1
|
Ojo AO, Castillo J, Cason ED, Valverde A. Biodegradation of chloroethene compounds under microoxic conditions. Biotechnol Bioeng 2024; 121:1036-1049. [PMID: 38116701 DOI: 10.1002/bit.28630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
The biodegradation of chloroethene compounds under oxic and anoxic conditions is well established. However, the biological reactions that take place under microoxic conditions are unknown. Here, we report the biostimulated (BIOST: addition of lactate) and natural attenuated (NAT) degradation of chloroethene compounds under microoxic conditions by bacterial communities from chloroethene compounds-contaminated groundwater. The degradation of tetrachloroethene was significantly higher in NAT (15.14% on average) than in BIOST (10.13% on average) conditions at the end of the experiment (90 days). Sporomusa, Paracoccus, Sedimentibacter, Pseudomonas, and Desulfosporosinus were overrepresented in NAT and BIOST compared to the source groundwater. The NAT metagenome contains phenol hydrolase P1 oxygenase (dmpL), catechol-1,2-dioxygenase (catA), catechol-2,3-dioxygenases (dmpB, todE, and xylE) genes, which could be involved in the cometabolic degradation of chloroethene compounds; and chlorate reductase (clrA), that could be associated with partial reductive dechlorination of chloroethene compounds. Our data provide a better understanding of the bacterial communities, genes, and pathways potentially implicated in the reductive and cometabolic degradation of chloroethene compounds under microoxic conditions.
Collapse
Affiliation(s)
- Abidemi Oluranti Ojo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
- Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, South Africa
| | - Julio Castillo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Errol Duncan Cason
- Department of Animal Sciences, University of the Free State, Bloemfontein, South Africa
| | - Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Salamanca, Spain
| |
Collapse
|
2
|
Richards PM, Ewald JM, Zhao W, Rectanus H, Fan D, Durant N, Pound M, Mattes TE. Natural Biodegradation of Vinyl Chloride and cis-Dichloroethene in Aerobic and Suboxic Conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:56154-56167. [PMID: 35322370 DOI: 10.1007/s11356-022-19755-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Chlorinated ethene (CE) groundwater contamination is commonly treated through anaerobic biodegradation (i.e., reductive dechlorination) either as part of an engineered system or through natural attenuation. Aerobic biodegradation has also been recognized as a potentially significant pathway for the removal of the lower CEs cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). However, the role of aerobic biodegradation under low oxygen conditions typical of contaminated groundwater is unclear. Bacteria capable of aerobic VC biodegradation appear to be common in the environment, while aerobic biodegradation of cDCE is less common and little is known regarding the organisms responsible. In this study, we investigate the role of aerobic cDCE and VC biodegradation in a mixed contaminant plume (including CEs, BTEX, and ketones) at Naval Air Station North Island, Installation Restoration Site 9. Sediment and groundwater collected from the plume source area, mid-plume, and shoreline were used to prepare microcosms under fully aerobic (8 mg/L dissolved oxygen (DO)) and suboxic (< 1 mg/L DO) conditions. In the shoreline microcosms, VC and cDCE were rapidly degraded under suboxic conditions (100% and 77% removal in < 62 days). In the suboxic VC microcosms, biodegradation was associated with a > 5 order of magnitude increase in the abundance of functional gene etnE, part of the aerobic VC utilization pathway. VC and cDCE were degraded more slowly under fully aerobic conditions (74% and 30% removal) in 110 days. High-throughput 16S rRNA and etnE sequencing suggest the presence of novel VC- and cDCE-degrading bacteria. These results suggest that natural aerobic biodegradation of cDCE and VC is occurring at the site and provide new evidence that low (< 1 mg/L) DO levels play a significant role in natural attenuation of cDCE and VC.
Collapse
Affiliation(s)
- Patrick M Richards
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Jessica M Ewald
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Weilun Zhao
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Heather Rectanus
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Dimin Fan
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Neal Durant
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Michael Pound
- Naval Facilities Engineering Systems Command (NAVFAC) Southwest, 750 Pacific Hwy, San Diego, CA, 92132, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA.
| |
Collapse
|
3
|
Desmarais M, Fraraccio S, Dolinova I, Ridl J, Strnad H, Kubatova H, Sevcu A, Suman J, Strejcek M, Uhlik O. Genomic analysis of Acinetobacter pittii CEP14 reveals its extensive biodegradation capabilities, including cometabolic degradation of cis-1,2-dichloroethene. Antonie Van Leeuwenhoek 2022; 115:1041-1057. [PMID: 35701646 DOI: 10.1007/s10482-022-01752-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022]
Abstract
Halogenated organic compounds are naturally occurring in subsurface environments; however, accumulation of the degradative intermediate cis-1,2-dichloroethene (cDCE) at soil and groundwater sites contaminated with xenobiotic chlorinated ethenes is a global environmental and public health issue. Identifying microorganisms capable of cDCE degradation in these environments is of interest because of their potential application to bioremediation techniques. In this study, we sequenced, assembled, and analyzed the complete genome of Acinetobacter pittii CEP14, a strain isolated from chloroethene-contaminated groundwater, that has demonstrated the ability for aerobic cometabolic degradation of cDCE in the presence of n-hexane, phenol, and toluene. The A. pittii CEP14 genome consists of a 3.93 Mbp-long chromosome (GenBank accession no. CP084921) with a GC content of 38.9% and three plasmids (GenBank accession no. CP084922, CP084923, and CP084924). Gene function was assigned to 83.4% of the 3,930 coding DNA sequences. Functional annotation of the genome revealed that the CEP14 strain possessed all genetic elements to mediate the degradation of a range of aliphatic and aromatic compounds, including n-hexane and phenol. In addition, it harbors gene clusters involved in cytosol detoxification and oxidative stress resistance, which could play a role in the mitigation of toxic chemical intermediates that can arise during the degradation of cDCE. Gene clusters for heavy metal and antibiotic resistance were also identified in the genome of CEP14. These results suggest that CEP14 may be a versatile degrader of xenobiotic compounds and well-adapted to polluted environments, where a combination of heavy metal and organic compound pollution is often found.
Collapse
Affiliation(s)
- Miguel Desmarais
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Iva Dolinova
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
- Department of Genetics and Molecular Diagnostics, Regional Hospital Liberec, Liberec, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Kubatova
- State Office for Nuclear Safety, Prague, Czech Republic
| | - Alena Sevcu
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic.
| |
Collapse
|
4
|
Dang H, Cupples AM. Identification of the phylotypes involved in cis-dichloroethene and 1,4-dioxane biodegradation in soil microcosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 794:148690. [PMID: 34198077 DOI: 10.1016/j.scitotenv.2021.148690] [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: 04/20/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Co-contamination with chlorinated compounds and 1,4-dioxane has been reported at many sites. Recently, there has been an increased interest in bioremediation because of the potential to degrade multiple contaminants concurrently. Towards improving bioremediation efficacy, the current study examined laboratory microcosms (inoculated separately with two soils) to determine the phylotypes and functional genes associated with the biodegradation of two common co-contaminants (cis-dichloroethene [cDCE] and 1,4-dioxane). The impact of amending microcosms with lactate on cDCE and 1,4-dioxane biodegradation was also investigated. The presence of either lactate or cDCE did not impact 1,4-dioxane biodegradation one of the two soils. Lactate appeared to improve the initiation of the biological removal of cDCE in microcosms inoculated with either soil. Stable isotope probing (SIP) was then used to determine which phylotypes were actively involved in carbon uptake from cDCE and 1,4-dioxane in both soil communities. The most enriched phylotypes for 13C assimilation from 1,4-dioxane included Rhodopseudomonas and Rhodanobacter. Propane monooxygenase was predicted (by PICRUSt2) to be dominant in the 1,4-dioxane amended microbial communities and propane monooxygenase gene abundance values correlated with other enriched (but less abundant) phylotypes for 13C-1,4-dioxane assimilation. The dominant enriched phylotypes for 13C assimilation from cDCE included Bacteriovorax, Pseudomonas and Sphingomonas. In the cDCE amended soil microcosms, PICRUSt2 predicted the presence of DNA encoding glutathione S-transferase (a known cDCE upregulated enzyme). Overall, the work demonstrated concurrent removal of cDCE and 1,4-dioxane by indigenous soil microbial communities and the enhancement of cDCE removal by lactate. The data generated on the phylotypes responsible for carbon uptake (as determined by SIP) could be incorporated into diagnostic molecular methods for site characterization. The results suggest concurrent biodegradation of cDCE and 1,4-dioxane should be considered for chlorinated solvent site remediation.
Collapse
Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
5
|
Zalesak M, Ruzicka J, Vicha R, Dvorackova M. Examining aerobic degradation of chloroethenes mixture in consortium composed of Comamonas testosteroni RF2 and Mycobacterium aurum L1. CHEMOSPHERE 2021; 269:128770. [PMID: 33139045 DOI: 10.1016/j.chemosphere.2020.128770] [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: 04/28/2020] [Revised: 09/07/2020] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
An environmental isolate Comamonas testosteroni RF2 has been previously described to cometabolize trichloroethene (TCE), 1,2-cis-dichloroethene (cDCE), 1,2-trans-dichloroethene (tDCE), and 1,1-dichloroethene (1,1DCE) when grown on phenol and lactate sodium. In this study, three vinyl chloride (VC) degrading strains, Mycobacterium aurum L1, Pseudomonas putida PS, and Rhodococcus ruber Sm-1 were used to form consortia with the strain RF2 in terms to achieve the removal of VC along with above-mentioned chloroethenes. Degradation assays were performed for a binary mixture of cDCE and VC as well as for a mixture of TCE, all DCEs and VC. The consortium composed of C. testosteroni RF2 and M. aurum L1 showed to be the most efficient towards the removal of cDCE (6.01 mg L-1) in the binary mixture with VC (10 mg L-1) and was capable of efficiently removing chloroethenes in the mixture sample at the initial concentrations of 116 μg L-1 for TCE, 662 μg L-1 for cDCE, 42 μg L-1 for tDCE, 16 μg L-1 for 1,1DCE, and 7 mg L-1 for VC with a removal efficiency of nearly 100% for all of the compounds. Although complete removal of VC took a significantly longer time than the removal of other chloroethenes, the consortium composed of C. testosteroni RF2 and M. aurum L1 displayed strong bioremediation potential for aquifers with downstream contamination characterized by the presence of less chlorinated ethenes.
Collapse
Affiliation(s)
- Michal Zalesak
- Department of Environment Protection Engineering, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| | - Jan Ruzicka
- Department of Environment Protection Engineering, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| | - Robert Vicha
- Department of Chemistry, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| | - Marie Dvorackova
- Department of Environment Protection Engineering, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| |
Collapse
|
6
|
Mundle SOC, Spain JC, Lacrampe-Couloume G, Nishino SF, Sherwood Lollar B. Branched pathways in the degradation of cDCE by cytochrome P450 in Polaromonas sp. JS666. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 605-606:99-105. [PMID: 28662431 DOI: 10.1016/j.scitotenv.2017.06.166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
Compound specific isotope analysis (CSIA) is widely used to monitor contaminant remediation in groundwater. CSIA-based approaches that use enrichment (ε) values to assess degradative processes rely on the assumption that the contaminant being investigated will have an ε value that is constant and specific to a catalytic pathway of a microorganism. Distinct ε values have been reported for aerobic degradation of cis-dichloroethene (cDCE), which has led to a number of proposed degradation mechanisms; however, cytochrome P450 catalyzed oxidation is the only biochemical mechanism that has been established in Polaromonas sp. JS666. Using CSIA we measured the ε values for microbial oxidation of cDCE (-18.8‰±1.5‰) and 1,2-dichloroethane (1,2-DCA) (-16.6‰±0.9‰) in wild-type JS666 and the oxidation of cDCE (-13.5‰±2.3‰) from a recombinant E. coli strain expressing the cytochrome P450 enzyme from JS666. This study supports the hypothesis that cytochrome P450 catalyzes the initial step in the degradation pathway of both cDCE and 1,2-DCA and provides evidence that a single enzyme can catalyze multiple pathways with different products and distinct ε values for a single substrate. Therefore, in cases where the products of the reaction cannot, or have not been characterized, caution must be used when employing ε values to interpret mechanisms, pathways, and their applications to environmental contaminant remediation.
Collapse
Affiliation(s)
- Scott O C Mundle
- Department of Earth Sciences, University of Toronto, 22 Russell St., Toronto, Ontario M5S 3B5, Canada; Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave., Windsor, ON N9B 3P4, Canada.
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, United States; Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL 32514-5750, United States
| | - Georges Lacrampe-Couloume
- Department of Earth Sciences, University of Toronto, 22 Russell St., Toronto, Ontario M5S 3B5, Canada
| | - Shirley F Nishino
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0512, United States
| | - Barbara Sherwood Lollar
- Department of Earth Sciences, University of Toronto, 22 Russell St., Toronto, Ontario M5S 3B5, Canada
| |
Collapse
|
7
|
Zalesak M, Ruzicka J, Vicha R, Dvorackova M. Cometabolic degradation of dichloroethenes by Comamonas testosteroni RF2. CHEMOSPHERE 2017; 186:919-927. [PMID: 28830064 DOI: 10.1016/j.chemosphere.2017.07.156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/28/2017] [Accepted: 07/29/2017] [Indexed: 06/07/2023]
Abstract
An environmental isolate Comamonas testosteroni strain RF2, which has been found to cometabolize trichloroethene (TCE) in the presence of phenol and sodium lactate as growth substrates, was tested to investigate its capacity for degrading 1,2-cis-dichloroethene (cDCE), 1,2-trans-dichlorothene (tDCE), and 1,1-dichloroethene (1,1DCE). Degradation assays were performed for single DCEs, as well as for a mixture of DCEs with TCE, which resembled contaminated plume in groundwater. RF2 was capable of efficiently removing all three dichloroethenes (DCEs) at the initial aqueous concentrations of 6.01 mg L-1 for cDCE, 3.80 mg L-1 for tDCE and 0.65 mg L-1 for 1,1DCE, with a removal efficiency of 100% for cDCE, 65.8% for tDCE, and 46.8% for 1,1DCE. Furthermore, complete removal of TCE, cDCE and 1,1DCE (122.5 μg L-1, 84.3 μg L-1 and 51.4 μg L-1, respectively) was observed in a mixture sample that also contained 72.33 μg L-1 of tDCE, which was removed to the amount of 72.3%. Moreover, degradation of cDCE (6.01 mg L-1) led to a 93.8% release of inorganic chloride, and 2,2-dichloroacetaldehyde was determined as the first intermediate of cDCE transformation. The findings of this study suggest that the strain RF2 exhibits the potential to remediate groundwater contaminated with less chlorinated ethenes.
Collapse
Affiliation(s)
- Michal Zalesak
- Department of Environment Protection Engineering, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| | - Jan Ruzicka
- Department of Environment Protection Engineering, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| | - Robert Vicha
- Department of Chemistry, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| | - Marie Dvorackova
- Department of Environment Protection Engineering, Tomas Bata University in Zlin, Faculty of Technology, Vavreckova 275, 760 01, Zlin, Czech Republic.
| |
Collapse
|
8
|
Munro JE, Kimyon Ö, Rich DJ, Koenig J, Tang S, Low A, Lee M, Manefield M, Coleman NV. Co-occurrence of genes for aerobic and anaerobic biodegradation of dichloroethane in organochlorine-contaminated groundwater. FEMS Microbiol Ecol 2017; 93:4494361. [DOI: 10.1093/femsec/fix133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 10/10/2017] [Indexed: 12/15/2022] Open
|
9
|
Dolinová I, Štrojsová M, Černík M, Němeček J, Macháčková J, Ševců A. Microbial degradation of chloroethenes: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13262-13283. [PMID: 28378313 DOI: 10.1007/s11356-017-8867-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/17/2017] [Indexed: 05/28/2023]
Abstract
Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.
Collapse
Affiliation(s)
- Iva Dolinová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Martina Štrojsová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jan Němeček
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jiřina Macháčková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| |
Collapse
|
10
|
Munro JE, Liew EF, Ly MA, Coleman NV. A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site. Appl Environ Microbiol 2016; 82:5298-308. [PMID: 27342553 PMCID: PMC4988179 DOI: 10.1128/aem.01373-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED 1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1 Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination. IMPORTANCE Earlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes.
Collapse
Affiliation(s)
- Jacob E Munro
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Elissa F Liew
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Mai-Anh Ly
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
11
|
Kumar A, Pillay B, Olaniran AO. Enzyme activity and gene expression profiles of Xanthobacter autotrophicus GJ10 during aerobic biodegradation of 1,2-dichloroethane. World J Microbiol Biotechnol 2015; 31:1211-6. [DOI: 10.1007/s11274-015-1868-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/05/2015] [Indexed: 11/29/2022]
|
12
|
A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria. Appl Biochem Biotechnol 2015; 176:670-99. [PMID: 25935219 DOI: 10.1007/s12010-015-1603-5] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 03/31/2015] [Indexed: 02/07/2023]
Abstract
Hydrocarbons are relatively recalcitrant compounds and are classified as high-priority pollutants. However, these compounds are slowly degraded by a large variety of microorganisms. Bacteria are able to degrade aliphatic saturated and unsaturated hydrocarbons via both aerobic and anaerobic pathways. Branched hydrocarbons and cyclic hydrocarbons are also degraded by bacteria. The aerobic bacteria use different types of oxygenases, including monooxygenase, cytochrome-dependent oxygenase and dioxygenase, to insert one or two atoms of oxygen into their targets. Anaerobic bacteria, on the other hand, employ a variety of simple organic and inorganic molecules, including sulphate, nitrate, carbonate and metals, for hydrocarbon oxidation.
Collapse
|
13
|
Coleman NV. Primers: Functional Genes for Aerobic Chlorinated Hydrocarbon-Degrading Microbes. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_91] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
14
|
Kurt Z, Mack EE, Spain JC. Biodegradation of cis-dichloroethene and vinyl chloride in the capillary fringe. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13350-13357. [PMID: 25329424 DOI: 10.1021/es503071m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Volatile chlorinated compounds are major pollutants in groundwater, and they pose a risk of vapor intrusion into buildings. Vapor intrusion can be prevented by natural attenuation in the vadose zone if biodegradation mechanisms can be established. In this study, we tested the hypothesis that bacteria can use cis-dichloroethene (cis-DCE) or vinyl chloride (VC) as an electron donor in the vadose zone. Anoxic water containing cis-DCE or VC was pumped continuously beneath laboratory columns that represented the vadose zone. Columns were inoculated with Polaromonas sp. strain JS666, which grows aerobically on cis-DCE, or with Mycobacterium sp. JS60 and Nocardiodes sp. JS614 that grow on VC. Complete biodegradation with fluxes of 84 ± 15 μmol of cis-DCE · m(-2) · hr(-1) and 218 ± 25 μmole VC·m(-2) · h(-1) within the 23 cm column indicated that microbial activities can prevent the migration of cis-DCE and VC vapors. Oxygen and volatile compound profiles along with enumeration of bacterial populations indicated that most of the biodegradation took place in the first 10 cm above the saturated zone within the capillary fringe. The results revealed that cis-DCE and VC can be biodegraded readily at the oxic/anoxic interfaces in the vadose zone if appropriate microbes are present.
Collapse
Affiliation(s)
- Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0512, United States
| | | | | |
Collapse
|