1
|
Song Q, Kong F, Liu BF, Song X, Ren HY. Biochar-based composites for removing chlorinated organic pollutants: Applications, mechanisms, and perspectives. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100420. [PMID: 38765891 PMCID: PMC11099330 DOI: 10.1016/j.ese.2024.100420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 05/22/2024]
Abstract
Chlorinated organic pollutants constitute a significant category of persistent organic pollutants due to their widespread presence in the environment, which is primarily attributed to the expansion of agricultural and industrial activities. These pollutants are characterized by their persistence, potent toxicity, and capability for long-range dispersion, emphasizing the importance of their eradication to mitigate environmental pollution. While conventional methods for removing chlorinated organic pollutants encompass advanced oxidation, catalytic oxidation, and bioremediation, the utilization of biochar has emerged as a prominent green and efficacious method in recent years. Here we review biochar's role in remediating typical chlorinated organics, including polychlorinated biphenyls (PCBs), triclosan (TCS), trichloroethene (TCE), tetrachloroethylene (PCE), organochlorine pesticides (OCPs), and chlorobenzenes (CBs). We focus on the impact of biochar material properties on the adsorption mechanisms of chlorinated organics. This review highlights the use of biochar as a sustainable and eco-friendly method for removing chlorinated organic pollutants, especially when combined with biological or chemical strategies. Biochar facilitates electron transfer efficiency between microorganisms, promoting the growth of dechlorinating bacteria and mitigating the toxicity of chlorinated organics through adsorption. Furthermore, biochar can activate processes such as advanced oxidation or nano zero-valent iron, generating free radicals to decompose chlorinated organic compounds. We observe a broader application of biochar and bioprocesses for treating chlorinated organic pollutants in soil, reducing environmental impacts. Conversely, for water-based pollutants, integrating biochar with chemical methods proved more effective, leading to superior purification results. This review contributes to the theoretical and practical application of biochar for removing environmental chlorinated organic pollutants.
Collapse
Affiliation(s)
- Qingqing Song
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Fanying Kong
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Xueting Song
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Hong-Yu Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| |
Collapse
|
2
|
Bulka O, Picott K, Mahadevan R, Edwards EA. From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium. Appl Environ Microbiol 2024; 90:e0073224. [PMID: 38819127 PMCID: PMC11218628 DOI: 10.1128/aem.00732-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the mec cassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase-named acdA-and a complete mec cassette were found to be encoded on a single contig belonging to Dehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a Dehalobacter capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the mec cassette. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of Dehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.
Collapse
Affiliation(s)
- Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
3
|
Kuang Y, Zhou S, Liu Y, Feng X, Chen L, Zheng J, Ouyang G. Nanoscale-controlled organicinorganic hybrid spheres for comprehensive enrichment of ultratrace chlorobenzenes in marine and fresh water. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133541. [PMID: 38286049 DOI: 10.1016/j.jhazmat.2024.133541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/26/2023] [Accepted: 01/14/2024] [Indexed: 01/31/2024]
Abstract
The size of the adsorbent has the potential to influence extraction performance, but the size effect at the nanoscale is still poorly understood. In this study, organic-inorganic hybrid nanospheres (OIHNs) with controllable nanoscale sizes of 30, 50, and 100 nm were successfully prepared. These materials were further fabricated as solid phase microextraction (SPME) coatings with similar thicknesses, and coupled with gas chromatography-mass spectrometry (GC-MS) to investigate their extraction performance. The results showed that the extraction capacities of OIHNs for chlorobenzenes (CBs) and polycyclic aromatic hydrocarbons (PAHs) were much better than those of their corresponding derived carbon materials, despite the smaller specific surface areas and lower porosities of them. In addition, the enrichment performance increased significantly with decreasing particle size, and the OIHN-30 coating demonstrated the best performance, with enrichment factors ranging from 1098 to 6853 for CBs. Finally, a highly sensitive and practical analytical method was established with a wide linear range of 0.5-5000 ng·L-1, and the limits of quantification (LOQs) were 0.43-1.7 ng·L-1. The determinations of ultratrace CBs in five marine water samples and five fresh water samples were realized successfully. This study is expected to contribute to a deep understanding of the environmental effects of nanoparticles and the design of high-performance adsorbents.
Collapse
Affiliation(s)
- Yixin Kuang
- Ministry of Education (MOE) Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Suxin Zhou
- Ministry of Education (MOE) Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuefan Liu
- Key Laboratory of Hunan Province for Advanced Carbon-based Functional Materials, School of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Yueyang 414006, China
| | - Xiaoying Feng
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China
| | - Luyi Chen
- School of Chemistry, Guangzhou Key Laboratory of Materials for Energy Conversion and Storage, Guangdong Provincial Engineering Technology Research Center for Materials for Energy Conversion and Storage, South China Normal University, Guangzhou 510006, China.
| | - Juan Zheng
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China.
| | - Gangfeng Ouyang
- Ministry of Education (MOE) Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China; School of Chemical Engineering and Technology, Sun Yat-sen University, Zhuhai 519082, China
| |
Collapse
|
4
|
Soder-Walz JM, Wasmund K, Deobald D, Vicent T, Adrian L, Marco-Urrea E. Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses. Environ Microbiol 2023; 25:2604-2620. [PMID: 37452527 DOI: 10.1111/1462-2920.16464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
Dehalobacter (Firmicutes) encompass obligate organohalide-respiring bacteria used for bioremediation of groundwater contaminated with halogenated organics. Various aspects of their biochemistry remain unknown, including the identities and interactions of respiratory proteins. Here, we sequenced the genome of Dehalobacter sp. strain 8M and analysed its protein expression. Strain 8M encodes 22 reductive dehalogenase homologous (RdhA) proteins. RdhA D8M_v2_40029 (TmrA) was among the two most abundant proteins during growth with trichloromethane and 1,1,2-trichloroethane. To examine interactions of respiratory proteins, we used blue native gel electrophoresis together with dehalogenation activity tests and mass spectrometry. The highest activities were found in gel slices with the highest abundance of TmrA. Protein distributions across gel lanes provided biochemical evidence that the large and small subunits of the membrane-bound [NiFe] uptake hydrogenase (HupL and HupS) interacted strongly and that HupL/S interacted weakly with RdhA. Moreover, the interaction of RdhB and membrane-bound b-type cytochrome HupC was detected. RdhC proteins, often encoded in rdh operons but without described function, migrated in a protein complex not associated with HupL/S or RdhA. This study provides the first biochemical evidence of respiratory protein interactions in Dehalobacter, discusses implications for the respiratory architecture and advances the molecular comprehension of this unique respiratory chain.
Collapse
Affiliation(s)
- Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Darja Deobald
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Chair of Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| |
Collapse
|
5
|
Fan J, Liu C, Zheng J, Song Y. Dithionite promoted microbial dechlorination of hexachlorobenzene while goethite further accelerated abiotic degradation by sulfidation in paddy soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 259:115047. [PMID: 37220705 DOI: 10.1016/j.ecoenv.2023.115047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/25/2023]
Abstract
It is of great scientific and practical importance to explore the mechanisms of accelerated degradation of Hexachlorobenzene (HCB) in soil. Both iron oxide and dithionite may promote the reductive dechlorination of HCB, but their effects on the microbial community and the biotic and abiotic mechanisms behind it remain unclear. This study investigated the effects of goethite, dithionite, and their interaction on microbial community composition and structure, and their potential contribution to HCB dechlorination in a paddy soil to reveal the underlying mechanism. The results showed that goethite addition alone did not significantly affect HCB dechlorination because the studied soil lacked iron-reducing bacteria. In contrast, dithionite addition significantly decreased the HCB contents by 44.0-54.9%, while the coexistence of dithionite and goethite further decreased the HCB content by 57.9-69.3%. Random Forest analysis suggested that indicator taxa (Paenibacillus, Acidothermus, Haliagium, G12-WMSP1, and Frankia), Pseudomonas, richness and Shannon's index of microbial community, and immobilized Fe content were dominant driving factors for HCB dechlorination. The dithionite addition, either with or without goethite, accelerated HCB anaerobic dechlorination by increasing microbial diversity and richness as well as the relative abundance of the above specific bacterial genera. When goethite and dithionite coexist, sulfidation of goethite with dithionite could remarkably increase FeS formation and then further promote HCB dechlorination rates. Overall, our results suggested that the combined application of goethite and dithionite could be a practicable strategy for the remediation of HCB contaminated soil.
Collapse
Affiliation(s)
- Jianling Fan
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, 219 Ningliu Road, Nanjing 210044, China
| | - Cuiying Liu
- Jiangsu Key Laboratory of Agricultural Meteorology, School of Applied Meteorology, Nanjing University of Information Science and Technology, 219 Ningliu Road, Nanjing 210044, China.
| | - Jinjin Zheng
- School of Changwang, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| |
Collapse
|
6
|
Zhang F, Ge R, Wan Z, Li G, Cao L. Dual effects of PFOA or PFOS on reductive dechlorination of trichloroethylene (TCE). WATER RESEARCH 2023; 240:120093. [PMID: 37210970 DOI: 10.1016/j.watres.2023.120093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/02/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
PFASs and chlorinated solvents are the common co-contaminants in soil and groundwater at firefighter training areas (FTAs). Although PFASs mixtures could have adverse impacts on bioremediation of trichloroethylene (TCE) by inhibiting Dehalococcoides (Dhc), little is known about the effect and contribution of PFOA or PFOS on dechlorination of TCE by non-Dhc organohalide-respiring bacteria (OHRB). To study this, PFOA and PFOS were amended to the growth medium of a non-Dhc OHRB-containing enrichment culture to determine the impact on dechlorination. This study demonstrated that high levels of PFOA or PFOS (100 mg L-1) inhibited TCE dechlorination in four non-Dhc OHRB-containing community including Geobacter, Desulfuromonas, Desulfitobacterium, and Dehalobacter, but low levels of PFOA or PFOS (≤10 mg L-1) enhanced TCE dechlorination. Four non-Dhc OHRB were less inhibited by PFOA than that by PFOS, and high level of PFOS killed Desulfitobacterium and Dehalobacter and decreased the biodiversity of bacterial community. Although most fermenters were killed by the presence of 100 mg L-1 PFOS, two important co-cultures (Desulfovibrio and Sedimentibacter) of OHRB were enriched, indicating that the syntrophic relationships between OHRB and co-cultures still remained, and PFOA or PFOS inhibited TCE dechlorination by directly repressing non-Dhc OHRB. Our results highlight that the bioattenuation of chloroethene contamination could be confounded by non-Dhc OHRB in high levels of PFOS contaminated subsurface environments at FTAs.
Collapse
Affiliation(s)
- Fang Zhang
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Runlei Ge
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Ziren Wan
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Guanghe Li
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Lifeng Cao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China.
| |
Collapse
|
7
|
Yin X, Hua H, Dyer J, Landis R, Fennell D, Axe L. Degradation of chlorinated solvents with reactive iron minerals in subsurface sediments from redox transition zones. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130470. [PMID: 36493644 DOI: 10.1016/j.jhazmat.2022.130470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Reactive iron (Fe) mineral coatings found in subsurface reduction-oxidation transition zones (RTZs) contribute to the attenuation of contaminants. An 18.3-m anoxic core was collected from the site, where constituents of concern (COCs) in groundwater included chlorinated solvents. Reactive Fe mineral coatings were found to be abundant in the RTZs. This research focused on evaluating reaction kinetics with anoxic sediments bearing ferrous mineral nano-coatings spiked with either tetrachloroethylene (PCE), trichloroethylene (TCE), or 1,4-dichlorobenzene (1,4-DCB). Reaction kinetics with RTZ sediments followed pseudo-first-order reactions for the three contaminants with 90% degradation achieved in less than 39 days. The second-order rate constants for the three COCs ranged from 6.20 × 10-4 to 1.73 × 10-3 Lg-1h-1 with pyrite (FeS2), 4.97 × 10-5 to 1.24 × 10-3 Lg-1h-1with mackinawite (FeS), 1.25 × 10-4 to 1.89 × 10-4 Lg-1h-1 with siderite (FeCO3), and 1.79 × 10-4 to 1.10 × 10-3 Lg-1h-1 with magnetite (Fe3O4). For these three chlorinated solvents, the trend for the rate constants followed: Fe(II) sulfide minerals > magnetite > siderite. The high reactivity of Fe mineral coatings is hypothesized to be due to the large surface areas of the nano-mineral coatings. As a result, these surfaces are expected to play an important role in the attenuation of chlorinated solvents in contaminated subsurface environments.
Collapse
Affiliation(s)
- Xin Yin
- Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07032, USA
| | - Han Hua
- Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07032, USA; Department of Civil, Construction & Environmental Engineering, University of New Mexico, Albuquerque, NM 87131, USA
| | - James Dyer
- Savannah River National Laboratory, Aiken, SC 29808, USA
| | | | - Donna Fennell
- Rutgers University, Department of Environmental Sciences, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Lisa Axe
- Otto H. York Department of Chemical and Materials Engineering, New Jersey Institute of Technzhaology, Newark, NJ 07032, USA.
| |
Collapse
|
8
|
Yue B, Wang X, Lian L, Wang Y, Gao W, Zhang H, Zhao J, Lou D. A fiber-packed needle-type extraction device with ionic liquid-based molecularly imprinted polymer as coating for extraction of chlorobenzenes in water samples. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
|
9
|
Semerád J, Lhotský O, Filipová A, Urban O, Šírová K, Boháčková J, Komárek M, Cajthaml T. Remedial trial of sequential anoxic/oxic chemico-biological treatment for decontamination of extreme hexachlorocyclohexane concentrations in polluted soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130199. [PMID: 36279651 DOI: 10.1016/j.jhazmat.2022.130199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
During production of γ-hexachlorocyclohexane (γ-HCH), thousands of tons of other isomers were synthesized as byproducts, and after dumping represent sources of contamination for the environment. Several microbes have the potential for aerobic and anaerobic degradation of HCHs, and zero-valent iron is an effective remediation agent for abiotic dechlorination of HCHs, whereas the combination of the processes has not yet been explored. In this study, a sequence of anoxic/oxic chemico-biological treatments for the degradation of HCHs in a real extremely contaminated soil (10-30 g/kg) was applied. Approximately 1500 kg of the soil was employed, and various combinations of reducing and oxygen-releasing chemicals were used for setting up the aerobic and anaerobic phases. The best results were obtained with mZVI/nZVI, grass cuttings, and oxygen-releasing compounds. In this case, 80 % removal of HCHs was achieved in 129 days, and 98 % degradation was achieved after 1106 days. The analysis of HCHs and their transformation products proved active degradation when slight accumulation of the transformation product during the anaerobic phase was followed by aerobic degradation. The results document that switching between aerobic and anaerobic phases, together with the addition of grass, also created suitable conditions for the biodegradation of HCHs and monochlorobenzene/benzene by microbes.
Collapse
Affiliation(s)
- Jaroslav Semerád
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic
| | - Ondřej Lhotský
- Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic; Dekonta a.s., Dřetovice 109, CZ-27342 Stehelčeves, Czech Republic
| | - Alena Filipová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic
| | - Ondřej Urban
- Dekonta a.s., Dřetovice 109, CZ-27342 Stehelčeves, Czech Republic
| | - Kateřina Šírová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic
| | - Jana Boháčková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic
| | - Michael Komárek
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague - Suchdol, CZ-165 00, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01, Prague 2, Czech Republic.
| |
Collapse
|
10
|
Gribble GW. Naturally Occurring Organohalogen Compounds-A Comprehensive Review. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 121:1-546. [PMID: 37488466 DOI: 10.1007/978-3-031-26629-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.
Collapse
Affiliation(s)
- Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA.
| |
Collapse
|
11
|
Wang Y, Li G, Wang Q, Chen X, Sun C. The kinetic reaction of anaerobic microbial chloerobenzenes degradation in contaminated soil. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
|
12
|
De Vera J, Chen W, Phillips E, Gilevska T, Morgan SA, Norcross S, West K, Mack EE, Lollar BS. Compound-specific isotope analysis (CSIA) evaluation of degradation of chlorinated benzenes (CBs) and benzene in a contaminated aquifer. JOURNAL OF CONTAMINANT HYDROLOGY 2022; 250:104051. [PMID: 35901656 DOI: 10.1016/j.jconhyd.2022.104051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 05/18/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Compound-specific isotope analysis (CSIA) has become a valuable tool in understanding the fate of organic contaminants at field sites. However, its application to chlorinated benzenes (CBs), a group of toxic and persistent groundwater contaminants, has received less attention. This study employed CSIA to investigate the occurrence of natural degradation of various CBs and benzene in a contaminated aquifer. Despite the complexity of the study area (e.g., installation of a sheet pile barrier and the presence of a complex set of contaminants), the substantial enrichments in δ13C values (i.e., >2‰) for all CBs and benzene across the sampling wells indicate in situ degradation of these compounds. In particular, the 13C enrichments for 1,2,4-trichlorobenzene (1,2,4-TCB) and 1,2-dichlorobenzene (1,2-DCB) display good correlations with decreasing groundwater concentrations, consistent with the effects of in situ biodegradation. Using the Rayleigh model, the extent of degradation (EoD) is estimated to be 47-99% for 1,2-DCB, and 21-73% for 1,2,4-TCB. The enrichments observed for the other CBs (1,4-DCB and chlorobenzene (MCB)) and benzene at the site are also suggestive of in situ biodegradation. Due to simultaneous degradation and production of 1,4-DCB (a major 1,2,4-TCB degradation product), MCB (from DCB degradation), and benzene (from MCB degradation), the estimation of EoD for these intermediate compounds is more complex but a modelling simulation supports in situ biodegradation of these daughter products. In particular, the fact that the δ13C values of MCB and benzene (i.e., daughter products of 1,2,4-TCB) are more enriched than the original δ13C value of their parent 1,2,4-TCB provides definitive evidence for the occurrence of in situ biodegradation of the MCB and benzene.
Collapse
Affiliation(s)
- Joan De Vera
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | - Weibin Chen
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | - Elizabeth Phillips
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | - Tetyana Gilevska
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada
| | | | | | - Kathryn West
- AECOM, 1 Canal Rd, Pennsville, NJ 08023, United States
| | - E Erin Mack
- Corteva Agriscience, 974 Centre Road, Wilmington, DE 19805, United States
| | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, M5S 3B1, Ontario, Canada.
| |
Collapse
|
13
|
Trueba-Santiso A, Palau J, Soder-Walz JM, Vicent T, Marco-Urrea E. Assessment of aerobic biodegradation of lower-chlorinated benzenes in contaminated groundwater using field-derived microcosms and compound-specific carbon isotope fractionation. J Environ Sci (China) 2022; 118:204-213. [PMID: 35305769 DOI: 10.1016/j.jes.2021.12.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Biodegradation of lower chlorinated benzenes (tri-, di- and monochlorobenzene) was assessed at a coastal aquifer contaminated with multiple chlorinated aromatic hydrocarbons. Field-derived microcosms, established with groundwater from the source zone and amended with a mixture of lower chlorinated benzenes, evidenced biodegradation of monochlorobenzene (MCB) and 1,4-dichlorobenzene (1,4-DCB) in aerobic microcosms, whereas the addition of lactate in anaerobic microcosms did not enhance anaerobic reductive dechlorination. Aerobic microcosms established with groundwater from the plume consumed several doses of MCB and concomitantly degraded the three isomers of dichlorobenzene with no observable inhibitory effect. In the light of these results, we assessed the applicability of compound stable isotope analysis to monitor a potential aerobic remediation treatment of MCB and 1,4-DCB in this site. The carbon isotopic fractionation factors (ε) obtained from field-derived microcosms were -0.7‰ ± 0.1 ‰ and -1.0‰ ± 0.2 ‰ for MCB and 1,4-DCB, respectively. For 1,4-DCB, the carbon isotope fractionation during aerobic biodegradation was reported for the first time. The weak carbon isotope fractionation values for the aerobic pathway would only allow tracing of in situ degradation in aquifer parts with high extent of biodegradation. However, based on the carbon isotope effects measured in this and previous studies, relatively high carbon isotope shifts (i.e., ∆δ13C > 4.0 ‰) of MCB or 1,4-DCB in contaminated groundwater would suggest that their biodegradation is controlled by anaerobic reductive dechlorination.
Collapse
Affiliation(s)
- Alba Trueba-Santiso
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Jordi Palau
- MAiMA group, SGR Applied Mineralogy, Geochemistry and Geomicrobiology, Department of Mineralogy, Petrology and Applied Geology, Faculty of Earth Sciences, Universitat de Barcelona (UB), Martí Franquès s/n, 08028 Barcelona, Spain
| | - Jesica M Soder-Walz
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Teresa Vicent
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Ernest Marco-Urrea
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain.
| |
Collapse
|
14
|
Hudari MSB, Richnow H, Vogt C, Nijenhuis I. Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review. FEMS Microbiol Ecol 2022; 98:6638985. [PMID: 35810002 DOI: 10.1093/femsec/fiac081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.
Collapse
Affiliation(s)
- Mohammad Sufian Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| |
Collapse
|
15
|
Saikia SS, Borah BK, Baruah G, Rokozeno, Deka MK. Characterization of the gut microbes of greater wax moth (Galleria mellonella Linnaeus) shows presence of potential polymer degraders. Folia Microbiol (Praha) 2021; 67:133-141. [PMID: 34628573 DOI: 10.1007/s12223-021-00925-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/01/2021] [Indexed: 11/27/2022]
Abstract
Greater wax moth (GWM), Galleria mellonella (Lepidoptera: Pyralidae), is a highly destructive honey bee pest prevalent throughout the world. It is considered as a major factor to the alarming decline in honey bee population. GWM destroys active honey combs as it feeds on the beeswax and lays eggs in bee hives, and the primary food of their larva is beeswax. Beeswax is a polymer composed mainly of saturated and unsaturated, linear and complex monoesters, and hydrocarbons. The most frequent bond in beeswax is ethene (CH2-CH2) which is also found in the common plastic polyethylene. As wax-digestion is not a common animal character, we hypothesized about a possible role of GWM gut microflora in the process; which could possibly degrade polyethylene-like polymers as well. This study was aimed to identify the GWM gut microflora via culture-dependant approach. We characterized several bacterial species based on the culture characteristics, Gram-reaction, and various biochemical tests. Sequencing of 16S-rDNA revealed nine bacterial and one microalgal species from GWM gut. The bacterial species included Gram-positive Exiguobacterium aestuarii, Bacillus circulans, Microbacterium zaea, Microbacterium sp. and Enterococcus faecalis; Gram-negative Agrobacterium sp., Sphingomonas pseudosanguinis, Sphingobium yanoikuyae and Acinetobacter radioresistens; the microalgae was Picochlorum oklahomensis. Some of them have been previously reported to degrade polycyclic aromatic hydrocarbon, low-density polyethylene, and 2-methylphenanthrene. Meanwhile, the microalga, P. oklahomensis, was reported to steal bacterial genes to adapt with abiotic stresses. Further investigation is necessary to explore the precise details about polymer degrading capabilities of these microbes; nevertheless, this study builds a foundation for elaborate and advanced future research.
Collapse
Affiliation(s)
- Silpi Shikha Saikia
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Basanta Kumar Borah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India.
| | - Geetanjali Baruah
- Environment Division, Assam Science Technology & Environment Council, Bigyan Bhawan, Guwahati, 781005, Assam, India
| | - Rokozeno
- Department of Entomology, Assam Agricultural University, Jorhat, 785013, Assam, India
| | - Mukul Kumar Deka
- Department of Entomology, Assam Agricultural University, Jorhat, 785013, Assam, India
| |
Collapse
|
16
|
Puentes Jácome LA, Lomheim L, Gaspard S, Edwards EA. Biodegradation of Lindane (γ-Hexachlorocyclohexane) To Nontoxic End Products by Sequential Treatment with Three Mixed Anaerobic Microbial Cultures. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:2968-2979. [PMID: 33557520 DOI: 10.1021/acs.est.0c07221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The γ isomer of hexachlorocyclohexane (HCH), also known as lindane, is a carcinogenic persistent organic pollutant. Lindane was used worldwide as an agricultural insecticide. Legacy soil and groundwater contamination with lindane and other HCH isomers is still a big concern. The biotic reductive dechlorination of HCH to nondesirable and toxic lower chlorinated compounds such as monochlorobenzene (MCB) and benzene, among others, has been broadly documented. Here, we demonstrate that complete biodegradation of lindane to nontoxic end products is attainable using a sequential treatment approach with three mixed anaerobic microbial cultures referred to as culture I, II, and III. Biaugmentation with culture I achieved dechlorination of lindane to MCB and benzene. Culture II was able to dechlorinate MCB to benzene, and finally, culture III carried out methanogenic benzene degradation. Distinct Dehalobacter populations, corresponding to different 16S rRNA amplicon sequence variants in culture I and culture II, were responsible for lindane and MCB dechlorination, respectively. This study continues to highlight key roles of Dehalobacter as chlorobenzene- and HCH -respiring bacteria and demonstrates that sequential treatment with specialized anaerobic cultures may be explored at field sites in order to address legacy soil and groundwater contamination with HCH.
Collapse
Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Sarra Gaspard
- Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre, Guadeloupe, French West-Indies 97157, France
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| |
Collapse
|
17
|
Abstract
Emerging pollutants in nature are linked to various acute and chronic detriments in biotic components and subsequently deteriorate the ecosystem with serious hazards. Conventional methods for removing pollutants are not efficient; instead, they end up with the formation of secondary pollutants. Significant destructive impacts of pollutants are perinatal disorders, mortality, respiratory disorders, allergy, cancer, cardiovascular and mental disorders, and other harmful effects. The pollutant substrate can recognize different microbial enzymes at optimum conditions (temperature/pH/contact time/concentration) to efficiently transform them into other rather unharmful products. The most representative enzymes involved in bioremediation include cytochrome P450s, laccases, hydrolases, dehalogenases, dehydrogenases, proteases, and lipases, which have shown promising potential degradation of polymers, aromatic hydrocarbons, halogenated compounds, dyes, detergents, agrochemical compounds, etc. Such bioremediation is favored by various mechanisms such as oxidation, reduction, elimination, and ring-opening. The significant degradation of pollutants can be upgraded utilizing genetically engineered microorganisms that produce many recombinant enzymes through eco-friendly new technology. So far, few microbial enzymes have been exploited, and vast microbial diversity is still unexplored. This review would also be useful for further research to enhance the efficiency of degradation of xenobiotic pollutants, including agrochemical, microplastic, polyhalogenated compounds, and other hydrocarbons.
Collapse
|
18
|
Yu Y, Zhang K, Li Z, Ren C, Chen J, Lin YH, Liu J, Men Y. Microbial Cleavage of C-F Bonds in Two C 6 Per- and Polyfluorinated Compounds via Reductive Defluorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14393-14402. [PMID: 33121241 DOI: 10.1021/acs.est.0c04483] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The C-F bond is one of the strongest single bonds in nature. Although microbial reductive dehalogenation is well known for the other organohalides, no microbial reductive defluorination has been documented for perfluorinated compounds except for a single, nonreproducible study on trifluoroacetate. Here, we report on C-F bond cleavage in two C6 per- and polyfluorinated compounds via reductive defluorination by an organohalide-respiring microbial community. The reductive defluorination was demonstrated by the release of F- and the formation of the corresponding product when lactate was the electron donor, and the fluorinated compound was the sole electron acceptor. The major dechlorinating species in the seed culture, Dehalococcoides, were not responsible for the defluorination as no growth of Dehalococcoides or active expression of Dehalococcoides-reductive dehalogenases was observed. It suggests that minor phylogenetic groups in the community might be responsible for the reductive defluorination. These findings expand our fundamental knowledge of microbial reductive dehalogenation and warrant further studies on the enrichment, identification, and isolation of responsible microorganisms and enzymes. Given the wide use and emerging concerns of fluorinated organics (e.g., per- and polyfluoroalkyl substances), particularly the perfluorinated ones, the discovery of microbial defluorination under common anaerobic conditions may provide valuable insights into the environmental fate and potential bioremediation strategies of these notorious contaminants.
Collapse
Affiliation(s)
- Yaochun Yu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kunyang Zhang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhong Li
- Metabolomics Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Changxu Ren
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Jin Chen
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Ying-Hsuan Lin
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
- Department of Environmental Sciences, University of California, Riverside, California 92521, United States
| | - Jinyong Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
19
|
Temme HR, Novak PJ. Diverse dechlorinators and dechlorination genes enriched through amendment of chlorinated natural organic matter fractions. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:595-605. [PMID: 31942582 DOI: 10.1039/c9em00499h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In uncontaminated environments, chlorinated natural organic matter (Cl-NOM) can act as an electron acceptor for organohalide-respiring bacteria. It is unknown, however, whether different types of Cl-NOM are preferentially dechlorinated or whether enrichment with Cl-NOM affects the ability of bacteria to dechlorinate contaminants. In this research NOM was extracted from sediment, fractionated based on hydrophobicity, and either amended to polychlorinated biphenyl-contaminated soil directly or chlorinated and then amended to soil. Amendments of the least hydrophobic Cl-NOM fraction were dechlorinated most rapidly, followed by the moderately hydrophobic Cl-NOM fraction. Soil that had been enriched on the moderately hydrophobic fraction of Cl-NOM was also capable of faster dechlorination of the contaminants trichloroethene and tetrachlorobenzene. Community analysis of the soil during enrichment showed that some known organohalide-respiring bacteria were present and may have played a role in dechlorination; nevertheless, many bacteria appeared to be enriched during both Cl-NOM and contaminant dechlorination. In addition, the quantities of two haloalkane dehalogenase genes increased during enrichment on Cl-NOM. These results show for the first time that Cl-NOM can prime contaminant dechlorination and also suggest that hydrolytic dechlorination processes were involved in both Cl-NOM and contaminant dechlorination.
Collapse
Affiliation(s)
- Hanna R Temme
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, USA.
| | | |
Collapse
|
20
|
Qiao W, Puentes Jácome LA, Tang X, Lomheim L, Yang MI, Gaspard S, Avanzi IR, Wu J, Ye S, Edwards EA. Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:255-265. [PMID: 31830788 DOI: 10.1021/acs.est.9b05558] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intensive historical and worldwide use of pesticide formulations containing hexachlorocyclohexane (HCH) has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates, inferred from production rates of the dechlorinated products, MCB and benzene, increased progressively from <3 to ∼12 μM/day over 2 years. The molar ratio of benzene to MCB produced was a function of the substrate isomer and ranged from β (0.77 ± 0.15), α (0.55 ± 0.09), γ (0.13 ± 0.02), to δ (0.06 ± 0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundances of Pelobacter and Dehalobacter, most notably in the α-HCH and δ-HCH cultures. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step toward better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.
Collapse
Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
| | - Xianjin Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
- Institute of Soil and Water Resources and Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
| | - Sarra Gaspard
- Laboratory COVACHIMM2E, EA 3592, Université des Antilles, Pointe à Pitre 97157, Guadeloupe, French West-Indies, France
| | - Ingrid Regina Avanzi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
- Laboratory of Biomaterial and Tissue Engineering, Federal University of Sao Paulo, 136 Silva Jardim Street, Santos 11015-020, São Paulo, Brazil
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
| |
Collapse
|
21
|
Liang Z, Li G, Xiong J, Mai B, An T. Purification, molecular characterization and metabolic mechanism of an aerobic tetrabromobisphenol A dehalogenase, a key enzyme of halorespiration in Ochrobactrum sp. T. CHEMOSPHERE 2019; 237:124461. [PMID: 31374395 DOI: 10.1016/j.chemosphere.2019.124461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Due to the detoxification of tetrabromobisphenol A (TBBPA) varies from different bacterial strains and depends on their specific enzymatic machinery, it is necessary to understand them for potential in situ bioremediation application. The special ability of our previously isolated Ochrobactrum sp. T to simultaneously debrominate and aerobic mineralize TBBPA urgent us to continuously study its degradation molecular mechanism. Herein, the purification and characterization of the dehalogenase which can debrominate TBBPA was investigated based on its corresponding encoding gene tbbpaA. Results showed that an enzyme with molecular mass of 117 kDa, Km of 26.6 μM and Vmax of 0.133 μM min-1 mg-1 was purified and designated as bromophenol dehalogenase. It was the only detected dehalogenase which exhibited TBBPA degradation ability (78%). Moreover, its activity was significantly enhanced by adding NADPH or methyl viologen to the reaction solution. The high similarity of substrate spectrum between the dehalogenase from the recombinant strain and the wild strain further indicated that it was the main dehalogenase responsible for the debromination in wild strain. Based on three identified metabolites, a metabolic pathway of TBBPA by purified enzyme under oxic condition was proposed. This study provides an excellent dehalogenase candidate for mechanistic study of aerobic dehalogenation of brominated aromatic compound.
Collapse
Affiliation(s)
- Zhishu Liang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guiying Li
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Jukun Xiong
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Bixian Mai
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Taicheng An
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| |
Collapse
|
22
|
Cheng H, Song Y, Bian Y, Ji R, Wang F, Gu C, Yang X, Ye M, Ouyang G, Jiang X. Meso-/microporous carbon as an adsorbent for enhanced performance in solid-phase microextraction of chlorobenzenes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 681:392-399. [PMID: 31108359 DOI: 10.1016/j.scitotenv.2019.05.150] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 06/09/2023]
Abstract
There is urgent demand for the design of advanced coating materials for solid-phase microextraction (SPME) for water quality monitoring and assessment because of the global occurrence of chlorobenzenes (CBs). In this study, we proposed a dual-order activation method in which potassium hydroxide is used to modify pre-activated calcium citrate to synthesize a highly developed meso-/microporous carbon (MMC). The as-obtained MMC presented well-developed porosity with a super-high specific surface area (2638.09 m2 g-1), abundant meso-/micropores (0.5-10 nm), high hydrophobicity, excellent thermal stability (>720 °C), and a partly graphitized structure. As a coating material for headspace-SPME, the MMC-coated fiber exhibited outstanding extraction capability for CBs (up to 48.5 times higher than that of commercial fibers), which may be attributed to multiple interactions between the MMC and the pollutants, including size selectivity, micropore filling, π-π stacking and hydrophobicity. Finally, a satisfactory method using an MMC-coated fiber coupled with gas chromatography and electron capture detection was developed with good linearity (1-1000 ng L-1, R2 > 0.9982), high enrichment efficiencies (enrichment factors, 861-7819), low limits of detection (0.003-0.072 ng L-1), excellent repeatability (0.7-5.3%) and reproducibility (1.7-5.1%), and outstanding recoveries (90.18-103.02%) when applied to determine trace CBs in real water samples. These results suggest that MMC is a promising coating material for the SPME of CBs.
Collapse
Affiliation(s)
- Hu Cheng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yang Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongrong Bian
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Rongting Ji
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenggang Gu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xinglun Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Aquatic Product Safety/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| |
Collapse
|
23
|
Qiao W, Luo F, Lomheim L, Mack EE, Ye S, Wu J, Edwards EA. A Dehalogenimonas Population Respires 1,2,4-Trichlorobenzene and Dichlorobenzenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13391-13398. [PMID: 30371071 DOI: 10.1021/acs.est.8b04239] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chlorobenzenes are ubiquitous contaminants in groundwater and soil at many industrial sites. Previously, we demonstrated the natural attenuation of chlorobenzenes and benzene at a contaminated site inferred from a 5 year site investigation and parallel laboratory microcosm studies. To identify the microbes responsible for the observed dechlorination of chlorobenzenes, the microbial community was surveyed using 16S rRNA gene amplicon sequencing. Members of the Dehalobacter and Dehalococcoides are reported to respire chlorobenzenes; however, neither were abundant in our sediment microcosms. Instead, we observed a significant increase in the relative abundance of Dehalogenimonas from <1% to 16-30% during dechlorination of 1,2,4-trichlorobenzene (TCB), 1,2-dichlorobenzene (DCB), and 1,3-DCB over 19 months. Quantitative PCR (qPCR) confirmed that Dehalogenimonas gene copies increased by 2 orders of magnitude with an average yield of 3.6 ± 2.3 g cells per mol Cl- released ( N = 12). In transfer cultures derived from sediment microcosms, dechlorination of 1,4-DCB and monochlorobenzene (MCB) was carried out by Dehalobacter spp. with a growth yield of 3.0 ± 2.1 g cells per mol Cl- released ( N = 5). Here we show that a Dehalogenimonas population respire 1,2,4-TCB and 1,2-/1,3-DCB isomers. This finding emphasizes the need to monitor a broader spectrum of organohalide-respiring bacteria, including Dehalogenimonas, at sites contaminated with halogenated organic compounds.
Collapse
Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - E Erin Mack
- DuPont Corporate Remediation Group , Wilmington , Delaware 19805 , United States
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| |
Collapse
|
24
|
Capozzi SL, Rodenburg LA, Krumins V, Fennell DE, Mack EE. Using positive matrix factorization to investigate microbial dehalogenation of chlorinated benzenes in groundwater at a historically contaminated site. CHEMOSPHERE 2018; 211:515-523. [PMID: 30086528 DOI: 10.1016/j.chemosphere.2018.07.180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/26/2018] [Accepted: 07/29/2018] [Indexed: 06/08/2023]
Abstract
Chlorinated benzenes are common groundwater contaminants in the United States, so demonstrating whether they undergo degradation in the subsurface is important in determining the best remedy for this contamination. The purpose of this work was to use a new data mining approach to investigate chlorinated benzene degradation pathways in the subsurface. Positive Matrix Factorization (PMF) was used to analyze long-term measurements of chlorinated benzene concentrations in groundwater at a contaminated site in New Jersey. A dataset containing 597 groundwater samples and 5 chlorinated benzenes and benzene collected from 144 wells over 20 years was investigated using PMF2 software. Despite the heterogeneity of this dataset, PMF analysis revealed patterns indicative of microbial dechlorination in the groundwater and provided insight about where dechlorination is occurring, to what extent, and under which geochemical conditions. PMF resolved a factor indicative of a source of 1,2,4-trichlorobenzene and 1,2-dichlorobenzene and two factors representing stages of dechlorination, one more advanced than the other. The PMF results indicated that virtually all of the 1,2-dichlorobenzene at the site arises from its use onsite, not from the dechlorination of trichlorobenzenes. Factors were further interpreted using ancillary data such as geochemical indicators and field parameters also measured in the samples. Analysis suggested that the partial and advanced dechlorination signals occur under different subsurface physical conditions. The results provided field validation of the current understanding of anaerobic dechlorination of chlorinated benzenes in the subsurface developed from laboratory studies. PMF is thereby shown to be a useful tool for investigating chlorinated benzene dechlorination.
Collapse
Affiliation(s)
- Staci L Capozzi
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, United States.
| | - Lisa A Rodenburg
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Donna E Fennell
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, United States
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Wilmington, DE, 19805, United States
| |
Collapse
|
25
|
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: 44] [Impact Index Per Article: 7.3] [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.
Collapse
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.
| |
Collapse
|
26
|
Puentes Jácome LA, Edwards EA. A switch of chlorinated substrate causes emergence of a previously undetected native Dehalobacter population in an established Dehalococcoides-dominated chloroethene-dechlorinating enrichment culture. FEMS Microbiol Ecol 2018; 93:4569067. [PMID: 29088371 DOI: 10.1093/femsec/fix141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/26/2017] [Indexed: 01/08/2023] Open
Abstract
Chlorobenzenes are soil and groundwater pollutants of concern that can be reductively dehalogenated by organohalide-respiring bacteria from the genera Dehalococcoides and Dehalobacter. The bioaugmentation culture KB-1® harbours Dehalococcoides mccartyi spp. that reductively dehalogenate trichloroethene to ethene. It contains more than 30 reductive dehalogenase genes; some of them are highly similar to genes found in the chlorobenzene-respiring Dehalococcoides mccartyi strain CBDB1. We explored the chlorobenzene dehalogenation capability of the KB-1 enrichment culture using 1,2,4-trichlorobenzene (1,2,4-TCB). We achieved adaptation of KB-1 to 1,2,4-TCB that is dehalogenated to a mixture of dichlorobenzenes, and subsequently to monochlorobenzene and benzene. Surprisingly, a native Dehalobacter population, and not a Dehalococcoides population, couples the dechlorination of 1,2,4-TCB to growth achieving an average yield of 1.1 ± 0.6 × 1013 cells per mole of Cl- released. Interestingly, the dechlorination of 1,2,4-TCB occurs alongside the complete dechlorination of trichloroethene to ethene in cultures fed both electron acceptors. Dehalobacter was not previously identified as a major player in KB-1, but its ecological niche was favoured by the introduction of 1,2,4-TCB. Based on 16S rRNA phylogeny, Dehalobacter populations seem to cluster into specialised clades, and are likely undergoing substrate specialisation as a strategy to reduce competition for electron acceptors.
Collapse
Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada.,Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
| |
Collapse
|
27
|
Qiao W, Luo F, Lomheim L, Mack EE, Ye S, Wu J, Edwards EA. Natural Attenuation and Anaerobic Benzene Detoxification Processes at a Chlorobenzene-Contaminated Industrial Site Inferred from Field Investigations and Microcosm Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:22-31. [PMID: 29178800 DOI: 10.1021/acs.est.7b04145] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A five-year site investigation was conducted at a former chemical plant in Nanjing, China. The main contaminants were 1,2,4-trichlorobenzene (TCB) reaching concentrations up to 7300 μg/L, dichlorobenzene (DCB) isomers, monochlorobenzene (MCB), and benzene. Over time, these contaminants naturally attenuated to below regulatory levels under anaerobic conditions. To confirm the transformation processes and to explore the mechanisms, a corresponding laboratory microcosm study was completed demonstrating that 1,2,4-TCB was dechlorinated to 1,2-DCB, 1,3-DCB, and 1,4-DCB in approximately 2%/10%/88% molar proportions. The DCB isomers were dechlorinated via MCB to benzene, and, finally, benzene was degraded under prevailing sulfate-reducing conditions. Dechlorination could not be attributed to known dechlorinators Dehalobacter or Dehalococcoides, while anaerobic benzene degradation was mediated by microbes affiliated to a Deltaproteobacterium ORM2, previously associated with this activity. Unidentified organic compounds, possibly aromatic compounds related to past on-site production processes, were fueling the dechlorination reactions in situ. The microcosm study confirmed transformation processes inferred from field data and provided needed assurance for natural attenuation. Activity-based microcosm studies are often omitted from site characterization in favor of rapid and less expensive molecular surveys. However, the value of microcosm studies for confirming transformation processes, establishing electron balances, assessing cocontaminant inhibition, and validating appropriate monitoring tools is clear. At complex sites impacted by multiple compounds with poorly characterized transformation mechanisms, activity assays provide valuable data to incorporate into the conceptual site model to most effectively inform remediation alternatives.
Collapse
Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Elizabeth Erin Mack
- DuPont Corporate Remediation Group , Wilmington, Delaware 19805, United States
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| |
Collapse
|
28
|
Liang X, Li M, Mack J, Lobb K, Zhu W. Iron( iii)porphyrin electrocatalyzed enantioselective carbon-chloride bond cleavage of hexachlorocyclohexanes (HCHs): combined experimental investigation and theoretical calculations. Dalton Trans 2018; 47:11470-11476. [DOI: 10.1039/c8dt02510j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enantioselective electrocatalysis of α-, β-, γ- and δ-hexachlorocyclohexanes (HCHs) by tetrakis-pentafluorophenyl-Fe(iii)porphyrin is described.
Collapse
Affiliation(s)
- Xu Liang
- School of Chemistry and Chemical Engineering
- Jiangsu University
- Zhenjiang 212013
- P. R. China
- State Key Laboratory of Coordination Chemistry
| | - Minzhi Li
- School of Chemistry and Chemical Engineering
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - John Mack
- Department of Chemistry
- Rhodes University
- South Africa
| | - Kevin Lobb
- Department of Chemistry
- Rhodes University
- South Africa
| | - Weihua Zhu
- School of Chemistry and Chemical Engineering
- Jiangsu University
- Zhenjiang 212013
- P. R. China
- State Key Laboratory of Coordination Chemistry
| |
Collapse
|
29
|
Song Y, Bian Y, Wang F, Herzberger A, Yang X, Gu C, Jiang X. Effects of biochar on dechlorination of hexachlorobenzene and the bacterial community in paddy soil. CHEMOSPHERE 2017; 186:116-123. [PMID: 28772178 DOI: 10.1016/j.chemosphere.2017.07.139] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/13/2017] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic reductive dechlorination is an important degradation pathway for chlorinated organic contaminants in paddy soil. This study investigated the effects of amending paddy soil with wheat straw biochar on both the dechlorination of hexachlorobenzene (HCB), a typical highly chlorinated contaminant, and on the structure of soil bacteria communities. Soil amendment of 0.1% biochar did not significantly affect the dechlorination of HCB in the soil. However, biochar amendment at higher application levels (5%) stimulated the dechlorination of HCB in the first month of anaerobic incubation and inhibited the dechlorination of HCB after that period. The stimulation effect may be ascribed to the graphite carbon and carbon-centered persistent radicals, which are redox active, in biochar. The inhibiting effect could be partly ascribed to the reduced bioavailability of HCB in biochar-amended soils. High-throughput sequencing revealed that the amendment of biochar changed the soil bacterial community structure but not the bacterial abundances and diversities. The relative abundance of Dehalococcoidaceae in the tested soils showed a significant relationship with the dechlorination percentages of HCB, indicating that Dehalococcoidaceae may be the main HCB-dechlorinating bacteria in the studied paddy soil. The results indicated that low application levels of biochar did not affect the dechlorination of HCB in the paddy soil, while high application levels of biochar mainly inhibited the dechlorination of HCB due to the reduced bioavailability of HCB and the reduced abundances of certain dechlorinating bacteria in the biochar-amended paddy soil.
Collapse
Affiliation(s)
- Yang Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, PR China.
| | - Yongrong Bian
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, PR China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, PR China
| | - Anna Herzberger
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Xinglun Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, PR China
| | - Chenggang Gu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, PR China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, PR China.
| |
Collapse
|
30
|
Munro JE, Kimyon Ö, Rich DJ, Koenig J, Tang S, Low A, Lee M, Manefield M, Coleman NV. Co-occurrence of genes for aerobic and anaerobic biodegradation of dichloroethane in organochlorine-contaminated groundwater. FEMS Microbiol Ecol 2017; 93:4494361. [DOI: 10.1093/femsec/fix133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
|
31
|
Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture. Appl Microbiol Biotechnol 2017; 101:5481-5492. [DOI: 10.1007/s00253-017-8236-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 10/19/2022]
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Alfán-Guzmán R, Ertan H, Manefield M, Lee M. Isolation and Characterization of Dehalobacter sp. Strain TeCB1 Including Identification of TcbA: A Novel Tetra- and Trichlorobenzene Reductive Dehalogenase. Front Microbiol 2017; 8:558. [PMID: 28421054 PMCID: PMC5379058 DOI: 10.3389/fmicb.2017.00558] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/16/2017] [Indexed: 11/13/2022] Open
Abstract
Dehalobacter sp. strain TeCB1 was isolated from groundwater near Sydney, Australia, that is polluted with a range of organochlorines. The isolated strain is able to grow by reductive dechlorination of 1,2,4,5-tetrachlorobenzene to 1,3- and 1,4-dichlorobenzene with 1,2,4-trichlorobenzene being the intermediate daughter product. Transient production of 1,2-dichlorobenzene was detected with subsequent conversion to monochlorobenzene. The dehalogenation capability of strain TeCB1 to respire 23 alternative organochlorines was examined and shown to be limited to the use of 1,2,4,5-tetrachlorobenzene and 1,2,4-trichlorobenzene. Growth on 1,2,4-trichlorobenzene resulted in the production of predominantly 1,3- and 1,4-dichlorobenzene. The inability of strain TeCB1 to grow on 1,2-dichlorobenzene indicated that the production of monochlorobenzene during growth on 1,2,4,5-tetarchlorobezene was cometabolic. The annotated genome of strain TeCB1 contained only one detectable 16S rRNA gene copy and genes for 23 full-length and one truncated Reductive Dehalogenase (RDase) homologs, five unique to strain TeCB1. Identification and functional characterization of the 1,2,4,5-tetrachlorobenzene and 1,2,4-trichlorobenzene RDase (TcbA) was achieved using native-PAGE coupled with liquid chromatography tandem mass spectrometry. Interestingly, TcbA showed higher amino acid identity with tetrachloroethene reductases PceA (95% identity) from Dehalobacter restrictus PER-K23 and Desulfitobacterium hafniense Y51 than with the only other chlorinated benzene reductase [i.e., CbrA (30% identity)] functionally characterized to date.
Collapse
Affiliation(s)
- Ricardo Alfán-Guzmán
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia.,Department of Molecular Biology and Genetics, Istanbul UniversityIstanbul, Turkey
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, SydneyNSW, Australia
| |
Collapse
|
34
|
Lu Y, Ramiro-Garcia J, Vandermeeren P, Herrmann S, Cichocka D, Springael D, Atashgahi S, Smidt H. Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions. Appl Microbiol Biotechnol 2017; 101:2589-2601. [PMID: 27909745 PMCID: PMC5320011 DOI: 10.1007/s00253-016-8004-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/27/2023]
Abstract
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms.
Collapse
Affiliation(s)
- Yue Lu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | | | - Steffi Herrmann
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Danuta Cichocka
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
| |
Collapse
|
35
|
Genome Sequence of Dehalobacter sp. Strain TeCB1, Able To Respire Chlorinated Benzenes. GENOME ANNOUNCEMENTS 2017; 5:5/8/e01681-16. [PMID: 28232453 PMCID: PMC5323632 DOI: 10.1128/genomea.01681-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Dehalobacter sp. strain TeCB1 was isolated from groundwater contaminated with a mixture of organohalides and is able to respire 1,2,4,5-tetrachlorobenzene and 1,2,4-trichlorobenzene. Here, we report its 3.13-Mb draft genome sequence.
Collapse
|
36
|
Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, Löffler FE. 'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Syst Appl Microbiol 2016; 40:150-159. [PMID: 28292625 DOI: 10.1016/j.syapm.2016.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
Abstract
Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160±3μmolL-1 d-1. The DCM degrader attained 5.25×107±1.0×107 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4±0.8μm long and 0.4±0.1μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, 'Candidatus Dichloromethanomonas elyunquensis'.
Collapse
Affiliation(s)
- Sara Kleindienst
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Steven A Higgins
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Despina Tsementzi
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, DE 19714, USA
| | - Frank E Löffler
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.
| |
Collapse
|
37
|
Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME JOURNAL 2016; 11:626-640. [PMID: 27898054 DOI: 10.1038/ismej.2016.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/25/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional. Using strain CF to experimentally verify annotations, we determined that the predicted defective serine biosynthesis pathway can be rescued with a promiscuous serine hydroxymethyltransferase. Strain CF grew without added thiamine although the thiamine biosynthesis pathway is predicted to be absent; intracellular thiamine diphosphate, the cofactor of carboxylases in central metabolism, was not detected in cell extracts. Thus, strain CF may use amino acids to replenish central metabolites, portending entangled metabolite exchanges in ACT-3. Consistent with annotation, strain CF possesses a functional corrinoid biosynthesis pathway, demonstrated by increasing corrinoid content during growth and guided cobalamin biosynthesis in corrinoid-free medium. Chloroform toxicity to corrinoid-producing methanogens and acetogens may drive the conservation of corrinoid autotrophy in Dehalobacter strains. Heme detection in strain CF cell extracts suggests the 'archaeal' heme biosynthesis pathway also functions in anaerobic Firmicutes. This study reinforces the importance of incorporating enzyme promiscuity and cofactor availability in genome-scale functional predictions and identifies essential nutrient interdependencies in anaerobic dechlorinating microbial communities.
Collapse
|
38
|
Wong YK, Holland SI, Ertan H, Manefield M, Lee M. Isolation and characterization ofDehalobacter sp.strain UNSWDHB capable of chloroform and chlorinated ethane respiration. Environ Microbiol 2016; 18:3092-105. [DOI: 10.1111/1462-2920.13287] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Yie K. Wong
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Sophie I. Holland
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
- Department of Molecular Biology and Genetics; Istanbul University; Turkey
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| | - Matthew Lee
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney Australia
| |
Collapse
|
39
|
Nijenhuis I, Kuntze K. Anaerobic microbial dehalogenation of organohalides — state of the art and remediation strategies. Curr Opin Biotechnol 2016; 38:33-8. [DOI: 10.1016/j.copbio.2015.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/03/2015] [Indexed: 11/26/2022]
|
40
|
Tang S, Wang PH, Higgins SA, Löffler FE, Edwards EA. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates. Front Microbiol 2016; 7:100. [PMID: 26903979 PMCID: PMC4751268 DOI: 10.3389/fmicb.2016.00100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. This analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.
Collapse
Affiliation(s)
- Shuiquan Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Po Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Steven A Higgins
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Frank E Löffler
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA; Department of Civil and Environmental Engineering, University of TennesseeKnoxville, TN, USA
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| |
Collapse
|
41
|
Souchier M, Casellas C, Ingrand V, Chiron S. Insights into reductive dechlorination of triclocarban in river sediments: Field measurements and in vitro mechanism investigations. CHEMOSPHERE 2016; 144:425-432. [PMID: 26386432 DOI: 10.1016/j.chemosphere.2015.08.083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/19/2015] [Accepted: 08/29/2015] [Indexed: 06/05/2023]
Abstract
Triclocarban (TCC) reductive dechlorination was investigated using a combination of field and laboratory experiments. Field monitoring revealed that TCC reductive dechlorination in river sediments leads to formation of two isomers of its lesser chlorinated congener namely 3,4'-dichlorocarbanilide and 4,4'-dichlorocarbanilide. Monochlorocarbanilide was not detected in sediments supporting that transformation of dichlorocarbanilide into monochlorocarbanilide is the rate limiting step of TCC dechlorination. In vitro experiments were conducted to study TCC potential reductive dechlorination mechanisms. These experiments demonstrated that 4,4'-dichlorocarbanilide was specifically formed upon a nucleophilic addition reaction under anaerobic conditions. The 3,4'-diclorocarbanilide was formed upon a two steps radical mechanism under aerobic conditions which includes TCC activation by one electron oxidation followed by a nucleophilic substitution reaction with glutathione. In vitro results suggested that strict anaerobic conditions might not be required for TCC reductive dechlorination in the environment. Moreover, in vitro reactions were performed using biomimetic or enzymatic systems supposing that TCC dechlorination might occur through microbial action in situ. Measured dichlorocarbanilide isomers/triclocarban ratios were used to evaluate the relative significance of both dechlorination pathways and the pathway leading to 3,4'-dichlorocarbanilide was found significant in all investigated river sediment samples.
Collapse
Affiliation(s)
- Marine Souchier
- Veolia Recherche et Innovation, Chemin de la Digue, BP 76, 78603 Maisons-Laffitte Cedex, France
| | - Claude Casellas
- UMR Hydrosciences 5569, Université Montpellier, 15 Avenue Ch. Flahault, 34093 Montpellier Cedex 5, France
| | - Valérie Ingrand
- Veolia Recherche et Innovation, Chemin de la Digue, BP 76, 78603 Maisons-Laffitte Cedex, France
| | - Serge Chiron
- UMR Hydrosciences 5569, Université Montpellier, 15 Avenue Ch. Flahault, 34093 Montpellier Cedex 5, France.
| |
Collapse
|
42
|
Zhou X, Zhang C, Zhang D, Awata T, Xiao Z, Yang Q, Katayama A. Polyphasic characterization of an anaerobic hexachlorobenzene-dechlorinating microbial consortium with a wide dechlorination spectrum for chlorobenzenes. J Biosci Bioeng 2015; 120:62-8. [PMID: 25795569 DOI: 10.1016/j.jbiosc.2014.11.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/23/2014] [Accepted: 11/28/2014] [Indexed: 10/23/2022]
Abstract
An anaerobic consortium that was capable of reductively dechlorinating hexachlorobenzene (HCB) to benzene was enriched from contaminated sediment. The consortium was capable of dechlorinating all chlorobenzene isomers except 1,4-dichlorobenzene. Singly and doubly flanked chlorines, as well as unflanked meta-substituted chlorines, were dechlorinated, although doubly flanked chlorines were preferred. Formate, acetate and lactate (but not ethanol) could be utilized as optimum electron donors for reductive dechlorination. Alternative electron acceptors, including nitrate and sulfate, completely inhibited HCB degradation, whereas amorphous iron oxide (FeOOH) did not suppress dechlorination activity. No degradation was found in chloramphenicol-treated consortium; however, vancomycin, molybdate, and 2-bromoethanesulfonate did not inhibit HCB dechlorination. The results of inhibitory treatments suggested that the dechlorinators were non-sulfate-reducing gram-negative or vancomycin resistant gram-positive bacteria. In addition to physiological characterization, analyses of 16S rRNA gene library of the consortium and quantitative PCR of 16S rRNA genes suggested that Dehalococcoides sp. was involved in the reductive dechlorination of HCB, and Geobacter sp. may serve as a dechlorinating candidate.
Collapse
Affiliation(s)
- Xue Zhou
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8603, Japan
| | - Chunfang Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Hangzhou 310058, China; EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan
| | - Dongdong Zhang
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Takanori Awata
- EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan; Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Zhixing Xiao
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Qi Yang
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Arata Katayama
- Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8603, Japan; EcoTopia Science Institute, Nagoya University, Nagoya 464-8603, Japan; Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
| |
Collapse
|
43
|
Liang X, Mundle SOC, Nelson JL, Passeport E, Chan CCH, Lacrampe-Couloume G, Zinder SH, Sherwood Lollar B. Distinct carbon isotope fractionation during anaerobic degradation of dichlorobenzene isomers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:4844-4851. [PMID: 24758692 DOI: 10.1021/es4054384] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Chlorinated benzenes are ubiquitous organic contaminants found in groundwater and soils. Compound specific isotope analysis (CSIA) has been increasingly used to assess natural attenuation of chlorinated contaminants, in which anaerobic reductive dechlorination plays an essential role. In this work, carbon isotope fractionation of the three dichlorobenzene (DCB) isomers was investigated during anaerobic reductive dehalogenation in methanogenic laboratory microcosms. Large isotope fractionation of 1,3-DCB and 1,4-DCB was observed while only a small isotope effect occurred for 1,2-DCB. Bulk enrichment factors (εbulk) were determined from a Rayleigh model: -0.8 ± 0.1 ‰ for 1,2-DCB, -5.4 ± 0.4 ‰ for 1,3-DCB, and -6.3 ± 0.2 ‰ for 1,4-DCB. εbulk values were converted to apparent kinetic isotope effects for carbon (AKIE) in order to characterize the carbon isotope effect at the reactive positions for the DCB isomers. AKIE values are 1.005 ± 0.001, 1.034 ± 0.003, and 1.039 ± 0.001 for 1,2-DCB, 1,3-DCB, and 1,4-DCB, respectively. The large difference in AKIE values between 1,2-DCB and 1,3-DCB (or 1,4-DCB) suggests distinct reaction pathways may be involved for different DCB isomers during microbial reductive dechlorination by the methanogenic cultures.
Collapse
Affiliation(s)
- Xiaoming Liang
- Department of Earth Sciences, University of Toronto , Toronto, Ontario M5S 3B1, Canada
| | | | | | | | | | | | | | | |
Collapse
|