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Elsey JL, Miller EL, Christ JA, Abriola LM. On the reliable estimation of sequential Monod kinetic parameters. JOURNAL OF CONTAMINANT HYDROLOGY 2024; 262:104323. [PMID: 38430692 DOI: 10.1016/j.jconhyd.2024.104323] [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: 07/26/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
While dozens of studies have attempted to estimate the Monod kinetic parameters of microbial reductive dechlorination, published values in the literature vary by 2-6 orders of magnitude. This lack of consensus can be attributed in part to limitations of both experimental design and parameter estimation techniques. To address these issues, Hamiltonian Monte Carlo was used to produce more than one million sets of realistic simulated microcosm data under a variety of experimental conditions. These data were then employed in model fitting experiments using a number of parameter estimation algorithms for determining Monod kinetic parameters. Analysis of data from conventional triplicate microcosms yielded parameter estimates characterized by high collinearity, resulting in poor estimation accuracy and precision. Additionally, confidence intervals computed by commonly used classical regression analysis techniques contained true parameter values much less frequently than their nominal confidence levels. Use of an alternative experimental design, requiring the same number of analyses as conventional experiments but comprised of microcosms with varying initial chlorinated ethene concentrations, is shown to result in order-of-magnitude decreases in parameter uncertainty. A Metropolis algorithm which can be run on a typical personal computer is demonstrated to return more reliable parameter interval estimates.
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Affiliation(s)
- Jack L Elsey
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, USA
| | - Eric L Miller
- Department of Electrical and Computer Engineering, Tufts University, Medford, MA 02155, USA
| | | | - Linda M Abriola
- School of Engineering, Brown University, Providence, RI 02912, USA.
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2
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Wu Z, Yu X, Liu G, Li W, Lu L, Li P, Xu X, Jiang J, Wang B, Qiao W. Sustained detoxification of 1,2-dichloroethane to ethylene by a symbiotic consortium containing Dehalococcoides species. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 325:121443. [PMID: 36921661 DOI: 10.1016/j.envpol.2023.121443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
1,2-Dichloroethane (1,2-DCA) is a ubiquitous volatile halogenated organic pollutant in groundwater and soil, which poses a serious threat to the ecosystem and human health. Microbial reductive dechlorination has been recognized as an environmentally-friendly strategy for the remediation of sites contaminated with 1,2-DCA. In this study, we obtained an anaerobic microbiota derived from 1,2-DCA contaminated groundwater, which was able to sustainably convert 1,2-DCA into non-toxic ethylene with an average dechlorination rate of 30.70 ± 11.06 μM d-1 (N = 6). The microbial community profile demonstrated that the relative abundance of Dehalococcoides species increased from 0.53 ± 0.08% to 44.68 ± 3.61% in parallel with the dechlorination of 1,2-DCA. Quantitative PCR results showed that the Dehalococcoides species 16S rRNA gene increased from 2.40 ± 1.71 × 108 copies∙mL-1 culture to 4.07 ± 2.45 × 108 copies∙mL-1 culture after dechlorinating 110.69 ± 30.61 μmol of 1,2-DCA with a growth yield of 1.55 ± 0.93 × 108 cells per μmol Cl- released (N = 6), suggesting that Dehalococcoides species used 1,2-DCA for organohalide respiration to maintain cell growth. Notably, the relative abundances of Methanobacterium sp. (p = 0.0618) and Desulfovibrio sp. (p = 0.0001995) also increased significantly during the dechlorination of 1,2-DCA and were clustered in the same module with Dehalococcoides species in the co-occurrence network. These results hinted that Dehalococcoides species, the obligate organohalide-respiring bacterium, exhibited potential symbiotic relationships with Methanobacterium and Desulfovibrio species. This study illustrates the importance of microbial interactions within functional microbiota and provides a promising microbial resource for in situ bioremediation in sites contaminated with 1,2-DCA.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianghua Lu
- Jiangsu Provincial Key Laboratory of Environmental Engineering, Jiangsu Provincial Academy of Environmental Science, Nanjing 210036, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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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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Elsey JL, Christ JA, Abriola LM. Quantifying Impacts of Microcosm Mass Loss on Kinetic Constant Estimation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:13822-13833. [PMID: 34618436 DOI: 10.1021/acs.est.1c03452] [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] [Indexed: 06/13/2023]
Abstract
Microcosm experiments to assess microbial reductive dechlorination of chlorinated aliphatic hydrocarbons typically experience 5-50% mass loss due to frequent sampling events and diffusion through septa. A literature review, however, reveals that models fit to such experiments for kinetic constant estimation have generally failed to account for experimental mass loss. To investigate possible resultant bias in best-fit parameters, a series of numerical experiments was conducted in which Monod kinetic models with and without mass loss were fit to more than 1300 synthetic data sets, generated using published microcosm data. Models that failed to account for mass loss resulted in significant fitted parameter bias. Bias ranged from 5 to 45% of the parameter magnitude for Monte Carlo simulations with low (approximately 10%) mass loss to 20-120% for simulations with high (approximately 40%) mass loss. In addition, for high mass loss simulations, best-fit values consistently fell along the bounds of the optimization range. These results suggest that failure to properly account for mass loss in microcosms may lead to inaccurate estimation of kinetic constants and may explain some of the literature-reported variability in these parameters. A model is presented that provides a method for including sampling and diffusional mass losses to improve kinetic constant estimation accuracy.
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Affiliation(s)
- Jack L Elsey
- Department of Civil and Environmental Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - John A Christ
- S&B Christ Consulting, Las Vegas, Nevada 89134, United States
| | - Linda M Abriola
- School of Engineering, Brown University, Providence, Rhode Island 02912, United States
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The influence of electrokinetic bioremediation on subsurface microbial communities at a perchloroethylene contaminated site. Appl Microbiol Biotechnol 2021; 105:6489-6497. [PMID: 34417847 DOI: 10.1007/s00253-021-11458-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 06/09/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
There is an increased interest in finding remedies for contamination in low permeability and advection-limited aquifers. A technology applicable at these sites, electrokinetic-enhanced bioremediation (EK-BIO), combines traditional bioremediation and electrokinetic technologies by applying direct current to transport bioremediation amendments and microbes in situ. The effect of this technology on the native soil microbial community has only been previously investigated at the bench scale. This research explored the influence of EK-BIO on subsurface microbial communities at a field-scale demonstration site. The results showed that, similar to the findings in laboratory studies, alpha diversity decreased and beta diversity differed temporally, based on treatment phase. Enrichments in specific taxa were linked to the bioaugmentation culture and electron donor. Overall, findings from our study, one of the first field-scale investigations of the influence of electrokinetic bioremediation on subsurface microbial communities, are very similar to bench-scale studies on the topic, suggesting good correlation between laboratory and field experiments on EK-BIO and showing that lessons learned at the benchtop are important and relevant to field-scale implementation. KEY POINTS: • Microbial community analysis of field samples validates laboratory study results • Bioaugmentation cultures and electron donors have largest effect on microbial community.
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Tian X, Shen Z, Zhou Y, Wang K. Acidification inhibition, biodechlorination, and biotransformation of chlorinated acetaldehydes on acidogenic sludge and microbial community changes. CHEMOSPHERE 2021; 277:130231. [PMID: 33774258 DOI: 10.1016/j.chemosphere.2021.130231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/04/2020] [Accepted: 03/06/2021] [Indexed: 06/12/2023]
Abstract
Chlorinated acetaldehydes (CALs) are typical chlorinated organic compounds that posing a great threat to biological wastewater treatment plants. In this study, volatile batch acid (VFA) tests were employed to investigate the acidification inhibition, biodechlorination, and biotransformation of high-strength CALs on hydrolytic acidification. The results indicated that the optimum parameters were 4 g/L sludge, pH = 8, and glucose as an electron donor. Moreover, the acidification inhibition and biodechlorination showed a strongly positive correlation with the degree of chlorination and CAL concentrations. Extracellular polymeric substances (EPS) decreased dramatically, while DNA increased sharply under higher CAL concentrations, which was the result of cell death caused by the toxicity of the CALs. Additionally, the relative toxicities of the CALs were as follows: trichloroacetaldehyde > dichloroacetaldehyde > chloroacetaldehyde. Furthermore, Excitation-Emission-Matrix (EEM) spectra of EPS revealed that aromatic protein-like substances I interacted with CALs to achieve a slight removal of CALs. The detected products revealed that some of the chlorine atoms and aldehyde groups in the CALs were removed by microbes to certain degree. Moreover, microbial community analysis indicated that the dominant phyla were Actinobacteria, Bacteroidetes, and Synergistetes, which had a stronger tolerance to CALs. Notably, biodechlorination was closely related to a remarkable increase in members of the genus Trichococcus.
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Affiliation(s)
- Xiangmiao Tian
- School of Environment, Tsinghua University, Beijing, 100084, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing, 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China
| | - Zhiqiang Shen
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing, 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Yuexi Zhou
- School of Environment, Tsinghua University, Beijing, 100084, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing, 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China.
| | - Kaijun Wang
- School of Environment, Tsinghua University, Beijing, 100084, PR China
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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: 5] [Impact Index Per Article: 1.7] [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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8
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Gobbi A, Santini RG, Filippi E, Ellegaard-Jensen L, Jacobsen CS, Hansen LH. Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR. PLoS One 2019; 14:e0200979. [PMID: 30973938 PMCID: PMC6459482 DOI: 10.1371/journal.pone.0200979] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/03/2019] [Indexed: 01/18/2023] Open
Abstract
Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition. To address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer, marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers from 1.00 to 2.20 m. Importantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition. Finally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier. These outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.
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Affiliation(s)
- Alex Gobbi
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Rui G. Santini
- Natural History Museum of Denmark, Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Elisa Filippi
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | | | - Lars H. Hansen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- * E-mail:
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9
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Yin Y, Yan J, Chen G, Murdoch FK, Pfisterer N, Löffler FE. Nitrous Oxide Is a Potent Inhibitor of Bacterial Reductive Dechlorination. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:692-701. [PMID: 30558413 PMCID: PMC6944068 DOI: 10.1021/acs.est.8b05871] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Organohalide-respiring bacteria are key players for the turnover of organohalogens. At sites impacted with chlorinated ethenes, bioremediation promotes reductive dechlorination; however, stoichiometric conversion to environmentally benign ethene is not always achieved. We demonstrate that nitrous oxide (N2O), a compound commonly present in groundwater, inhibits organohalide respiration. N2O concentrations in the low micromolar range decreased dechlorination rates and resulted in incomplete dechlorination of tetrachloroethene (PCE) in Geobacter lovleyi strain SZ and of cis-1,2-dichloroethene ( cDCE) and vinyl chloride (VC) in Dehalococcoides mccartyi strain BAV1 axenic cultures. Presumably, N2O interferes with reductive dechlorination by reacting with super-reduced Co(I)-corrinoids of reductive dehalogenases, which is supported by the finding that N2O did not inhibit corrinoid-independent fumarate-to-succinate reduction in strain SZ. Kinetic analyses revealed a best fit to the noncompetitive Michaelis-Menten inhibition model and determined N2O inhibitory constants, KI, for PCE and cDCE dechlorination of 40.8 ± 3.8 and 21.2 ± 3.5 μM in strain SZ and strain BAV1, respectively. The lowest KI value of 9.6 ± 0.4 μM was determined for VC to ethene reductive dechlorination in strain BAV1, suggesting that this crucial dechlorination step for achieving detoxification is most susceptible to N2O inhibition. Groundwater N2O concentrations exceeding 100 μM are not uncommon, especially in watersheds impacted by nitrate runoff from agricultural sources. Thus, dissolved N2O measurements can inform about cDCE and VC stalls at sites impacted with chlorinated ethenes.
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Affiliation(s)
- Yongchao Yin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jun Yan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Liaoning 110016, People’s Republic of China
| | - Gao Chen
- 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
| | - Fadime Kara Murdoch
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nina Pfisterer
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, 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
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Corresponding Author: Phone: (865) 974-4933.
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10
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Wang W, Liu X, Li K, Li T. Dechlorinating performance of Dehalococcoides spp. mixed culture enhanced by tourmaline. CHEMOSPHERE 2018; 194:9-19. [PMID: 29195092 DOI: 10.1016/j.chemosphere.2017.11.096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Dehalococcoides spp. were extensively studied and applied to in-situ trichloroethylene (TCE) remediation since it is the only genus that can reduce TCE to harmless ethene completely. However, this technology was hindered because of the requirement of electron donor (i.e. hydrogen or fermentable organic substrate). Considering the spontaneous electric field and in-situ hydrogen production capacity of tourmaline, this mineral was used as an environmental-friendly bio-promoter for dechlorinating mixed culture containing Dehalococcoides spp. in this work. Research results showed that biodegradation of TCE and the intermediates were both significantly improved by tourmaline. The first-order TCE degradation rate coefficient increased from 0.0125 h-1 for the tourmaline-free system to 0.0306 h-1 for the system combined with 5 g L-1 tourmaline, and ethene production increased by 36%. The outstanding TCE-degrading ability in the tourmaline-bacteria system without the addition of fermentative electron donor (i.e. methanol) indicated that tourmaline could also produce electron donor to support dechlorinating bacteria. Tourmaline could have direct electric biostimulatory effect and indirect enhanced effect associated with water-derived H2 production in the electric field of tourmaline. Meanwhile, PCR-DGGE analysis exhibited that tourmaline could accelerate the succession of a bacterial, dechlorinating community. The distinctive effects of tourmaline on bacteria were related to its stable electric properties. Therefore, tourmaline could be continuously used in the bioremediation. The present study provided a safe, convenient and persistent alternative to the commonly used enhancement approaches for anaerobic reductive dechlorination process.
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Affiliation(s)
- Wei Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Xingyu Liu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Kerui Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Tielong Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Tianjin Advanced Water Treatment Technology International Joint Research Center, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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11
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Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 2016; 350:434-8. [PMID: 26494757 DOI: 10.1126/science.aac7745] [Citation(s) in RCA: 423] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl-coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.
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Affiliation(s)
- Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Suzanne D Golding
- School of Earth Sciences, University of Queensland, St Lucia 4072, Queensland, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia. Advanced Water Management Centre, University of Queensland, St Lucia 4072, Queensland, Australia.
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Raudsepp MJ, Gagen EJ, Evans P, Tyson GW, Golding SD, Southam G. The influence of hydrogeological disturbance and mining on coal seam microbial communities. GEOBIOLOGY 2016; 14:163-175. [PMID: 26541089 DOI: 10.1111/gbi.12166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 10/01/2015] [Indexed: 06/05/2023]
Abstract
The microbial communities present in two underground coal mines in the Bowen Basin, Queensland, Australia, were investigated to deduce the effect of pumping and mining on subsurface methanogens and methanotrophs. The micro-organisms in pumped water from the actively mined areas, as well as, pre- and post-mining formation waters were analyzed using 16S rRNA gene amplicon sequencing. The methane stable isotope composition of Bowen Basin coal seam indicates that methanogenesis has occurred in the geological past. More recently at the mine site, changing groundwater flow dynamics and the introduction of oxygen in the subsurface has increased microbial biomass and diversity. Consistent with microbial communities found in other coal seam environments, pumped coal mine waters from the subsurface were dominated by bacteria belonging to the genera Pseudomonas and the family Rhodocyclaceae. These environments and bacterial communities supported a methanogen population, including Methanobacteriaceae, Methanococcaceae and Methanosaeta. However, one of the most ubiquitous micro-organisms in anoxic coal mine waters belonged to the family 'Candidatus Methanoperedenaceae'. As the Archaeal family 'Candidatus Methanoperedenaceae' has not been extensively defined, the one studied species in the family is capable of anaerobic methane oxidation coupled to nitrate reduction. This introduces the possibility that a methane cycle between archaeal methanogenesis and methanotrophy may exist in the anoxic waters of the coal seam after hydrogeological disturbance.
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Affiliation(s)
- M J Raudsepp
- School of Earth Sciences, The University of Queensland, St. Lucia, Qld, Australia
| | - E J Gagen
- School of Earth Sciences, The University of Queensland, St. Lucia, Qld, Australia
| | - P Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, Australia
| | - G W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, Australia
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Qld, Australia
| | - S D Golding
- School of Earth Sciences, The University of Queensland, St. Lucia, Qld, Australia
| | - G Southam
- School of Earth Sciences, The University of Queensland, St. Lucia, Qld, Australia
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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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