Browsing by Author "Gieg, Lisa Marie"
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Item Open Access Assessment of Anaerobic Bioremediation Potential in Hydrocarbon Contaminated Aquifers in Alberta, Canada(2019-04-30) Kharey, Gurpreet Singh; Gieg, Lisa Marie; Hubert, Casey R. J.; Turner, Raymond JosephAnaerobic biodegradation of hydrocarbon fuels (mono-aromatic and short chain alkane hydrocarbon) was demonstrated under both field and microcosm experiments, with detection of signature metabolites, fumarate addition genes, and microbial community composition to determine the potential of hydrocarbon-contaminated sites for bioremediation and assess the evidence of its past and/or present occurrence. It was determined here that the potential for bioremediation is unique to both the contaminated sites, but also to the hydrocarbon load present. Quantification of the fumarate addition genes using a newly-designed mixture of primers was done. These qPCR assays for assA and bssA abundances concluded that an upper limit to gene abundance is present according to hydrocarbon concentrations, of approximately 5 ppm hydrocarbon. Monitoring hydrocarbon loss from groundwater collected at these sites, paired with fumarate addition gene abundances concluded that the contaminated sites in question have the potential for bioremediation, but is limited with higher hydrocarbon concentrations.Item Open Access Biodegradation of Aromatic Hydrocarbons by Methanogenic Consortia and Groundwater-Associated Microbial Communities(2021-01-08) Taylor, Nicole; Gieg, Lisa Marie; Hubert, Casey R. J.; Dunfield, Peter F.The biodegradation of hydrocarbons is an important environmental process responsible for in situ remediation of crude oil and gas components. Microorganisms of many lineages and redox conditions have been characterized to degrade numerous types of petroleum hydrocarbons, including those with aromatic structures. Alkyl-substituted mono- and polycyclic aromatic hydrocarbons are more chemically reactive than their unsubstituted counterparts, and as such their anaerobic degradation pathways have been studied to varying degrees. Aromatic hydrocarbons require enzymatic functionalization before biodegradation can occur; these activation enzymes and products are often unique to anaerobic reactions, therefore identifying the metabolites produced or the enzymes carrying out these reactions lends evidence to identifying in situ bioremediation of aromatic hydrocarbon contamination. Hydrocarbon biodegradation in the deep subsurface is often associated with methanogenesis. Anaerobic toluene degradation has been extensively studied and has been shown in multiple studies to involve an activation process known as fumarate addition, however methanogenic biodegradation of other alkylbenzenes and polycyclic aromatic hydrocarbons is comparatively poorly understood. In this work, the biodegradation of ethylbenzene and p-xylene was examined in the presence of toluene; p-toluic acid was found as a metabolite of p-xylene biotransformation, but no evidence of fumarate addition to either p-xylene or ethylbenzene were observed. A second methanogenic biodegradation study of naphthalene, 2-methylnaphthalene, and phenanthrene revealed 2-naphthoic acid as the primary metabolite produced by microbial cultures. A third study involved evaluating the use of a trapping device for passively sampling microorganisms from groundwater contaminated with aromatic hydrocarbons; this study showed that the chosen sorptive material did not influence the biodiversity of microbial communities, did not influence the rate of hydrocarbon biodegradation, and the presence of hydrocarbons was correlated to higher biomass recovery.Item Open Access Biodegradation of Naphthenic Acids by Microorganisms Originating from Alberta's Oil Sands Surface Mining Operations(2021-01) Paulssen, Julie Maria; Gieg, Lisa Marie; Muench, Douglas G.; Chua, GordonBillions of liters of tailings water are produced from oil sands surface mining operations each year. Reclamation of tailings ponds is now a legislated process that must occur within 10 years after the end of an oil sands mining operation. To reclaim these waste ponds back to a natural landscape, toxic compounds must first be removed, including naphthenic acids (NAs), which are the primary toxic components. I investigated the biodegradation ability of three different microbial culture sets - photosynthetic algal-bacterial communities, aerobic bacterial communities, and a nitrate-reducing bacterial community - for their ability to metabolize the two model NAs cyclohexanecarboxylic acid (CHCA) and 1-adamantanecarboxylic acid (1-ADCA). Using gas chromatography-mass spectrophotometry, DNA stable isotope probing, and 16S/18S rRNA gene sequencing techniques, the work in this thesis illustrates the metabolism and organisms responsible for the biodegradation of the model NAs studied. All three microbial culture sets successfully biodegraded CHCA, while the structurally more complex 1-ADCA could only be biodegraded by the algal-bacterial communities, suggesting the potential value of such consortia for treating NA in oil sands tailings ponds. The DNA stable isotope probing experiments revealed that of the algae, members of the family Scenedesmaceae and the class Trebouxiophyceae both contribute to the biodegradation of CHCA. Brevundimonas and Rhodococcus were the two primary genera found associated with the biodegradation of CHCA in the aerobic bacterial communities. Sequencing results revealed that the nitrate-reducing bacterial community was primarily composed of known sulfate-reducing microorganisms, an intriguing result that warrants additional study.Item Open Access Biological and Advanced Oxidation Processes for the Treatment of Sulfolane Contaminated Waters(2020-01-07) Khan, Muhammad Faizan; Achari, Gopal; Black, Kerry E.; Kimura, Susana Y.; Gieg, Lisa Marie; Khan, Faisal MasoodSulfolane contamination has increasingly become a major environmental concern around the world. This research builds on past research on sulfolane degradation using a variety of different advanced treatment technologies. Initially, the performance of an integrated technology combining biological activated sludge with advanced oxidation process (AOP) (UVC/H2O2) in sequence was evaluated in a batch reactor resulting in >81% sulfolane degradation in less than 24 h. Evaluation of the impact of biological process on AOP showed sulfolane concentration beyond 30 mg/L and presence of TSS >44 mg/L can negatively impact the UVC/H2O2 efficiency for sulfolane degradation. The application of UVC/H2O2 after biological treatment was an advantage as UVC/H2O2 could perform dual roles of oxidation and disinfection. As aerobic granulation is perceived to be more advanced than activated sludge process, two approaches of forming sulfolane degrading aerobic granules (SDAG) were investigated. The adaptation of pre-grown granules to sulfolane environment required a longer period to form SDAG compared to coaggregation of pre-grown granules with bacterial culture native to sulfolane contaminated site. Scanning electron microscopic images revealed dominant filamentous bacteria on the surface of granules. The stability and settleability of SDAG were also investigated under different environmental conditions. Subsequently, a novel integration of aerobic granulation with UV/H2O2 process in a continuous flow-through operation sequence showed elimination of more than 99.99% of sulfolane in less than 6.3 h of combined retention time. The degradation kinetics of sulfolane were also evaluated and the flow-through system showed generation and maintenance of a healthy aerobic granular system. Additionally, various key factors were also identified that govern residual H2O2 concentration in UV/H2O2 effluents. Finally, a pilot-scale field investigation was conducted using a pressurized ozone treatment system to degrade sulfolane in contaminated groundwaters. A series of batch and continuous flow systems were studied to determine the degradation kinetics and evaluate augmentation of oxidation process with the addition of secondary chemicals with ozone. Groundwater matrix played a crucial role in the efficacy of ozone treatment and intermittently sparged ozone injection was evaluated as a viable option for ozone field applications. Nevertheless, bromate concentrations higher than drinking water guidelines were detected in treated groundwater after ozone treatment and this will need further research.Item Open Access Biosensors for the Detection of Naphthenic Acids in Wastewater from Oil Sands Operations(2019-09-19) Shideler, Steven Mark; DeVinney, Rebekah; Lewenza, Shawn; Gieg, Lisa Marie; Savchenko, AlexeiNaphthenic acids (NA) are a complex group of acyclic and cyclic alkyl-substituted carboxylic acids that are present in the bitumen mined from the oil sands. NAs accumulate in the tailings waste produced from processing bitumen, are toxic to living organisms and are difficult, both in terms of time and resources, to remediate. In this study, we established a high throughput pipeline using bacterial genomics and synthetic biology methods to build biosensor constructs using promoters from Pseudomonas synxantha, an organism isolated from oilsands process-affected water (OSPW). By observing the gene expression profiles of P. synxantha, we have been able to identify genes that are induced by NAs, and that likely play a role in the transport and catabolism of various NA species. We have identified a catabolic operon that is expressed in a dose-dependent manner, in response to NA exposure. In addition, we identified a TetR regulator that is divergent from this operon, that represses expression of the catabolic operon during normal conditions. The TetR regulator was purified and was shown to bind to the target promoter in electrophoretic mobility shift assays. In the presence of specific naphthenic acids, the repressor loses DNA binding affinity and no longer interacts with the promoter. Based on these findings, we have proposed a model of naphthenic acid sensing through a TetR repressor protein and have therefore identified all the components required to build an NA sensing biosensor using P. synxantha as a chassis. We have therefore identified all the components required to build an NA biosensor using P. synxantha as a chassis. The NA biosensor can be employed as a method to detect NA contamination in the environment, and also to aid in the discovery of novel genes for the purpose of supporting the bioremediation of the 1.2 trillion liters of NA contaminated water currently being stored in Northern Alberta.Item Open Access Enzymatic degradation of carboxymethyl cellulose – A biotechnological approach for hydraulic fracturing operations(2019-12-19) Scheffer, Gabrielle; Gieg, Lisa Marie; Ng, Kenneth Kai Sing; Sen, ArindomCarboxymethyl cellulose (CMC) is a polymer used in different industrial sectors. In the oil and gas industry, CMC is often used during hydraulic fracturing (fracking) operations as a thickening agent helping for proppant delivery. Accumulations of CMC at fracture faces (filter cakes) can impede oil and gas recovery. Although chemical oxidizers are added to disrupt these accumulations, there is industrial interest in developing alternative, enzyme-based treatments. Little is known about whether CMC can be biodegraded under fracking conditions. Here, we enriched a methanogenic CMC-degrading culture, and demonstrated its ability to express extracellular enzymes able to utilize CMC under various conditions that typify oil fields. Finally, isolation and purification of the enzymes allowed for complete degradation of the polymer within 3 h, and allowed for the identification of putative purified cellulases. This study demonstrates that enzyme technology holds great promise as a viable approach to treating CMC filter cakes under field conditions.Item Open Access Health Impact Assessment of Sulfolane on Embryonic Development of Zebrafish (Danio rerio)(2018-07-30) Shah, Soham Manoj; Habibi, Hamid R.; Achari, Gopal; Gieg, Lisa Marie; Ruckstuhl, K. E.Sulfolane is a widely used polar, aprotic solvent for multiple applications in numerous industries. Through problems with storage, leaks, spills and leeching; sulfolane has been introduced into the environment and has been detected through chemical analysis in groundwater and creeks around the world including Alberta, Canada (800 µg·mL-1), Louisiana, USA (2900 µg·mL-1) and Brisbane, Australia (4344 µg·mL-1). Previous research on terrestrial organisms has demonstrated hyperactivity, shortness of breath, convulsions, and internal molecular changes following sulfolane exposure. However, relatively little information is available on the adverse impacts of sulfolane on aquatic organisms. This study investigates the adverse effects of sulfolane on morphological, behavioural and transcript abundance in developing zebrafish embryos. A wide range of concentrations (0 – 5000 µg·mL-1) were tested on survival, hatching, morphometric characteristics (yolk sac and pericardial edema, hemorrhaging, spinal malformations, swim bladder inflation), growth (larval length, condition factor, eye volume), yolk sac utilization, behavior (response to touch stimuli and light stimuli) and transcript abundances of a number of genes (ahr1a, cyp1a, thraa, dio1, dio2, dio3, 11βhsd2, gr, aqp3a, cyp19a1b, ddc, gria2b, hsp70). Minimum effective doses were different for morphometrics and growth parameters (800-1000 µg·mL-1), behaviour (200-500 µg·mL-1) and transcript abundance (10 µg·mL-1). The overall results provide novel information on the adverse effects of sulfolane on an aquatic vertebrate model organism, and a framework for better understanding of potential adverse health impacts of environmental levels of sulfolane in fish and other vertebrates.Item Open Access Methane Cycling and Methanotrophic Bacteria in Base Mine Lake, a Model End-Pit Lake in the Alberta Oilsands(2018-08-29) Albakistani, Emad; Dunfield, Peter F.; Voordouw, Gerrit; Gieg, Lisa MarieWe studied methanotrophic bacteria over three years (2015 - 2018) in Base Mine Lake, Fort McMurray, Canada. The lake represents the first large scale demonstration of end-pit lake technology in the Alberta oilsands. 16S rRNA gene amplicon sequencing and measurement of methanotrophic rates were applied to evaluate the effect of seasonal changes on methanotrophic diversity and activity, and to understand the biogeochemical cycling of methane and oxygen. Based on 16S rRNA gene sequence relative abundance, the predominantly detected methanotrophic genera were Methylobacter/Crenothrix in the winter and Methylocaldum in the summer. Methanotrophs were most abundant in winter throughout the water column, and in summer at the bottom of the lake near the fluid fine tailings interface. Potential methanotrophic rates decreased over three years from 2015-2018.Item Open Access Microbial Ecology of Subsurface Oil Sands Deposits in Northern Alberta, Canada(2018-08-09) Ridley, Christina M.; Gieg, Lisa Marie; Voordouw, Gerrit; Strous, Marc; Biddle, Jennifer; Hubert, Casey R. J.The subsurface Athabasca Oil Sands in northern Alberta, Canada, is an important yet understudied microbial habitat. Over geological time, progressive biodegradation of low molecular weight hydrocarbons by indigenous microorganisms has resulted in an enrichment of high molecular weight hydrocarbons known as bitumen. This is an extreme environment characterized by low water and nutrient availability, thereby resulting in low microbial biomass. The objective of this study was to characterize the microbial ecology of this unique ecosystem, which could ultimately provide a basis for the development of microbially enhanced oil recovery (MEOR) technologies. To that end, pristine core samples were collected from 220 to 320 meters below the surface during 3 annual field trips. Due to the high bitumen and low biomass content of the core samples, extensive method development and validation was performed to identify a robust molecular biological workflow that would allow for consistently successful extraction, amplification and sequencing of genomic DNA from core samples. This molecular biological method was then used to characterize the prokaryotic and eukaryotic microbial communities of the subsurface oil sands through 16S and 18S rRNA gene sequencing. Results revealed a surprising predominance of aerobic and facultative microorganisms in an environment that is traditionally considered anoxic. The genera Pseudomonas, Acinetobacter and Fontibacter were the dominant prokaryotes in all core samples (average relative sequence abundance >5%). Methanoculleus was the only methanogen detected at an average relative sequence abundance >1%. Fungi from the family Trichocomaceae and the order Hypocreales were the prevailing Eukaryotes. Core sample incubations were used to determine the effects of atmosphere and temperature on microbial community succession. Microcosms were established under aerobic, microaerobic and anaerobic atmospheres at reservoir (8°C), mesophilic (33°C) and thermophilic (60°C) temperatures. Results indicate that the predominant community members remained similar to the controls; however, some microcosms incubated at 60°C experienced enrichment of thermophiles, including the genera Thermus, Geobacillus and Thermanaerothrix. Many of the dominant taxa observed in this study could have potential MEOR applications, including hydrocarbon degradation, biosurfactant production and methanogenesis. Thus, the information revealed in this study could be used as the basis for MEOR technologies.Item Open Access Microbial Nitrogen and Sulfur Metabolism and its Relation to Corrosion Risk on Offshore Oil Production Platforms(2020-04-07) Nicoletti, Danika Susianne; Gieg, Lisa Marie; Ng, Kenneth Kai Sing; Hubert, Casey R. J.The potential for microbiologically-influenced corrosion (MIC) of oilfield produced waters collected from the topsides of two offshore FPSO (floating, production, storage, and offloading) vessels exposed to various sulfur (S) and nitrogen (N) chemistries was investigated. Produced water was incubated at high temperature (54 °C) for 154 days with exposure to various nitrate and nitrite injection chemistries under sour and non-sour conditions, and microbial community analysis, N and S transformation monitoring, and corrosion coupon weight loss were used to assess MIC risk. Low concentrations of nitrate or nitrite (0.5 mM) did not effectively inhibit detrimental sulfate reduction by sulfate-reducing microorganisms (SRM), while 5 mM nitrate and nitrite treatments displayed successful sulfate reduction inhibition. Microbial community compositions did not differ dramatically between topside sampling locations from a single FPSO in response to various nitrate, nitrite, and sulfide treatments determined by microbial community analysis, however the microbial community structures between the two FPSO platforms revealed differences. The highest corrosion rates which may be MIC-attributed based on comparisons with sterile controls were measured in microcosms wherein no nitrate, nitrite or sulfide was added (0.48 mm/year). Despite its successful sulfate reduction inhibition, the addition of 5 mM nitrite into produced water microcosms conferred corrosion rates of up to 0.17 mm/year in sterile controls, indicating a chemical corrosion effect. In related work, the purification of the sulfide utilizing enzyme sulfide:quinone oxidoreductase (SQR) from Thiobacillus denitrificans was also performed successfully using a reproducible and scalable method for future use on a previously developed biosensor for sulfide detection. The knowledge gained from this thesis work can be used to inform the MIC risks associated with nitrate and nitrite injection within the topside machinery of offshore oil recovery operations, a previously poorly characterized environment. The efficient enzyme purification method offered in this thesis provides an avenue for continued development of a sulfide biosensor for future use in monitoring sulfidogenesis in produced water samples such as those on offshore oil production facilities.