Elizabeth Edwards

• Doctor of Engineering
• Professor (Full) at University of Toronto

SC05-UT is an anaerobic mixed microbial enrichment culture that reduces chloroform (CF) to dichloromethane (DCM) through reductive dechlorination, which it further mineralizes to carbon dioxide. This DCM mineralization yields electron equivalents that are used to reduce CF without addition of exogenous electron donor. By studying this self-feeding...

2,3-dichloroaniline (2,3-DCA) has widespread use in chemical manufacturing and remains a persistent groundwater contaminant. To better understand the mechanism and kinetics of its anaerobic biotransformation, we conducted a laboratory kinetic experiment using an anaerobic enrichment culture dominated by Dehalobacter . At an initial field-relevant c...

Reductive dehalogenases (RDases) are essential in the anaerobic degradation of various organohalide contaminants. This family of enzymes has broad sequence diversity, but high structural conservation. There have been few studies assessing how RDase amino acid sequences affect their substrate selectivity. Here, we focus on two chloroalkane RDases, C...

The potential for bioremediation of dichloroanilines (2,3- and 3,4-DCA) and dichloronitrobenzenes (3,4-, 2,5- and 2,3-DCNB) was investigated using inocula from an industrial site in northeast of Brazil. Anaerobic biotransformation of these chlorinated compounds was observed in microcosms simulating site conditions, particularly when electron donor...

The Oil Refinery (OR) consortium is a model methanogenic enrichment culture for studying anaerobic benzene degradation. Over 80% of the culture’s bacterial community is comprised of two closely related strains of benzene-fermenting Desulfobacterota (designated ORM2a and ORM2b) whose mechanism of benzene degradation is unknown. Two new metagenomes,...

The archaeal class Bathyarchaeia are widely and abundantly distributed in anoxic habitats. Metagenomic studies have suggested that they are mixotrophic, capable of CO2 fixation and heterotrophic growth, and involved in acetogenesis and lignin degradation. We analysed 35 Bathyarchaeia metagenome assembled genomes (MAGs), including the first complete...

Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed gen...

We present a dataset of six metagenomes and 323 metagenome assembled genomes (MAGs) describing the microbial community of anaerobic digesters at three Canadian pulp and paper mills. Our objective was to assess the coding potential of the microbial community and obtain draft genomes of key organisms in the digesters.

Here we present two metagenomes and two Dehalobacter metagenome-assembled genomes from subcultures of an anaerobic chloroform and dichloromethane degrading microbial community used for bioremediation. Our objective was to assemble and curate the genome(s) of Dehalobacter, key biodegraders in the culture, through repeated sequencing and joint assemb...

The archaeal class Bathyarchaeia are widely and abundantly distributed in anoxic habitats. Metagenomic studies have suggested that they are mixotrophic, capable of CO2 fixation and heterotrophic growth, and involved in acetogenesis and lignin degradation. We analysed 35 Bathyarchaeia metagenome assembled genomes (MAGs), including the first complete...

Here, we present the metagenome of an anaerobic chloroform respiring mixed microbial community used for bioremediation. Our objective was to obtain draft genomes of key microorganisms in the culture.

Metagenome-assembled genomes (MAGs) were recovered from metagenomic assemblies from a nitrate-reducing benzene-degrading enrichment culture. Ten MAGs of high quality or functional interest to benzene degradation are reported, seven of which are single contig genomes.

Carbon and chlorine isotope effects for biotransformation of chloroform by different microbes show significant variability. Reductive dehalogenases (RDase) enzymes contain different cobamides, affecting substrate preferences, growth yields, and dechlorination rates and extent. We investigate the role of cobamide type on carbon and chlorine isotopic...

We present a metagenome assembled genome (MAG) of an anaerobic bacterium from a nitrate-reducing, benzene-degrading enrichment culture (NRBC). The draft Thermincolales genome consists of 20 contigs with a total length of 4.09 Mbp and includes putative carboxylase genes likely involved in benzene activation.

Reductive dehalogenases (RDases) are essential in the anaerobic degradation of various organohalide contaminants. This family of enzymes has broad sequence diversity, but high structural conservation. There have been few studies assessing how RDase peptide sequences affect their substrate selectivity. Here we focus on two chloroalkane RDases, CfrA...

Chloroform and trichloroethanes are pervasive groundwater contaminants for which bioremediation has been an effective treatment strategy. Reductive dehalogenase (RDase) enzymes from organohalide-respiring bacteria are essential for their remediation under anaerobic conditions. RDases are responsible for dehalogenating these chlorinated solvents, le...

Here, we present metagenomes from two cultures derived from an anaerobic microbial consortium used for bioremediation. One culture dechlorinates chloroform to dichloromethane, which is further mineralized to CO2. A second subculture was amended with only dichloromethane. We sought draft genomes of key microorganisms to identify metabolic potential...

During the COVID-19 pandemic, the Province of Ontario, Canada, launched a wastewater surveillance program to monitor SARS-CoV-2, inspired by the early work and successful forecasts of COVID-19 waves in the city of Ottawa, Ontario. This manuscript presents a dataset from January 1, 2021, to March 31, 2023, with RT-qPCR results for SARS-CoV-2 genes a...

Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-...

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewersheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between the two biomarkers has been noticed by independent studies using these methods since late 2021. The...

Wastewater surveillance of coronavirus disease 2019 (COVID-19) commonly applies reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in wastewater over time. In most applications worldwide, maximal sensitivity and specificity of RT-qPCR has...

Wastewater surveillance using RT-qPCR has now been widely adopted to track circulating levels of SARS-CoV-2 virus in many sewer sheds. The CDC qPCR assays targeting two regions (N1 and N2) within the N gene are commonly used, but a discrepancy between the two biomarkers has been noticed by many groups using this method since late 2021. The reason i...

We present a data set of four metagenomes and 281 metagenome-assembled genomes describing the microbial community of a laboratory-scale high solids anaerobic digester. Our objective was to obtain information on the coding potential of the microbial community and draft genomes of the most abundant organisms in the digester.

Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes. Biotransformation of CF and DCM have been well documented but always independent of one another. CF is dechlorinated to DCM by organohalide-respiring bacteria using reductive dehalogenase...

Sulfidated nano zerovalent iron (S-nZVI) has garnered significant attention from researchers due to its potential for effective in-situ remediation applications. Compared to bare nZVI, sulfidation process enhances its reactivity towards chlorinated volatile organic compounds (cVOCs) and improves its longevity (Nunez Garcia et al. 2021). Stabilizing...

In situ chemical reduction of chlorinated volatile organic compounds (cVOCs) by nano zero-valent iron (nZVI) has been widely applied in the past 20 years, but with limited effectiveness for bare nZVI due to rapid particle settling, short lifespan, and low reactivity. Stabilization and sulfidation of nZVI have improved its mobility and longevity, in...

Constructed wetlands can be a suitable remediation technique for the treatment of industrial contaminants via transfer (i.e., non-destructive) and transformation (i.e., destructive) processes. Providing direct evidence of in situ transformation using concentrations and biogeochemical parameters alone is challenging. Compound specific isotope analys...

Metagenomes of lignocellulose-degrading microbial communities are reservoirs of carbohydrate-active enzymes relevant to biomass processing. Whereas several metagenomes of natural digestive systems have been sequenced, the current study analyses metagenomes originating from an industrial anaerobic digester that processes effluent from a cellulose pu...

Amplicon sequencing data and operating data from anaerobic wastewater treatment plants from three Canadian pulp and paper mills were used to explore the microbial community organization and identify relationships between organisms and operating conditions. These relationships were identified using Local Similarity Analysis (LSA). Each of the digest...

Chloroform (CF) and dichloromethane (DCM) contaminate groundwater sites around the world, which can be remediated through bioaugmentation. Although several strains of Dehalobacter restrictus can reduce CF to DCM, and multiple Peptococcaceae can ferment DCM, these processes cannot happen simultaneously due to CF sensitivity in the known DCM-degrader...

Although benzene degradation under strictly anoxic conditions was first reported over 25 years ago, the mechanism for benzene activation in the absence of oxygen is still elusive. A major limitation has been the difficulty to grow anaerobic benzene-degrading enrichment cultures. Our laboratory has maintained a methanogenic enrichment culture for de...

As technological advances allow the development of new products, the number of synthetic chemical compounds released into the soil, surface water and groundwater increases, posing a threat to the environment. Therefore, treatability studies to improve bioremediation strategies (biostimulation and bioaugmentation) were applied to samples of soil con...

The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent i...

Draft and complete metagenome assembled genomes (MAGs) were created from multiple metagenomic assemblies of DGG-B, a strictly anaerobic, stable mixed microbial consortium that degrades benzene completely to methane and CO2. Our objective was to obtain closed genome sequences of benzene-fermenting bacteria to enable the elucidation of their elusive...

Wastewater-based surveillance has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription polymerase chain reaction (RT-PCR) or whole genome sequencing (WGS). Rapid, reliable RT-PCR assays continue to be needed to determ...

A 50 kg-scale, high solids anaerobic digestor (AD) comprising six sequentially-fed leach beds with a leachate recirculation system was operated at 37°C for 88 weeks. The solid feedstock contained a constant fibre fraction (a mix of cardboard, boxboard, newsprint, and fine paper) and varying proportions of food waste. Previously, we reported on the...

Here, we review the contributions of Professor Barbara Sherwood Lollar to Compound Specific Isotope Analysis (CSIA) in contaminant hydrogeology and environmental chemistry. We first discuss the seminal work by Professor Sherwood Lollar’s lab on establishing CSIA as a quantitative tool for contaminant (bio)transformation at contaminated groundwater...

We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A one-time injection of 0.1 mL air , simulating...

Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) will have greater value as an important diagnostic tool. An in-de...

Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile, TePN) is one of the most widely used fungicides all over the world. Its major environmental transformation product 4-hydroxy-chlorothalonil (4-hydroxy-2,5,6-trichloroisophthalonitrile, 4-OH-TPN) is more persistent, mobile, and toxic and is frequently detected at a higher concentration in various...

Compound specific isotope analysis (CSIA) is an established tool for evaluating in situ transformation of organic contaminants. To date, CSIA has never been applied to understand the in situ fate of 2,3-dichloroaniline (2,3-DCA). Although persistent in the environment, several microorganisms were identified as able to degrade 2,3-DCA, thus making t...

Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and therefore believed to participate in horizontal gene transfer. To try to induce horizontal ge...

Wastewater surveillance has rapidly emerged as an early warning tool to track COVID-19. However, the early warning measurement of new SARS-CoV-2 variants of concern (VOCs) in wastewaters remains a major challenge. We herein report a rapid analytical strategy for quantitative measurement of VOCs, which couples nested polymerase chain reaction and li...

Compound specific isotope analysis (CSIA) is an established tool to demonstrate in situ degradation of traditional groundwater contaminants at heavily contaminated sites, usually at mg/L range aqueous concentrations. Currently, an efficient preconcentration method is lacking to expand CSIA to low aqueous concentration environmental samples. This wo...

Reductive dehalogenases (RDases) are corrinoid-dependent enzymes that reductively dehalogenate organohalides in respiratory processes. By comparing isotope effects in biotically-catalyzed reactions to reference experiments with abiotic corrinoid-catalysts, compound-specific isotope analysis (CSIA) has been shown to yield valuable insights into enzy...

The Candidate Phyla Radiation (CPR, or superphylum Patescibacteria) is a very large group of bacteria with few cultivated representatives first discovered by culture-independent metagenomic analyses. Within the CPR, the candidate phylum Parcubacteria (previously OD1) is prevalent in anoxic lake sediments and groundwater. We identified a bacterium b...

Clinical testing has been the cornerstone of public health monitoring and infection control efforts in communities throughout the COVID-19 pandemic. With the extant and anticipated reduction of clinical testing as the disease moves into an endemic state, SARS-CoV-2 wastewater surveillance (WWS) is likely to have greater value as an important diagno...

Wastewater-based surveillance (WBS) has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Quantities of viral fragments of SARS-CoV-2 in wastewater are related to numbers of clinical cases of COVID-19 reported within the corresponding sewershed. Variants of Concern (VOCs) have been detected in wastewater...

We investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria Candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A relatively small one-time injection of air, si...

A 50 kg-scale high solids anaerobic digestor comprising six sequentially-fed leach beds with a leachate recirculation system and an upflow anaerobic sludge blanket reactor was operated at 37°C for 88 weeks. The feedstock contained a constant fibre fraction (a mix of cardboard, boxboard, newsprint, and fine paper) and varying proportions of food was...

We present and demonstrate a quantitative statistical linear trend analysis (QTA) approach to analyze and interpret SARS-CoV-2 RNA wastewater surveillance results concurrently with clinical case data. This demonstration is based on the work completed under the Ontario (Canada) Wastewater Surveillance Initiative (WSI) by two laboratories in four lar...

Wastewater-based surveillance of SARS-CoV-2 RNA has been implemented at building, neighbourhood, and city levels throughout the world. Implementation strategies and analysis methods differ, but they all aim to provide rapid and reliable information about community COVID-19 health states. A viable and sustainable SARS-CoV-2 surveillance network must...

Wastewater-based surveillance of SARS-CoV-2 RNA has been implemented at building, neighbourhood, and city levels throughout the world. Implementation strategies and analysis methods differ, but they all aim to provide rapid and reliable information about community COVID-19 health states. A viable and sustainable SARS-CoV-2 surveillance network must...

Reductive dehalogenases (RDases) are a family of redox enzymes that are required for anaerobic organohalide respiration, a microbial process that is useful in bioremediation. Structural and mechanistic studies of these enzymes have been greatly impeded due to challenges in RDase heterologous expression, potentially because of their cobamide-depende...

This Protocol has been developed collaboratively with stakeholders of Ontario Ministry of the Environment, Conservation and Parks' Wastewater Surveillance Initiative. It is a technical guidance document that prescribes a streamlined list of definitions and a framework related to quality assurance/quality control of data emanating from RT-qPCR-based...

l‐2‐Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon‐halogen bond in s‐2‐halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. A screen for novel dehalogenase activities revealed fo...

Reductive dehalogenases (RDases) are a family of redox enzymes that are required for anaerobic organohalide respiration, a microbial process that is useful in bioremediation. Structural and mechanistic studies of these enzymes have been greatly impeded due to challenges in RDase heterologous expression, primarily because of their cobamide-dependenc...

Anaerobic microcosms constructed with soil from Guadeloupe, amended with ethanol and acetone and incubated anaerobically for more than a decade, transformed chlordecone (CLD) into a suite of progressively more dechlorinated products, including a fully dechlorinated carboxylated indene product. This fully dechlorinated transformation product has nev...

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...

A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.

Anaerobic microcosms constructed with soil from Guadeloupe, amended with electron donor (ethanol and acetone) and incubated for more than a decade, transformed chlordecone (CLD) into a suite of progressively more dechlorinated products, including a fully dechlorinated carboxylated indene product. This fully dechlorinated transformation product has...

Open science means sharing all information in the research process as early as possible and making the output available without restriction on use. In the most expansive definition of open science, this includes sharing early‐stage inventions that could be the subject of patent applications. We illustrate how this expansive open science definition...

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...

Reliance on bioremediation to remove benzene from anoxic environments has proven risky for decades but for unknown reasons. Years of research have revealed a strong link between anaerobic benzene biodegradation and the enrichment of highly specific microbes, namely Thermincola in the family Peptococcaceae and the deltaproteobacterial Candidate Sva0...

Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and therefore believed to participate in horizontal gene transfer. To try to induce horizontal ge...

Efficient biotransformation of lignin requires the activity of different oxidative enzymes. In this work, 19 bacterial multi-copper oxidases were screened for oxidase activity against 19 soluble substrates and revealed the highest activity in the laccase CotABsu (BSU0630) from Bacillus subtilis. Structure-based site-directed mutagenesis of CotABsu...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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 non-desirable and toxic lowe...

The hardest problems that engineers tackle, such as climate change, energy sustainability, food security, and water quality and quantity, cannot be solved without partnerships among universities, governments, and industry. These solutions must also be global, as low and middle income countries are particularly affected. In this Perspective, we ask...

Chlorinated ethanes are environmental pollutants found frequently at many contaminated industrial sites. 1,1,1-Trichloroethane (1,1,1-TCA) can be dechlorinated and detoxified via abiotic transformation or biologically by the action of dechlorinating microorganisms such as Dehalobacter (Dhb). At a field site, it is challenging to distinguish abiotic...

Reversible UbiD-like (de)carboxylases represent a large family of mostly uncharacterized enzymes, which require the recently discovered prenylated FMN (prFMN) cofactor for activity. Functional characterization of novel UbiDs is hampered by lack of robust protocols for prFMN generation and UbiD activation. Here, we report two systems for in vitro an...