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Suchana S, Edwards E, Mack EE, Lomheim L, Melo N, Gavazza S, Passeport E. Compatibility of polar organic chemical integrative sampler (POCIS) with compound specific isotope analysis (CSIA) of substituted chlorobenzenes. Sci Total Environ 2024; 906:167628. [PMID: 37804973 DOI: 10.1016/j.scitotenv.2023.167628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Compound specific isotope analysis (CSIA) is a powerful technique to demonstrate in situ degradation of traditional groundwater contaminants when concentrations are typically in the mg/L range. Currently, an efficient preconcentration method is lacking to expand CSIA to low aqueous concentration environmental samples. Specially for the H- and N-CSIA of heteroatom-bearing non-traditional compounds, the CSIA analytical detection limits are significantly higher than that of the C-CSIA. This work demonstrates the compatibility of polar organic chemical integrative sampler (POCIS) with C-, H-, and N-CSIA using four nitro- and amino-substituted chlorobenzenes that are common industrial feedstocks for numerous applications and are commonly detected in the environment at mg/L to μg/L range. Using lab experiments, we showed isotopic equilibrium in POCIS was achieved after 30 days with either a negligible (<0.5 ‰) or a constant shift for C (<1 ‰) and N (<2 ‰). Similar negligible (<5 ‰) or constant shift (<20 ‰) was evident for H isotope except for 3,4-dichloroaniline. The method quantification limits for the combined sorbent and membrane of one POCIS were comparable to that of the solid phase extraction (SPE) using 10 L water. Next, we demonstrated the field applicability of POCIS for C- and N-CSIA after a 60-day deployment in a pilot constructed wetland by showing <1 ‰ difference between the δ13C and δ15N obtained from POCIS and SPE. Finally, we evaluated whether the biofilm development on POCIS membrane could affect the isotope signature of the sampled compounds during field deployment. Although a diverse microbial community was identified on the membrane after a 60-day deployment, we did not observe significant isotope fractionation. This was likely due to either slower diffusion in the biofilm or microbial degradation of the sampled compounds. This work demonstrates the potential of using POCIS-CSIA as a simple, fast, and sensitive method for low-concentration contaminants, such as pesticides, pharmaceuticals, and flame-retardants.
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Affiliation(s)
- Shamsunnahar Suchana
- Department of Civil & Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Elizabeth Edwards
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - E Erin Mack
- Corteva Environmental Remediation, Corteva Agriscience, Wilmington, DE 19805, USA
| | - Line Lomheim
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Natanna Melo
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, PE 50740-530, Brazil
| | - Sávia Gavazza
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, PE 50740-530, Brazil
| | - Elodie Passeport
- Department of Civil & Mineral Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada; Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada.
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Inglis AM, Head NA, Chowdhury AIA, Nunez Garcia A, Reynolds DA, Hogberg D, Edwards E, Lomheim L, Weber K, Wallace SJ, Austrins LM, Hayman J, Auger M, Sidebottom A, Eimers J, Gerhard JI, O'Carroll DM. Electrokinetically-enhanced emplacement of lactate in a chlorinated solvent contaminated clay site to promote bioremediation. Water Res 2021; 201:117305. [PMID: 34119968 DOI: 10.1016/j.watres.2021.117305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/27/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Bioremediation through the injection of electron donors and bacterial cultures is effective at treating chlorinated solvent contamination. However, it has had limited application in low permeability zones where amendments cannot be delivered successfully. This field-scale study investigated the application of electrokinetics to enhance the delivery of lactate at a clay site contaminated with chlorinated solvents. Groundwater and soil samples were collected before, during and for 1 year after the 71-day field test and analyzed for a wide suite of chemical and biological parameters. Lactate was successfully delivered to all monitoring locations. Lactate emplacement resulted in the stimulation of bacterial populations, specifically within the phylum Firmicutes, which contains fermenters and strict anaerobes. This likely led to biodegradation, as the field trial resulted in significant decreases in both soil and aqueous phase chlorinated solvent concentrations. Contaminant decreases were also partially attributable to dilution, given evidence of some advective lactate flux. This research provides evidence that electrokinetically-enhanced bioremediation has potential as a treatment strategy for contaminated low permeability strata.
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Affiliation(s)
- Ainsley M Inglis
- Department of Civil and Environmental Engineering, University of Western Ontario, 1151 Richmond Rd., London, Ontario, N6A 5B8, Canada
| | - Nicholas A Head
- Department of Civil and Environmental Engineering, University of Western Ontario, 1151 Richmond Rd., London, Ontario, N6A 5B8, Canada
| | - Ahmed I A Chowdhury
- Institute of Water and Flood Management, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Ariel Nunez Garcia
- Department of Civil and Environmental Engineering, University of Western Ontario, 1151 Richmond Rd., London, Ontario, N6A 5B8, Canada
| | - David A Reynolds
- Geosyntec Consultants, 130 Stone Road W, Guelph, N1G 3Z2, ON, Canada
| | - Dave Hogberg
- Geosyntec Consultants, 130 Stone Road W, Guelph, N1G 3Z2, ON, Canada
| | - Elizabeth Edwards
- University of Toronto, 27 King's College Cir, Toronto, ON M5S 3H7, Canada
| | - Line Lomheim
- University of Toronto, 27 King's College Cir, Toronto, ON M5S 3H7, Canada
| | - Kela Weber
- Royal Military College of Canada, 13 General Crerar Crescent, Kingston, ON K7K 7B4, Canada
| | - Sarah J Wallace
- Royal Military College of Canada, 13 General Crerar Crescent, Kingston, ON K7K 7B4, Canada
| | - Leanne M Austrins
- Dow Chemical, Environmental Remediation and Compliance, Midland, MI, 48674, USA
| | | | - Marlaina Auger
- Geosyntec Consultants, 130 Stone Road W, Guelph, N1G 3Z2, ON, Canada
| | | | - Jake Eimers
- Jacobs, 72 Victoria St S, Kitchener, N2G 4Y9, ON, Canada
| | - Jason I Gerhard
- Department of Civil and Environmental Engineering, University of Western Ontario, 1151 Richmond Rd., London, Ontario, N6A 5B8, Canada
| | - Denis M O'Carroll
- School of Civil and Environmental Engineering, Water Research Centre, University of New South Wales, Sydney, NSW 2052 Australia.
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Puentes Jácome LA, Lomheim L, Gaspard S, Edwards EA. Biodegradation of Lindane (γ-Hexachlorocyclohexane) To Nontoxic End Products by Sequential Treatment with Three Mixed Anaerobic Microbial Cultures. Environ Sci Technol 2021; 55:2968-2979. [PMID: 33557520 DOI: 10.1021/acs.est.0c07221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The γ isomer of hexachlorocyclohexane (HCH), also known as lindane, is a carcinogenic persistent organic pollutant. Lindane was used worldwide as an agricultural insecticide. Legacy soil and groundwater contamination with lindane and other HCH isomers is still a big concern. The biotic reductive dechlorination of HCH to nondesirable and toxic lower chlorinated compounds such as monochlorobenzene (MCB) and benzene, among others, has been broadly documented. Here, we demonstrate that complete biodegradation of lindane to nontoxic end products is attainable using a sequential treatment approach with three mixed anaerobic microbial cultures referred to as culture I, II, and III. Biaugmentation with culture I achieved dechlorination of lindane to MCB and benzene. Culture II was able to dechlorinate MCB to benzene, and finally, culture III carried out methanogenic benzene degradation. Distinct Dehalobacter populations, corresponding to different 16S rRNA amplicon sequence variants in culture I and culture II, were responsible for lindane and MCB dechlorination, respectively. This study continues to highlight key roles of Dehalobacter as chlorobenzene- and HCH -respiring bacteria and demonstrates that sequential treatment with specialized anaerobic cultures may be explored at field sites in order to address legacy soil and groundwater contamination with HCH.
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Affiliation(s)
- Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Sarra Gaspard
- Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre, Guadeloupe, French West-Indies 97157, France
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3E5, Canada
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Lomheim L, Laquitaine L, Rambinaising S, Flick R, Starostine A, Jean-Marius C, Edwards EA, Gaspard S. Evidence for extensive anaerobic dechlorination and transformation of the pesticide chlordecone (C10Cl10O) by indigenous microbes in microcosms from Guadeloupe soil. PLoS One 2020; 15:e0231219. [PMID: 32282845 PMCID: PMC7153859 DOI: 10.1371/journal.pone.0231219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/18/2020] [Indexed: 11/19/2022] Open
Abstract
The historic use of chlordecone (C10Cl10O) as a pesticide to control banana weevil infestations has resulted in pollution of large land areas in the French West Indies. Although currently banned, chlordecone persists because it adsorbs strongly to soil and its complex bis-homocubane structure is stable, particularly under aerobic conditions. Abiotic chemical transformation catalyzed by reduced vitamin B12 has been shown to break down chlordecone by opening the cage structure to produce C9 polychloroindenes. More recently these C9 polychloroindenes were also observed as products of anaerobic microbiological transformation. To investigate the anaerobic biotransformation of chlordecone by microbes native to the French West Indies, microcosms were constructed anaerobically from chlordecone impacted Guadeloupe soil and sludge to mimic natural attenuation and eletron donor-stimulated reductive dechlorination. Original microcosms and transfers were incubated over a period of 8 years, during which they were repeatedly amended with chlordecone and electron donor (ethanol and acetone). Using LC-MS, chlordecone and degradation products were detected in all the biologically active microcosms. Observed products included monohydro-, dihydro- and trihydrochlordecone derivatives (C10Cl10-nO2Hn; n = 1,2,3), as well as “open cage” C9 polychloroindene compounds (C9Cl5-nH3+n n = 0,1,2) and C10 carboxylated polychloroindene derivatives (C10Cl4-nO2H4+n, n = 0–3). Products with as many as 9 chlorine atoms removed were detected. These products were not observed in sterile (poisoned) microcosms. Chlordecone concentrations decreased in active microcosms as concentrations of products increased, indicating that anaerobic dechlorination processes have occurred. The data enabled a crude estimation of partitioning coefficients between soil and water, showing that carboxylated intermediates sorb poorly and as a consequence may be flushed away, while polychlorinated indenes sorb strongly to soil. Microbial community analysis in microcosms revealed enrichment of anaerobic fermenting and acetogenic microbes possibly involved in anaerobic chlordecone biotransformation. It thus should be possible to stimuilate anaerobic dechlorination through donor amendment to contaminated soils, particularly as some metabolites (in particular pentachloroindene) were already detected in field samples as a result of intrinsic processes. Extensive dechlorination in the microcosms, with evidence for up to 9 Cl atoms removed from the parent molecule is game-changing, giving hope to the possibility of using bioremediation to reduce the impact of CLD contamination.
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Affiliation(s)
- Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Laurent Laquitaine
- Département de Chimie, Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre Cedex, Guadeloupe (FWI), France
| | - Suly Rambinaising
- Département de Chimie, Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre Cedex, Guadeloupe (FWI), France
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrei Starostine
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Corine Jean-Marius
- Département de Chimie, Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre Cedex, Guadeloupe (FWI), France
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (EAE); (SG)
| | - Sarra Gaspard
- Département de Chimie, Laboratory COVACHIMM2E, Université des Antilles, Pointe à Pitre Cedex, Guadeloupe (FWI), France
- * E-mail: (EAE); (SG)
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Molenda O, Puentes Jácome LA, Cao X, Nesbø CL, Tang S, Morson N, Patron J, Lomheim L, Wishart DS, Edwards EA. Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification. Environ Sci Process Impacts 2020; 22:663-678. [PMID: 32159535 DOI: 10.1039/c9em00605b] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Organohalide respiring bacteria (OHRB) express reductive dehalogenases for energy conservation and growth. Some of these enzymes catalyze the reductive dehalogenation of chlorinated and brominated pollutants in anaerobic subsurface environments, providing a valuable ecosystem service. Dehalococcoides mccartyi strains have been most extensively studied owing to their ability to dechlorinate all chlorinated ethenes - most notably carcinogenic vinyl chloride - to ethene. The genomes of OHRB, particularly obligate OHRB, often harbour multiple putative reductive dehalogenase genes (rdhA), most of which have yet to be characterized. We recently sequenced and closed the genomes of eight new strains, increasing the number of available D. mccartyi genomes in NCBI from 16 to 24. From all available OHRB genomes, we classified predicted translations of reductive dehalogenase genes using a previously established 90% amino acid pairwise identity cut-off to identify Ortholog Groups (OGs). Interestingly, the majority of D. mccartyi dehalogenase gene sequences, once classified into OGs, exhibited a remarkable degree of synteny (gene order) in all genomes sequenced to date. This organization was not apparent without the classification. A high degree of synteny indicates that differences arose from rdhA gene loss rather than recombination. Phylogenetic analysis suggests that most rdhA genes have a long evolutionary history in the Dehalococcoidia with origin prior to speciation of Dehalococcoides and Dehalogenimonas. We also looked for evidence of synteny in the genomes of other species of OHRB. Unfortunately, there are too few closed Dehalogenimonas genomes to compare at this time. There is some partial evidence for synteny in the Dehalobacter restrictus genomes, but here too more closed genomes are needed for confirmation. Interestingly, we found that the rdhA genes that encode enzymes that catalyze dehalogenation of industrial pollutants are the only rdhA genes with strong evidence of recent lateral transfer - at least in the genomes examined herein. Given the utility of the RdhA sequence classification to comparative analyses, we are building a public web server () for the community to use, which allows users to add and classify new sequences, and download the entire curated database of reductive dehalogenases.
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Affiliation(s)
- Olivia Molenda
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.
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6
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Qiao W, Puentes Jácome LA, Tang X, Lomheim L, Yang MI, Gaspard S, Avanzi IR, Wu J, Ye S, Edwards EA. Microbial Communities Associated with Sustained Anaerobic Reductive Dechlorination of α-, β-, γ-, and δ-Hexachlorocyclohexane Isomers to Monochlorobenzene and Benzene. Environ Sci Technol 2020; 54:255-265. [PMID: 31830788 DOI: 10.1021/acs.est.9b05558] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intensive historical and worldwide use of pesticide formulations containing hexachlorocyclohexane (HCH) has led to widespread contamination. We derived four anaerobic enrichment cultures from HCH-contaminated soil capable of sustainably dechlorinating each of α-, β-, γ-, and δ-HCH isomers stoichiometrically to benzene and monochlorobenzene (MCB). For each isomer, the dechlorination rates, inferred from production rates of the dechlorinated products, MCB and benzene, increased progressively from <3 to ∼12 μM/day over 2 years. The molar ratio of benzene to MCB produced was a function of the substrate isomer and ranged from β (0.77 ± 0.15), α (0.55 ± 0.09), γ (0.13 ± 0.02), to δ (0.06 ± 0.02) in accordance with pathway predictions based on prevalence of antiperiplanar geometry. Data from 16S rRNA gene amplicon sequencing and quantitative PCR revealed significant increases in the absolute abundances of Pelobacter and Dehalobacter, most notably in the α-HCH and δ-HCH cultures. Cultivation with a different HCH isomer resulted in distinct bacterial communities, but similar archaeal communities. This study provides the first direct comparison of shifts in anaerobic microbial communities induced by the dechlorination of distinct HCH isomers. It also uncovers candidate microorganisms responsible for the dechlorination of α-, β-, γ-, and δ-HCH, a key step toward better understanding and monitoring of natural attenuation processes and improving bioremediation technologies for HCH-contaminated sites.
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Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Luz A Puentes Jácome
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
| | - Xianjin Tang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
- Institute of Soil and Water Resources and Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
| | - Sarra Gaspard
- Laboratory COVACHIMM2E, EA 3592, Université des Antilles, Pointe à Pitre 97157, Guadeloupe, French West-Indies, France
| | - Ingrid Regina Avanzi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
- Laboratory of Biomaterial and Tissue Engineering, Federal University of Sao Paulo, 136 Silva Jardim Street, Santos 11015-020, São Paulo, Brazil
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto M5S 3E5, Canada
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Qiao W, Luo F, Lomheim L, Mack EE, Ye S, Wu J, Edwards EA. A Dehalogenimonas Population Respires 1,2,4-Trichlorobenzene and Dichlorobenzenes. Environ Sci Technol 2018; 52:13391-13398. [PMID: 30371071 DOI: 10.1021/acs.est.8b04239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chlorobenzenes are ubiquitous contaminants in groundwater and soil at many industrial sites. Previously, we demonstrated the natural attenuation of chlorobenzenes and benzene at a contaminated site inferred from a 5 year site investigation and parallel laboratory microcosm studies. To identify the microbes responsible for the observed dechlorination of chlorobenzenes, the microbial community was surveyed using 16S rRNA gene amplicon sequencing. Members of the Dehalobacter and Dehalococcoides are reported to respire chlorobenzenes; however, neither were abundant in our sediment microcosms. Instead, we observed a significant increase in the relative abundance of Dehalogenimonas from <1% to 16-30% during dechlorination of 1,2,4-trichlorobenzene (TCB), 1,2-dichlorobenzene (DCB), and 1,3-DCB over 19 months. Quantitative PCR (qPCR) confirmed that Dehalogenimonas gene copies increased by 2 orders of magnitude with an average yield of 3.6 ± 2.3 g cells per mol Cl- released ( N = 12). In transfer cultures derived from sediment microcosms, dechlorination of 1,4-DCB and monochlorobenzene (MCB) was carried out by Dehalobacter spp. with a growth yield of 3.0 ± 2.1 g cells per mol Cl- released ( N = 5). Here we show that a Dehalogenimonas population respire 1,2,4-TCB and 1,2-/1,3-DCB isomers. This finding emphasizes the need to monitor a broader spectrum of organohalide-respiring bacteria, including Dehalogenimonas, at sites contaminated with halogenated organic compounds.
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Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
| | - E Erin Mack
- DuPont Corporate Remediation Group , Wilmington , Delaware 19805 , United States
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education; School of Earth Sciences and Engineering , Nanjing University , Nanjing 210023 , China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5S 3E5 , Canada
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8
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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 J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Qiao W, Luo F, Lomheim L, Mack EE, Ye S, Wu J, Edwards EA. Natural Attenuation and Anaerobic Benzene Detoxification Processes at a Chlorobenzene-Contaminated Industrial Site Inferred from Field Investigations and Microcosm Studies. Environ Sci Technol 2018; 52:22-31. [PMID: 29178800 DOI: 10.1021/acs.est.7b04145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A five-year site investigation was conducted at a former chemical plant in Nanjing, China. The main contaminants were 1,2,4-trichlorobenzene (TCB) reaching concentrations up to 7300 μg/L, dichlorobenzene (DCB) isomers, monochlorobenzene (MCB), and benzene. Over time, these contaminants naturally attenuated to below regulatory levels under anaerobic conditions. To confirm the transformation processes and to explore the mechanisms, a corresponding laboratory microcosm study was completed demonstrating that 1,2,4-TCB was dechlorinated to 1,2-DCB, 1,3-DCB, and 1,4-DCB in approximately 2%/10%/88% molar proportions. The DCB isomers were dechlorinated via MCB to benzene, and, finally, benzene was degraded under prevailing sulfate-reducing conditions. Dechlorination could not be attributed to known dechlorinators Dehalobacter or Dehalococcoides, while anaerobic benzene degradation was mediated by microbes affiliated to a Deltaproteobacterium ORM2, previously associated with this activity. Unidentified organic compounds, possibly aromatic compounds related to past on-site production processes, were fueling the dechlorination reactions in situ. The microcosm study confirmed transformation processes inferred from field data and provided needed assurance for natural attenuation. Activity-based microcosm studies are often omitted from site characterization in favor of rapid and less expensive molecular surveys. However, the value of microcosm studies for confirming transformation processes, establishing electron balances, assessing cocontaminant inhibition, and validating appropriate monitoring tools is clear. At complex sites impacted by multiple compounds with poorly characterized transformation mechanisms, activity assays provide valuable data to incorporate into the conceptual site model to most effectively inform remediation alternatives.
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Affiliation(s)
- Wenjing Qiao
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Fei Luo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Line Lomheim
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
| | - Elizabeth Erin Mack
- DuPont Corporate Remediation Group , Wilmington, Delaware 19805, United States
| | - Shujun Ye
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry, Ministry of Education, School of Earth Sciences and Engineering, Nanjing University , Nanjing 210046, China
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , Toronto M5S 3E5, Canada
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10
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Mondal PK, Lima G, Zhang D, Lomheim L, Tossell RW, Patel P, Sleep BE. Evaluation of peat and sawdust as permeable reactive barrier materials for stimulating in situ biodegradation of trichloroethene. J Hazard Mater 2016; 313:37-48. [PMID: 27054663 DOI: 10.1016/j.jhazmat.2016.03.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/29/2016] [Accepted: 03/19/2016] [Indexed: 06/05/2023]
Abstract
Two low cost solid organic materials, sawdust and peat, were tested in laboratory batch microcosm and flow-through column experiments to determine their suitability for application in permeable reactive barriers (PRBs) supporting biodegradation of trichloroethene (TCE). In microcosms with peat, TCE (∼30μM) was sequentially and completely degraded to cis-dichloroethene (cDCE), vinyl chloride, and ethene through reductive dechlorination. In microcosms with sawdust, reductive dechlorination of TCE stopped at cDCE and high methane production (up to 3000μM) was observed. 16S rRNA gene copy numbers of Dehalobacter and Archaea were higher (1000 and 10 times, respectively) in sawdust microcosms than those in peat microcosms. Dehalococcoides and vcrA gene copy numbers were 10 times higher in peat microcosms than in sawdust microcosms. These gene copy number differences are consistent with the extent of TCE degradation and production of methane in the microcosms. Flow-through column experiments showed that hydraulic conductivity reduction with time was consistently greater in the sawdust column compared to the peat column. The greater conductivity reduction was likely due to biofouling and methane gas bubble formation. The experimental observations indicate that peat has potential to be a better solid organic material than sawdust to support reductive dechlorination of TCE in PRB applications.
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Affiliation(s)
- Pulin K Mondal
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Glaucia Lima
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - David Zhang
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
| | - Line Lomheim
- BioZone, University of Toronto, 200 College Avenue, Toronto, Ontario M5S 3E5, Canada
| | - Robert W Tossell
- Pinchin Ltd., 2470 Milltower Court, Mississauga, Ontario L5 N 7W5, Canada
| | - Paresh Patel
- Pinchin Ltd., 2470 Milltower Court, Mississauga, Ontario L5 N 7W5, Canada
| | - Brent E Sleep
- Department of Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada.
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11
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Kocur CMD, Lomheim L, Molenda O, Weber KP, Austrins LM, Sleep BE, Boparai HK, Edwards EA, O'Carroll DM. Long-Term Field Study of Microbial Community and Dechlorinating Activity Following Carboxymethyl Cellulose-Stabilized Nanoscale Zero-Valent Iron Injection. Environ Sci Technol 2016; 50:7658-7670. [PMID: 27305345 DOI: 10.1021/acs.est.6b01745] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells. The entire microbial community was tracked using 16S rRNA gene amplicon pyrosequencing. Following nZVI-CMC injection, a clear shift in microbial community was observed, with most notable increases in the dechlorinating genera Dehalococcoides and Dehalogenimonas. This study suggests that coupled abiotic degradation (i.e., from reaction with nZVI) and biotic degradation fueled by CMC led to the long-term degradation of chlorinated ethenes at this field site. Furthermore, nZVI-CMC addition stimulated dehalogenator growth (e.g., Dehalococcoides) and biotic degradation of chlorinated ethenes.
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Affiliation(s)
- Chris M D Kocur
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
- CH2M HILL Canada Limited , 72 Victoria Street Kitchener, Ontario, Canada , N2G 4Y9
| | - Line Lomheim
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Olivia Molenda
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Kela P Weber
- Environmental Sciences Group, Chemistry and Chemical Engineering, Royal Military College of Canada , PO Box 17000, Station Forces, Kingston, Ontario, Canada , K7K 7B4
| | - Leanne M Austrins
- CH2M HILL Canada Limited , 72 Victoria Street Kitchener, Ontario, Canada , N2G 4Y9
| | - Brent E Sleep
- Civil Engineering, University of Toronto , 35 Saint George Street, Toronto, Ontario, Canada , M5S 1A4
| | - Hardiljeet K Boparai
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
| | - Elizabeth A Edwards
- Chemical Engineering & Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada , M5S 3E5
| | - Denis M O'Carroll
- Civil & Environmental Engineering, Western University , 1151 Richmond Street, London, Ontario, Canada , N6A 5B8
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12
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Kocur CMD, Lomheim L, Boparai HK, Chowdhury AIA, Weber KP, Austrins LM, Edwards EA, Sleep BE, O'Carroll DM. Contributions of Abiotic and Biotic Dechlorination Following Carboxymethyl Cellulose Stabilized Nanoscale Zero Valent Iron Injection. Environ Sci Technol 2015; 49:8648-56. [PMID: 26090687 DOI: 10.1021/acs.est.5b00719] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A pilot scale injection of nanoscale zerovalent iron (nZVI) stabilized with carboxymethyl cellulose (CMC) was performed at an active field site contaminated with a range of chlorinated volatile organic compounds (cVOC). The cVOC concentrations and microbial populations were monitored at the site before and after nZVI injection. The remedial injection successfully reduced parent compound concentrations on site. A period of abiotic degradation was followed by a period of enhanced biotic degradation. Results suggest that the nZVI/CMC injection created conditions that stimulated the native populations of organohalide-respiring microorganisms. The abundance of Dehalococcoides spp. immediately following the nZVI/CMC injection increased by 1 order of magnitude throughout the nZVI/CMC affected area relative to preinjection abundance. Distinctly higher cVOC degradation occurred as a result of the nZVI/CMC injection over a 3 week evaluation period when compared to control wells. This suggests that both abiotic and biotic degradation occurred following injection.
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Affiliation(s)
- Chris M D Kocur
- ∥CH2M HILL Canada Limited, 72 Victoria Street, Kitchener, Ontario N2G 4Y9, Canada
| | | | | | | | - Kela P Weber
- §Environmental Sciences Group, Chemistry and Chemical Engineering, Royal Military College of Canada, P.O. Box 17000, Station Forces, Kingston, Ontario K7K 7B4, Canada
| | - Leanne M Austrins
- ∥CH2M HILL Canada Limited, 72 Victoria Street, Kitchener, Ontario N2G 4Y9, Canada
| | | | - Brent E Sleep
- ⊥Civil Engineering, University of Toronto, 35 St. George Street, Toronto, Ontario M5S 1A4, Canada
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