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Bulka O, Picott K, Mahadevan R, Edwards EA. From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium. Appl Environ Microbiol 2024; 90:e0073224. [PMID: 38819127 DOI: 10.1128/aem.00732-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the mec cassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase-named acdA-and a complete mec cassette were found to be encoded on a single contig belonging to Dehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a Dehalobacter capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the mec cassette. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of Dehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.
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Affiliation(s)
- Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
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Huang W, Cao L, Ge R, Wan Z, Zheng D, Li F, Li G, Zhang F. Higher thermal remediation temperature facilitates the sequential bioaugmented reductive dechlorination. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134825. [PMID: 38876014 DOI: 10.1016/j.jhazmat.2024.134825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/07/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
The coupling of thermal remediation with microbial reductive dechlorination (MRD) has shown promising potential for the cleanup of chlorinated solvent contaminated sites. In this study, thermal treatment and bioaugmentation were applied in series, where prior higher thermal remediation temperature led to improved TCE dechlorination performance with both better organohalide-respiring bacteria (OHRB) colonization and electron donor availability. The 60 °C was found to be a key temperature point where the promotion effect became obvious. Amplicon sequencing and co-occurrence network analysis demonstrated that temperature was a more dominating factor than bioaugmentation that impacted microbial community structure. Higher temperature of prior thermal treatment resulted in the decrease of richness, diversity of indigenous microbial communities, and simplified the network structure, which benefited the build-up of newcoming microorganisms during bioaugmentation. Thus, the abundance of Desulfitobacterium increased from 0.11 % (25 °C) to 3.10 % (90 °C). Meanwhile, released volatile fatty acids (VFAs) during thermal remediation functioned as electron donors and boosted MRD. Our results provided temperature-specific information on synergistic effect of sequential thermal remediation and bioaugmentation, which contributed to better implementation of the coupled technologies in chloroethene-impacted sites.
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Affiliation(s)
- Wan Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Lifeng Cao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, 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; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Runlei Ge
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ziren Wan
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Di Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Fangzhou Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, 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
| | - Fang Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, 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.
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3
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Du X, Hong M, Yang Y, Li J, Su Y, Liu N. Removal mechanisms of aqueous Cr(VI) by anaerobic fermentation sludge. ENVIRONMENTAL TECHNOLOGY 2023; 44:3975-3987. [PMID: 35549986 DOI: 10.1080/09593330.2022.2077136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
After fermentation, activated sludge contains many acid-producing bacteria and their metabolites, which have a good reducing effect. Various active groups (e.g., hydroxyl, amino, carboxyl, and phosphate) on microbial cell surfaces can adsorb heavy metals through complexation or chelation, forming heavy metal precipitates and thereby reducing the toxicity of heavy metals. However, the effects and mechanisms of using sludge after anaerobic fermentation to remove Cr(VI) are unclear, such as the dominance of direct versus indirect biological reduction, the contribution of abiotic effects, and the influence of fermentation conditions. This paper compares Cr(VI) removal in fermented and unfermented sludges. After fermentation for 24 h, 99.9% of the Cr(VI) (50 mg/L) in anaerobic sludge was removed within 7 h, which was twice the rate in unfermented activated sludge. A series of comparative experiments demonstrated that Cr(VI) removal primarily occurred through biological effects (about 92%), which included biological reduction and biosorption. 16SrRNA gene sequencing revealed that Cr(VI) transformation primarily occurred through direct biological reduction, with the related genera being Trichococcus, Acetobacter, Aeromonas, and Tolumonas. Fourier-transform infrared (FTIR) spectroscopy results showed that the C = O and C-O functionalities on sludge were likely involved in the Cr(VI) conversion. Majority of the Cr(VI) in the system was reduced to Cr(III) and existed in the suspension, with a small amount deposited on the sludge surface. The X-ray photoelectron spectroscopy (XPS) results indicated that the majority of Cr was present as reduced Cr(III) on the sludge. These results demonstrate that after fermentation in an aqueous environment, activated sludge is an effective medium for the remediation of Cr(VI). These results are useful for designing a green and sustainable bioreduction system for the remediation of Cr(VI)-polluted water.
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Affiliation(s)
- Xiaoyan Du
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of Environment and Resources, Jilin University, Changchun, People's Republic of China
| | - Mei Hong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of Environment and Resources, Jilin University, Changchun, People's Republic of China
| | - Yadong Yang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of Environment and Resources, Jilin University, Changchun, People's Republic of China
| | - Jing Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of Environment and Resources, Jilin University, Changchun, People's Republic of China
| | - Yaoming Su
- South China Institute of Environmental Sciences, MEP, People's Republic of China
| | - Na Liu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of Environment and Resources, Jilin University, Changchun, People's Republic of China
- Institute of Groundwater and Earth Science, Jinan University, Guangzhou City, People's Republic of China
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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.
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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.
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5
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Xu G, Ng HL, Chen C, Zhao S, He J. Efficient and Complete Detoxification of Polybrominated Diphenyl Ethers in Sediments Achieved by Bioaugmentation with Dehalococcoides and Microbial Ecological Insights. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8008-8019. [PMID: 35549250 DOI: 10.1021/acs.est.2c00914] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are prevalent environmental pollutants, but bioremediation of PBDEs remains to be reported. Here we report accelerated remediation of a penta-BDE mixture in sediments by bioaugmentation with Dehalococcoides mccartyi strains CG1 and TZ50. Bioaugmentation with different amounts of each Dehalococcoides strain enhanced debromination of penta-BDEs compared with the controls. The sediment microcosm spiked with 6.8 × 106 cells/mL strain CG1 showed the highest penta-BDEs removal (89.9 ± 7.3%) to diphenyl ether within 60 days. Interestingly, co-contaminant tetrachloroethene (PCE) improved bioaugmentation performance, resulting in faster and more extensive penta-BDEs debromination using less bioinoculants, which was also completely dechlorinated to ethene by introducing D. mccartyi strain 11a. The better bioaugmentation performance in sediments with PCE could be attributed to the boosted growth of the augmented Dehalococcoides and capability of the PCE-induced reductive dehalogenases to debrominate penta-BDEs. Finally, ecological analyses showed that bioaugmentation resulted in more deterministic microbial communities, where the augmented Dehalococcoides established linkages with indigenous microorganisms but without causing obvious alterations of the overall community diversity and structure. Collectively, this study demonstrates that bioaugmentation with Dehalococcoides is a feasible strategy to completely remove PBDEs in sediments.
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Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
- NUS Graduate School─Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore 119077
| | - Hung Liang Ng
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| | - Chen Chen
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
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6
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Phillips E, Bulka O, Picott K, Kümmel S, Edwards E, Nijenhuis I, Gehre M, Dworatzek S, Webb J, Lollar BS. Investigation of Active Site Amino Acid Influence on Carbon and Chlorine Isotope Fractionation during Reductive Dechlorination. FEMS Microbiol Ecol 2022; 98:6608266. [PMID: 35700008 DOI: 10.1093/femsec/fiac072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Reductive dehalogenases (RDases) are corrinoid-dependent enzymes that reductively dehalogenate organohalides in respiratory processes. By comparing isotope effects in biotically-catalyzed reactions to reference experiments with abiotic corrinoid-catalysts, compound-specific isotope analysis (CSIA) has been shown to yield valuable insights into enzyme mechanisms and kinetics, including RDases. Here, we report isotopic fractionation (ε) during biotransformation of chloroform (CF) for carbon (εC = -1.52 ± 0.34‰) and chlorine (εCl = -1.84 ± 0.19‰), corresponding to a ΛC/Cl value of 1.13 ± 0.35. These results are highly suppressed compared to isotope effects observed both during CF biotransformation by another organism with a highly similar RDase (> 95% sequence identity) at the amino acid level, and to those observed during abiotic dehalogenation of CF. Amino acid differences occur at four locations within the two different RDases' active sites, and this study examines whether these differences potentially affect the observed εC, εCl, and ΛC/Cl. Structural protein models approximating the locations of the residues elucidate possible controls on reaction mechanisms and/or substrate binding efficiency. These four locations are not conserved among other chloroalkane reducing RDases with high amino acid similarity (> 90%), suggesting that these locations may be important in determining isotope fractionation within this homologous group of RDases.
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Affiliation(s)
- Elizabeth Phillips
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, Toronto, Ontario M5S 3B1, Canada
| | - Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Elizabeth Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Matthias Gehre
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | | | | | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, 22 Ursula Franklin Street, Toronto, Ontario M5S 3B1, Canada
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7
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Illy VD, Cohen GJV, Verardo E, Höhener P, Guiserix N, Atteia O. Using 1,1,1-Trichloroethane degradation data to understand NAPL dissolution and solute transport at real sites. JOURNAL OF CONTAMINANT HYDROLOGY 2022; 245:103934. [PMID: 34922184 DOI: 10.1016/j.jconhyd.2021.103934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Analytical and numerical models describing the evolution of contaminant concentrations in the plume associated with the dissolution of NAPL source and degradation processes were presented in the literature. At real sites and particularly in complex aquifers like chalk, it is difficult to understand how the sources of contaminants evolve with time. 1,1,1-Trichloroethane (1,1,1-TCA) is one of the few compounds with a well-known hydrolysis constant, that can help to improve knowledge of the contaminant sources and transport rates of dissolved contaminants in groundwater by dating the spill. In this work, different scenarios that could explain the evolution of the concentrations of 1,1,1-TCA and its degradation product 1,1-Dichloroethene (1,1-DCE) at a real contaminated site were investigated by analytical and numerical modelling. The results show that (1) the peaks of concentration time series do not correspond to a single contamination event even in the case of a complex medium, (2) the multiphasic behavior of the concentration time series is dictated by the dissolution in a heterogeneous medium, and (3) the persistence of the concentrations can arise from a small residual organic phase or transport in dual domain medium.
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Affiliation(s)
- Valeureux D Illy
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France; Renault SAS, 1 Allée du Golf, Guyancourt 78 280, France.
| | - Gregory J V Cohen
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France
| | - Elicia Verardo
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France
| | - Patrick Höhener
- Laboratoire de Chimie Environnementale-UMR 7376, Aix-Marseille Université-CNRS, 3 place Victor Hugo - Case 29, 13331 Marseille Cedex 3, France
| | | | - Olivier Atteia
- EA 4592, Géoressources et Environnement, Bordeaux INP, Université Bordeaux Montaigne, 1 Avenue Dr Schweitzer, 33400 Talence, France
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Yi S, Morson N, Edwards EA, Yang D, Liu R, Zhu L, Mabury SA. Anaerobic Microbial Dechlorination of 6:2 Chlorinated Polyfluorooctane Ether Sulfonate and the Underlying Mechanisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:907-916. [PMID: 34978445 DOI: 10.1021/acs.est.1c05475] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The microbial transformation potential of 6:2 chlorinated polyfluorooctane ether sulfonate (6:2 Cl-PFESA) was explored in anaerobic microbial systems. Microbial communities from anaerobic wastewater sludge, an anaerobic digester, and anaerobic dechlorinating cultures enriched from aquifer materials reductively dechlorinated 6:2 Cl-PFESA to 6:2 hydrogen-substituted polyfluorooctane ether sulfonate (6:2 H-PFESA), which was identified as the sole metabolite by non-target analysis. Rapid and complete reductive dechlorination of 6:2 Cl-PFESA was achieved by the anaerobic dechlorinating cultures. The microbial community of the anaerobic dechlorinating cultures was impacted by 6:2 Cl-PFESA exposure. Organohalide-respiring bacteria originally present in the anaerobic dechlorinating cultures, including Geobacter, Dehalobacter, and Dehalococcoides, decreased in relative abundance over time. As the relative abundance of organohalide-respiring bacteria decreased, the rates of 6:2 Cl-PFESA dechlorination decreased, suggesting that the most likely mechanism for reductive dechlorination of 6:2 Cl-PFESA was co-metabolism rather than organohalide respiration. Reductive defluorination of 6:2 Cl-PFESA was not observed. Furthermore, 6:2 H-PFESA exhibited 5.5 times lower sorption affinity to the suspended biosolids than 6:2 Cl-PFESA, with the prospect of increased mobility in the environment. These results show the susceptibility of 6:2 Cl-PFESA to microbially mediated reductive dechlorination and the likely persistence of the product, 6:2 H-PFESA, in anaerobic environments.
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Affiliation(s)
- Shujun Yi
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
| | - Nadia Morson
- Department of Chemical Engineering and Applied Chemistry and BioZone, University of Toronto, Toronto M5S 3E5, Ontario, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry and BioZone, University of Toronto, Toronto M5S 3E5, Ontario, Canada
| | - Diwen Yang
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
| | - Runzeng Liu
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
| | - Lingyan Zhu
- Key Laboratory of Pollution Processes and Environmental Criteria, Ministry of Education, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Scott A Mabury
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
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9
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Heterologous expression of active Dehalobacter spp. respiratory reductive dehalogenases in Escherichia coli. Appl Environ Microbiol 2021; 88:e0199321. [PMID: 34851719 DOI: 10.1128/aem.01993-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reductive dehalogenases (RDases) are a family of redox enzymes that are required for anaerobic organohalide respiration, a microbial process that is useful in bioremediation. Structural and mechanistic studies of these enzymes have been greatly impeded due to challenges in RDase heterologous expression, potentially because of their cobamide-dependence. There have been a few successful attempts at RDase production in unconventional heterologous hosts, but a robust method has yet to be developed. Here we outline a novel respiratory RDase expression system using Escherichia coli. The overexpression of E. coli's cobamide transport system, btu, and anaerobic expression conditions were found to be essential for production of active RDases from Dehalobacter - an obligate organohalide respiring bacterium. The expression system was validated on six enzymes with amino acid sequence identities as low as 28%. Dehalogenation activity was verified for each RDase by assaying cell-free extracts of small-scale expression cultures on various chlorinated substrates including chloroalkanes, chloroethenes, and hexachlorocyclohexanes. Two RDases, TmrA from Dehalobacter sp. UNSWDHB and HchA from Dehalobacter sp. HCH1, were purified by nickel affinity chromatography. Incorporation of the cobamide and iron-sulfur cluster cofactors was verified; though, the precise cobalamin incorporation could not be determined due to variance between methodologies, and the specific activity of TmrA was consistent with that of the native enzyme. The heterologous expression of respiratory RDases, particularly from obligate organohalide respiring bacteria, has been extremely challenging and unreliable. Here we present a relatively straightforward E. coli expression system that has performed well for a variety of Dehalobacter spp. RDases. IMPORTANCE Understanding microbial reductive dehalogenation is important to refine the global halogen cycle and to improve bioremediation of halogenated contaminants; however, studies of the family of enzymes responsible are limited. Characterization of reductive dehalogenase enzymes has largely eluded researchers due to the lack of a reliable and high-yielding production method. We are presenting an approach to express reductive dehalogenase enzymes from Dehalobacter, a key group of organisms used in bioremediation, in E. coli. This expression system will propel the study of reductive dehalogenases by facilitating their production and isolation, allowing researchers to pursue more in-depth questions about the activity and structure of these enzymes. This platform will also provide a starting point to improve the expression of reductive dehalogenases from many other organisms.
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10
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Giannari D, Ho CH, Mahadevan R. A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PLoS Comput Biol 2021; 17:e1009060. [PMID: 34723959 PMCID: PMC8584699 DOI: 10.1371/journal.pcbi.1009060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/11/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
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Affiliation(s)
- Dafni Giannari
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- The Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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11
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Fernández-Verdejo D, Cortés P, Blánquez P, Marco-Urrea E, Guisasola A. Enhanced dechlorination of 1,2-dichloropropane to propene in a bioelectrochemical system mediated by Dehalogenimonas. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:126234. [PMID: 34492987 DOI: 10.1016/j.jhazmat.2021.126234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Bioelectrochemical systems (BES) are promising technologies to enhance the growth of organohalide-respiring bacteria and to treat chlorinated aliphatic hydrocarbons. In this study, two carbon-based cathodic electrode materials, a graphite brush and a carbon cloth, were used as hydrogen suppliers to couple growth of Dehalogenimonas and dechlorination of 1,2-DCP to nontoxic propene in the cathode vessel. The BES with graphite brush electrode consumed ~4000 µM 1,2-DCP during 110 days and exhibited a degradation rate 5.6-fold higher than the maximum value obtained with the carbon cloth electrode, with a cathode potential set at -0.7 V. Quantitative PCR confirmed that Dehalogenimonas gene copies increased by two orders of magnitude in the graphite brush BES, with an average yield of 1.2·108±5·107 cells per µmol of 1,2-DCP degraded. The use of a pulsed voltage operation (cathode potential set at -0.6 V for 16 h and -1.1 V for 8 h) increased the coulombic efficiency and degradation of 1,2-DCP when compared with a continuous voltage operation of -1.1 V. Bacterial cell aggregates were observed in the surface of the graphite brush electrodes by electron scanning microscopy, suggesting biofilm formation. This study expands the range of chlorinated compounds degradable and organohalide-respiring bacteria capable of growing in BES.
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Affiliation(s)
- David Fernández-Verdejo
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Facultat de BioCiències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Paqui Blánquez
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ernest Marco-Urrea
- Biorem UAB, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Albert Guisasola
- GENOCOV, Department of Chemical, Biological and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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12
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Ghezzi D, Filippini M, Cappelletti M, Firrincieli A, Zannoni D, Gargini A, Fedi S. Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23017-23035. [PMID: 33438126 DOI: 10.1007/s11356-020-12236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
- Laboratory of NanoBiotechnology, IRCSS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Maria Filippini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Alessandro Gargini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
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13
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Yang MI, Previdsa M, Edwards EA, Sleep BE. Two distinct Dehalobacter strains sequentially dechlorinate 1,1,1-trichloroethane and 1,1-dichloroethane at a field site treated with granular zero valent iron and guar gum. WATER RESEARCH 2020; 186:116310. [PMID: 32858243 DOI: 10.1016/j.watres.2020.116310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Chlorinated ethanes are environmental pollutants found frequently at many contaminated industrial sites. 1,1,1-Trichloroethane (1,1,1-TCA) can be dechlorinated and detoxified via abiotic transformation or biologically by the action of dechlorinating microorganisms such as Dehalobacter (Dhb). At a field site, it is challenging to distinguish abiotic vs. biotic mechanisms as both processes share common transformation products. In this study, we evaluated using the Dhb 16S rRNA gene and specific reductive dehalogenase genes as biomarkers for 1,1,1-TCA and 1,1-dichloroethane (1,1-DCA) dechlorination. We analyzed samples from laboratory groundwater microcosms and from an industrial site where a mixture of granular zero valent iron (ZVI) and guar gum was injected for 1,1,1-TCA remediation. Abiotic and biotic transformation products were monitored and the changes in dechlorinating organisms were tracked using quantitative PCR (qPCR) with primers targeting the Dhb 16S rRNA gene and two functional genes cfrA and dcrA encoding enzymes that dechlorinate 1,1,1-TCA to 1,1-DCA and 1,1-DCA to chloroethane (CA), respectively. The abundance of the cfrA- and dcrA-like genes confirmed that the two dechlorination steps were carried out by two distinct Dhb populations at the site. The biomarkers used in this study proved useful for monitoring different Dhb populations responsible for step-wise dechlorination and tracking biodegradation of 1,1,1-TCA and 1,1-DCA where both abiotic (e.g., with ZVI) and biotic processes co-occur.
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Affiliation(s)
- M Ivy Yang
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada
| | - Michael Previdsa
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, M5S 3E5, Canada.
| | - Brent E Sleep
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada.
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14
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Li T, Li H, Li C. A review and perspective of recent research in biological treatment applied in removal of chlorinated volatile organic compounds from waste air. CHEMOSPHERE 2020; 250:126338. [PMID: 32126329 DOI: 10.1016/j.chemosphere.2020.126338] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Chlorinated volatile organic compounds (Cl-VOCs) waste air is a kind of typical recalcitrant organic compounds, which poses a great threat to the ecological environment and human health. At present, the biotechnology is considered as a potential strategy for the Cl-VOCs removal due to the advantages of low energy consumption and less possibility of secondary pollution. This work summarizes the recent researches on strains, bioreactors and technology integration. The dominant pure strains for biodegradation of Cl-VOCs are first outlined with a special focus on the co-metabolism of multi-components. It then summarizes two bioreactors (optimized airlift reactor (ALR) and two-phase partitioning bioreactor (TPPB)) and strategy (addition of surfactant) for improvement of biotrickling filter (BTF), which are benefit to achieve the mass transfer enhancement in the removal of hydrophobic Cl-VOCs from waste air. After that, the integration technologies, such as magnetic field (MF)-BTF, non-thermal plasma (NTP)/ultraviolet light (UV)-BTF, and microbial electrolytic cells (MEC), are elucidated, which provide opportunities for complete mineralization of Cl-VOCs in a more efficient, energy-saving and economical way. Finally, current challenges and a perspective of future research on biotechnology for Cl-VOCs removal are thoroughly discussed.
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Affiliation(s)
- Tong Li
- National-Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources Utilization, Tianjin Key Laboratory of Chemical Process Safety, School of Chemical Engineering and Technology, Hebei University of Technology, 8 Guangrong Road, Tianjin, 300000, China
| | - Hao Li
- National-Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources Utilization, Tianjin Key Laboratory of Chemical Process Safety, School of Chemical Engineering and Technology, Hebei University of Technology, 8 Guangrong Road, Tianjin, 300000, China.
| | - Chunli Li
- National-Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources Utilization, Tianjin Key Laboratory of Chemical Process Safety, School of Chemical Engineering and Technology, Hebei University of Technology, 8 Guangrong Road, Tianjin, 300000, China
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15
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Trueba-Santiso A, Fernández-Verdejo D, Marco-Rius I, Soder-Walz JM, Casabella O, Vicent T, Marco-Urrea E. Interspecies interaction and effect of co-contaminants in an anaerobic dichloromethane-degrading culture. CHEMOSPHERE 2020; 240:124877. [PMID: 31541898 DOI: 10.1016/j.chemosphere.2019.124877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/30/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
An anaerobic stable mixed culture dominated by bacteria belonging to the genera Dehalobacterium, Acetobacterium, Desulfovibrio, and Wolinella was used as a model to study the microbial interactions during DCM degradation. Physiological studies indicated that DCM was degraded in this mixed culture at least in a three-step process: i) fermentation of DCM to acetate and formate, ii) formate oxidation to CO2 and H2, and iii) H2/CO2 reductive acetogenesis. The 16S rRNA gene sequencing of cultures enriched with formate or H2 showed that Desulfovibrio was the dominant population followed by Acetobacterium, but sequences representing Dehalobacterium were only present in cultures amended with DCM. Nuclear magnetic resonance analyses confirmed that acetate produced from 13C-labelled DCM was marked at the methyl ([2-13C]acetate), carboxyl ([1-13C]acetate), and both ([1,2-13C]acetate) positions, which is in accordance to acetate formed by both direct DCM fermentation and H2/CO2 acetogenesis. The inhibitory effect of ten different co-contaminants frequently detected in groundwaters on DCM degradation was also investigated. Complete inhibition of DCM degradation was observed when chloroform, perfluorooctanesulfonic acid, and diuron were added at 838, 400, and 107 μM, respectively. However, the inhibited cultures recovered the DCM degradation capability when transferred to fresh medium without co-contaminants. Findings derived from this work are of significant relevance to provide a better understanding of the synergistic interactions among bacteria to accomplish DCM degradation as well as to predict the effect of co-contaminants during anaerobic DCM bioremediation in groundwater.
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Affiliation(s)
- Alba Trueba-Santiso
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Vallès, Spain
| | - David Fernández-Verdejo
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Vallès, Spain
| | - Irene Marco-Rius
- Institute for Bioengineering of Catalonia, Parc Científic de Barcelona, Edifici Clúster c/ Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Vallès, Spain
| | - Oriol Casabella
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Vallès, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Vallès, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Vallès, Spain.
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16
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Wang Q, Yang M, Song X, Tang S, Yu L. Aerobic and Anaerobic Biodegradation of 1,2-Dibromoethane by a Microbial Consortium under Simulated Groundwater Conditions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16193775. [PMID: 31597267 PMCID: PMC6802363 DOI: 10.3390/ijerph16193775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/24/2019] [Accepted: 09/28/2019] [Indexed: 11/16/2022]
Abstract
This study was conducted to explore the potential for 1,2-Dibromoethane (EDB) biodegradation by an acclimated microbial consortium under simulated dynamic groundwater conditions. The enriched EDB-degrading consortium consisted of anaerobic bacteria Desulfovibrio, facultative anaerobe Chromobacterium, and other potential EDB degraders. The results showed that the biodegradation efficiency of EDB was more than 61% at 15 °C, and the EDB biodegradation can be best described by the apparent pseudo-first-order kinetics. EDB biodegradation occurred at a relatively broad range of initial dissolved oxygen (DO) from 1.2 to 5.1 mg/L, indicating that the microbial consortium had a strong ability to adapt. The addition of 40 mg/L of rhamnolipid and 0.3 mM of sodium lactate increased the biodegradation. A two-phase biodegradation scheme was proposed for the EDB biodegradation in this study: an aerobic biodegradation to carbon dioxide and an anaerobic biodegradation via a two-electron transfer pathway of dihaloelimination. To our knowledge, this is the first study that reported EDB biodegradation by an acclimated consortium under both aerobic and anaerobic conditions, a dynamic DO condition often encountered during enhanced biodegradation of EDB in the field.
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Affiliation(s)
- Qing Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
| | - Miaoyan Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xin Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
| | - Shiyue Tang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lei Yu
- Department of Environmental Engineering, Nanjing Forestry University, Nanjing 210037, China.
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17
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He C, Cheng J, Zhang X, Douthwaite M, Pattisson S, Hao Z. Recent Advances in the Catalytic Oxidation of Volatile Organic Compounds: A Review Based on Pollutant Sorts and Sources. Chem Rev 2019; 119:4471-4568. [DOI: 10.1021/acs.chemrev.8b00408] [Citation(s) in RCA: 769] [Impact Index Per Article: 153.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chi He
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
- Department of Environmental Science and Engineering, State Key Laboratory of Multiphase Flow in Power Engineering, School of Energy and Power Engineering, Xi’an Jiaotong University, Xi’an 710049, Shaanxi, P.R. China
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Jie Cheng
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Xin Zhang
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
| | - Mark Douthwaite
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Samuel Pattisson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K
| | - Zhengping Hao
- National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing 101408, P.R. China
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18
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Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME JOURNAL 2019; 13:1042-1055. [PMID: 30607026 DOI: 10.1038/s41396-018-0333-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
Abstract
Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate-pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.
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Affiliation(s)
- Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Han-Chen Ho
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
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19
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Wen LL, Chen JX, Fang JY, Li A, Zhao HP. Effects of 1,1,1-Trichloroethane and Triclocarban on Reductive Dechlorination of Trichloroethene in a TCE-Reducing Culture. Front Microbiol 2017; 8:1439. [PMID: 28824572 PMCID: PMC5541058 DOI: 10.3389/fmicb.2017.01439] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/17/2017] [Indexed: 11/13/2022] Open
Abstract
Chlorinated compounds were generally present in the environment due to widespread use in the industry. A short-term study was performed to evaluate the effects of 1,1,1- trichloroethane (TCA) and triclocarban (TCC) on trichloroethene (TCE) removal in a reactor fed with lactate as the sole electron donor. Both TCA and TCC inhibited TCE reduction, but the TCC had a more pronounced effect compared to TCA. The TCE-reducing culture, which had never been exposed to TCA before, reductively dechlorinated TCA to 1,1-dichloroethane (DCA). Below 15 μM, TCA had little effect on the transformation of TCE to cis-dichloroethene (DCE); however, the reduction of cis-DCE and vinyl chloride (VC) were more sensitive to TCA, and ethene production was completely inhibited when the concentration of TCA was above 15 μM. In cultures amended with TCC, the reduction of TCE was severely affected, even at concentrations as low as 0.3 μM; all the cultures stalled at VC, and no ethene was detected. The cultures that fully transformed TCE to ethene contained 5.2–8.1% Dehalococcoides. Geobacter and Desulfovibrio, the bacteria capable of partially reducing TCE to DCE, were detected in all cultures, but both represented a larger proportion of the community in TCC-amended cultures. All cultures were dominated by Clostridium_sensu_stricto_7, a genus that belongs to Firmicutes with proportions ranging from 40.9% (in a high TCC (15 μM) culture) to 88.2%. Methanobacteria was detected at levels of 1.1–12.7%, except in cultures added with 15 and 30 μM TCA, in which they only accounted for ∼0.4%. This study implies further environmental factors needed to be considered in the successful bioremediation of TCE in contaminated sites.
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Affiliation(s)
- Li-Lian Wen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang UniversityHangzhou, China.,Zhejiang Provincial Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang UniversityHangzhou, China
| | - Jia-Xian Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang UniversityHangzhou, China.,Zhejiang Provincial Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang UniversityHangzhou, China
| | - Jia-Yi Fang
- College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Ang Li
- School of Environment, Harbin Institute of TechnologyHarbin, China
| | - He-Ping Zhao
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang UniversityHangzhou, China.,Zhejiang Provincial Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang UniversityHangzhou, China
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20
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Şimşir B, Yan J, Im J, Graves D, Löffler FE. Natural Attenuation in Streambed Sediment Receiving Chlorinated Solvents from Underlying Fracture Networks. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:4821-4830. [PMID: 28328216 PMCID: PMC6944067 DOI: 10.1021/acs.est.6b05554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Contaminant discharge from fractured bedrock formations remains a remediation challenge. We applied an integrated approach to assess the natural attenuation potential of sediment that forms the transition zone between upwelling groundwater from a chlorinated solvent-contaminated fractured bedrock aquifer and the receiving surface water. In situ measurements demonstrated that reductive dechlorination in the sediment attenuated chlorinated compounds before reaching the water column. Microcosms established with creek sediment or in situ incubated Bio-Sep beads degraded C1-C3 chlorinated solvents to less-chlorinated or innocuous products. Quantitative PCR and 16S rRNA gene amplicon sequencing revealed the abundance and spatial distribution of known dechlorinator biomarker genes within the creek sediment and demonstrated that multiple dechlorinator populations degrading chlorinated C1-C3 alkanes and alkenes co-inhabit the sediment. Phylogenetic classification of bacterial and archaeal sequences indicated a relatively uniform distribution over spatial (300 m horizontally) scale, but Dehalococcoides and Dehalobacter were more abundant in deeper sediment, where 5.7 ± 0.4 × 105 and 5.4 ± 0.9 × 106 16S rRNA gene copies per g of sediment, respectively, were measured. The microbiological and hydrogeological characterization demonstrated that microbial processes at the fractured bedrock-sediment interface were crucial for preventing contaminants reaching the water column, emphasizing the relevance of this critical zone environment for contaminant attenuation.
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Affiliation(s)
- Burcu Şimşir
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jun Yan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Jeongdae Im
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01002, United States
| | - Duane Graves
- Geosyntec Consultants, Knoxville, Tennessee 37922, United States
| | - Frank E. Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Trueba-Santiso A, Parladé E, Rosell M, Lliros M, Mortan SH, Martínez-Alonso M, Gaju N, Martín-González L, Vicent T, Marco-Urrea E. Molecular and carbon isotopic characterization of an anaerobic stable enrichment culture containing Dehalobacterium sp. during dichloromethane fermentation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 581-582:640-648. [PMID: 28063652 DOI: 10.1016/j.scitotenv.2016.12.174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
UNLABELLED Biodegradation of dichloromethane (DCM) under reducing conditions is of major concern due to its widespread detection in contaminated groundwaters. Here, we report an anaerobic enrichment culture derived from a membrane bioreactor operating in an industrial wastewater treatment plant, capable of fermenting DCM and the brominated analogue dibromomethane (DBM). Comparative analysis of bacterial 16S rDNA-DGGE profiles from fresh liquid medium inoculated with single colonies picked from serial dilution-to-extinction agar vials showed that cultures degrading DCM contained a predominant band belonging to Dehalobacterium, however this band was absent in cultures unable to degrade DCM. Analysis of the microbial composition of the enrichment by bacterial 16S rRNA gene amplicon paired-end sequencing confirmed the presence of Dehalobacterium together with three additional phylotypes belonging to Acetobacterium, Desulfovibrio, and Wolinella, representing all four operational taxonomic units >99.9% of the retrieved sequences. The carbon isotopic fractionation (ε) determined for DCM degradation in this culture was -27±2‰. This value differs from the ε previously reported for the DCM-fermentative bacteria Dehalobacter (-15.5±1.5‰) but they are both significantly different from those reported for facultative methylotrophic organisms (ranging from -45 to -61‰). This significant difference in the ε allows differentiating between hydrolytic transformation of DCM via glutathione-dependent dehalogenases and fermentation pathway. CAPSULE The carbon isotopic fractionation of dichloromethane by an enriched Dehalobacterium-containing culture has significant potential to monitor biodegradation of DCM in groundwaters.
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Affiliation(s)
- Alba Trueba-Santiso
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Eloi Parladé
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Mònica Rosell
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Martí Franquès s/n, 08028 Barcelona, Spain
| | - Marc Lliros
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Siti Hatijah Mortan
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Maira Martínez-Alonso
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Nuria Gaju
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lucía Martín-González
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain.
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Zhang X, Wu Y. Application of coupled zero-valent iron/biochar system for degradation of chlorobenzene-contaminated groundwater. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 75:571-580. [PMID: 28192351 DOI: 10.2166/wst.2016.503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel iron-carbon micro-electrolysis system, bamboo-derived biochar coupled with zero-valent iron (ZVI), was investigated for chlorobenzene (CB)-contaminated groundwater removal. Influences of initial pH value, mass ratio of the ZVI/Biochar, initial CB concentration and ionic strength of the ZVI/Biochar micro-electrolysis were studied. The results indicated that the increase of initial pH led to the decrease of the CB removal efficiency. While the optimum mass ratio of ZVI to biochar was 2:1, the improved initial concentration and reaction time were 33.68 mg/L and 4 h, respectively. When pH of 2, mass ratio of 2:1 and reaction time of 4 h were applied, the CB removal efficiency was 99.92%. Enhanced degradation of CB was observed with increased Cl- concentration. When the Cl- concentration of 1,000 mg/L and reaction time of 1 h were applied, the CB removal efficiency arrived at 98.2%. Additionally, considering that biochar is cost-effective and readily produced, the coupled ZVI/Biochar micro-electrolysis could represent an effective approach for the treatment of groundwater containing chlorinated organic compounds in the future.
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Affiliation(s)
- Xu Zhang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China E-mail:
| | - Yanqing Wu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China E-mail:
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Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, Löffler FE. 'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Syst Appl Microbiol 2016; 40:150-159. [PMID: 28292625 DOI: 10.1016/j.syapm.2016.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
Abstract
Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160±3μmolL-1 d-1. The DCM degrader attained 5.25×107±1.0×107 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4±0.8μm long and 0.4±0.1μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, 'Candidatus Dichloromethanomonas elyunquensis'.
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Affiliation(s)
- Sara Kleindienst
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Steven A Higgins
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Despina Tsementzi
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, DE 19714, USA
| | - Frank E Löffler
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.
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Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME JOURNAL 2016; 11:626-640. [PMID: 27898054 DOI: 10.1038/ismej.2016.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/25/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional. Using strain CF to experimentally verify annotations, we determined that the predicted defective serine biosynthesis pathway can be rescued with a promiscuous serine hydroxymethyltransferase. Strain CF grew without added thiamine although the thiamine biosynthesis pathway is predicted to be absent; intracellular thiamine diphosphate, the cofactor of carboxylases in central metabolism, was not detected in cell extracts. Thus, strain CF may use amino acids to replenish central metabolites, portending entangled metabolite exchanges in ACT-3. Consistent with annotation, strain CF possesses a functional corrinoid biosynthesis pathway, demonstrated by increasing corrinoid content during growth and guided cobalamin biosynthesis in corrinoid-free medium. Chloroform toxicity to corrinoid-producing methanogens and acetogens may drive the conservation of corrinoid autotrophy in Dehalobacter strains. Heme detection in strain CF cell extracts suggests the 'archaeal' heme biosynthesis pathway also functions in anaerobic Firmicutes. This study reinforces the importance of incorporating enzyme promiscuity and cofactor availability in genome-scale functional predictions and identifies essential nutrient interdependencies in anaerobic dechlorinating microbial communities.
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Stedtfeld RD, Stedtfeld TM, Samhan F, Kanitkar YH, Hatzinger PB, Cupples AM, Hashsham SA. Direct loop mediated isothermal amplification on filters for quantification of Dehalobacter in groundwater. J Microbiol Methods 2016; 131:61-67. [PMID: 27720723 DOI: 10.1016/j.mimet.2016.09.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 12/12/2022]
Abstract
Nucleic acid amplification of biomarkers is increasingly used to monitor microbial activity and assess remedial performance in contaminated aquifers. Previous studies described the use of filtration, elution, and direct isothermal amplification (i.e. no DNA extraction and purification) as a field-able means to quantify Dehalococcoides spp. in groundwater. This study expands previous work with direct loop mediated isothermal amplification (LAMP) for the detection and quantification of Dehalobacter spp. in groundwater. Experiments tested amplification of DNA with and without crude lysis and varying concentrations of humic acid. Three separate field-able methods of biomass concentration with eight aquifer samples were also tested, comparing direct LAMP with traditional DNA extraction and quantitative PCR (qPCR). A new technique was developed where filters were amplified directly within disposable Gene-Z chips. The direct filter amplification (DFA) method eliminated an elution step and provided a detection limit of 102Dehalobacter cells per 100mL. LAMP with crudely lysed Dehalobacter had a negligible effect on threshold time and sensitivity compared to lysed samples. The LAMP assay was more resilient than traditional qPCR to humic acid in sample, amplifying with up to 100mg per L of humic acid per reaction compared to 1mg per L for qPCR. Of the tested field-able concentrations methods, DFA had the lowest coefficient of variation among Dehalobacter spiked groundwater samples and lowest threshold time indicating high capture efficiency and low inhibition. While demonstrated with Dehalobacter, the DFA method can potentially be used for a number of applications requiring field-able, rapid (<60min) and highly sensitive quantification of microorganisms in environmental water samples.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Farag Samhan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA; Department of Water Pollution Control, National Research Centre, 33 El-Bohouth, P.O. 12622, Ad-Doqi, Giza, Egypt
| | - Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | | | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
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Linear free energy relationships of electrochemical and thermodynamic parameters for the electrochemical reductive dechlorination of chlorinated volatile organic compounds (Cl-VOCs). Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2016.04.182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Impact of Ammonium on Syntrophic Organohalide-Respiring and Fermenting Microbial Communities. mSphere 2016; 1:mSphere00053-16. [PMID: 27303735 PMCID: PMC4894693 DOI: 10.1128/msphere.00053-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/10/2016] [Indexed: 01/27/2023] Open
Abstract
Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4+-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium. Syntrophic interactions between organohalide-respiring and fermentative microorganisms are critical for effective bioremediation of halogenated compounds. This work investigated the effect of ammonium concentration (up to 4 g liter−1 NH4+-N) on trichloroethene-reducing Dehalococcoides mccartyi and Geobacteraceae in microbial communities fed lactate and methanol. We found that production of ethene by D. mccartyi occurred in mineral medium containing ≤2 g liter−1 NH4+-N and in landfill leachate. For the partial reduction of trichloroethene (TCE) to cis-dichloroethene (cis-DCE) at ≥1 g liter−1 NH4+-N, organohalide-respiring dynamics shifted from D. mccartyi and Geobacteraceae to mainly D. mccartyi. An increasing concentration of ammonium was coupled to lower metabolic rates, longer lag times, and lower gene abundances for all microbial processes studied. The methanol fermentation pathway to acetate and H2 was conserved, regardless of the ammonium concentration provided. However, lactate fermentation shifted from propionic to acetogenic at concentrations of ≥2 g liter−1 NH4+-N. Our study findings strongly support a tolerance of D. mccartyi to high ammonium concentrations, highlighting the feasibility of organohalide respiration in ammonium-contaminated subsurface environments. IMPORTANCE Contamination with ammonium and chlorinated solvents has been reported in numerous subsurface environments, and these chemicals bring significant challenges for in situ bioremediation. Dehalococcoides mccartyi is able to reduce the chlorinated solvent trichloroethene to the nontoxic end product ethene. Fermentative bacteria are of central importance for organohalide respiration and bioremediation to provide D. mccartyi with H2, their electron donor, acetate, their carbon source, and other micronutrients. In this study, we found that high concentrations of ammonium negatively correlated with rates of trichloroethene reductive dehalogenation and fermentation. However, detoxification of trichloroethene to nontoxic ethene occurred even at ammonium concentrations typical of those found in animal waste (up to 2 g liter−1 NH4+-N). To date, hundreds of subsurface environments have been bioremediated through the unique metabolic capability of D. mccartyi. These findings extend our knowledge of D. mccartyi and provide insight for bioremediation of sites contaminated with chlorinated solvents and ammonium.
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Schiffmacher EN, Becker JG, Lorah MM, Voytek MA. The effects of co-contaminants and native wetland sediments on the activity and dominant transformation mechanisms of a 1,1,2,2-tetrachloroethane (TeCA)-degrading enrichment culture. CHEMOSPHERE 2016; 147:239-247. [PMID: 26766361 DOI: 10.1016/j.chemosphere.2015.12.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/03/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
Bioremediation strategies, including bioaugmentation with chlorinated ethene-degrading enrichment cultures, have been successfully applied in the cleanup of subsurface environments contaminated with tetrachloroethene (PCE) and/or trichloroethene (TCE). However, these compounds are frequently found in the environment as components of mixtures that may also contain chlorinated ethanes and methanes. Under these conditions, the implementation of bioremediation may be complicated by inhibition effects, particularly when multiple dehalorespirers are present. We investigated the ability of the 1,1,2,2-tetrachloroethane (TeCA)-dechlorinating culture WBC-2 to biotransform TeCA alone, or a mixture of TeCA plus PCE and carbon tetrachloride (CT), in microcosms. The microcosms contained electron donors provided to biostimulate the added culture and sediment collected from a wetland where numerous "hotspots" of contamination with chlorinated solvent mixtures exist. The dominant TeCA biodegradation mechanism mediated by the WBC-2 culture in the microcosms was different in the presence of these wetland sediments than in the sediment-free enrichment culture or in previous WBC-2 bioaugmented microcosms and column tests conducted with wetland sediment collected at nearby sites. The co-contaminants and their daughter products also inhibited TeCA biodegradation by WBC-2. These results highlight the need to conduct biodegradability assays at new sites, particularly when multiple contaminants and dehalorespiring populations are present.
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Affiliation(s)
- Emily N Schiffmacher
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Jennifer G Becker
- Department of Environmental Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Michelle M Lorah
- United States Geological Survey, MD-DE-DC Water Science Center, 5522 Research Park Drive, Baltimore, MD 21228, USA.
| | - Mary A Voytek
- United States Geological Survey, 430 National Center, Reston, VA 20192, USA.
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Tang S, Wang PH, Higgins SA, Löffler FE, Edwards EA. Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates. Front Microbiol 2016; 7:100. [PMID: 26903979 PMCID: PMC4751268 DOI: 10.3389/fmicb.2016.00100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
The genomes of two closely related Dehalobacter strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous (rdh) genes. These two genomes were systematically compared to three other available organohalide-respiring Dehalobacter genomes (Dehalobacter restrictus strain PER-K23, Dehalobacter sp. strain E1 and Dehalobacter sp. strain UNSWDHB), and to the genomes of Dehalococcoides mccartyi strain 195 and Desulfitobacterium hafniense strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes, cfrA and dcrA, that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five Dehalobacter genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five Dehalobacter genomes, yet D. restrictus can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to D. mccartyi, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. This analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.
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Affiliation(s)
- Shuiquan Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Po Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
| | - Steven A Higgins
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Frank E Löffler
- Department of Microbiology, University of TennesseeKnoxville, TN, USA; Center for Environmental Biotechnology, University of TennesseeKnoxville, TN, USA; University of Tennessee and Oak Ridge National Laboratory Joint Institute for Biological Sciences and Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA; Department of Civil and Environmental Engineering, University of TennesseeKnoxville, TN, USA
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto, ON, Canada
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Characterization of Chlorinated Aliphatic Hydrocarbons and Environmental Variables in a Shallow Groundwater in Shanghai Using Kriging Interpolation and Multifactorial Analysis. PLoS One 2015; 10:e0142241. [PMID: 26565796 PMCID: PMC4643907 DOI: 10.1371/journal.pone.0142241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/18/2015] [Indexed: 11/19/2022] Open
Abstract
CAHs, as a cleaning solvent, widely contaminated shallow groundwater with the development of manufacturing in China's Yangtze River Delta. This study focused on the distribution of CAHs, and correlations between CAHs and environmental variables in a shallow groundwater in Shanghai, using kriging interpolation and multifactorial analysis. The results showed that the overall CAHs plume area (above DIV) was approximately 9,000 m(2) and located in the 2-4 m underground, DNAPL was accumulated at an area of approximately 1,400 m(2) and located in the 6-8m sandy silt layer on the top of the muddy silty clay. Heatmap of PPC for CAHs and environmental variables showed that the correlation between "Fe(2+)" and most CAHs such as "1,1,1-TCA", "1,1-DCA", "1,1-DCE" and "%TCA" were significantly positive (p<0.001), but "%CA" and/or "%VC" was not, and "Cl-" was significantly positive correlated with "1,1-DCA" and "1,1-DCE" (p<0.001). The PCA demonstrated that the relative proportions of CAHs in groundwater were mostly controlled by the sources and the natural attenuation. In conclusion, the combination of geographical and chemometrics was helpful to establishing an aerial perspective of CAHs and identifying reasons for the accumulation of toxic dechlorination intermediates, and could become a useful tool for characterizing contaminated sites in general.
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Lu Q, Zhu RL, Yang J, Li H, Liu YD, Lu SG, Luo QS, Lin KF. Natural attenuation model and biodegradation for 1,1,1-trichloroethane contaminant in shallow groundwater. Front Microbiol 2015; 6:839. [PMID: 26379629 PMCID: PMC4548683 DOI: 10.3389/fmicb.2015.00839] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/31/2015] [Indexed: 12/03/2022] Open
Abstract
Natural attenuation is an effective and feasible technology for controlling groundwater contamination. This study investigated the potential effectiveness and mechanisms of natural attenuation of 1,1,1-trichloroethane (TCA) contaminants in shallow groundwater in Shanghai by using a column simulation experiment, reactive transport model, and 16S rRNA gene clone library. The results indicated that the majority of the contaminant mass was present at 2–6 m in depth, the contaminated area was approximately 1000 m × 1000 m, and natural attenuation processes were occurring at the site. The effluent breakthrough curves from the column experiments demonstrated that the effectiveness of TCA natural attenuation in the groundwater accorded with the advection-dispersion-reaction equation. The kinetic parameter of adsorption and biotic dehydrochlorination of TCA was 0.068 m3/kg and 0.0045 d–1. The contamination plume was predicted to diminish and the maximum concentration of TCA decreased to 280 μg/L. The bacterial community during TCA degradation in groundwater belonged to Trichococcus, Geobacteraceae, Geobacter, Mucilaginibacter, and Arthrobacter.
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Affiliation(s)
- Qiang Lu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology , Shanghai, China
| | - Rui-Li Zhu
- Shanghai Academy of Environmental Sciences , Shanghai, China
| | - Jie Yang
- Shanghai Academy of Environmental Sciences , Shanghai, China
| | - Hui Li
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology , Shanghai, China
| | - Yong-Di Liu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology , Shanghai, China
| | - Shu-Guang Lu
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology , Shanghai, China
| | - Qi-Shi Luo
- Shanghai Engineering Research Center of Contaminated Sites Remediation, Shanghai Institute for Design and Research on Environmental Engineering , Shanghai, China
| | - Kuang-Fei Lin
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resource and Environmental Engineering, East China University of Science and Technology , Shanghai, China
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Zhang Y, Hu M, Li P, Wang X, Meng Q. Trichloroethylene removal and bacterial variations in the up-flow anaerobic sludge blanket reactor in response to temperature shifts. Appl Microbiol Biotechnol 2015; 99:6091-102. [DOI: 10.1007/s00253-015-6480-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/07/2015] [Accepted: 02/12/2015] [Indexed: 12/26/2022]
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Ndong LBB, Gu X, Lu S, Ibondou MP, Qiu Z, Sui Q, Mbadinga SM, Mu B. Role of reactive oxygen species in the dechlorination of trichloroethene and 1.1.1-trichloroethane in aqueous phase in UV/TiO 2 systems. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.11.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Palau J, Shouakar-Stash O, Hunkeler D. Carbon and chlorine isotope analysis to identify abiotic degradation pathways of 1,1,1-trichloroethane. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:14400-14408. [PMID: 25379605 DOI: 10.1021/es504252z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This study investigates dual C-Cl isotope fractionation during 1,1,1-TCA transformation by heat-activated persulfate (PS), hydrolysis/dehydrohalogenation (HY/DH) and Fe(0). Compound-specific chlorine isotope analysis of 1,1,1-TCA was performed for the first time, and transformation-associated isotope fractionation ε bulk C and ε bulk Cl values were -4.0 ± 0.2‰ and no chlorine isotope fractionation with PS, -1.6 ± 0.2‰ and -4.7 ± 0.1‰ for HY/DH, -7.8 ± 0.4‰ and -5.2 ± 0.2‰ with Fe(0). Distinctly different dual isotope slopes (Δδ13C/Δδ37Cl): ∞ with PS, 0.33 ± 0.04 for HY/DH and 1.5 ± 0.1 with Fe(0) highlight the potential of this approach to identify abiotic degradation pathways of 1,1,1-TCA in the field. The trend observed with PS agreed with a C-H bond oxidation mechanism in the first reaction step. For HY/DH and Fe(0) pathways, different slopes were obtained although both pathways involve cleavage of a C-Cl bond in their initial reaction step. In contrast to the expected larger primary carbon isotope effects relative to chlorine for C-Cl bond cleavage, ε bulk C < ε bulk Cl was observed for HY/DH and in a similar range for reduction by Fe(0), suggesting the contribution of secondary chlorine isotope effects. Therefore, different magnitude of secondary chlorine isotope effects could at least be partly responsible for the distinct slopes between HY/DH and Fe(0) pathways. Following this dual isotope approach, abiotic transformation processes can unambiguously be identified and quantified.
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Affiliation(s)
- Jordi Palau
- Centre for Hydrogeology and Geothermics, University of Neuchâtel , Neuchâtel CH-2000, Switzerland
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Zhou YZ, Yang J, Wang XL, Pan YQ, Li H, Zhou D, Liu YD, Wang P, Gu JD, Lu Q, Qiu YF, Lin KF. Bio-beads with immobilized anaerobic bacteria, zero-valent iron, and active carbon for the removal of trichloroethane from groundwater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:11500-11509. [PMID: 24906831 DOI: 10.1007/s11356-014-3110-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/26/2014] [Indexed: 06/03/2023]
Abstract
Chlorinated hydrocarbons are the most common organic pollutants in groundwater systems worldwide. In this study, we developed bio-beads with immobilized anaerobic bacteria, zero-valent iron (ZVI), and activated carbon (AC) powder and evaluated their efficacy in removing 1,1,1-trichloroethane (TCA) from groundwater. Bio-beads were produced by polyvinyl alcohol, alginate, and AC powder. We found that the concentration of AC powder used significantly affected the mechanical properties of immobilized bio-beads and that 1.0 % (w/v) was the optimal concentration. The bio-beads effectively degraded TCA (160 mg L(-1)) in the anaerobic medium and could be reused up to six times. The TCA degradation rate of bio-beads was 1.5 and 2.3 times greater, respectively, than ZVI + AC treatment or microbes + AC treatment. Measuring FeS produced by microbial reactions indicated that TCA removal occurred via FeS-catalyzed dechlorination. Analysis of clonal libraries derived from bio-beads demonstrated that the dominant species in the community were Betaproteobacteria and Gammaproteobacteria, which may contribute to the long-term stability of ZVI reactivity during TCA dechlorination. This study shows that the combined use of immobilized anaerobic bacteria, ZVI, and AC in bio-beads is effective and practical for TCA dechlorination and suggests they may be applicable towards developing a groundwater treatment system for the removal of TCA.
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Affiliation(s)
- Ya-Zhen Zhou
- State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, State Key Laboratory of Bioreactor Engineering, School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
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Huang B, Lei C, Wei C, Zeng G. Chlorinated volatile organic compounds (Cl-VOCs) in environment - sources, potential human health impacts, and current remediation technologies. ENVIRONMENT INTERNATIONAL 2014; 71:118-38. [PMID: 25016450 DOI: 10.1016/j.envint.2014.06.013] [Citation(s) in RCA: 332] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 06/20/2014] [Accepted: 06/24/2014] [Indexed: 05/03/2023]
Abstract
Chlorinated volatile organic compounds (Cl-VOCs), including polychloromethanes, polychloroethanes and polychloroethylenes, are widely used as solvents, degreasing agents and a variety of commercial products. These compounds belong to a group of ubiquitous contaminants that can be found in contaminated soil, air and any kind of fluvial mediums such as groundwater, rivers and lakes. This review presents a summary of the research concerning the production levels and sources of Cl-VOCs, their potential impacts on human health as well as state-of-the-art remediation technologies. Important sources of Cl-VOCs principally include the emissions from industrial processes, the consumption of Cl-VOC-containing products, the disinfection process, as well as improper storage and disposal methods. Human exposure to Cl-VOCs can occur through different routes, including ingestion, inhalation and dermal contact. The toxicological impacts of these compounds have been carefully assessed, and the results demonstrate the potential associations of cancer incidence with exposure to Cl-VOCs. Most Cl-VOCs thus have been listed as priority pollutants by the Ministry of Environmental Protection (MEP) of China, Environmental Protection Agency of the U.S. (U.S. EPA) and European Commission (EC), and are under close monitor and strict control. Yet, more efforts will be put into the epidemiological studies for the risk of human exposure to Cl-VOCs and the exposure level measurements in contaminated sites in the future. State-of-the-art remediation technologies for Cl-VOCs employ non-destructive methods and destructive methods (e.g. thermal incineration, phytoremediation, biodegradation, advanced oxidation processes (AOPs) and reductive dechlorination), whose advantages, drawbacks and future developments are thoroughly discussed in the later sections.
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Affiliation(s)
- Binbin Huang
- College of Environment Science and Engineering, Hunan University, Changsha 410082, P.R. China
| | - Chao Lei
- School of Hydraulic Engineering, Changsha University of Science & Technology, Changsha 410114, P.R. China
| | - Chaohai Wei
- Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institutions, South China University of Technology, Guangzhou 510006, P.R. China
| | - Guangming Zeng
- College of Environment Science and Engineering, Hunan University, Changsha 410082, P.R. China
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Broholm MM, Hunkeler D, Tuxen N, Jeannottat S, Scheutz C. Stable carbon isotope analysis to distinguish biotic and abiotic degradation of 1,1,1-trichloroethane in groundwater sediments. CHEMOSPHERE 2014; 108:265-273. [PMID: 24559936 DOI: 10.1016/j.chemosphere.2014.01.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 12/06/2013] [Accepted: 01/05/2014] [Indexed: 06/03/2023]
Abstract
The fate and treatability of 1,1,1-TCA by natural and enhanced reductive dechlorination was studied in laboratory microcosms. The study shows that compound-specific isotope analysis (CSIA) identified an alternative 1,1,1-TCA degradation pathway that cannot be explained by assuming biotic reductive dechlorination. In all biotic microcosms 1,1,1-TCA was degraded with no apparent increase in the biotic degradation product 1,1-DCA. 1,1,1-TCA degradation was documented by a clear enrichment in (13)C in all biotic microcosms, but not in the abiotic control, which suggests biotic or biotically mediated degradation. Biotic degradation by reductive dechlorination of 1,1-DCA to CA only occurred in bioaugmented microcosms and in donor stimulated microcosms with low initial 1,1,1-TCA or after significant decrease in 1,1,1-TCA concentration (after∼day 200). Hence, the primary degradation pathway for 1,1,1-TCA does not appear to be reductive dechlorination via 1,1-DCA. In the biotic microcosms, the degradation of 1,1,1-TCA occurred under iron and sulfate reducing conditions. Biotic reduction of iron and sulfate likely resulted in formation of FeS, which can abiotically degrade 1,1,1-TCA. Hence, abiotic degradation of 1,1,1-TCA mediated by biotic FeS formation constitute an explanation for the observed 1,1,1-TCA degradation. This is supported by a high 1,1,1-TCA (13)C enrichment factor consistent with abiotic degradation in biotic microcosms. 1,1-DCA carbon isotope field data suggest that this abiotic degradation of 1,1,1-TCA is a relevant process also at the field site.
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Affiliation(s)
- Mette M Broholm
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Daniel Hunkeler
- Centre for Hydrogeology, University of Neuchâtel, Neuchâtel, Switzerland.
| | | | - Simon Jeannottat
- Centre for Hydrogeology, University of Neuchâtel, Neuchâtel, Switzerland.
| | - Charlotte Scheutz
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Ding C, Zhao S, He J. A Desulfitobacterium sp. strain PR reductively dechlorinates both 1,1,1-trichloroethane and chloroform. Environ Microbiol 2014; 16:3387-97. [PMID: 24428759 DOI: 10.1111/1462-2920.12387] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 01/04/2014] [Indexed: 11/30/2022]
Abstract
1,1,1-Trichloroethane (TCA) and chloroform are two notorious groundwater pollutants. Here we report the isolation and characterization of Desulfitobacterium sp. strain PR that rapidly dechlorinates both compounds. In pyruvate-amended medium, strain PR reductively dechlorinates ∼ 1.0 mM TCA completely to monochloroethane within 15 days. Under the same conditions, strain PR dechlorinates ∼ 1.2 mM chloroform to predominantly dichloromethane (∼ 1.14 mM) and trace amount of monochloromethane (∼ 0.06 mM) within 10 days. Strain PR shares 96.7% 16S rRNA gene sequence similarity with its closest relative - Desulfitobacterium metallireducens strain 853-15; however, it distinguishes itself from known Desulfitobacterium strains by its inability of utilizing several of their commonly shared substrates such as lactate, thiosulfate and sulfite. A reductive dehalogenase gene (ctrA) in strain PR was identified to be responsible for dechlorination of both TCA and chloroform, showing a maximum expression level of 5.95 ∼ 6.25 copies of transcripts cell(-1) . CtrA shares 94% amino acid sequence identity with CfrA in Dehalobacter sp. strain CF50 and DcrA in Dehalobacter sp. strain DCA. Interestingly, strain PR could tolerate high aqueous concentrations (up to 0.45 mM) of trichloroethene, another groundwater pollutant that often coexists with TCA/chloroform. As the first chloroform-respiring and the second TCA-respiring isolate that has been identified, Desulfitobacterium sp. strain PR may prove useful in remediation of halogenated alkanes with trihalomethyl (-CX₃) groups.
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Affiliation(s)
- Chang Ding
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
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Justicia-Leon SD, Higgins S, Mack EE, Griffiths DR, Tang S, Edwards EA, Löffler FE. Bioaugmentation with distinct Dehalobacter strains achieves chloroform detoxification in microcosms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:1851-1858. [PMID: 24392834 DOI: 10.1021/es403582f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Chloroform (CF) is a widespread groundwater contaminant not susceptible to aerobic degradation. Under anoxic conditions, CF can undergo abiotic and cometabolic transformation but detoxification is generally not achieved. The recent discovery of distinct Dehalobacter strains that respire CF to dichloromethane (DCM) and ferment DCM to nonchlorinated products promises that bioremediation of CF plumes is feasible. To track both strains, 16S rRNA gene-based qPCR assays specific for either Dehalobacter strain were designed and validated. A laboratory treatability study explored the value of bioaugmentation and biostimulation to achieve CF detoxification using anoxic microcosms established with aquifer material from a CF-contaminated site. Microcosms that received 6% (v/v) of the CF-to-DCM-dechlorinating culture Dhb-CF to achieve an initial Dehalobacter cell titer of 1.6 ± 0.9 × 10(4) mL(-1) dechlorinated CF to stoichiometric amounts of DCM. Subsequent augmentation with 3% (v/v) of the DCM-degrading consortium RM to an initial Dehalobacter cell abundance of 1.2 ± 0.2 × 10(2) mL(-1) achieved complete DCM degradation in microcosms amended with 10 mM bicarbonate. Growth of the CF-respiring and the DCM-degrading Dehalobacter populations and detoxification were also observed in microcosms that received both inocula simultaneously. These findings suggest that anaerobic bioremediation (e.g., bioaugmentation) is a possible remedy at CF- and DCM-contaminated sites without CT, which strongly inhibited CF organohalide respiration and DCM organohalide fermentation.
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40
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Effects of bioaugmentation on enhanced reductive dechlorination of 1,1,1-trichloroethane in groundwater: a comparison of three sites. Biodegradation 2013; 25:459-78. [DOI: 10.1007/s10532-013-9674-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 10/31/2013] [Indexed: 10/26/2022]
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41
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Isolation and characterization of a novel Dehalobacter species strain TCP1 that reductively dechlorinates 2,4,6-trichlorophenol. Biodegradation 2013; 25:313-23. [PMID: 23995979 DOI: 10.1007/s10532-013-9662-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
Chlorophenols are widely used as biocides, leading them to being prevalent environmental contaminants that pose toxic threats to ecosystems. In this study, a Dehalobacter species strain TCP1 was isolated from a digester sludge sample, which is able to dechlorinate 2,4,6-trichlorophenol (2,4,6-TCP) to 4-monochlorophenol (4-MCP) with H2 as the sole electron donor and acetate as the carbon source. Strain TCP1 also distinguishes itself from other Dehalobacter species with its capability to dechlorinate tetrachloroethene or trichloroethene (TCE) to both cis- and trans-dichloroethenes in a ratio of 5.6 (±0.2):1. The growth yields of strain TCP1 on TCE and 2,4,6-TCP were 4.14 × 10(13) and 5.77 × 10(13) cells mol(-1) of Cl(-) released, respectively. Strain TCP1 contains five unusually long 16S rRNA gene copies per genome, and the extra length is due to the ~110 bp insertion sequences at their 5'-ends. This suggests that strain TCP1 may represent a novel Dehalobacter species. A putative chlorophenol reductive dehalogenase gene-debcprA-was identified to catalyze the ortho-chlorine removal from 2,4,6-TCP. Both the culture-dependent and housekeeping rpoB gene-based approaches indicate the purity of the culture. Strain TCP1 can serve as a promising candidate for the bioremediation of 2,4,6-TCP contaminated sites, and its discovery expands our understanding of metabolic capabilities of Dehalobacter species.
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42
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Dillehay JL, Bowman KS, Yan J, Rainey FA, Moe WM. Substrate interactions in dehalogenation of 1,2-dichloroethane, 1,2-dichloropropane, and 1,1,2-trichloroethane mixtures by Dehalogenimonas spp. Biodegradation 2013; 25:301-12. [DOI: 10.1007/s10532-013-9661-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/22/2013] [Indexed: 12/01/2022]
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Tang S, Edwards EA. Identification of Dehalobacter reductive dehalogenases that catalyse dechlorination of chloroform, 1,1,1-trichloroethane and 1,1-dichloroethane. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120318. [PMID: 23479748 DOI: 10.1098/rstb.2012.0318] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two novel reductive dehalogenases (RDases) that are highly similar to each other but catalyse distinct dechlorination reactions were identified from Dehalobacter-containing mixed cultures. These two RDases were partially purified from crude protein extracts of anaerobic dechlorinating enrichment cultures using blue native polyacrylamide gel electrophoresis. Gel slices were assayed for dechlorinating activity, and associated proteins were identified using liquid chromatography tandem mass spectrometry with the metagenome of the parent culture as the reference database. The two RDases identified, annotated as CfrA and DcrA, share an amino acid identity of 95.2 per cent, but use different substrates: CfrA dechlorinates chloroform (CF) and 1,1,1-trichloroethane (1,1,1-TCA), but not 1,1-dichloroethane; DcrA dechlorinates 1,1-dichloroethane, but not CF or 1,1,1-TCA. These two novel RDases share no more than 40 per cent amino acid identity to any other known or putative RDases, but both have a twin-arginine motif and two iron-sulfur binding motifs conserved in most RDases. Peptides specific to two putative membrane anchor proteins, annotated as CfrB and DcrB, were also detected in gel slices.
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Affiliation(s)
- Shuiquan Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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Hug LA, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L. Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120322. [PMID: 23479752 DOI: 10.1098/rstb.2012.0322] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.
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Affiliation(s)
- Laura A Hug
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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45
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Damgaard I, Bjerg PL, Bælum J, Scheutz C, Hunkeler D, Jacobsen CS, Tuxen N, Broholm MM. Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis. JOURNAL OF CONTAMINANT HYDROLOGY 2013; 146:37-50. [PMID: 23357226 DOI: 10.1016/j.jconhyd.2012.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 10/17/2012] [Accepted: 11/29/2012] [Indexed: 06/01/2023]
Abstract
The degradation of chlorinated ethenes and ethanes in clay till was investigated at a contaminated site (Vadsby, Denmark) by high resolution sampling of intact cores combined with groundwater sampling. Over decades of contamination, bioactive zones with degradation of trichloroethene (TCE) and 1,1,1-trichloroethane (1,1,1-TCA) to 1,2-cis-dichloroethene (cis-DCE) and 1,1-dichloroethane, respectively, had developed in most of the clay till matrix. Dehalobacter dominated over Dehalococcoides (Dhc) in the clay till matrix corresponding with stagnation of sequential dechlorination at cis-DCE. Sporadically distributed bioactive zones with partial degradation to ethene were identified in the clay till matrix (thickness from 0.10 to 0.22 m). In one sub-section profile the presence of Dhc with the vcrA gene supported the occurrence of degradation of cis-DCE and VC, and in another enriched δ(13)C for TCE, cis-DCE and VC documented degradation. Highly enriched δ(13)C for 1,1,1-TCA (25‰) and cis-DCE (-4‰) suggested the occurrence of abiotic degradation in a third sub-section profile. Due to fine scale heterogeneity the identification of active degradation zones in the clay till matrix depended on high resolution subsampling of the clay till cores. The study demonstrates that an integrated approach combining chemical analysis, molecular microbial tools and compound specific isotope analysis (CSIA) was required in order to document biotic and abiotic degradations in the clay till system.
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Affiliation(s)
- Ida Damgaard
- DTU Environment (Department of Environmental Engineering, Technical University of Denmark), Miljoevej bldn 113, DK-2800 Lyngby, Denmark.
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46
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Lai Y, Becker JG. Compounded effects of chlorinated ethene inhibition on ecological interactions and population abundance in a Dehalococcoides - Dehalobacter coculture. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:1518-25. [PMID: 23281935 DOI: 10.1021/es3034582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The development of rational and effective engineered bioremediation approaches for sites contaminated with chlorinated solvents requires a fundamental understanding of the factors limiting the in situ activity of dehalorespiring bacteria. Frequently, multiple dehalorespiring bacteria are present at contaminated sites, particularly when bioaugmentation is applied. The ecological interactions between different dehalorespiring populations can-along with hydrodynamic and other environmental factors-affect their activity and thus the rates and extent of dehalorespiration. An integrated experimental and modeling approach was used to evaluate the ecological interactions between two hydrogenotrophic, dehalorespiring strains. A dual Monod model of dehalorespiration provided a good fit to the chlorinated ethene concentrations measured in a coculture of Dehalococcoides mccartyi 195 and Dehalobacter restrictus growing on tetrachloroethene (PCE) and excess H(2) in a continuous-flow reactor. Inhibition of dehalorespiration by chlorinated ethenes was previously observed in cultures containing Dehalococcoides or Dehalobacter strains. Therefore, inhibition coefficients were estimated for Dhc. mccartyi 195 and Dhb. restrictus. The inhibition effects of PCE and TCE on VC dechlorination by Dhc. mccartyi 195, and of VC on PCE and TCE dechlorination by Dhb. restrictus, were compounded when these strains were grown in coculture, and dehalorespiring population abundance and survival could be accurately predicted only by incorporating these complex interactions into the dual Monod model.
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Affiliation(s)
- Yenjung Lai
- Swette Center for Environmental Biotechnology, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287-5701, United States
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47
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Tang S, Gong Y, Edwards EA. Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data. PLoS One 2012; 7:e52038. [PMID: 23284863 PMCID: PMC3528712 DOI: 10.1371/journal.pone.0052038] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 11/13/2012] [Indexed: 11/18/2022] Open
Abstract
Typically, the assembly and closure of a complete bacterial genome requires substantial additional effort spent in a wet lab for gap resolution and genome polishing. Assembly is further confounded by subspecies polymorphism when starting from metagenome sequence data. In this paper, we describe an in silico gap-resolution strategy that can substantially improve assembly. This strategy resolves assembly gaps in scaffolds using pre-assembled contigs, followed by verification with read mapping. It is capable of resolving assembly gaps caused by repetitive elements and subspecies polymorphisms. Using this strategy, we realized the de novo assembly of the first two Dehalobacter genomes from the metagenomes of two anaerobic mixed microbial cultures capable of reductive dechlorination of chlorinated ethanes and chloroform. Only four additional PCR reactions were required even though the initial assembly with Newbler v. 2.5 produced 101 contigs within 9 scaffolds belonging to two Dehalobacter strains. By applying this strategy to the re-assembly of a recently published genome of Bacteroides, we demonstrate its potential utility for other sequencing projects, both metagenomic and genomic.
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Affiliation(s)
- Shuiquan Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Yunchen Gong
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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48
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Preston J, Watts JEM, Jones M. Novel bacterial community associated with 500-year-old unpreserved archaeological wood from King Henry VIII's Tudor Warship the Mary Rose. Appl Environ Microbiol 2012; 78:8822-8. [PMID: 23023757 PMCID: PMC3502903 DOI: 10.1128/aem.02387-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/22/2012] [Indexed: 02/01/2023] Open
Abstract
A 500-year-old unpreserved Mary Rose sample, historically containing an iron bolt, was analyzed using enrichment cultures and 16S sequencing. The novel community of bacteria present demonstrates a biological pathway of Fe and S oxidation and a range of acid-generating metabolisms, with implications for preservation and biogeochemical cycling.
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Affiliation(s)
- Joanne Preston
- University of Portsmouth, School of Biological Sciences, Portsmouth, Hants, United Kingdom.
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49
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Yamasaki S, Nomura N, Nakajima T, Uchiyama H. Cultivation-independent identification of candidate dehalorespiring bacteria in tetrachloroethylene degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:7709-7716. [PMID: 22708499 DOI: 10.1021/es301288y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Tetrachloroethylene (PCE) is one of the major pollutants and is degraded by dissimilation by dehalorespiring bacteria. The dehalorespiring bacteria are anaerobic, and most cannot be cultured by conventional agar plating methods. Therefore, to identify the dehalorespiring bacteria that dissimilatively degrade PCE, a cultivation-independent method is required. To achieve accurate and detailed analysis of the bacteria, we developed a novel stable isotope probing (SIP) method. This technique involves 2 steps, namely, a labeling step, in which a labeled carbon source is incorporated into the sample's DNA, and an analysis step, in which the DNA is isolated, fractionated, and analyzed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Subsequently, 16S rRNA sequencing and phylogenetic analysis were performed to identify the bacteria. Initially, we examined the effectiveness of this method by using Dehalococcoides ethenogenes 195 consortium as a defined model system. The result indicated the method was able to correctly identify the dehalorespiring bacteria D. ethenogenes 195 from the consortium. Moreover, in an artificially contaminated microcosm experiment, we confirmed that the method was able to identify the indigenous dehalorespiring bacteria Dehalobacter sp. Thus, we concluded that this novel method was a feasible tool to identify dehalorespiring bacteria in natural environments.
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Affiliation(s)
- Shouhei Yamasaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Li H, Zhang W, Li L, Liu YD, Lin KF, Lu SG, Mu BZ, Du XM, Lu Q, Zhang Q, Shen TT, Li BZ, Zhao LM, Li YY. Effects of 1,1,1-trichloroethane on enzymatic activity and bacterial community in anaerobic microcosm form sequencing batch reactors. ECOTOXICOLOGY (LONDON, ENGLAND) 2012; 21:1426-1435. [PMID: 22543958 DOI: 10.1007/s10646-012-0896-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/15/2012] [Indexed: 05/31/2023]
Abstract
1,1,1-Trichloroethane (TCA), a major organic and groundwater contaminant, has very strong toxic effects on humans, plants and microorganisms. Effects of TCA on enzymatic activity and microbial diversity were investigated in the anaerobic sequencing batch reactor (ASBR) under methanogenic, nitrate-reducing, sulfate-reducing and benzene/toluene degrading conditions. The activities of three enzymes (lactate dehydrogenase, phosphatase and protease) were significantly decreased in the presence of 5 mg/L TCA. Within these three affected enzymes, phosphatase activity may serve as a noteworthy marker of bacterial toxicity. The activity of phosphatase was 0.2 U/L in methanogenic conditions with 5 mg/L TCA, which was 99% lower than the controls, and the enzyme activity was 18.6 U/L in methanogenic conditions with 1 mg/L TCA, which was 7% lower than the controls. DGGE profiles showed that TCA altered the bacterial community distribution and diversity obviously during the 21 day of TCA exposure. The enzyme activities decreased second lowest but TCA degrading strains Clostridium sp. DhR-2/LM-G01, Bacterial clone DCE25 and Bacterial clone DPHB06 were enriched in the methanogenic ASBR amended TCA.
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Affiliation(s)
- Hui Li
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, People's Republic of China
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