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Lu CW, Lo KH, Wang SC, Kao CM, Chen SC. An innovative permeable reactive bio-barrier to remediate trichloroethene-contaminated groundwater: A field study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170885. [PMID: 38342459 DOI: 10.1016/j.scitotenv.2024.170885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/13/2024]
Abstract
Permeable reactive bio-barrier (PRBB), an innovative technology, could treat many contaminants via the natural gradient flow of groundwater based on immobilization or transformation of pollutants into less toxic and harmful forms. In this field study, we developed an innovative PRBB system comprising immobilized Dehalococcoides mccartyi (Dhc) and Clostridium butyricum embedded into the silica gel for long-term treatment of trichloroethene (TCE) polluted groundwater. Four injection wells and two monitoring wells were installed at the downstream of the TCE plume. Without PRBB, results showed that the TCE (6.23 ± 0.43 μmole/L) was converted to cis-dichloroethene (0.52 ± 0.63 μmole/L), and ethene was not detected, whereas TCE was completely converted to ethene (3.31 μmole/L) with PRBB treatment, indicating that PRBB could promote complete dechlorination of TCE. Noticeably, PRBB showed the long-term capability to maintain a high dechlorinating efficiency for TCE removal during the 300-day operational period. Furthermore, with qPCR analysis, the PRBB application could stably maintain the populations of Dhc and functional genes (bvcA, tceA, and vcrA) at >108 copies/L within the remediation course and change the bacterial communities in the contaminated groundwater. We concluded that our PRBB was first set up for cleaning up TCE-contaminated groundwater in a field trial.
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Affiliation(s)
- Che-Wei Lu
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan
| | - Kai-Hung Lo
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Sun-Chong Wang
- Systems Biology and Bioinformatics Institute, National Central University, Taoyuan 32001, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan.
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, Taoyuan 32001, Taiwan.
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2
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Kucharzyk KH, Murdoch FK, Wilson J, Michalsen M, Löffler FE, Murdoch RW, Istok JD, Hatzinger PB, Mullins L, Hill A. Integrated Advanced Molecular Tools Predict In Situ cVOC Degradation Rates: Field Demonstration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:557-569. [PMID: 38109066 DOI: 10.1021/acs.est.3c06231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Chlorinated volatile organic compound (cVOC) degradation rate constants are crucial information for site management. Conventional approaches generate rate estimates from the monitoring and modeling of cVOC concentrations. This requires time series data collected along the flow path of the plume. The estimates of rate constants are often plagued by confounding issues, making predictions cumbersome and unreliable. Laboratory data suggest that targeted quantitative analysis of Dehalococcoides mccartyi (Dhc) biomarker genes (qPCR) and proteins (qProt) can be directly correlated with reductive dechlorination activity. To assess the potential of qPCR and qProt measurements to predict rates, we collected data from cVOC-contaminated aquifers. At the benchmark study site, the rate constant for degradation of cis-dichloroethene (cDCE) extracted from monitoring data was 11.0 ± 3.4 yr-1, and the rate constant predicted from the abundance of TceA peptides was 6.9 yr-1. The rate constant for degradation of vinyl chloride (VC) from monitoring data was 8.4 ± 5.7 yr-1, and the rate constant predicted from the abundance of TceA peptides was 5.2 yr-1. At the other study sites, the rate constants for cDCE degradation predicted from qPCR and qProt measurements agreed within a factor of 4. Under the right circumstances, qPCR and qProt measurements can be useful to rapidly predict rates of cDCE and VC biodegradation, providing a major advance in effective site management.
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Affiliation(s)
| | | | - John Wilson
- Scissortail Environmental Solutions, LLC, Ada, Oklahoma 74820, United States
| | - Mandy Michalsen
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, Mississippi 39180, United States
| | - Frank E Löffler
- Department of Civil and Environmental Engineering, Department of Microbiology, Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert W Murdoch
- Battelle Memorial Institute, Columbus, Ohio 43220, United States
| | - Jack D Istok
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, Tennessee 37831, United States
| | - Paul B Hatzinger
- Aptim Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Larry Mullins
- Battelle Memorial Institute, Columbus, Ohio 43220, United States
| | - Amy Hill
- Battelle Memorial Institute, Columbus, Ohio 43220, United States
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3
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Underwood JC, Akob DM, Lorah MM, Imbrigiotta TE, Harvey RW, Tiedeman CR. Microbial Community Response to a Bioaugmentation Test to Degrade Trichloroethylene in a Fractured Rock Aquifer, Trenton, N.J. FEMS Microbiol Ecol 2022; 98:6617591. [PMID: 35749571 DOI: 10.1093/femsec/fiac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/12/2022] [Accepted: 06/22/2022] [Indexed: 11/12/2022] Open
Abstract
Bioaugmentation is a promising strategy for enhancing trichloroethylene (TCE) degradation in fractured rock. However, slow or incomplete biodegradation can lead to stalling at degradation byproducts such as 1,2-dichloroethene (cis-DCE) and vinyl chloride (VC). Over the course of 7 years, we examined the response of groundwater microbial populations in a bioaugmentation test where an emulsified vegetable oil solution (EOS®) and a dechlorinating consortium (KB-1®), containing the established dechlorinator Dehalococcoides, were injected into a TCE-contaminated fractured rock aquifer. Indigenous microbial communities responded within 2 days to added substrate and outcompeted KB-1®, and over the years of monitoring, several other notable turnover events were observed. Concentrations of ethene, the end product in reductive dechlorination, had the strongest correlations (p< 0.05) with members of Candidatus Colwellbacteria but their involvement in reductive dechlorination is unknown and warrants further investigation. Dehalococcoides never exceeded 0.6% relative abundance of groundwater microbial communities, despite its previously presumed importance at the site. Increased concentrations of carbon dioxide, acetic acid, and methane were positively correlated with increasing ethene concentrations; however, concentrations of cis-DCE and VC remained high by the end of the monitoring period suggesting preferential enrichment of indigenous partial dechlorinators over bioaugmented complete dechlorinators. This study highlights the importance of characterizing in situ microbial populations to understand how they can potentially enhance or inhibit augmented TCE degradation.
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Affiliation(s)
- J C Underwood
- U.S. Geological Survey, Water Mission Area, Boulder CO 80303USA
| | - D M Akob
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, 12201 Sunrise Valley Drive, Mailstop 954, Reston, VA 20192USA
| | - M M Lorah
- U.S. Geological Survey, MD-DE-DC Water Science Center, 5522 Research Park Drive, Baltimore, MD 21228USA
| | - T E Imbrigiotta
- U.S. Geological Survey, New Jersey Water Science Center, 3450 Princeton Pike, Suite 110, Lawrenceville, NJ 08648USA
| | - R W Harvey
- U.S. Geological Survey, Water Mission Area, Boulder CO 80303USA
| | - C R Tiedeman
- U.S. Geological Survey, Water Mission Area, Menlo Park, CA 94025USA
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4
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Yan J, Wang J, Villalobos Solis MI, Jin H, Chourey K, Li X, Yang Y, Yin Y, Hettich RL, Löffler FE. Respiratory Vinyl Chloride Reductive Dechlorination to Ethene in TceA-Expressing Dehalococcoides mccartyi. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:4831-4841. [PMID: 33683880 DOI: 10.1021/acs.est.0c07354] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioremediation of chlorinated ethenes in anoxic aquifers hinges on organohalide-respiring Dehalococcoidia expressing vinyl chloride (VC) reductive dehalogenase (RDase). The tceA gene encoding the trichloroethene-dechlorinating RDase TceA is frequently detected in contaminated groundwater but not recognized as a biomarker for VC detoxification. We demonstrate that tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as an electron acceptor when sufficient vitamin B12 (B12) is provided. Strain FL2 cultures that received 50 μg L-1 B12 completely dechlorinated VC to ethene at rates of 14.80 ± 1.30 μM day-1 and attained 1.64 ± 0.11 × 108 cells per μmol of VC consumed. Strain 195 attained similar growth yields of 1.80 ± 1.00 × 108 cells per μmol of VC consumed, and both strains could be consecutively transferred with VC as the electron acceptor. Proteomic analysis demonstrated TceA expression in VC-grown strain FL2 cultures. Resequencing of the strain FL2 and strain 195 tceA genes identified non-synonymous substitutions, although their consequences for TceA function are currently unknown. The finding that Dhc strains expressing TceA respire VC can explain ethene formation at chlorinated solvent sites, where quantitative polymerase chain reaction analysis indicates that tceA dominates the RDase gene pool.
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Affiliation(s)
- Jun Yan
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jingjing Wang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Huijuan Jin
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Karuna Chourey
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiuying Li
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yi Yang
- Key Laboratory of Pollution Control and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
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Yang L, Hnatko JP, Elsey JL, Christ JA, Pennell KD, Cápiro NL, Abriola LM. Exploration of processes governing microbial reductive dechlorination in a heterogeneous aquifer flow cell. WATER RESEARCH 2021; 193:116842. [PMID: 33545437 DOI: 10.1016/j.watres.2021.116842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Although microbial reductive dechlorination (MRD) has proven to be an effective approach for in situ treatment of chlorinated ethenes, field implementation of this technology is complicated by many factors, including subsurface heterogeneity, electron donor availability, and distribution of microbial populations. This work presents a coupled experimental and mathematical modeling study designed to explore the influence of heterogeneity on MRD and to assess the suitability of microcosm-derived rate parameters for modeling complex heterogeneous systems. A Monod-based model is applied to simulate a bioremediation experiment conducted in a laboratory-scale aquifer cell packed with aquifer material from the Commerce Street Superfund site in Williston, VT. Results reveal that (uncalibrated) model application of microcosm-derived dechlorination and microbial growth rates for transformation of trichloroethene (TCE), cis-1,2-dichloroethene (cis-DCE), and vinyl chloride (VC) reproduced observed aquifer cell concentration levels and trends. Mean relative errors between predicted and measured effluent concentrations were quantified as 6.7%, 27.0%, 41.5%, 32.0% and 21.6% over time for TCE, cis-DCE, VC, ethene and total volatile fatty acids (fermentable electron donor substrate and carbon source), respectively. The time-averaged extent of MRD (i.e., ethene formation) was well-predicted (4% underprediction), with modeled MRD exhibiting increased deviation from measured values under electron donor limiting conditions (maximum discrepancy of 14%). In contrast, simulations employing a homogeneous (uniform flow) domain resulted in underprediction of MRD extent by an average of 13%, with a maximum discrepancy of 45%. Model sensitivity analysis suggested that trace amounts of natural dissolved organic carbon served as an important fermentable substrate, providing up to 69% of the reducing equivalents consumed for MRD under donor-limiting conditions. Aquifer cell port concentration data and model simulations revealed that ethene formation varied spatially within the domain and was associated with regions of longer residence times. These results demonstrate the strong influence of subsurface heterogeneity on the accuracy of MRD predictions, and highlight the importance of subsurface characterization and the incorporation of flow field uncertainty in model applications for successful design and assessment of in situ bioremediation.
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Affiliation(s)
- Lurong Yang
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jason P Hnatko
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts, USA; ERM, Boston, Massachusetts, USA
| | - Jack L Elsey
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts, USA
| | | | - Kurt D Pennell
- School of Engineering, Brown University, Providence, Rhode Island, USA
| | - Natalie L Cápiro
- Department of Civil and Environmental Engineering, Auburn University, Auburn, Alabama, USA
| | - Linda M Abriola
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts, USA; School of Engineering, Brown University, Providence, Rhode Island, USA.
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Ottosen CB, Rønde V, McKnight US, Annable MD, Broholm MM, Devlin JF, Bjerg PL. Natural attenuation of a chlorinated ethene plume discharging to a stream: Integrated assessment of hydrogeological, chemical and microbial interactions. WATER RESEARCH 2020; 186:116332. [PMID: 32871289 DOI: 10.1016/j.watres.2020.116332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Attenuation processes of chlorinated ethenes in complex near-stream systems result in site-specific outcomes of great importance for risk assessment of contaminated sites. Additional interdisciplinary and comprehensive field research is required to enhance process understanding in these systems. In this study, several methods were combined in a multi-scale interdisciplinary in-situ approach to assess and quantify the near-stream attenuation of a chlorinated ethene plume, mainly consisting of cis-dichloroethene (cis-DCE) and vinyl chloride (VC), discharging to a lowland stream (Grindsted stream, Denmark) over a monitoring period of seven years. The approach included: hydrogeological characterisation, reach scale contaminant mass balance analysis, quantification of contaminant mass discharge, streambed fluxes of chlorinated ethenes quantified using Sediment Bed Passive Flux Meters (SBPFMs), assessment of redox conditions, temporal assessment of contaminant concentrations, microbial analysis, and compound-specific isotope analysis (CSIA). This study site exhibits a special attenuation behaviour not commonly encountered in field studies: the conversion from an initially limited degradation case (2012-16), despite seemingly optimal conditions, to one presenting notable levels of degradation (2019). Hence, this study site provides a new piece to the puzzle, as sites with different attenuation behaviours are required in order to acquire the full picture of the role groundwater-surface water interfaces have in risk mitigation. In spite of the increased degradation in the near-stream plume core, the contaminant attenuation was still incomplete in the discharging plume. A conceptualization of flow, transport and processes clarified that hydrogeology was the main control on the natural attenuation, as short residence times of 0.5-37 days restricted the time in which dechlorination could occur. This study reveals the importance of: taking an integrated approach to understand the influence of all attenuation processes in groundwater - surface water interactions; considering the scale and domain of interest when determining the main processes; and monitoring sufficiently both spatially and temporally to cover the transient conditions.
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Affiliation(s)
- Cecilie B Ottosen
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Vinni Rønde
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ursula S McKnight
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael D Annable
- Department of Environmental Engineering Sciences, University of Florida, FL, United States
| | - Mette M Broholm
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - John F Devlin
- Department of Geology, University of Kansas, Lawrence, KS, United States
| | - Poul L Bjerg
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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7
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Waseem H, Ali J, Syed JH, Jones KC. Establishing the relationship between molecular biomarkers and biotransformation rates: Extension of knowledge for dechlorination of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114676. [PMID: 33618452 DOI: 10.1016/j.envpol.2020.114676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 06/12/2023]
Abstract
Anaerobic reductive treatment technologies offer cost-effective and large-scale treatment of chlorinated compounds, including polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs). The information about the degradation rates of these compounds in natural settings is critical but difficult to obtain because of slow degradation processes. Establishing a relationship between biotransformation rate and abundance of biomarkers is one of the most critical challenges faced by the bioremediation industry. When solved for a given contaminant, it may result in significant cost savings because of serving as a basis for action. In the current review, we have summarized the studies highlighting the use of biomarkers, particularly DNA and RNA, as a proxy for reductive dechlorination of chlorinated ethenes. As the use of biomarkers for predicting biotransformation rates has not yet been executed for PCDD/Fs, we propose the extension of the same knowledge for dioxins, where slow degradation rates further necessitate the need for developing the biomarker-rate relationship. For this, we have first retrieved and calculated the bioremediation rates of different PCDD/Fs and then highlighted the key sequences that can be used as potential biomarkers. We have also discussed the implications and hurdles in developing such a relationship. Improvements in current techniques and collaboration with some other fields, such as biokinetic modeling, can improve the predictive capability of the biomarkers so that they can be used for effectively predicting biotransformation rates of dioxins and related compounds. In the future, a valid and established relationship between biomarkers and biotransformation rates of dioxin may result in significant cost savings, whilst also serving as a basis for action.
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Affiliation(s)
- Hassan Waseem
- Department of Civil & Environmental Engineering, Michigan State University, East Lansing, MI, 48823, USA; Department of Biotechnology, University of Sialkot, Sialkot, Punjab 51310, Pakistan
| | - Jafar Ali
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS University, Tarlai Kalan Park Road, Islamabad, 45550, Pakistan.
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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Kaya D, Kjellerup BV, Chourey K, Hettich RL, Taggart DM, Löffler FE. Impact of Fixed Nitrogen Availability on Dehalococcoides mccartyi Reductive Dechlorination Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14548-14558. [PMID: 31693350 DOI: 10.1021/acs.est.9b04463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biostimulation to promote reductive dechlorination is widely practiced, but the value of adding an exogenous nitrogen (N) source (e.g., NH4+) during treatment is unclear. This study investigates the effect of NH4+ availability on organohalide-respiring Dehalococcoides mccartyi (Dhc) growth and reductive dechlorination in enrichment cultures derived from groundwater (PW4) and river sediment (TC) impacted with chlorinated ethenes. In PW4 cultures, the addition of NH4+ increased cis-1,2-dichloroethene (cDCE)-to-ethene dechlorination rates about 5-fold (20.6 ± 1.6 versus 3.8 ± 0.5 μM Cl- d-1), and the total number of Dhc 16S rRNA gene copies were about 43-fold higher in incubations with NH4+ ((1.8 ± 0.9) × 108 mL-1) compared to incubations without NH4+ ((4.1 ± 0.8) × 107 mL-1). In TC cultures, NH4+ also stimulated cDCE-to-ethene dechlorination and Dhc growth. Quantitative polymerase chain reaction (qPCR) revealed that Cornell-type Dhc capable of N2 fixation dominated PW4 cultures without NH4+, but their relative abundance decreased in cultures with NH4+ amendment (i.e., 99 versus 54% of total Dhc). Pinellas-type Dhc incapable of N2 fixation were responsible for cDCE dechlorination in TC cultures, and diazotrophic community members met their fixed N requirement in the medium without NH4+. Responses to NH4+ were apparent at the community level, and N2-fixing bacterial populations increased in incubations without NH4+. Quantitative assessment of Dhc nitrogenase genes, transcripts, and proteomics data linked Cornell-type Dhc nifD and nifK expression with fixed N limitation. NH4+ additions also demonstrated positive effects on Dhc in situ dechlorination activity in the vicinity of well PW4. These findings demonstrate that biostimulation with NH4+ can enhance Dhc reductive dechlorination rates; however, a "do nothing" approach that relies on indigenous diazotrophs can achieve similar dechlorination end points and avoids the potential for stalled dechlorination due to inhibitory levels of NH4+ or transformation products (i.e., nitrous oxide).
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Affiliation(s)
- Devrim Kaya
- Biosciences Division and ⊥Chemical Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Department of Civil and Environmental Engineering , University of Maryland College Park , College Park , Maryland 20742 , United States
| | - Birthe V Kjellerup
- Department of Civil and Environmental Engineering , University of Maryland College Park , College Park , Maryland 20742 , United States
| | | | | | - Dora M Taggart
- Microbial Insights, Inc. , Knoxville , Tennessee 37932 , United States
| | - Frank E Löffler
- Biosciences Division and ⊥Chemical Sciences Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
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Wu YJ, Liu PWG, Hsu YS, Whang LM, Lin TF, Hung WN, Cho KC. Application of molecular biological tools for monitoring efficiency of trichloroethylene remediation. CHEMOSPHERE 2019; 233:697-704. [PMID: 31195274 DOI: 10.1016/j.chemosphere.2019.05.203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/11/2019] [Accepted: 05/23/2019] [Indexed: 05/20/2023]
Abstract
Trichloroethylene (TCE) is one of the most ubiquitous halogenated organic compounds of concerns of carcinogens in groundwater in Taiwan. Bioremediation has been recognized as a cost-effective approach in reducing TCE concentration. Five pilot-scale wells were constructed to monitor TCE concentrations in contaminated groundwater. With injection of EOS®, TCE was effectively degraded to 42%-93% by the end of 175 days. The biostimulation with EOS® was useful in establishing a micro-site anaerobic but with limited contribution. Dilution of the aquifer movement also caused the TCE reduction among injection and monitoring wells. The degradability was affected by the location and the proximity from the injection well. TCE concentrations found to be negatively correlated with the associated Dehalococcoides spp. and functional genes levels. Dhc concentration of 108 copies L-1 caused the initial 40% of TCE degradation. The well with the optimal degradation owned tceA of 109 cells L-1. T-RFLP results indicate the wells with the superior TCE degradability also performed the highest Shannon index number (means the highest diversity), which occurred on the same day that Dhc levels started to enlarge. Desulfovibrio desulfuricans and Desulfuromonas chloroethenica were predominant species identified in the T-RFLP fingerprint profile. In brief, a variety of different factors including well locations, geochemical indicators, and microbial contribution were useful to explain the site-specific optimal TCE remediation approach. The consistence among TCE degradation, Dhc growing pattern, functional gene levels, and the dynamics of the microbial community structure present the novelty of this study.
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Affiliation(s)
- Yi-Ju Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Pao-Wen Grace Liu
- Department of Safety Health and Environmental Engineering, Chung Hwa University of Medical Technology, Tainan 71703, Taiwan.
| | - You-Siang Hsu
- Department of Safety Health and Environmental Engineering, Chung Hwa University of Medical Technology, Tainan 71703, Taiwan
| | - Liang-Ming Whang
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Tsair-Fuh Lin
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Nung Hung
- Industrial Technology Research Institute of Taiwan, Taiwan
| | - Kun-Ching Cho
- Industrial Technology Research Institute of Taiwan, Taiwan
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Clark K, Taggart DM, Baldwin BR, Ritalahti KM, Murdoch RW, Hatt JK, Löffler FE. Normalized Quantitative PCR Measurements as Predictors for Ethene Formation at Sites Impacted with Chlorinated Ethenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13410-13420. [PMID: 30365883 PMCID: PMC6945293 DOI: 10.1021/acs.est.8b04373] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Quantitative PCR (qPCR) targeting Dehalococcoides mccartyi ( Dhc) biomarker genes supports effective management at sites impacted with chlorinated ethenes. To establish correlations between Dhc biomarker gene abundances and ethene formation (i.e., detoxification), 859 groundwater samples representing 62 sites undergoing monitored natural attenuation or enhanced remediation were analyzed. Dhc 16S rRNA genes and the vinyl chloride (VC) reductive dehalogenase genes bvcA and vcrA were detected in 88% and 61% of samples, respectively, from wells with ethene. Dhc 16S rRNA, bvcA, vcrA, and tceA (implicated in cometabolic reductive VC dechlorination) gene abundances all positively correlated with ethene formation. Significantly greater ethene concentrations were observed when Dhc 16S rRNA gene and VC RDase gene abundances exceeded 107 and 106 copies L-1, respectively, and when Dhc 16S rRNA- and bvcA + vcrA-to-total bacterial 16S rRNA gene ratios exceeded 0.1%. Dhc 16S rRNA gene-to- vcrA/ bvcA ratios near unity also indicated elevated ethene; however, no increased ethene was observed in 19 wells where vcrA and/or bvcA gene copy numbers exceeded Dhc cell numbers 10- to 10 000-fold. Approximately one-third of samples with detectable ethene lacked bvcA, vcrA, and tceA, suggesting that comprehensive understanding of VC detoxification biomarkers has not been achieved. Although the current biomarker suite is incomplete, the data analysis corroborates the value of the available Dhc DNA biomarkers for prognostic and diagnostic groundwater monitoring at sites impacted with chlorinated ethenes.
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Affiliation(s)
- Katherine Clark
- Microbial Insights, Incorporated, 10515 Research Drive, Knoxville, Tennessee 37932, United States
| | - Dora M. Taggart
- Microbial Insights, Incorporated, 10515 Research Drive, Knoxville, Tennessee 37932, United States
| | - Brett R. Baldwin
- Microbial Insights, Incorporated, 10515 Research Drive, Knoxville, Tennessee 37932, United States
| | - Kirsti M. Ritalahti
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Robert W. Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Janet K. Hatt
- School of Civil and Environmental Engineering, Atlanta, Georgia 30332-0512
| | - Frank E. Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division and Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge Tennessee 37831, United States
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11
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Molenda O, Tang S, Lomheim L, Gautam VK, Lemak S, Yakunin AF, Maxwell KL, Edwards EA. Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes. ISME JOURNAL 2018; 13:24-38. [PMID: 30104577 DOI: 10.1038/s41396-018-0254-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 01/12/2023]
Abstract
Dehalococcoides mccartyi are obligate organohalide-respiring bacteria that play an important detoxifying role in the environment. They have small genomes (~1.4 Mb) with a core region interrupted by two high plasticity regions (HPRs) containing dozens of genes encoding reductive dehalogenases involved in organohalide respiration. The genomes of eight new strains of D. mccartyi were closed from metagenomic data from a related set of enrichment cultures, bringing the total number of genomes to 24. Two of the newly sequenced strains and three previously sequenced strains contain CRISPR-Cas systems. These D. mccartyi CRISPR-Cas systems were found to primarily target prophages and genomic islands. The genomic islands were identified either as integrated into D. mccartyi genomes or as circular extrachromosomal elements. We observed active circularization of the integrated genomic island containing vcrABC operon encoding the dehalogenase (VcrA) responsible for the transformation of vinyl chloride to non-toxic ethene. We interrogated archived DNA from established enrichment cultures and found that the CRISPR array acquired three new spacers in 11 years. These data provide a glimpse into dynamic processes operating on the genomes distinct to D. mccartyi strains found in enrichment cultures and provide the first insights into possible mechanisms of lateral DNA exchange in D. mccartyi.
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Affiliation(s)
- Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Vasu K Gautam
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada. .,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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12
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Pérez-de-Mora A, Lacourt A, McMaster ML, Liang X, Dworatzek SM, Edwards EA. Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi ( D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments. Front Microbiol 2018; 9:812. [PMID: 29867784 PMCID: PMC5968391 DOI: 10.3389/fmicb.2018.00812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023] Open
Abstract
Dehalococcoides mccartyi (D. mccartyi) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed D. mccartyi-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 D. mccartyi rdhA genes and used to measure population diversity in 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to D. mccartyi 16S rRNA gene copies revealed the presence of multiple distinct D. mccartyi strains in each culture, many more than the two strains inferred from 16S rRNA analysis. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi strains and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant D. mccartyi strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative rdhA abundances revealed D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene. These shifts indicate a selective pressure of the most abundant chlorinated electron acceptor, as was also observed in lab cultures. These results also suggest that reductive dechlorination at contaminated sites is brought about by multiple strains of D. mccartyi whether or not the site is bioaugmented. Understanding the driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.
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Affiliation(s)
- Alfredo Pérez-de-Mora
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Research Unit Analytical Biogeochemistry, Department of Environmental Sciences, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anna Lacourt
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Xiaoming Liang
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Elizabeth A Edwards
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
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13
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Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Most probable number with visual based LAMP for the quantification of reductive dehalogenase genes in groundwater samples. J Microbiol Methods 2017; 143:44-49. [PMID: 29031631 DOI: 10.1016/j.mimet.2017.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 01/26/2023]
Abstract
The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation). Despite having a detection limit less than the threshold recommended for effective remediation, the application of the assay was limited because of the semi-quantitative nature of the data. Moreover, the assay was prone to false positives due to the aerosolization of amplicons. In this study, deoxyuridine triphosphate (dUTP) and uracil DNA glycosylase (UNG) were incorporated into the assay to reduce the probability of false positives. Optimization experiments revealed a UNG concentration of 0.2units per reaction was adequate for degrading trace levels of AUGC based contamination (~1.4×104 gene copies/reaction) without significant changes to the detection limit (~100 gene copies/reaction). Additionally, the optimized assay was used with the most probable number (MPN) method to quantify RDase genes (vcrA and tceA) in multiple groundwater samples from a chlorinated solvent contaminated site. Using this approach, gene concentrations were significantly correlated to concentrations obtained using traditional methods (qPCR and DNA templates). Although the assay underestimated RDase genes concentrations, a strong correlation (R2=0.78 and 0.94) was observed between the two data sets. The regression equations obtained will be valuable to determine gene copies in groundwater using the newly developed, low cost and time saving method.
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Affiliation(s)
- Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Paul B Hatzinger
- APTIM Federal Services, 17 Princess Road, Lawrenceville, NJ 08648, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
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14
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Yang Y, Higgins SA, Yan J, Şimşir B, Chourey K, Iyer R, Hettich RL, Baldwin B, Ogles DM, Löffler FE. Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes. ISME JOURNAL 2017; 11:2767-2780. [PMID: 28809851 DOI: 10.1038/ismej.2017.127] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 06/12/2017] [Accepted: 06/16/2017] [Indexed: 12/15/2022]
Abstract
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene. 16S rRNA gene amplicon and qPCR analyses revealed a predominance of Dhgm sequences, but Dehalococcoides mccartyi (Dhc) biomarker genes were not detected. The enumeration of Dhgm 16S rRNA genes demonstrated VC-dependent growth, and 6.55±0.64 × 108 cells were measured per μmole of chloride released. Metagenome sequencing enabled the assembly of a Dhgm draft genome, and 52 putative reductive dehalogenase (RDase) genes were identified. Proteomic workflows identified a putative VC RDase with 49 and 56.1% amino acid similarity to the known VC RDases VcrA and BvcA, respectively. A survey of 1,173 groundwater samples collected from 111 chlorinated solvent-contaminated sites in the United States and Australia revealed that Dhgm 16S rRNA genes were frequently detected and outnumbered Dhc in 65% of the samples. Dhgm are likely greater contributors to reductive dechlorination of chlorinated solvents in contaminated aquifers than is currently recognized, and non-polluted environments represent sources of organohalide-respiring bacteria with novel RDase genes.
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Affiliation(s)
- Yi Yang
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Steven A Higgins
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jun Yan
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Burcu Şimşir
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | - Robert L Hettich
- Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA.,Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
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15
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Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater. Appl Microbiol Biotechnol 2017; 101:4827-4835. [PMID: 28238079 DOI: 10.1007/s00253-017-8203-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 10/20/2022]
Abstract
TaqMan probe-based quantitative polymerase chain reaction (qPCR) specific to the biomarker reductive dehalogenase (RDase) genes is a widely accepted molecular biological tool (MBT) for determining the abundance of Dehalococcoides sp. in groundwater samples from chlorinated solvent-contaminated sites. However, there are significant costs associated with this MBT. In this study, we describe an approach that requires only low-cost laboratory equipment (a bench top centrifuge and a water bath) and requires less time and resources compared to qPCR. The method involves the concentration of biomass from groundwater, without DNA extraction, and loop-mediated isothermal amplification (LAMP) of the cell templates. The amplification products are detected by a simple visual color change (orange/green). The detection limits of the assay were determined using groundwater from a contaminated site. In addition, the assay was tested with groundwater from three additional contaminated sites. The final approach to detect RDase genes, without DNA extraction or a thermal cycler, was successful to 1.8 × 105 gene copies per L for vcrA and 1.3 × 105 gene copies per L for tceA. Both values are below the threshold recommended for effective in situ dechlorination.
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Affiliation(s)
- Yogendra H Kanitkar
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA
| | - Paul B Hatzinger
- CB&I Federal Services, 17 Princess Road, Lawrenceville, NJ, 08648, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA.,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, A135, 1449 Engineering Research Court, East Lansing, MI, 48824, USA.
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16
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Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, J.M. Stams A, Springael D, Dejonghe W, Smidt H. Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol. Environ Microbiol 2016; 19:968-981. [DOI: 10.1111/1462-2920.13531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Yue Lu
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Ying Zheng
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | | | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health; Ingolstädter Landstrasse 1 Neuherberg D-85764 Germany
| | - Alfons J.M. Stams
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Centre of Biological Engineering; University of Minho; Braga Portugal
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - 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; Wageningen The Netherlands
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17
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Lee J, Im J, Kim U, Löffler FE. A Data Mining Approach to Predict In Situ Detoxification Potential of Chlorinated Ethenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5181-5188. [PMID: 27116079 DOI: 10.1021/acs.est.5b05090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite advances in physicochemical remediation technologies, in situ bioremediation treatment based on Dehalococcoides mccartyi (Dhc) reductive dechlorination activity remains a cornerstone approach to remedy sites impacted with chlorinated ethenes. Selecting the best remedial strategy is challenging due to uncertainties and complexity associated with biological and geochemical factors influencing Dhc activity. Guidelines based on measurable biogeochemical parameters have been proposed, but contemporary efforts fall short of meaningfully integrating the available information. Extensive groundwater monitoring data sets have been collected for decades, but have not been systematically analyzed and used for developing tools to guide decision-making. In the present study, geochemical and microbial data sets collected from 35 wells at five contaminated sites were used to demonstrate that a data mining prediction model using the classification and regression tree (CART) algorithm can provide improved predictive understanding of a site's reductive dechlorination potential. The CART model successfully predicted the 3-month-ahead reductive dechlorination potential with 75.8% and 69.5% true positive rate (i.e., sensitivity) for the training set and the test set, respectively. The machine learning algorithm ranked parameters by relative importance for assessing in situ reductive dechlorination potential. The abundance of Dhc 16S rRNA genes, CH4, Fe(2+), NO3(-), NO2(-), and SO4(2-) concentrations, total organic carbon (TOC) amounts, and oxidation-reduction potential (ORP) displayed significant correlations (p < 0.01) with dechlorination potential, with NO3(-), NO2(-), and Fe(2+) concentrations exhibiting precedence over other parameters. Contrary to prior efforts, the power of data mining approaches lies in the ability to discern synergetic effects between multiple parameters that affect reductive dechlorination activity. Overall, these findings demonstrate that data mining techniques (e.g., machine learning algorithms) effectively utilize groundwater monitoring data to derive predictive understanding of contaminant degradation, and thus have great potential for improving decision-making tools. A major need for realizing the predictive capabilities of data mining approaches is a curated, open-access, up-to-date and comprehensive collection of biogeochemical groundwater monitoring data.
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Affiliation(s)
- Jaejin Lee
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jeongdae Im
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Ungtae Kim
- Department of Civil and Environmental Engineering, Cleveland State University , Cleveland, Ohio 44115, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division , Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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18
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Mirza BS, Sorensen DL, Dupont RR, McLean JE. Dehalococcoides abundance and alternate electron acceptor effects on large, flow-through trichloroethene dechlorinating columns. Appl Microbiol Biotechnol 2015; 100:2367-79. [PMID: 26536878 DOI: 10.1007/s00253-015-7112-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/18/2015] [Accepted: 10/20/2015] [Indexed: 11/25/2022]
Abstract
Trichloroethene (TCE) in groundwater is a major health concern and biostimulation/bioaugmentation-based strategies have been evaluated to achieve complete reductive dechlorination with varying success. Different carbon sources were hypothesized to stimulate different extents of TCE reductive dechlorination. Ecological conditions that developed different dechlorination stages were investigated by quantitating Dehalococcoides 16S rRNA (Dhc) and reductive dehalogenase gene abundance, and by describing biogeochemical properties of laboratory columns in response to this biostimulation. Eight large columns (183 cm × 15.2 cm), packed with aquifer material from Hill AFB, Utah, that were continuously fed TCE for 7.5 years. Duplicate columns were biostimulated with whey or one of two different Newman Zone® emulsified oil formulations containing either nonionic surfactant (EOLN) or standard surfactant (EOL). Two columns were non-stimulated controls. Complete (whey amended), partial (EOLN amended), limited (EOL), and non-TCE dehalogenating systems (controls) developed over the course of the study. Bioaugmentation of half of the columns with Bachman Road culture 3 years prior to dismantling did not influence the extent of TCE dehalogenation. Multivariate analysis clustered samples by biostimulation treatments and extent of TCE dehalogenation. Dhc, tceA, and bvcA gene concentrations did not show a consistent relationship with TCE dehalogenation but the vcrA gene was more abundant in completely dehalogenating, whey-treated columns. The whey columns developed strongly reducing conditions producing Fe(II), sulfide, and methane. Biostimulation with different carbon and energy sources can support high concentrations of diverse Dhc, but carbon addition has a major influence on biogeochemical processes effecting the extent of TCE dehalogenation.
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Affiliation(s)
- Babur S Mirza
- Utah Water Research Laboratory, Utah State University, Logan, UT, 84322-8200, USA
| | - Darwin L Sorensen
- Utah Water Research Laboratory, Utah State University, Logan, UT, 84322-8200, USA
| | - R Ryan Dupont
- Utah Water Research Laboratory, Utah State University, Logan, UT, 84322-8200, USA.,Department of Civil and Environmental Engineering, Utah State University, Logan, UT, 84322-8200, USA
| | - Joan E McLean
- Utah Water Research Laboratory, Utah State University, Logan, UT, 84322-8200, USA. .,Department of Civil and Environmental Engineering, Utah State University, Logan, UT, 84322-8200, USA.
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19
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Cápiro NL, Löffler FE, Pennell KD. Spatial and temporal dynamics of organohalide-respiring bacteria in a heterogeneous PCE-DNAPL source zone. JOURNAL OF CONTAMINANT HYDROLOGY 2015; 182:78-90. [PMID: 26348832 DOI: 10.1016/j.jconhyd.2015.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/15/2015] [Accepted: 08/19/2015] [Indexed: 06/05/2023]
Abstract
Effective treatment of sites contaminated with dense non-aqueous phase liquids (DNAPLs) requires detailed understanding of the microbial community responses to changes in source zone strength and architecture. Changes in the spatial and temporal distributions of the organohalide-respiring Dehalococcoides mccartyi (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ) were examined in a heterogeneous tetrachloroethene- (PCE-) DNAPL source zone within a two-dimensional laboratory-scale aquifer flow cell. As part of a combined remedy approach, flushing with 2.3 pore volumes (PVs) of 4% (w/w) solution of the nonionic, biodegradable surfactant Tween® 80 removed 55% of the initial contaminant mass, and resulted in a PCE-DNAPL distribution that contained 51% discrete ganglia and 49% pools (ganglia-to-pool ratio of 1.06). Subsequent bioaugmentation with the PCE-to-ethene-dechlorinating consortium BDI-SZ resulted in cis-1,2-dichloroethene (cis-DCE) formation after 1 PV (ca. 7 days), while vinyl chloride (VC) and ethene were detected 10 PVs after bioaugmentation. Maximum ethene yields (ca. 90 μM) within DNAPL pool and ganglia regions coincided with the detection of the vcrA reductive dehalogenase (RDase) gene that exceeded the Dhc 16S rRNA genes by 2.0±1.3 and 4.0±1.7 fold in the pool and ganglia regions, respectively. Dhc and GeoSZ cell abundance increased by up to 4 orders-of-magnitude after 28 PVs of steady-state operation, with 1 to 2 orders-of-magnitude increases observed in close proximity to residual PCE-DNAPL. These observations suggest the involvement of these dechlorinators the in observed PCE dissolution enhancements of up to 2.3 and 6.0-fold within pool and ganglia regions, respectively. Analysis of the solid and aqueous samples at the conclusion of the experiment revealed that the highest VC (≥155 μM) and ethene (≥65 μM) concentrations were measured in zones where Dhc and GeoSZ were predominately attached to the solids. These findings demonstrate dynamic responses of organohalide-respiring bacteria in a heterogeneous DNAPL source zone, and emphasize the influence of source zone architecture on bioremediation performance.
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Affiliation(s)
- Natalie L Cápiro
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, United States.
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, United States; University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Kurt D Pennell
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, United States.
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20
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Lee PKH, Men Y, Wang S, He J, Alvarez-Cohen L. Development of a fluorescence-activated cell sorting method coupled with whole genome amplification to analyze minority and trace Dehalococcoides genomes in microbial communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1585-1593. [PMID: 25565465 DOI: 10.1021/es503888y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10(6) cells or ∼1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing ∼10% and ∼1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.
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Affiliation(s)
- Patrick K H Lee
- Department of Civil and Environmental Engineering, University of California , Berkeley, California 94720, United States
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21
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Doğan-Subaşi E, Bastiaens L, Leys N, Boon N, Dejonghe W. Quantitative and functional dynamics of Dehalococcoides spp. and its tceA and vcrA genes under TCE exposure. Biodegradation 2015; 25:493-504. [PMID: 25025097 DOI: 10.1007/s10532-013-9676-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This study aimed at monitoring the dynamics of phylogenetic and catabolic genes of a dechlorinating enrichment culture before, during, and after complete dechlorination of chlorinated compounds. More specifically, the effect of 40 μM trichloroethene (TCE) and 5.6 mM lactate on the gene abundance and activity of an enrichment culture was investigated for 40 days. Although tceA and vcrA gene copy numbers were relatively stable in DNA extracts over time, tceA and vcrA mRNA abundances were upregulated from undetectable levels to 2.96 × and 6.33 × 10⁴ transcripts/mL, respectively, only after exposure to TCE and lactate. While tceA gene transcripts decreased over time with TCE dechlorination, the vcrA gene was expressed steadily even when the concentration of vinyl chloride was at undetectable levels. In addition, ratios between catabolic and phylogenetic genes indicated that tceA and vcrA gene carrying organisms dechlorinated TCE and its produced daughter products, while vcrA gene was mainly responsible for the dechlorination of the lower VC concentrations in a later stage of degradation.
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Stedtfeld RD, Stedtfeld TM, Kronlein M, Seyrig G, Steffan RJ, Cupples AM, Hashsham SA. DNA extraction-free quantification of Dehalococcoides spp. in groundwater using a hand-held device. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13855-63. [PMID: 25360694 DOI: 10.1021/es503472h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nucleic acid amplification of biomarkers is increasingly used to measure microbial activity and predict remedial performance in sites with trichloroethene (TCE) contamination. Field-based genetic quantification of microorganisms associated with bioremediation may help increase accuracy that is diminished through transport and processing of groundwater samples. Sterivex cartridges and a previously undescribed mechanism for eluting biomass was used to concentrate cells. DNA extraction-free loop mediated isothermal amplification (LAMP) was monitored in real-time with a point of use device (termed Gene-Z). A detection limit of 10(5) cells L(–1) was obtained, corresponding to sensitivity between 10 to 100 genomic copies per reaction for assays targeting the Dehalococcoides spp. specific 16S rRNA gene and vcrA gene, respectively. The quantity of Dehalococcoides spp. genomic copies measured from two TCE contaminated groundwater samples with conventional means of quantification including filtration, DNA extraction, purification, and qPCR was comparable to the field ready technique. Overall, this method of measuring Dehalococcoides spp. and vcrA genes in groundwater via direct amplification without intentional DNA extraction and purification is demonstrated, which may provide a more accurate mechanism of predicting remediation rates.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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23
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Cápiro NL, Wang Y, Hatt JK, Lebrón CA, Pennell KD, Löffler FE. Distribution of organohalide-respiring bacteria between solid and aqueous phases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:10878-87. [PMID: 25105899 DOI: 10.1021/es501320h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Contemporary microbial monitoring of aquifers relies on groundwater samples to enumerate nonattached cells of interest. One-dimensional column studies quantified the distribution of bacterial cells in solid and the aqueous phases as a function of microbial species, growth substrate availability and porous medium (i.e., Appling soil versus Federal Fine Ottawa sand with 0.75% and 0.01% [w/w] organic carbon, respectively). Without supplied growth substrates, effluent from columns inoculated with the tetrachloroethene- (PCE-) to-ethene-dechlorinating bacterial consortium BDI-SZ containing Dehalococcoides mccartyi (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ), or inoculated with Anaeromyxobacter dehalogenans strain W (AdehalW), captured 94-96, 81-99, and 73-84% of the Dhc, GeoSZ, and AdehalW cells, respectively. Cell retention was organism-specific and increased in the order Dhc < GeoSZ < AdehalW. When amended with 10 mM lactate and 0.11 mM PCE, aqueous samples accounted for 1.3-27 and 0.02-22% of the total Dhc and GeoSZ biomass, respectively. In Appling soil, up to three orders-of-magnitude more cells were associated with the solid phase, and attachment rate coefficients (katt) were consistently greater compared to Federal Fine sand. Cell-solid interaction energies ranged from -2.5 to 787 kT and were consistent with organism-specific deposition behavior, where GeoSZ and AdehalW exhibited greater attachment than Dhc cells. The observed disparities in microbial cell distributions between the aqueous and solid phases imply that groundwater analysis can underestimate the total cell abundance in the aquifer by orders-of-magnitude under conditions of growth and in porous media with elevated organic carbon content. The implications of these findings for monitoring chlorinated solvent sites are discussed.
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Affiliation(s)
- Natalie L Cápiro
- Department of Civil and Environmental Engineering, Tufts University , Medford, Massachusetts 02155, United States
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Biostimulation of indigenous communities for the successful dechlorination of tetrachloroethene (perchloroethylene)-contaminated groundwater. Biotechnol Lett 2013; 36:75-83. [DOI: 10.1007/s10529-013-1369-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/05/2013] [Indexed: 11/26/2022]
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25
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Hatt JK, Ritalahti KM, Ogles DM, Lebrón CA, Löffler FE. Design and application of an internal amplification control to improve Dehalococcoides mccartyi 16S rRNA gene enumeration by qPCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:11131-8. [PMID: 24053159 DOI: 10.1021/es4019817] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Dehalococcoides mccartyi (Dhc) strains are keystone bacteria for reductive dechlorination of chlorinated ethenes to nontoxic ethene in contaminated aquifers. Enumeration of Dhc biomarker genes using quantitative real-time PCR (qPCR) in groundwater is a key component of site assessment and bioremediation monitoring. Unfortunately, standardized qPCR procedures that recognize impaired measurements due to PCR inhibition, low template DNA concentrations, or analytical error are not available, thus limiting confidence in qPCR data. To improve contemporary approaches for enumerating Dhc in environmental samples, multiplex qPCR assays were designed to quantify the Dhc 16S rRNA gene and one of two different internal amplification controls (IACs): a modified Dhc 16S rRNA gene fragment (Dhc*) and the firefly luciferase gene luc. The Dhc* IAC exhibited competitive inhibition in qPCR with the Dhc 16S rRNA gene template when the ratio of either target was 100-fold greater than the other target. A multiplex qPCR assay with the luc IAC avoided competitive inhibition and accurately quantified Dhc abundances ranging from ∼10 to 10(7) 16S rRNA gene copies per reaction. The addition of ∼10(6) E. coli luc IAC to simulated groundwater amended with the Dhc-containing consortium KB-1 yielded reproducible luc counts after DNA extraction and multiplex qPCR enumeration. The application of the luc IAC assay improved Dhc biomarker gene quantification from simulated groundwater samples and is a valuable approach for "ground truthing" qPCR data obtained in different laboratories, thus reducing ambiguity associated with qPCR enumeration and reproducibility.
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Affiliation(s)
- Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology , 311 Ferst Drive, Atlanta, Georgia 30332, United States
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26
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Bælum J, Chambon JC, Scheutz C, Binning PJ, Laier T, Bjerg PL, Jacobsen CS. A conceptual model linking functional gene expression and reductive dechlorination rates of chlorinated ethenes in clay rich groundwater sediment. WATER RESEARCH 2013; 47:2467-78. [PMID: 23490098 DOI: 10.1016/j.watres.2013.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 05/26/2023]
Abstract
We used current knowledge of cellular processes involved in reductive dechlorination to develop a conceptual model to describe the regulatory system of dechlorination at the cell level; the model links bacterial growth and substrate consumption to the abundance of messenger RNA of functional genes involved in the dechlorination process. The applicability of the model was tested on a treatability study of biostimulated and bioaugmented microcosms. Using quantitative real time PCR, high-resolution expression profiles of the functional reductive dehalogenase genes bvcA and vcrA were obtained during two consecutive dechlorination events of trichlorethene, cis-dichlorethene and vinyl chloride. Up-regulation of the bvcA (for the biostimulated microcosms) and vcrA (for the bioaugmented microcosms) gene expression fitted well with high rates of dechlorination of vinyl chloride, while no known transcripts could be measured during trichloroethene and cis-dichlorethene dechlorination. Maximum concentrations of 2.1 and 1.7 transcripts per gene of the bvcA and vcrA genes, respectively, were measured at the same time points as maximum dechlorination rates were observed. The developed model compared well with the experimental data for both biostimulated and bioaugmented microcosms under non-steady state conditions and was supported by results from a recently published study under steady state conditions.
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Affiliation(s)
- Jacob Bælum
- The Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350 Copenhagen, Denmark
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Quantitative estimation of Dehalococcoides mccartyi at laboratory and field scale: Comparative study between CARD-FISH and Real Time PCR. J Microbiol Methods 2013; 93:127-33. [DOI: 10.1016/j.mimet.2013.02.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/28/2013] [Accepted: 02/28/2013] [Indexed: 11/22/2022]
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28
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Lee PKH, Cheng D, West KA, Alvarez-Cohen L, He J. Isolation of two newDehalococcoides mccartyistrains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis. Environ Microbiol 2013; 15:2293-305. [DOI: 10.1111/1462-2920.12099] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 01/02/2013] [Accepted: 01/18/2013] [Indexed: 11/29/2022]
Affiliation(s)
| | - Dan Cheng
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore; 117576
| | - Kimberlee A. West
- Department of Civil and Environmental Engineering; University of California; Berkeley; CA; 94720; USA
| | | | - Jianzhong He
- Department of Civil and Environmental Engineering; National University of Singapore; Singapore; 117576
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Matturro B, Aulenta F, Majone M, Papini MP, Tandoi V, Rossetti S. Field distribution and activity of chlorinated solvents degrading bacteria by combining CARD-FISH and real time PCR. N Biotechnol 2012; 30:23-32. [DOI: 10.1016/j.nbt.2012.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 07/12/2012] [Accepted: 07/14/2012] [Indexed: 11/27/2022]
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Rowe AR, Heavner GL, Mansfeldt CB, Werner JJ, Richardson RE. Relating chloroethene respiration rates in Dehalococcoides to protein and mRNA biomarkers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:9388-9397. [PMID: 22812668 DOI: 10.1021/es300996c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Molecular biomarkers could provide critical insight into myriad in situ microbial activities. In this study we explore correlations of both mRNA and protein biomarkers with chloroethene respiration rate in Dehalococcoides. In a series of continuously fed dechlorinating mixed-culture microcosm experiments (n = 26), we varied respiratory substrates, substrate ratios and feeding rates. Transcript levels for most biomarkers were responsive down to 0.01× the culture's maximum respiration rate. The dehalogenase TceA and the Ni-Fe hydrogenase HupL transcripts were positively correlated (Pearson's r of 0.89 and 0.88, respectively) with respiration rates on log-log plots between 1.5 and 280 μeeq/L-hr for mRNA abundances of 10(7) to 10(10) transcripts/mL (0.07-230 transcripts/genome). These trends were independent of the types of chloroethene or electron donors fed. Other mRNA target levels plateaued or declined at respiration rates above 5 μeeq/L-hr. Using both relative and absolute protein quantification methods, we found that per-genome protein abundances of most targeted biomarkers did not statistically change over the experimental time frames. However, quantified enzyme levels allowed us to calculate in vivo enzyme-specific rate constants (k(cat)) for the dehalogenases PceA and TceA: 400 and 22 substrate molecules/enzyme-sec, respectively. Overall, these data support the promise of both mRNA and protein biomarkers for estimating process rates through either empirical (mRNA-based) or kinetic (protein-based) models, but they require follow-up studies in other cultures and at active remediation sites.
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Affiliation(s)
- Annette R Rowe
- Field of Microbiology, Cornell University, Ithaca New York 14853, United States
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Discovery of a trans-dichloroethene-respiring Dehalogenimonas species in the 1,1,2,2-tetrachloroethane-dechlorinating WBC-2 consortium. Appl Environ Microbiol 2012; 78:5280-7. [PMID: 22635995 DOI: 10.1128/aem.00384-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The WBC-2 consortium is an organohalide-respiring anaerobic microbial enrichment culture capable of dechlorinating 1,1,2,2-tetrachloroethane (TeCA) to ethene. In the WBC-2 culture, TeCA is first transformed to trans-dichloroethene (tDCE) by dichloroelimination; tDCE is subsequently transformed to vinyl chloride (VC) and then to ethene by hydrogenolysis. Analysis of 16S rRNA gene clone libraries from culture DNA revealed sequences from three putative dechlorinating organisms belonging to Dehalococcoides, Dehalobacter, and Dehalogenimonas genera. Quantitative PCR primers were designed for each of these sequences, and their abundance was quantified in enrichment cultures over time. These data revealed that complete dechlorination of TeCA to ethene involves all three organisms. Dehalobacter spp. grew during the dihaloelimination of TeCA to tDCE, while Dehalococcoides and Dehalogenimonas spp. grew during hydrogenolysis of tDCE to ethene. This is the first time a genus other than Dehalococcoides has been implicated in dechlorination of tDCE to VC.
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Ding C, He J. Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments. Microb Biotechnol 2012; 5:347-67. [PMID: 22070763 PMCID: PMC3821678 DOI: 10.1111/j.1751-7915.2011.00313.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 09/24/2011] [Accepted: 09/28/2011] [Indexed: 11/28/2022] Open
Abstract
Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction-based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next-generation sequencing, provide unsurpassed detection ability, which has enabled large-scale comparative genomic and whole-genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic-acid-based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.
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Affiliation(s)
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576
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Hatt JK, Löffler FE. Quantitative real-time PCR (qPCR) detection chemistries affect enumeration of the Dehalococcoides 16S rRNA gene in groundwater. J Microbiol Methods 2012; 88:263-70. [DOI: 10.1016/j.mimet.2011.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 12/08/2011] [Accepted: 12/08/2011] [Indexed: 11/15/2022]
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Ise K, Suto K, Inoue C. Microbial diversity and changes in the distribution of dehalogenase genes during dechlorination with different concentrations of cis-DCE. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:5339-5345. [PMID: 21609008 DOI: 10.1021/es104199y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A dechlorinating consortium (designated as TES-1 culture) able to convert trichloroethene (TCE) to ethene was established from TCE-contaminated groundwater. This culture had the ability of complete dechlorination of TCE within about one month. From the clone library analysis of 16S rRNA gene, this culture was mainly composed of fermentation bacteria, such as Clostridium spp., and Desulfitobacterium spp. known as facultative dechlorinator. PCR using specific primers for Dehalococcoides spp. and the dehalogenase genes confirmed that the culture contained the Dehalococcoides spp. 16S rRNA gene and three dehalogenase genes, tceA, vcrA and bvcA. Dechlorination experiments using cis-dichloroethene (cis-DCE) at concentrations of 37-146 μM, revealed that the gene copy numbers of tceA, vcrA, and bvcA increased up to 10⁷ copy/mL, indicating that Dehalococcoides spp. containing these three dehalogenase genes were involved in cis-DCE dechlorination. However, in the culture to which 292 μM of cis-DCE was added, only the tceA gene and the Dehalococcoides spp. 16S rRNA gene increased up to 10⁷ copy/mL. The culture containing 292 μM of cis-DCE also exhibited about one tenth slower ethene production rate compared to the other cultures.
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Affiliation(s)
- Kotaro Ise
- Department of Environmental Studies, Graduate School of Environmental Studies, Tohoku University, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
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