmed reads on the genome of R. palustris and estimate the expression profiling for each transcript. A total of 341 differentially expressed genes (DEGs) in HBCD-treated R. palustris (RPH) versus control R. palustris (RPC) was identified by 2-fold changes, among which 305 genes were up-regulated and 36 genes were down-regulated. The regulated genes were mapped to the database of Gene Ontology (GO) and Genes and Genomes Encyclopedia of Kyoto (KEGG), resulting in 78 pathways being identified. Among those DEGs which annotated to important functions in several metabolic pathways, including those involved in two-component system (13.6%), ribosome assembly (10.7%), glyoxylate and dicarboxylate metabolism (5.3%), fatty acid degradation (4.7%), drug metabolism-cytochrome P450 (2.3%), and chlorocyclohexane and chlorobenzene degradation (3.0%) were differentially expressed in RPH and RPC samples. We also identified one transcript annotated as dehalogenase and other genes involved in the HBCD biotransformation in R. palustris. Furthermore, the putative HBCD biotransformation mechanism in R. palustris was proposed.
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Affiliation(s)
- Reuben Wang
- Department of Food Science, Tunghai University, Taiwan, No.1727, Sec.4, Taiwan Boulevard, Xitun District, Taichung 40704, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Taipei 11529, Taiwan
| | - Shu-Hwa Chen
- Institute of Information Science, Academia Sinica, No. 128, Sec. 2, Taipei 11529, Taiwan
| | - Kai-Jiun Lo
- Institute of Biotechnology, National Taiwan University, No. 81, Chang-Xing St., Taipei 10617, Taiwan
| | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, No. 81, Chang-Xing St., Taipei 10617, Taiwan
| | - Tzu-Ho Chou
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Yang-Hsin Shih
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan.
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31
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Yang X, Bennett B, Holz RC. Insights into the catalytic mechanism of a bacterial hydrolytic dehalogenase that degrades the fungicide chlorothalonil. J Biol Chem 2019; 294:13411-13420. [PMID: 31331935 DOI: 10.1074/jbc.ra119.009094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Indexed: 11/06/2022] Open
Abstract
Chlorothalonil (2,4,5,6-tetrachloroisophtalonitrile; TPN) is one of the most commonly used fungicides in the United States. Given TPN's widespread use, general toxicity, and potential carcinogenicity, its biodegradation has garnered significant attention. Here, we developed a direct spectrophotometric assay for the Zn(II)-dependent, chlorothalonil-hydrolyzing dehalogenase from Pseudomonas sp. CTN-3 (Chd), enabling determination of its metal-binding properties; pH dependence of the kinetic parameters k cat, Km , and k cat/Km ; and solvent isotope effects. We found that a single Zn(II) ion binds a Chd monomer with a Kd of 0.17 μm, consistent with inductively coupled plasma MS data for the as-isolated Chd dimer. We observed that Chd was maximally active toward chlorothalonil in the pH range 7.0-9.0, and fits of these data yielded a pK ES1 of 5.4 ± 0.2, a pK ES2 of 9.9 ± 0.1 (k'cat = 24 ± 2 s-1), a pK E1 of 5.4 ± 0.3, and a pK E2 of 9.5 ± 0.1 (k'cat/k' m = 220 ± 10 s-1 mm-1). Proton inventory studies indicated that one proton is transferred in the rate-limiting step of the reaction at pD 7.0. Fits of UV-visible stopped-flow data suggested a three-step model and provided apparent rate constants for intermediate formation (i.e. a k'2 of 35.2 ± 0.1 s-1) and product release (i.e. a k'3 of 1.1 ± 0.2 s-1), indicating that product release is the slow step in catalysis. On the basis of these results, along with those previously reported, we propose a mechanism for Chd catalysis.
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Affiliation(s)
- Xinhang Yang
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233
| | - Richard C Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201-1881; Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401.
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32
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Wu JH, Chen WY, Kuo HC, Li YM. Redox fluctuations shape the soil microbiome in the hypoxic bioremediation of octachlorinated dibenzodioxin- and dibenzofuran-contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:506-515. [PMID: 30831347 DOI: 10.1016/j.envpol.2019.02.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/16/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
The biodegradation of polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) has been recently demonstrated in a single reactor under hypoxic conditions. Maintaining hypoxic conditions through periodic aerations results in a marked fluctuation of reduction-oxidation (redox) potential. To further assess the effects of redox fluctuations, we operated two fed-batch continuously stirred tank reactors (CSTRs) with sophisticated redox controls at different anoxic/oxic fluctuations to reduce PCDD/Fs in contaminated soil. The results of long-term reactor operation showed that the CSTR with redox fluctuations at a narrow range (-63 ± 68 mV) (CSTR_A) revealed a higher substrate hydrolysis level and PCDD/F degradation rate than did the CSTR with a redox potential that fluctuated at a broad range (-13 ± 118 mV) (CSTR_B). In accordance with analyses of bacterial 16S rRNA genes, the designated hypoxic conditions with added compost supported survival of bacterial populations at a density of approximately 109 copies/g slurry. The evolved core microbiome was dominated by anoxic/oxic fluctuation-adapted Bacteroidetes, Alphaproteobacteria, and Actinobacteria, with higher species diversity and functionality, including hydrolysis and degradation of dioxin-like compounds in CSTR_A than in CSTR_B. Taken together, the overall results of this study expand the understanding of redox fluctuations in association with the degradation of recalcitrant substrates in soil and the corresponding microbiome.
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Affiliation(s)
- Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan.
| | - Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Hung-Chih Kuo
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Yun-Ming Li
- Mass Laboratory, National Chiao-Tung University, Hsinchu, Taiwan
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33
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Tu P, Gao B, Chi L, Lai Y, Bian X, Ru H, Lu K. Subchronic low-dose 2,4-D exposure changed plasma acylcarnitine levels and induced gut microbiome perturbations in mice. Sci Rep 2019; 9:4363. [PMID: 30867497 PMCID: PMC6416245 DOI: 10.1038/s41598-019-40776-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/21/2018] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota critically confers various health benefits, whereas environmental chemicals can affect its constitution and functionality thereby increasing disease risk. In the present study, we aim to evaluate the toxic effects of a wildly-used herbicide 2,4-D (2,4-dichlorophenoxyacetic acid) on the gut microbiome and host using an occupationally relevant dose. A mouse model was used combined with metagenomic sequencing and metabolomic profiling to examine the alterations induced by subchronic low-dose 2,4-D exposure in fecal and plasma samples. The metagenomics results revealed a distinct gut microbial community with profound changes in diverse microbial pathways including urea degradation, amino acid and carbohydrate metabolism in 2,4-D-treated mice. Moreover, the metabolomics results revealed that the metabolic profiles in treatment group were differentiated from control group in both fecal and plasma samples. Toxic effects on the host of 2,4-D at an occupationally relevant dose were observed indicated by decreased acylcarnitine levels in plasma. These findings indicated that 2,4-D can cause toxicity and substantially impact the gut microbiome in mice at occupationally relevant doses, inferring that the relationship between environmental contaminants and microbiota is largely underestimated calling for more comprehensive consideration of the toxicity of occupational exposures.
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Affiliation(s)
- Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bei Gao
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yunjia Lai
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Xiaoming Bian
- Department of Environmental Health Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Hongyu Ru
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Hanano A, Shaban M, Almutlk D, Almousally I. The cytochrome P450 BM-1 of Bacillus megaterium A14K is induced by 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin: Biophysical, molecular and biochemical determinants. CHEMOSPHERE 2019; 216:258-270. [PMID: 30384294 DOI: 10.1016/j.chemosphere.2018.10.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/10/2018] [Accepted: 10/16/2018] [Indexed: 06/08/2023]
Abstract
The current study describes biological changes in Bacillus megaterium A14K cells growing in the presence of 2,3,7,8-Tetrachlorinated dibenzo-p-dioxin (TCDD), the most potent congener of dioxins. The results indicate that the metabolizing of 2,3,7,8-TCDD by BmA14K was accompanied with a novel morphological and biophysical profile typified by the growth of single cells with high levels of biosurfactant production, surface hydrophobicity and cell membrane permeability. Moreover, the TCDD-grown bacteria exhibited a specific fatty acid profile characterized by low ratios of branched/straight chain fatty acids (BCFAs/SCFAs) and saturated/unsaturated fatty acids (SFAs/USFAs) with a specific "signature" due to the presence of branched chain unsaturated fatty acids (BCUFAs). This was synchronized with a significant induction of P450BM-1, an unsaturated fatty acid-metabolizing enzyme in B. megaterium. Subsequently, the profile of oxygenated fatty acids in the TCDD-grown bacteria was typified by the presence of 5,6-epoxy derived from unsaturated C15, C16 and C17 fatty acids, that were absent in control bacteria. A net increase was also detected in both hydroxylated and epoxidized fatty acids, especially those derived from C15:0 and C16:1, respectively, suggesting a specific TCDD-induced "signature" of oxygenated fatty acids in BmA14K. Overall, this study sheds light on the use of B. megaterium A14K as a promising bioindicator/biodegrader of dioxins.
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Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria.
| | - Mouhnad Shaban
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria
| | - Douaa Almutlk
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P.O. Box 6091, Damascus, Syria
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Seidel K, Kühnert J, Adrian L. The Complexome of Dehalococcoides mccartyi Reveals Its Organohalide Respiration-Complex Is Modular. Front Microbiol 2018; 9:1130. [PMID: 29946299 PMCID: PMC6005880 DOI: 10.3389/fmicb.2018.01130] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/14/2018] [Indexed: 11/30/2022] Open
Abstract
Dehalococcoides mccartyi strain CBDB1 is a slow growing strictly anaerobic microorganism dependent on halogenated compounds as terminal electron acceptor for anaerobic respiration. Indications have been described that the membrane-bound proteinaceous organohalide respiration complex of strain CBDB1 is functional without quinone-mediated electron transfer. We here study this multi-subunit protein complex in depth in regard to participating protein subunits and interactions between the subunits using blue native gel electrophoresis coupled to mass spectrometric label-free protein quantification. Applying three different solubilization modes to detach the respiration complex from the membrane we describe different solubilization snapshots of the organohalide respiration complex. The results demonstrate the existence of a two-subunit hydrogenase module loosely binding to the rest of the complex, tight binding of the subunit HupX to OmeA and OmeB, predicted to be the two subunits of a molybdopterin-binding redox subcomplex, to form a second module, and the presence of two distinct reductive dehalogenase module variants with different sizes. In our data we obtained biochemical evidence for the specificity between a reductive dehalogenase RdhA (CbdbA80) and its membrane anchor protein RdhB (CbdbB3). We also observed weak interactions between the reductive dehalogenase and the hydrogenase module suggesting a not yet recognized contact surface between these two modules. Especially an interaction between the two integral membrane subunits OmeB and RdhB seems to promote the integrity of the complex. With the different solubilization strengths we observe successive disintegration of the complex into its subunits. The observed architecture would allow the association of different reductive dehalogenase modules RdhA/RdhB with the other two protein complex modules when the strain is growing on different electron acceptors. In the search for other respiratory complexes in strain CBDB1 the remarkable result is not the detection of a standard ATPase but the absence of any other abundant membrane complex although an 11-subunit version of complex I (Nuo) is encoded in the genome.
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Affiliation(s)
- Katja Seidel
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Joana Kühnert
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
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Suzuki Y, Nakamura M, Otsuka Y, Suzuki N, Ohyama K, Kawakami T, Sato-Izawa K, Navarro RR, Hishiyama S, Inoue K, Kameyama T, Takahashi A, Katayama Y. Cloning and sequencing of the gene encoding the enzyme for the reductive cleavage of diaryl ether bonds of 2,3,7,8-tetrachlorodibenzo-p-dioxin in Geobacillus thermodenitrificans UZO 3. J Biosci Bioeng 2018; 126:488-496. [PMID: 29805114 DOI: 10.1016/j.jbiosc.2018.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 11/17/2022]
Abstract
We have previously reported that a cell-free extract prepared from Geobacillus thermodenitrificans UZO 3 reductively cleaves diaryl ether bonds of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD), a dioxin with the highest toxicity, in a sequential fashion producing 3',4',4,5-tetrachloro-2-hydroxydiphenyl ether (TCDE) as the intermediate, and 3,4-dichlorophenol (DCP) as the final reaction product. The detection of TCDE implicated the discovery of an unprecedented dioxin-degrading enzyme that reductively cleaves the diaryl ether bonds. In this study, we report the cloning and sequencing of the dioxin reductive etherase gene dreE which codes for the 2,3,7,8-TCDD-degrading enzyme. We showed that dreE was expressed in Escherichia coli and that the product of the expression could reductively cleave diaryl ether bonds of 2,3,7,8-TCDD to produce TCDE. Furthermore, we established that the amino acid sequence encoded by dreE was homologous to an enzyme with yet unknown function that is encoded by a gene located in the riboflavin (vitamin B2) biosynthesis operon in Bacillus subtilis. We also showed that the amino acid sequence possesses a coenzyme A (CoA) binding site that is conserved in the N-acyltransferase superfamily. For the first time, the degradation of 2,3,7,8-TCDD at the molecular level using a enzyme of bacterial origin has been demonstrated. A novel mechanism model for the reductive cleavage of diaryl ether bond of 2,3,7,8-TCDD was also proposed.
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Affiliation(s)
- Yuzo Suzuki
- Takasago Thermal Engineering Co. Ltd., Shinjyuku, Tokyo 160-0022, Japan
| | - Masaya Nakamura
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan.
| | - Yuichiro Otsuka
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Nao Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Keisuke Ohyama
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Takeshi Kawakami
- Takasago Thermal Engineering Co. Ltd., Shinjyuku, Tokyo 160-0022, Japan
| | - Kanna Sato-Izawa
- Department of Bioscience, Faculty of Life Sciences, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Ronald R Navarro
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Shojiro Hishiyama
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Kouya Inoue
- Kantteku Co. Ltd., Bunkyo, Tokyo 112-0004, Japan
| | | | - Atsushi Takahashi
- Takasago Thermal Engineering Co. Ltd., Shinjyuku, Tokyo 160-0022, Japan
| | - Yoshihiro Katayama
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
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Ang TF, Maiangwa J, Salleh AB, Normi YM, Leow TC. Dehalogenases: From Improved Performance to Potential Microbial Dehalogenation Applications. Molecules 2018; 23:E1100. [PMID: 29735886 PMCID: PMC6100074 DOI: 10.3390/molecules23051100] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/07/2018] [Accepted: 04/09/2018] [Indexed: 11/16/2022] Open
Abstract
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants. These group of enzymes catalyzing the cleavage of the carbon-halogen bond of organohalogen compounds have potential applications in the chemical industry and bioremediation. The dehalogenases make use of fundamentally different strategies with a common mechanism to cleave carbon-halogen bonds whereby, an active-site carboxylate group attacks the substrate C atom bound to the halogen atom to form an ester intermediate and a halide ion with subsequent hydrolysis of the intermediate. Structurally, these dehalogenases have been characterized and shown to use substitution mechanisms that proceed via a covalent aspartyl intermediate. More so, the widest dehalogenation spectrum of electron acceptors tested with bacterial strains which could dehalogenate recalcitrant organohalides has further proven the versatility of bacterial dehalogenators to be considered when determining the fate of halogenated organics at contaminated sites. In this review, the general features of most widely studied bacterial dehalogenases, their structural properties, basis of the degradation of organohalides and their derivatives and how they have been improved for various applications is discussed.
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Affiliation(s)
- Thiau-Fu Ang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Jonathan Maiangwa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Enzyme and Microbial Technology Research Centre, Centre of Excellence, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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Nijenhuis I, Stollberg R, Lechner U. Anaerobic microbial dehalogenation and its key players in the contaminated Bitterfeld-Wolfen megasite. FEMS Microbiol Ecol 2018; 94:4828323. [PMID: 29385441 DOI: 10.1093/femsec/fiy012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 01/25/2018] [Indexed: 11/14/2022] Open
Abstract
The megasite Bitterfeld-Wolfen is highly contaminated as a result of accidents and because of dumping of wastes from local chemical industries in the last century. A variety of contaminants including chlorinated ethenes and benzenes, hexachlorohexanes and chlorinated dioxins can still be found in the groundwater and (river) sediments. Investigations of the in situ microbial transformation of organohalides have been performed only over the last two decades at this megasite. In this review, we summarise the research on the activity of anaerobic dehalogenating bacteria at the field site in Bitterfeld-Wolfen, focusing on chlorinated ethenes, monochlorobenzene and chlorinated dioxins. Various methods and concepts were applied including ex situ cultivation and isolation, and in situ analysis of hydrochemical parameters, compound-specific stable isotope analysis of contaminants, 13C-tracer studies and molecular markers. Overall, biotransformation of organohalides is ongoing at the field site and Dehalococcoides mccartyi species play an important role in the detoxification process in the Bitterfeld-Wolfen region.
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Affiliation(s)
- Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Reiner Stollberg
- Department of Groundwater Remediation, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ute Lechner
- Institute of Biology/Microbiology Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
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Zhang S, Adrian L, Schüürmann G. Interaction Mode and Regioselectivity in Vitamin B 12-Dependent Dehalogenation of Aryl Halides by Dehalococcoides mccartyi Strain CBDB1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1834-1843. [PMID: 29283566 DOI: 10.1021/acs.est.7b04278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The bacterium Dehalococcoides, strain CBDB1, transforms aromatic halides through reductive dehalogenation. So far, however, the structures of its vitamin B12-containing dehalogenases are unknown, hampering clarification of the catalytic mechanism and substrate specificity as basis for targeted remediation strategies. This study employs a quantum chemical donor-acceptor approach for the Co(I)-substrate electron transfer. Computational characterization of the substrate electron affinity at carbon-halogen bonds enables discriminating aromatic halides ready for dehalogenation by strain CBDB1 (active substrates) from nondehalogenated (inactive) counterparts with 92% accuracy, covering 86 of 93 bromobenzenes, chlorobenzenes, chlorophenols, chloroanilines, polychlorinated biphenyls, and dibenzo-p-dioxins. Moreover, experimental regioselectivity is predicted with 78% accuracy by a site-specific parameter encoding the overlap potential between the Co(I) HOMO (highest occupied molecular orbital) and the lowest-energy unoccupied sigma-symmetry substrate MO (σ*), and the observed dehalogenation pathways are rationalized with a success rate of 81%. Molecular orbital analysis reveals that the most reactive unoccupied sigma-symmetry orbital of carbon-attached halogen X (σC-X*) mediates its reductive cleavage. The discussion includes predictions for untested substrates, thus providing opportunities for targeted experimental investigations. Overall, the presently introduced orbital interaction model supports the view that with bacterial strain CBDB1, an inner-sphere electron transfer from the supernucleophile B12 Co(I) to the halogen substituent of the aromatic halide is likely to represent the rate-determining step of the reductive dehalogenation.
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Affiliation(s)
- Shangwei Zhang
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Technical University Bergakademie Freiberg , Institute for Organic Chemistry, Leipziger Straße 29, 09596 Freiberg, German y
| | - Lorenz Adrian
- UFZ Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Technische Universität Berlin , Chair of Geobiotechnology, Ackerstraße 76, 13355 Berlin, Germany
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research , Permoserstraße 15, 04318 Leipzig, Germany
- Technical University Bergakademie Freiberg , Institute for Organic Chemistry, Leipziger Straße 29, 09596 Freiberg, German y
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40
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Wang S, Poon K, Cai Z. Removal and metabolism of triclosan by three different microalgal species in aquatic environment. JOURNAL OF HAZARDOUS MATERIALS 2018; 342:643-650. [PMID: 28898861 DOI: 10.1016/j.jhazmat.2017.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/02/2017] [Accepted: 09/04/2017] [Indexed: 06/07/2023]
Abstract
Triclosan, an antimicrobial additive widely used in personal care products, has caused the contamination of various aquatic environment. Biodegradation was proved to play a vital role in the treatment of triclosan in wastewater. However, there is limited information about the metabolic pathway. In this study, three common freshwater microalgae including Chlorella pyrenoidosa (C. pyrenoidosa), Desmodesmus sp., and Scenedesmus obliquus (S. obliquus) were applied to remove and biodegrade triclosan in aqueous culture medium. High removal rate up to 99.7% was observed during the treatment of 400μgL-1 triclosan by the three microalgae for 1day. The removal of triclosan attributed to cellular uptake by C. pyrenoidosa, and biotransformation by Desmodesmus sp. and S. obliquus. Simultaneously, triclosan metabolites resulted from hydroxylation, reductive dechlorination, or ether bond cleavage and their conjugates produced through glucosylation and/or methylation were detected in the biodegradation samples. Metabolic pathway of triclosan by algae were firstly proposed in this work, shedding light on the environmental fate of triclosan.
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Affiliation(s)
- Shujuan Wang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, P. R. China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing, Beijing, P. R. China; Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, P. R. China
| | - Karen Poon
- Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, P. R. China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, P. R. China; School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, P. R. China.
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Rodenburg LA, Dewani Y, Häggblom MM, Kerkhof LJ, Fennell DE. Forensic Analysis of Polychlorinated Dibenzo-p-Dioxin and Furan Fingerprints to Elucidate Dechlorination Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:10485-10493. [PMID: 28796943 DOI: 10.1021/acs.est.7b02705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Polychlorinated dibenzo-p-dioxins and -furans (PCDD/Fs) are persistent organic pollutants whose main removal process in the environment is due to biodegradation, and particularly anaerobic reductive dechlorination. Since PCDD/F congeners that are substituted in the lateral 2, 3, 7, and 8 positions are the most toxic, removal of these chlorines is advantageous, but previous studies have only demonstrated their removal under laboratory conditions. We evaluated a concentration data set of PCDD/F congeners with four or more chlorines along with all 209 polychlorinated biphenyl (PCB) congeners in surface water, treated and untreated wastewater, landfill leachate, and biosolids (NY CARP data set) to determine whether peri and peri/lateral dechlorination of PCDD/Fs occurs in these environments. Positive Matrix Factorization (PMF) applied to the data set revealed a factor indicative of the microbial dechlorination of PCBs, and this factor also contained a variety of non-2,3,7,8 substituted PCDD/F congeners. These results suggest that dechlorination of PCDD/Fs at the lateral positions is facile if not preferred in these environments. The relative lack of tetra- and penta-chlorinated PCDD/Fs suggested that dechlorination proceeds to PCDD/F congeners with less than four chlorines. The PMF results were confirmed by examining three samples that contained >90% PCB dechlorination products from the Fresh Kills Landfill and the Hudson River. Even without factor analysis, these samples demonstrated almost identical PCDD/F congener patterns. This study suggests that PCDD/Fs are reductively dechlorinated to nontoxic non-2,3,7,8 PCDD/F congeners in sewers and landfills as well as in the sediment of the Upper Hudson River.
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Affiliation(s)
- Lisa A Rodenburg
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Yashika Dewani
- Department of Environmental Sciences, Rutgers University , 14 College Farm Road, New Brunswick, New Jersey 08901, United States
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University , 76 Lipman Drive, New Brunswick, New Jersey 08901, United States
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University , 71 Dudley Rd, New Brunswick, New Jersey 08901, 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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Sun J, Qiu Y, Ding P, Peng P, Yang H, Li L. Conjugative Transfer of Dioxin-Catabolic Megaplasmids and Bioaugmentation Prospects of a Rhodococcus sp. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:6298-6307. [PMID: 28485586 DOI: 10.1021/acs.est.7b00188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genetic bioaugmentation, in which bacteria harboring conjugative plasmids provide catabolic functions, is a promising strategy to restore dioxin-contaminated environments. Here we examined the conjugative transfer of the dioxin-catabolic plasmids pDF01 and pDF02 harbored by Rhodococcus sp. strain p52. A mating experiment using strain p52 as a donor showed that pDF01 and pDF02 were concomitantly and conjugatively transferred from strain p52 to a Pseudomonas aeruginosa recipient at a conjugation frequency of 3 × 10-4 colonies per recipient. pDF01 and pDF02 were isolated from the P. aeruginosa transconjugant and identified by Southern hybridization, and they were localized in the transconjugant cells by fluorescence in situ hybridization. Moreover, the catabolic plasmids functioned in the transconjugant, which gained the ability to use dibenzofuran and chlorodibenzofuran for growth, and they were maintained in 50% of the transconjugant cells for 30 generations without selective pressure. Furthermore, conjugative transfer of the catabolic plasmids to activated sludge bacteria was detected. Sequencing of pDF01 and pDF02 revealed the genetic basis for the plasmids' conjugative transfer and stable maintenance, as well as their cooperation during dioxin catabolism. Therefore, strain p52 harboring pDF01 and pDF02 has potential for genetic bioaugmentation in dioxin-contaminated environments.
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Affiliation(s)
- Jiao Sun
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University , Jinan, China
| | - Yilun Qiu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University , Jinan, China
| | - Pengfei Ding
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University , Jinan, China
| | - Peng Peng
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University , Jinan, China
| | - Haiyan Yang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University , Jinan, China
| | - Li Li
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University , Jinan, China
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Ghattas AK, Fischer F, Wick A, Ternes TA. Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment. WATER RESEARCH 2017; 116:268-295. [PMID: 28347952 DOI: 10.1016/j.watres.2017.02.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 05/22/2023]
Abstract
Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.
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Affiliation(s)
- Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Ferdinand Fischer
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany.
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Zhang S, Wondrousch D, Cooper M, Zinder SH, Schüürmann G, Adrian L. Anaerobic Dehalogenation of Chloroanilines by Dehalococcoides mccartyi Strain CBDB1 and Dehalobacter Strain 14DCB1 via Different Pathways as Related to Molecular Electronic Structure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:3714-3724. [PMID: 28233989 DOI: 10.1021/acs.est.6b05730] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dehalococcoides mccartyi strain CBDB1 and Dehalobacter strain 14DCB1 are organohalide-respiring microbes of the phyla Chloroflexi and Firmicutes, respectively. Here, we report the transformation of chloroanilines by these two bacterial strains via dissimilar dehalogenation pathways and discuss the underlying mechanism with quantum chemically calculated net atomic charges of the substrate Cl, H, and C atoms. Strain CBDB1 preferentially removed Cl doubly flanked by two Cl or by one Cl and NH2, whereas strain 14DCB1 preferentially dechlorinated Cl that has an ortho H. For the CBDB1-mediated dechlorination, comparative analysis with Hirshfeld charges shows that the least-negative Cl discriminates active from nonactive substrates in 14 out of 15 cases and may represent the preferred site of primary attack through cob(I)alamin. For the latter trend, three of seven active substrates provide strong evidence, with partial support from three of the remaining four substrates. Regarding strain 14DCB1, the most positive carbon-attached H atom discriminates active from nonactive chloroanilines in again 14 out of 15 cases. Here, regioselectivity is governed for 10 of the 11 active substrates by the most positive H attached to the highest-charge (most positive or least negative) aromatic C carrying the Cl to be removed. These findings suggest the aromatic ring H as primary site of attack through the supernucleophile Co(I), converting an initial H bond to a full electron transfer as start of the reductive dehalogenation. For both mechanisms, one- and two-electron transfer to Cl (strain CBDB1) or H (strain 14DCB1) are compatible with the presently available data. Computational chemistry research into reaction intermediates and pathways may further aid in understanding the bacterial reductive dehalogenation at the molecular level.
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Affiliation(s)
- Shangwei Zhang
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
| | - Dominik Wondrousch
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
| | | | - Stephen H Zinder
- Department of Microbiology, Cornell University , Ithaca, New York 14853, United States
| | - Gerrit Schüürmann
- Institute for Organic Chemistry, Technical University Bergakademie Freiberg , Leipziger Straße 29, 09596 Freiberg, Germany
| | - Lorenz Adrian
- Fachgebiet Applied Biochemistry, Technische Universität Berlin , Gustav-Meyer-Allee 25, 13355 Berlin, Germany
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Chen M, He Y, Yang Y, Huang L, Zhang H, Ye Q, Wang H. Non-stereoselective transformation of the chiral insecticide cycloxaprid in aerobic soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 579:667-674. [PMID: 27847184 DOI: 10.1016/j.scitotenv.2016.11.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
Cycloxaprid (CYC) is one of the most effective neonicotinoid insecticides and is proposed to be a replacement of imidacloprid that has caused concerns over non-targeted resistance and ecological toxicity worldwide. The present study was performed with the 14C-labeled racemic CYC and its two enantiomers in aerobic soil. Racemic CYC and the enantiomers 1S2R-CYC and 1R2S-CYC underwent non-stereoselective degradation in the three soils tested. During the incubation period, CYC was transformed into three achiral degradation products which displayed varying degradation kinetics dependent upon soil properties. The soil properties were found to significantly influence the CYC metabolite profiles. The fastest degradation occurred in loamy soil, whereas the slowest reactions occurred in acidic clay soil. The primary transformation of CYC included cleavage of the oxabridged seven-member ring and CN between chloropyridinylmethyl and imidazalidine ring, carboxylation of the alkene group, and hydroxylation of imidazolidine ring. The results shed light on understanding of CYC degradation and provided useful information for applications and environmental assessments of chiral pesticides.
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Affiliation(s)
- Min Chen
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310029, China
| | - Yupeng He
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310029, China
| | - Yatian Yang
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310029, China
| | - Lei Huang
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310029, China
| | - Hanxue Zhang
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310029, China
| | - Qingfu Ye
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310029, China
| | - Haiyan Wang
- Institute of Nuclear Agricultural Sciences, Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Zhejiang University, Hangzhou 310029, China.
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Dam HT, Häggblom MM. Impact of estuarine gradients on reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin in river sediment enrichment cultures. CHEMOSPHERE 2017; 168:1177-1185. [PMID: 27817900 DOI: 10.1016/j.chemosphere.2016.10.082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/17/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
Polychlorinated dibenzo-p-dioxins (PCDDs) are among the most persistent organic pollutants. Although the total input of PCDDs into the environment has decreased substantially over the past four decades, their input via non-point sources is still increasing, especially in estuarine metropolitan areas. Here we report on the microbially mediated reductive dechlorination of PCDDs in anaerobic enrichment cultures established from sediments collected from five locations along the Hackensack River, NJ and investigate the impacts of sediment physicochemical characteristics on dechlorination activity. Dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD) and abundance of Dehalococcoides spp. negatively correlated with salinity and sulfate concentration in sediments used to establish the cultures. 1,2,3,4-TeCDD was dechlorinated to a lesser extent in cultures established from sediments from the tidally influenced estuarine mouth of the river. In cultures established from low salinity sediments, 1,2,3,4-TeCDD was reductively dechlorinated with the accumulation of 2-monochlorodibenzo-p-dioxin as the major product. Sulfate concentrations above 2 mM inhibited 1,2,3,4-TecDD dechlorination activity. Consecutive lateral- and peri- dechlorination took place in enrichment cultures with a minimal accumulation of 2,3-dichlorodibenzo-p-dioxin in active cultures. A Dehalococcoides spp. community was enriched and accounted for up to 64% of Chloroflexi detected in these sediment cultures.
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Affiliation(s)
- Hang T Dam
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, 76 Lipman Drive, New Brunswick, NJ 08901, USA.
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, 76 Lipman Drive, New Brunswick, NJ 08901, USA.
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Johannissen LO, Leys D, Hay S. A common mechanism for coenzyme cobalamin-dependent reductive dehalogenases. Phys Chem Chem Phys 2017; 19:6090-6094. [DOI: 10.1039/c6cp08659d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hieke ASC, Brinkmeyer R, Yeager KM, Schindler K, Zhang S, Xu C, Louchouarn P, Santschi PH. Widespread Distribution of Dehalococcoides mccartyi in the Houston Ship Channel and Galveston Bay, Texas, Sediments and the Potential for Reductive Dechlorination of PCDD/F in an Estuarine Environment. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:630-644. [PMID: 27844293 DOI: 10.1007/s10126-016-9723-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/04/2016] [Indexed: 05/14/2023]
Abstract
Sediments in the Houston Ship Channel and upper Galveston Bay, Texas, USA, are polluted with polychlorinated dibenzo-p-dioxins/furans (PCDD/F; ≤46,000 ng/kg dry weight (wt.)) with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the most toxic congener, contributing >50 % of the total toxic equivalents (TEQ) at most locations. We measured PCDD/F concentrations in sediments and evaluated the potential for enhanced in situ biodegradation by surveying for Dehalococcoides mccartyi, an obligate organohalide respiring bacterium. Dehalococcoides spp. (98 % similar to D. mccartyi) and 22 other members of the class Dehalococcoidia were predominant 16S ribosomal RNA (rRNA) phylotypes. Dehalococcoides spp. were also present in the active fraction of the bacterial community. Presence/absence PCR screening detected D. mccartyi in sediment cores and sediment grab samples having at least 1 ng/kg dry wt. TEQ at salinities ranging from 0.6 to 19.5 PSU, indicating that they are widespread in the estuarine environment. Organic carbon-only and organic carbon + sulfate-amended sediment microcosm experiments resulted in ∼60 % reduction of ambient 2,3,7,8-TCDD in just 24 months leading to reductions in total TEQs by 38.4 and 45.0 %, respectively, indicating that 2,3,7,8-TCDD degradation is occurring at appreciable rates.
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Affiliation(s)
- Anne-Sophie Charlotte Hieke
- Department of Oceanography, Texas A&M University, 3146 TAMU, College Station, TX, 77843, USA.
- Department of Poultry Science, Texas A&M University, 2472 TAMU, College Station, TX, 77843, USA.
| | - Robin Brinkmeyer
- Department of Marine Science, Texas A&M University, 200 Seawolf Parkway, Galveston, TX, 77553, USA
| | - Kevin M Yeager
- Department of Marine Science, Texas A&M University, 200 Seawolf Parkway, Galveston, TX, 77553, USA
- Department of Earth and Environmental Sciences, University of Kentucky, 101 Slone Research Building, Lexington, KY, 40506, USA
| | - Kimberly Schindler
- Department of Marine Science, Texas A&M University, 200 Seawolf Parkway, Galveston, TX, 77553, USA
- Department of Earth and Environmental Sciences, University of Kentucky, 101 Slone Research Building, Lexington, KY, 40506, USA
| | - Saijin Zhang
- Department of Marine Science, Texas A&M University, 200 Seawolf Parkway, Galveston, TX, 77553, USA
| | - Chen Xu
- Department of Marine Science, Texas A&M University, 200 Seawolf Parkway, Galveston, TX, 77553, USA
| | - Patrick Louchouarn
- Department of Marine Science, Texas A&M University, 200 Seawolf Parkway, Galveston, TX, 77553, USA
| | - Peter H Santschi
- Department of Marine Science, Texas A&M University, 200 Seawolf Parkway, Galveston, TX, 77553, USA
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Denk MK, Milutinović NS, Marczenko KM, Sadowski NM, Paschos A. Nature's hydrides: rapid reduction of halocarbons by folate model compounds. Chem Sci 2016; 8:1883-1887. [PMID: 28553478 PMCID: PMC5424806 DOI: 10.1039/c6sc04314c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/10/2016] [Indexed: 11/21/2022] Open
Abstract
Methylenetetrahydrofolate models (green substructure) reduce organohalides to the respective hydrocarbons under biomimetic conditions and mimic the activity of dehalohydrogenases.
Halocarbons R–X are reduced to hydrocarbons R–H by folate model compounds under biomimetic conditions. The reactions correspond to a halide–hydride exchange with the methylenetetrahydrofolate (MTHF) models acting as hydride donors. The MTHF models are also functional equivalents of dehalohydrogenases but, unlike these enzymes, do not require a metal cofactor. The reactions suggest that halocarbons have the potential to act as endocrinological disruptors of biochemical pathways involving MTHF. As a case in point, we observe the rapid reaction of the MTHF models with the inhalation anaesthetic halothane. The ready synthetic accessibility of the MTHF models as well as their dehalogenation activity in the presence of air and moisture allow for the remediation of toxic, halogenated hydrocarbons.
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Affiliation(s)
- Michael K Denk
- Department of Chemistry , University of Guelph , 50 Stone Road East , Guelph , Ontario N1G 2W1 , Canada
| | - Nicholas S Milutinović
- Department of Chemistry , University of Guelph , 50 Stone Road East , Guelph , Ontario N1G 2W1 , Canada
| | - Katherine M Marczenko
- Department of Chemistry , University of Guelph , 50 Stone Road East , Guelph , Ontario N1G 2W1 , Canada
| | - Natalie M Sadowski
- Department of Chemistry , University of Guelph , 50 Stone Road East , Guelph , Ontario N1G 2W1 , Canada
| | - Athanasios Paschos
- Department of Biology , McMaster University , 1280 Main Street West , Hamilton , Ontario L8S 4K1 , Canada.,Mohawk College of Applied Arts and Technology , Department of Chemical and Environmental Technology , 135 Fennell Ave West , Hamilton , Ontario L9C 1E9 , Canada
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50
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The MarR-Type Regulator Rdh2R Regulates rdh Gene Transcription in Dehalococcoides mccartyi Strain CBDB1. J Bacteriol 2016; 198:3130-3141. [PMID: 27621279 DOI: 10.1128/jb.00419-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/24/2016] [Indexed: 11/20/2022] Open
Abstract
Reductive dehalogenases are essential enzymes in organohalide respiration and consist of a catalytic subunit A and a membrane protein B, encoded by rdhAB genes. Thirty-two rdhAB genes exist in the genome of Dehalococcoides mccartyi strain CBDB1. To gain a first insight into the regulation of rdh operons, the control of gene expression of two rdhAB genes (cbdbA1453/cbdbA1452 and cbdbA1455/cbdbA1454) by the MarR-type regulator Rdh2R (cbdbA1456) encoded directly upstream was studied using heterologous expression and in vitro studies. Promoter-lacZ reporter fusions were generated and integrated into the genome of the Escherichia coli host. The lacZ reporter activities of both rdhA promoters decreased upon transformation of the cells with a plasmid carrying the rdh2R gene, suggesting that Rdh2R acts as repressor, whereas the lacZ reporter activity of the rdh2R promoter was not affected. The transcriptional start sites of both rdhA genes in strain CBDB1 and/or the heterologous host mapped to a conserved direct repeat with 11- to 13-bp half-sites. DNase I footprinting revealed binding of Rdh2R to a ∼30-bp sequence covering the complete direct repeat in both promoters, including the transcriptional start sites. Equilibrium sedimentation ultracentrifugation revealed that Rdh2R binds as tetramer to the direct-repeat motif of the rdhA (cbdbA1455) promoter. Using electrophoretic mobility shift assays, a similar binding affinity was found for both rdhA promoters. In the presence of only one half-site of the direct repeat, the interaction was strongly reduced, suggesting a positive cooperativity of binding, for which unusual short palindromes within the direct-repeat half-sites might play an important role. IMPORTANCE Dehalococcoides mccartyi strains are obligate anaerobes that grow by organohalide respiration. They have an important bioremediation potential because they are capable of reducing a multitude of halogenated compounds to less toxic products. We are now beginning to understand how these organisms make use of this large catabolic potential, whereby D. mccartyi expresses dehalogenases in a compound-specific fashion. MarR-type regulators are often encoded in the vicinity of reductive dehalogenase genes. In this study, we made use of heterologous expression and in vitro studies to demonstrate that the MarR-type transcription factor Rdh2R acts as a negative regulator. We identify its binding site on the DNA, which suggests a mechanism by which it controls the expression of two adjacent reductive dehalogenase operons.
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