1
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Contrasting regulatory effects of organic acids on aerobic vinyl chloride biodegradation in etheneotrophs. Appl Microbiol Biotechnol 2022; 106:6335-6346. [PMID: 36056199 DOI: 10.1007/s00253-022-12147-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 01/05/2023]
Abstract
Vinyl chloride (VC) is a common groundwater pollutant generated during anaerobic biodegradation of chlorinated solvents (e.g., trichloroethene (TCE) or tetrachloroethene (PCE)). Aerobic VC biodegradation by etheneotrophs can support anaerobic PCE and TCE bioremediation to achieve complete removal in situ. However, anaerobic bioremediation strategies necessitate biostimulation with electron donors that are fermented in situ, generating organic acids that could influence aerobic VC biodegradation processes. We examined the effect of organic acids (lactate, acetate, propionate, and butyrate) on aerobic VC biodegradation by VC-assimilating etheneotrophs Mycobacterium strain JS60 and Nocardioides strain JS614. Strain JS60 grew on all organic acids tested, while strain JS614 did not respond to lactate. VC-grown strain JS60 fed VC and one or more organic acids showed carbon catabolite repression (CCR) behavior where VC biodegradation occurred only after organic acids were depleted. In contrast, CCR was not evident in VC-grown strain JS614, which degraded VC and organic acids simultaneously. Acetate-grown JS60 showed similar CCR behavior when fed VC and a single organic acid, except that extended lag periods (5-12 days) occurred before VC oxidation ensued. Acetate-grown JS614 fed VC and either acetate or butyrate displayed 5-8 day lag periods before simultaneous VC and organic acid biodegradation. In contrast, acetate-grown JS614 degraded VC and propionate without a significant lag, suggesting a regulatory link between propionate and VC oxidation in JS614. Different global regulatory mechanisms controlling VC biodegradation in the presence of organic acids in etheneotrophs have implications for developing combined anaerobic-aerobic bioremediation strategies at chlorinated ethene-contaminated sites. KEY POINTS: • With organic acids present, VC utilization was repressed in JS60, but not in JS614 • Strain JS60 grew readily on lactate, while strain JS614 did not • Propionate alleviated lag periods for VC utilization in acetate-grown JS614.
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2
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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.
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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.
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3
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Di Franca ML, Matturro B, Crognale S, Zeppilli M, Dell’Armi E, Majone M, Petrangeli Papini M, Rossetti S. Microbiome Composition and Dynamics of a Reductive/Oxidative Bioelectrochemical System for Perchloroethylene Removal: Effect of the Feeding Composition. Front Microbiol 2022; 13:951911. [PMID: 35923400 PMCID: PMC9340161 DOI: 10.3389/fmicb.2022.951911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Chlorinated solvents still represent an environmental concern that requires sustainable and innovative bioremediation strategies. This study describes the microbiome composition of a novel bioelectrochemical system (BES) based on sequential reductive/oxidative dechlorination for complete perchloroethylene (PCE) removal occurring in two separate but sequential chambers. The BES has been tested under various feeding compositions [i.e., anaerobic mineral medium (MM), synthetic groundwater (SG), and real groundwater (RG)] differing in presence of sulfate, nitrate, and iron (III). In addition, the main biomarkers of the dechlorination process have been monitored in the system under various conditions. Among them, Dehalococcoides mccartyi 16S rRNA and reductive dehalogenase genes (tceA, bvcA, and vcrA) involved in anaerobic dechlorination have been quantified. The etnE and etnC genes involved in aerobic dechlorination have also been quantified. The feeding composition affected the microbiome, in particular when the BES was fed with RG. Sulfuricurvum, enriched in the reductive compartment, operated with MM and SG, suggesting complex interactions in the sulfur cycle mostly including sulfur oxidation occurring at the anodic counter electrode (MM) or coupled to nitrate reduction (SG). Moreover, the known Mycobacterium responsible for natural attenuation of VC by aerobic degradation was found abundant in the oxidative compartment fed with RG, which was in line with the high VC removal observed (92 ± 2%). D. mccartyi was observed in all the tested conditions ranging from 8.78E + 06 (with RG) to 2.35E + 07 (with MM) 16S rRNA gene copies/L. tceA was found as the most abundant reductive dehalogenase gene in all the conditions explored (up to 2.46 E + 07 gene copies/L in MM). The microbiome dynamics and the occurrence of biomarkers of dechlorination, along with the kinetic performance of the system under various feeding conditions, suggested promising implications for the scale-up of the BES, which couples reductive with oxidative dechlorination to ensure the complete removal of highly chlorinated ethylene and mobile low-chlorinated by-products.
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Affiliation(s)
- Maria L. Di Franca
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
| | - Bruna Matturro
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
- *Correspondence: Bruna Matturro,
| | - Simona Crognale
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
| | - Marco Zeppilli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Mauro Majone
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Simona Rossetti
- Water Research Institute-National Research Council (IRSA-CNR), Rome, Italy
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4
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Xing Z, Su X, Zhang X, Zhang L, Zhao T. Direct aerobic oxidation (DAO) of chlorinated aliphatic hydrocarbons: A review of key DAO bacteria, biometabolic pathways and in-situ bioremediation potential. ENVIRONMENT INTERNATIONAL 2022; 162:107165. [PMID: 35278801 DOI: 10.1016/j.envint.2022.107165] [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] [Received: 11/15/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Contamination of aquifers and vadose zones with chlorinated aliphatic hydrocarbons (CAH) is a world-wide issue. Unlike other reactions, direct aerobic oxidation (DAO) of CAHs does not require growth substrates and avoids the generation of toxic by-products. Here, we critically review the current understanding of chlorinated aliphatic hydrocarbons-DAO and its application in bioreactors and at the field scale. According to reports on chlorinated aliphatic hydrocarbons-DAO bacteria, isolates mainly consisted of Methylobacterium and Proteobacterium. Chlorinated aliphatic hydrocarbons-DAO bacteria are characterized by tolerance to a high concentration of CAHs and highly efficient removal of CAHs. Trans-1,2-dichloroethylene (t-DCE) is easily transformed biomass for bacteria, followed by 1,2-dichloroethane (1,2-DCA), dichloromethane (DCM), vinyl chloride (VC) and cis-1,2-dichloroethylene (c-DCE). Significant differences in the maximum specific growth rates were observed with different CAHs and biometabolic pathways for DCM, 1,2-DCA, VC and c-DCE degradation have been successfully parsed. Detection of the functional genes etnC and etnE is useful for the determination of active VC DAO bacteria. Additionally, DAO bacteria have been successfully applied to CAHs in new types of bioreactors with satisfactory results. To the best of the authors' knowledge, only one study on DAO-CAHs was conducted in-situ and resulted in 99% CAH removal. Lastly, we put forward future development prospect of chlorinated aliphatic hydrocarbons-DAO.
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Affiliation(s)
- Zhilin Xing
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xia Su
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Xiaoping Zhang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Lijie Zhang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Tiantao Zhao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China.
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5
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Cortés-Albayay C, Sangal V, Klenk HP, Nouioui I. Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov. Front Microbiol 2021; 12:767895. [PMID: 35003006 PMCID: PMC8727900 DOI: 10.3389/fmicb.2021.767895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/16/2021] [Indexed: 11/30/2022] Open
Abstract
Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1T (CECT 8761T = DSM 6695T) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027T. Phenotypic, chemotaxonomic and genomic data considering strain L1T (CECT 8761T = DSM 6695T) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov.
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Affiliation(s)
- Carlos Cortés-Albayay
- Faculty of Science, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Hans-Peter Klenk
- Faculty of Science, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Imen Nouioui
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- *Correspondence: Imen Nouioui,
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6
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Lhotský O, Kukačka J, Slunský J, Marková K, Němeček J, Knytl V, Cajthaml T. The effects of hydraulic/pneumatic fracturing-enhanced remediation (FRAC-IN) at a site contaminated by chlorinated ethenes: A case study. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125883. [PMID: 33971551 DOI: 10.1016/j.jhazmat.2021.125883] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
A low-permeability locality with heterogeneous geology contaminated primarily by tetrachloroethene (PCE) present partially in the free phase in the unsaturated zone was treated on a pilot scale via direct push pneumatic fracturing combined with the hydraulic delivery of a remediation suspension consisting of milled iron, sulphidated nanosized zerovalent iron and sand in guar gum solution. Afterwards, a whey solution was injected into the fractures as a carbon source for bacteria. The unsaturated and saturated zones were treated. Long-term monitoring of the groundwater revealed that the abiotic reduction of PCE and trichloroethene was the dominant remediation processes for several months after the injections. A complex microbial consortium was developed that was capable of effective, long-term chlorinated ethenes (ClE) dechlorination. The consortium consisted mainly of Dehalococcoides but also of other anaerobic bacterial strains capable of partial dechlorination of ClE, including the sulphate-reducing bacteria; Geobacter and Desulfitobacterium. The average chlorine number in the groundwater decreased from 3.65 to 1.38 within 2.5 years after the injections, while the average ClE concentration increased from 13.5 to 31.5 mgL-1 because of the substantial acceleration of the ClE mass-transfer to the groundwater caused by the treatment. The remediation processes remained fully active for 2.5 years.
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Affiliation(s)
- Ondřej Lhotský
- DEKONTA a.s., Volutová 2523, CZ-158 00 Prague 5, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - Jan Kukačka
- DEKONTA a.s., Volutová 2523, CZ-158 00 Prague 5, Czech Republic
| | - Jan Slunský
- NANO IRON, s.r.o., Topolová 933, CZ-667 01 Židlochovice, Czech Republic
| | - Kristýna Marková
- Technical University of Liberec, Studentská 2, CZ-461 17 Liberec, Czech Republic
| | - Jan Němeček
- Technical University of Liberec, Studentská 2, CZ-461 17 Liberec, Czech Republic
| | - Vladislav Knytl
- DEKONTA a.s., Volutová 2523, CZ-158 00 Prague 5, Czech Republic; Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic
| | - Tomáš Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Prague 2, Czech Republic; Institute of Microbiology Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic.
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7
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Czinnerová M, Vološčuková O, Marková K, Ševců A, Černík M, Nosek J. Combining nanoscale zero-valent iron with electrokinetic treatment for remediation of chlorinated ethenes and promoting biodegradation: A long-term field study. WATER RESEARCH 2020; 175:115692. [PMID: 32199189 DOI: 10.1016/j.watres.2020.115692] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
Nanoscale zero-valent iron (nZVI) is recognized as a powerful tool for the remediation of groundwater contaminated by chlorinated ethenes (CEs). This long-term field study explored nZVI-driven degradation of CEs supported by electrokinetic (EK) treatment, which positively affects nZVI longevity and migration, and its impact on indigenous bacteria. In particular, the impact of combined nZVI-EK treatment on organohalide-respiring bacteria, ethenotrophs and methanotrophs (all capable of CE degradation) was assessed using molecular genetic markers detecting Dehalococcoides spp., Desulfitobacterium spp., the reductive dehalogenase genes vcrA and bvcA and ethenotroph and methanotroph functional genes. The remediation treatment resulted in a rapid decrease of the major pollutant cis-1,2-dichloroethene (cDCE) by 75% in the affected area, followed by an increase in CE degradation products methane, ethane and ethene. The newly established geochemical conditions in the treated aquifer not only promoted growth of organohalide-respiring bacteria but also allowed for the concurrent presence of vinyl chloride- and cDCE-oxidizing methanotrophs and (especially) ethenotrophs, which proliferated preferentially in the vicinity of an anode where low levels of oxygen were produced. The nZVI treatment resulted in a temporary negative impact on indigenous bacteria in the application well close to the cathode; but even there, the microbiome was restored within 15 days. The nZVI-EK treatment proved highly effective in reducing CE contamination and creating a suitable environment for subsequent biodegradation by changing groundwater conditions, promoting transport of nutrients and improving CE availability to soil and groundwater bacteria.
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Affiliation(s)
- Marie Czinnerová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, CZ-46117, Liberec, Czech Republic; Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, CZ-46117, Liberec, Czech Republic
| | - Ondřejka Vološčuková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, CZ-46117, Liberec, Czech Republic
| | - Kristýna Marková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, CZ-46117, Liberec, Czech Republic
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, CZ-46117, Liberec, Czech Republic
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, CZ-46117, Liberec, Czech Republic
| | - Jaroslav Nosek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, CZ-46117, Liberec, Czech Republic.
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8
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Hydrochemical Conditions for Aerobic/Anaerobic Biodegradation of Chlorinated Ethenes—A Multi-Site Assessment. WATER 2020. [DOI: 10.3390/w12020322] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A stall of cis-1,2-DCE and vinyl chloride (VC) is frequently observed during bioremediation of groundwater chloroethenes via reductive dechlorination. These chloroethenes may be oxidised by aerobic methanotrophs or ethenotrophs co-metabolically and/or metabolically. We assessed the potential for such oxidation at 12 sites (49 groundwater samples) using hydrochemical and molecular biological tools. Both ethenotroph (etnC and etnE) and methanotroph (mmoX and pmoA) functional genes were identified in 90% of samples, while reductive dehalogenase functional genes (vcrA and bvcA) were identified in 82%. All functional genes were simultaneously detected in 78% of samples, in actively biostimulated sites in 88% of samples. Correlation analysis revealed that cis-1,2-DCE concentration was positively correlated with vcrA, etnC and etnE, while VC concentration was correlated with etnC, etnE, vcrA and bvcA. However, feature selection based on random forest classification indicated a significant relationship for the vcrA in relation to cis-1,2-DCE, and vcrA, bvcA and etnE for VC and no prove of relationship between cis-1,2-DCE or VC and the methanotroph functional genes. Analysis of hydrochemical parameters indicated that aerobic oxidation of chloroethenes by ethenotrophs may take place under a range of redox conditions of aquifers and coincide with high ethene and VC concentrations.
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9
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Richards PM, Liang Y, Johnson RL, Mattes TE. Cryogenic soil coring reveals coexistence of aerobic and anaerobic vinyl chloride degrading bacteria in a chlorinated ethene contaminated aquifer. WATER RESEARCH 2019; 157:281-291. [PMID: 30959331 DOI: 10.1016/j.watres.2019.03.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/04/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
Vinyl chloride (VC) is a common groundwater contaminant and known human carcinogen. Three major bacterial guilds are known to participate in VC biodegradation: aerobic etheneotrophs and methanotrophs, and anaerobic organohalide-respiring VC-dechlorinators. We investigated the spatial relationships between functional genes representing these three groups of bacteria (as determined by qPCR) with chlorinated ethene concentrations in a surficial aquifer at a contaminated site. We used cryogenic soil coring to collect high-resolution aquifer sediment samples and to preserve sample geochemistry and nucleic acids under field conditions. All samples appeared to be anaerobic (i.e., contained little to no dissolved oxygen). VC biodegradation associated functional genes from etheneotrophs (etnC and/or etnE), methanotrophs (mmoX and/or pmoA), and anaerobic VC-dechlorinators (bvcA and/or vcrA) coexisted in 48% of the samples. Transcripts of etnC/etnE and bvcA/vcrA were quantified in contemporaneous groundwater samples, indicating co-located gene expression. Functional genes from etheneotrophs and anaerobic VC-dechlorinators were correlated to VC concentrations in the lower surficial aquifer (p < 0.05). Methanotroph functional genes were not correlated to VC concentrations. Cryogenic soil coring proved to be a powerful tool for capturing high-spatial resolution trends in geochemical and nucleic acid data in aquifer sediments. We conclude that both aerobic etheneotrophs and anaerobic VC-dechlorinators may play a significant role in VC biodegradation in aquifers that have little dissolved oxygen.
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Affiliation(s)
- Patrick M Richards
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Yi Liang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Richard L Johnson
- OHSU-PSU School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA.
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10
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Dang H, Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13914-13924. [PMID: 30427665 DOI: 10.1021/acs.est.8b04895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Yogendra H Kanitkar
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Paul B Hatzinger
- APTIM , 17 Princess Road , Lawrenceville , New Jersey 08648 , United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
- Center for Microbial Ecology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Alison M Cupples
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
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11
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Liu X, Wu Y, Wilson FP, Yu K, Lintner C, Cupples AM, Mattes TE. Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride. FEMS Microbiol Ecol 2018; 94:5045312. [DOI: 10.1093/femsec/fiy124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/25/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Xikun Liu
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Yang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Nanshan District, Shenzhen 518055, China
| | - Fernanda P Wilson
- Department of Civil and Environmental Engineering, Engineering Building, 428 S. Shaw Lane, Room 3546, East Lansing, MI 48824, USA
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Nanshan District, Shenzhen 518055, China
| | - Carly Lintner
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Engineering Building, 428 S. Shaw Lane, Room 3546, East Lansing, MI 48824, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
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12
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Liang Y, Liu X, Singletary MA, Wang K, Mattes TE. Relationships between the Abundance and Expression of Functional Genes from Vinyl Chloride (VC)-Degrading Bacteria and Geochemical Parameters at VC-Contaminated Sites. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:12164-12174. [PMID: 28981261 DOI: 10.1021/acs.est.7b03521] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bioremediation of vinyl chloride (VC) contamination in groundwater could be mediated by three major bacterial guilds: anaerobic VC-dechlorinators, methanotrophs, and ethene-oxidizing bacteria (etheneotrophs) via metabolic or cometabolic pathways. We collected 95 groundwater samples across 6 chlorinated ethene-contaminated sites and searched for relationships among VC biodegradation gene abundance and expression and site geochemical parameters (e.g., VC concentrations). Functional genes from the three major VC-degrading bacterial guilds were present in 99% and expressed in 59% of the samples. Etheneotroph and methanotroph functional gene abundances ranged from 102 to 109 genes per liter of groundwater among the samples with VC reductive dehalogenase gene (bvcA and vcrA) abundances reaching 108 genes per liter of groundwater. Etheneotroph functional genes (etnC and etnE) and VC reductive dehalogenase genes (bvcA and vcrA) were strongly related to VC concentrations (p < 0.001). Methanotroph functional genes (mmoX and pmoA) were not related to VC concentration (p > 0.05). Samples from sites with bulk VC attenuation rates >0.08 year-1 contained higher levels of etheneotroph and anaerobic VC-dechlorinator functional genes and transcripts than those with bulk VC attenuation rates <0.004 year-1. We conclude that both etheneotrophs and anaerobic VC-dechlorinators have the potential to simultaneously contribute to VC biodegradation at these sites.
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Affiliation(s)
| | | | - Michael A Singletary
- NAVFAC Southeast, EV3 Environmental Restoration Building 135, Naval Air Station Jacksonville, Florida 32508, United States
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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.
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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.
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14
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Liang Y, Cook LJ, Mattes TE. Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13760-13774. [PMID: 28401391 DOI: 10.1007/s11356-017-8948-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
Assessment and monitoring of microbial community dynamics is useful when tracking the progress of vinyl chloride (VC) bioremediation strategies, particularly in dilute plumes where apparent VC attenuation rates are low. In a long-term field study, the abundance and the activity of microbial VC degraders were tracked in three monitoring wells (MW05, MW25, and MW19) along a dilute VC plume at Naval Air Station (NAS) Oceana. High-throughput sequencing of partial 16S ribosomal RNA (rRNA) genes and transcripts revealed diverse groundwater microbial communities and showed that methanotrophs and anaerobic respirers (e.g., methanogens, sulfate reducers, and iron reducers) were among the most active and abundant guilds. Quantitative PCR analysis showed that among bacterial guilds with a potential to contribute to VC biodegradation, methanotrophs were the most abundant and active microbial group. Ethene-oxidizing bacterial populations were less abundant and relatively inactive compared to methanotrophs. In MW19, expression of functional genes associated with both aerobic VC oxidation and anaerobic VC reduction was observed. Overall, our results reveal that the groundwater community contains various active bacterial guilds previously associated with metabolic and cometabolic VC degradation processes either under aerobic and anaerobic conditions that might have contributed to the slowly decreasing VC concentrations at the NAS Oceana site over the 6-year study period.
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Affiliation(s)
- Yi Liang
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Laura J Cook
- CH2M 5701 Cleveland Street Suite 200, Virginia Beach, VA, 23462, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA.
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15
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Atashgahi S, Lu Y, Ramiro-Garcia J, Peng P, Maphosa F, Sipkema D, Dejonghe W, Smidt H, Springael D. Geochemical Parameters and Reductive Dechlorination Determine Aerobic Cometabolic vs Aerobic Metabolic Vinyl Chloride Biodegradation at Oxic/Anoxic Interface of Hyporheic Zones. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:1626-1634. [PMID: 28004913 DOI: 10.1021/acs.est.6b05041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hyporheic zones mediate vinyl chloride (VC) biodegradation in groundwater discharging into surface waters. At the oxic/anoxic interface (OAI) of hyporheic zones subjected to redox oscillations, VC is degraded via coexisting aerobic ethenotrophic and anaerobic reductive dechlorination pathways. However, the identity of aerobic VC degradation pathways (cometabolic vs metabolic) and their interactions with reductive dechlorination in relation to riverbed sediment geochemistry remain ill-defined. We addressed this using microcosms containing OAI sediments incubated under fluctuating oxic/anoxic atmosphere. Under oxic atmosphere, aerobic metabolic VC oxidation was absent in sediments with high total organic carbon (TOC) and VC was reductively dechlorinated to ethene. Ethene was oxidized by ethenotrophs that can degrade VC cometabolically. Contrastingly, VC was metabolically oxidized by ethenotrophs in low-TOC sediments with low reductive dechlorination potential. Accordingly, enrichment and isolation of metabolic VC-oxidizing ethenotrophs was successful only from the low-TOC sediment. Sequence analysis of etnE genes from the microcosms as well phylogenetic typing of the isolates showed that ethenotrophs in the sediments were facultative anaerobic Proteobacteria capable of coping with OAI-associated redox fluctuations. Our results suggest that local sediment heterogeneity supports/selects divergent VC degradation processes at the OAI and that high reductive dechlorination potential suppresses development of aerobic metabolic VC oxidation potential.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
| | - Yue Lu
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Farai Maphosa
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Springael
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
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16
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Wilson FP, Liu X, Mattes TE, Cupples AM. Nocardioides, Sediminibacterium, Aquabacterium, Variovorax, and Pseudomonas linked to carbon uptake during aerobic vinyl chloride biodegradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:19062-19070. [PMID: 27343076 DOI: 10.1007/s11356-016-7099-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
Vinyl chloride (VC) is a frequent groundwater contaminant and a known human carcinogen. Bioremediation is a potential cleanup strategy for contaminated sites; however, little is known about the bacteria responsible for aerobic VC degradation in mixed microbial communities. In attempts to address this knowledge gap, the microorganisms able to assimilate labeled carbon ((13)C) from VC within a mixed culture capable of rapid VC degradation (120 μmol in 7 days) were identified using stable isotope probing (SIP). For this, at two time points during VC degradation (days 3 and 7), DNA was extracted from replicate cultures initially supplied with labeled or unlabeled VC. The extracted DNA was ultracentrifuged, fractioned, and the fractions of greater buoyant density (heavy fractions, 1.758 to 1.780 g mL(-1)) were subject to high-throughput sequencing. Following this, specific primers were designed for the most abundant phylotypes in the heavy fractions. Then, quantitative PCR (qPCR) was used across the buoyant density gradient to confirm label uptake by these phylotypes. From qPCR and/or sequencing data, five phylotypes were found to be dominant in the heavy fractions, including Nocardioides (∼40 %), Sediminibacterium (∼25 %), Aquabacterium (∼17 %), Variovorax (∼6 %), and Pseudomonas (∼1 %). The abundance of two functional genes (etnC and etnE) associated with VC degradation was also investigated in the SIP fractions. Peak shifts of etnC and etnE gene abundance toward heavier fractions were observed, indicating uptake of (13)C into the microorganisms harboring these genes. Analysis of the total microbial community indicated a significant dominance of Nocardioides over the other label-enriched phylotypes. Overall, the data indicate Nocardioides is primarily responsible for VC degradation in this mixed culture, with the other putative VC degraders generating a small growth benefit from VC degradation. The specific primers designed toward the putative VC degraders may be of use for investigating VC degradation potential at contaminated sites.
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Affiliation(s)
- Fernanda Paes Wilson
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, 48824, MI, USA
| | - Xikun Liu
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, 52242, IA, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, 52242, IA, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, 48824, MI, USA.
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17
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Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites. Appl Environ Microbiol 2016; 82:3269-3279. [PMID: 27016563 DOI: 10.1128/aem.00673-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Epoxyalkane:coenzyme M transferase (EaCoMT) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (VC). To improve our understanding of the diversity and distribution of EaCoMT genes in the environment, novel EaCoMT-specific terminal-restriction fragment length polymorphism (T-RFLP) and nested-PCR methods were developed and applied to groundwater samples from six different contaminated sites. T-RFLP analysis revealed 192 different EaCoMT T-RFs. Using clone libraries, we retrieved 139 EaCoMT gene sequences from these samples. Phylogenetic analysis revealed that a majority of the sequences (78.4%) grouped with EaCoMT genes found in VC- and ethene-assimilating Mycobacterium strains and Nocardioides sp. strain JS614. The four most-abundant T-RFs were also matched with EaCoMT clone sequences related to Mycobacterium and Nocardioides strains. The remaining EaCoMT sequences clustered within two emergent EaCoMT gene subgroups represented by sequences found in propene-assimilating Gordonia rubripertincta strain B-276 and Xanthobacter autotrophicus strain Py2. EaCoMT gene abundance was positively correlated with VC and ethene concentrations at the sites studied. IMPORTANCE The EaCoMT gene plays a critical role in assimilation of short-chain alkenes, such as ethene, VC, and propene. An improved understanding of EaCoMT gene diversity and distribution is significant to the field of bioremediation in several ways. The expansion of the EaCoMT gene database and identification of incorrectly annotated EaCoMT genes currently in the database will facilitate improved design of environmental molecular diagnostic tools and high-throughput sequencing approaches for future bioremediation studies. Our results further suggest that potentially significant aerobic VC degraders in the environment are not well represented in pure culture. Future research should aim to isolate and characterize aerobic VC-degrading bacteria from these underrepresented groups.
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18
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Findlay M, Smoler DF, Fogel S, Mattes TE. Aerobic Vinyl Chloride Metabolism in Groundwater Microcosms by Methanotrophic and Etheneotrophic Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3617-3625. [PMID: 26918370 DOI: 10.1021/acs.est.5b05798] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Vinyl chloride (VC) is a carcinogen generated in groundwater by reductive dechlorination of chloroethenes. Under aerobic conditions, etheneotrophs oxidize ethene and VC, while VC-assimilators can use VC as their sole source of carbon and energy. Methanotrophs utilize only methane but can oxidize ethene to epoxyethane and VC to chlorooxirane. Microcosms were constructed with groundwater from the Carver site in MA containing these three native microbial types. Methane, ethene, and VC were added to the microcosms singly or as mixtures. In the absence of VC, ethene degraded faster when methane was also present. We hypothesized that methanotroph oxidation of ethene to epoxyethane competed with their use of methane, and that epoxyethane stimulated the activity of starved etheneotrophs by inducing the enzyme alkene monooxygenase. We then developed separate enrichment cultures of Carver methanotrophs and etheneotrophs, and demonstrated that Carver methanotrophs can oxidize ethene to epoxyethane, and that starved Carver etheneotrophs exhibit significantly reduced lag time for ethene utilization when epoxyethane is added. In our groundwater microcosm tests, when all three substrates were present, the rate of VC removal was faster than with either methane or ethene alone, consistent with the idea that methanotrophs stimulate etheneotroph destruction of VC.
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Affiliation(s)
- Margaret Findlay
- Bioremediation Consulting , c/o 55 Halcyon Road, Newton Massachusetts 02459, United States
| | - Donna F Smoler
- Bioremediation Consulting , c/o 55 Halcyon Road, Newton Massachusetts 02459, United States
| | - Samuel Fogel
- Bioremediation Consulting , c/o 55 Halcyon Road, Newton Massachusetts 02459, United States
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa , 4105 Seamans Center, Iowa City, Iowa 52242, United States
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19
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Mattes TE, Jin YO, Livermore J, Pearl M, Liu X. Abundance and activity of vinyl chloride (VC)-oxidizing bacteria in a dilute groundwater VC plume biostimulated with oxygen and ethene. Appl Microbiol Biotechnol 2015; 99:9267-76. [DOI: 10.1007/s00253-015-6771-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
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20
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Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing. Appl Microbiol Biotechnol 2015; 99:7735-43. [DOI: 10.1007/s00253-015-6606-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/09/2015] [Accepted: 04/12/2015] [Indexed: 10/23/2022]
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21
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Momper LM, Reese BK, Carvalho G, Lee P, Webb EA. A novel cohabitation between two diazotrophic cyanobacteria in the oligotrophic ocean. ISME JOURNAL 2015; 9:882-93. [PMID: 25343510 DOI: 10.1038/ismej.2014.186] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/24/2014] [Accepted: 07/30/2014] [Indexed: 11/09/2022]
Abstract
The cyanobacterial genus Trichodesmium is biogeochemically significant because of its dual role in nitrogen and carbon fixation in the oligotrophic ocean. Trichodesmium species form colonies that can be easily enriched from the water column and used for shipboard rate measurements to estimate their contribution to oceanic carbon and nitrogen budgets. During a July 2010 cruise near the Hawaiian Islands in the oligotrophic North Pacific Subtropical Gyre, a specific morphology of Trichodesmium puff-form colonies were examined under epifluorescent microscopy and found to harbor a colonial endobiont, morphologically identified as the heterocystous diazotrophic cyanobacterium Calothrix. Using unialgal enrichments obtained from this cruise, we show that these Calothrix-like heterocystous cyanobionts (hetDA for 'Trichodesmium-associated heterocystous diazotroph') fix nitrogen on a diurnal cycle (maximally in the middle of the light cycle with a detectable minimum in the dark). Gene sequencing of nifH from the enrichments revealed that this genus was likely not quantified using currently described quantitative PCR (qPCR) primers. Guided by the sequence from the isolate, new hetDA-specific primers were designed and subsequent qPCR of environmental samples detected this diazotroph from surface water to a depth of 150 m, reaching densities up to ∼ 9 × 10(3) l(-1). Based on phylogenetic relatedness of nifH and 16S rRNA gene sequences, it is predicted that the distribution of this cyanobiont is not limited to subtropical North Pacific but likely reaches to the South Pacific and Atlantic Oceans. Therefore, this previously unrecognized cohabitation, if it reaches beyond the oligotrophic North Pacific, could potentially influence Trichodesmium-derived nitrogen fixation budgets in the world ocean.
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Affiliation(s)
- Lily M Momper
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Brandi Kiel Reese
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Gustavo Carvalho
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Patrick Lee
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Eric A Webb
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
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22
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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]
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23
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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.
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Affiliation(s)
- Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0512, United States
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24
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Fullerton H, Rogers R, Freedman DL, Zinder SH. Isolation of an aerobic vinyl chloride oxidizer from anaerobic groundwater. Biodegradation 2014; 25:893-901. [DOI: 10.1007/s10532-014-9708-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/13/2014] [Indexed: 11/24/2022]
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25
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Patterson BM, Aravena R, Davis GB, Furness AJ, Bastow TP, Bouchard D. Multiple lines of evidence to demonstrate vinyl chloride aerobic biodegradation in the vadose zone, and factors controlling rates. JOURNAL OF CONTAMINANT HYDROLOGY 2013; 153:69-77. [PMID: 23999077 DOI: 10.1016/j.jconhyd.2013.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/20/2013] [Accepted: 07/25/2013] [Indexed: 06/02/2023]
Abstract
A field-based investigation was conducted at a contaminated site where the vadose zone was contaminated with a range of chlorinated hydrocarbons. The investigation consisted of groundwater and multilevel soil-gas monitoring of a range of contaminants and gases, along with isotope measurements and microbiology studies. The investigation provided multiple lines of evidence that demonstrated aerobic biodegradation of vinyl chloride (VC) was occurring in the vadose zone (i) above the on-site source zone, and (ii) above the downgradient off-site groundwater plume location. Data from both the on-site and off-site locations were consistent in showing substantially greater (an order of magnitude greater) rates of VC removal from the aerobic vadose zone compared to more recalcitrant contaminants trichloroethene (TCE) and tetrachloroethene (PCE). Soil gas VC isotope analysis showed substantial isotopic enrichment of VC (δ¹³C -5.2 to -10.9‰) compared to groundwater (δ¹³C -39.5‰) at the on-site location. Soil gas CO₂ isotope analysis at both locations showed that CO₂ was highly isotopically depleted (δ¹³C -28.8 to -33.3‰), compared to soil gas CO₂ data originating from natural sediment organic matter (δ¹³C= -14.7 to -21.3‰). The soil gas CO2 δ¹³C values were consistent with near-water table VC groundwater δ¹³C values (-36.8 to -39.5‰), suggesting CO₂ originating from aerobic biodegradation of VC. Bacteria that had functional genes (ethene monooxygenase (etnC) and epoxyalkane transferase (etnE)) involved in ethene metabolism and VC oxidation were more abundant at the source zone where oxygen co-existed with VC. The distribution of VC and oxygen vadose zone vapour plumes, together with long-term changes in soil gas CO₂ concentrations and temperature, provided information to elucidate the factors controlling aerobic biodegradation of VC in the vadose zone. Based on the overlapping VC and oxygen vadose zone vapour plumes, aerobic vapour biodegradation rates were independent of substrate (VC and/or oxygen) concentration. The high correlation (R=0.962 to 0.975) between CO₂ concentrations and temperature suggested that aerobic biodegradation of VC was controlled by bacterial activity that was regulated by the temperature within the vadose zone. When assessing a contaminated site for possible vapour intrusion into buildings, accounting for environmental conditions for aerobic biodegradation of VC in the vadose zone should improve the assessment of environmental risk of VC intrusion into buildings, enabling better identification and prioritisation of contaminated sites to be remediated.
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Affiliation(s)
- B M Patterson
- CSIRO Land and Water, Floreat, Australia; School of Chemistry and Biochemistry, University of Western Australia, Crawley, Australia.
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Presence, diversity and enumeration of functional genes (bssA and bamA) relating to toluene degradation across a range of redox conditions and inoculum sources. Biodegradation 2013; 25:189-203. [DOI: 10.1007/s10532-013-9651-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/23/2013] [Indexed: 10/26/2022]
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Atashgahi S, Maphosa F, Doğan E, Smidt H, Springael D, Dejonghe W. Small-scale oxygen distribution determines the vinyl chloride biodegradation pathway in surficial sediments of riverbed hyporheic zones. FEMS Microbiol Ecol 2012; 84:133-42. [DOI: 10.1111/1574-6941.12044] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 10/18/2012] [Accepted: 11/07/2012] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Farai Maphosa
- Laboratory of Microbiology; Wageningen University; Wageningen; the Netherlands
| | - Eylem Doğan
- Separation and Conversion Technology; Flemish Institute for Technological Research (VITO); Mol; Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University; Wageningen; the Netherlands
| | - Dirk Springael
- Division Soil and Water Management; KU Leuven; Heverlee; Belgium
| | - Winnie Dejonghe
- Separation and Conversion Technology; Flemish Institute for Technological Research (VITO); Mol; Belgium
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Mills HJ, Reese BK, Shepard AK, Riedinger N, Dowd SE, Morono Y, Inagaki F. Characterization of Metabolically Active Bacterial Populations in Subseafloor Nankai Trough Sediments above, within, and below the Sulfate-Methane Transition Zone. Front Microbiol 2012; 3:113. [PMID: 22485111 PMCID: PMC3317506 DOI: 10.3389/fmicb.2012.00113] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 03/12/2012] [Indexed: 11/13/2022] Open
Abstract
A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate-methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques.
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Affiliation(s)
- Heath J. Mills
- Department of Oceanography, Texas A&M UniversityCollege Station, TX, USA
| | - Brandi Kiel Reese
- Department of Oceanography, Texas A&M UniversityCollege Station, TX, USA
- Department of Biological Sciences, University of Southern CaliforniaLos Angeles, CA, USA
| | - Alicia K. Shepard
- Department of Marine Biology, Texas A&M University at GalvestonGalveston, TX, USA
| | - Natascha Riedinger
- Department of Earth Sciences, University of CaliforniaRiverside, CA, USA
| | - Scot E. Dowd
- Research and Testing Laboratory, Medical Biofilm Research InstituteLubbock, TX, USA
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and TechnologyKochi, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and TechnologyKochi, Japan
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Jin YO, Mattes TE. Assessment and modification of degenerate qPCR primers that amplify functional genes from etheneotrophs and vinyl chloride-assimilators. Lett Appl Microbiol 2011; 53:576-80. [PMID: 21880051 DOI: 10.1111/j.1472-765x.2011.03144.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Degenerate qPCR primer sets that target the functional genes etnC and etnE in etheneotrophs and vinyl chloride-assimilating bacteria were assessed and modified in an effort to improve performance. METHODS AND RESULTS Functional gene abundance in four pure cultures was estimated by qPCR using novel (MRTC and MRTE) and existing (RTC and RTE) degenerate primer sets and compared to abundances estimated with nondegenerate gene-specific primers (GSPs). Functional gene abundance in groundwater DNA extracted from several contaminated sites was also estimated with MRTC and MRTE primers. CONCLUSIONS MRTC primers displayed significantly improved etnC quantification in both pure cultures and environmental samples. SIGNIFICANCE AND IMPACT OF THE STUDY Application of MRTC and MRTE primer sets will enhance microbial ecology studies involving etheneotrophs and qPCR analyses that support vinyl chloride bioremediation strategies.
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Affiliation(s)
- Y O Jin
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA 52242, USA
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