Browsing by Author "Gieg, Lisa M."

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    Biostimulation for Enhanced Bioremediation of Crude Oil and Diesel Fuel by Marine Sediment Communities of Canada’s Subarctic: A Microcosm-Simulated Oil Spill Study
    (2020-01-23) Murphy, Sean Michael Colin; Hubert, Casey R. J.; Gieg, Lisa M.; Vamosi, Steven M.
    Increases in shipping traffic, future mining, and oil and gas developments represent significant oil spill risks in Canada’s subarctic marine environment. The impact of oil on marine ecosystems and the traditional activities of local indigenous peoples are of major concern. To understand the response of local microbial communities to oil contamination and nutrient biostimulation, microcosm-simulated oil spills contaminated with diesel fuel or crude oil and incubated at 4°C were constructed using marine sediments from Hudson Bay and the Labrador Sea. Changes in microbial community structure, diversity, and composition were monitored by DNA extraction, the amplification of 16S rRNA genes, followed by sequencing and taxonomic classifications. Additionally, hydrocarbon degradation in response to bioremediation was monitored by changes in gas compositions with GC, and through hydrocarbon extractions and GC-MS analysis. Results suggested that petroleum hydrocarbons decreased observed microbial diversity and led to dominance by Gammaproteobacteria in both sediments, where many hydrocarbonoclastic bacteria (HCB) increased heavily in abundance at both sites, including Cycloclasticus, Marinobacter, Oleispira, Paraperlucidibaca, Pseudomonas, Thalassolituus, and Zhongshania. The same OTUs were found to increase in abundance in both high and low nutrient treatments, but biostimulation was found to increase initial rates of biodegradation by accelerating the succession and dominance of these HCB. Increase in the relative abundance of Cycloclasticus was noted as signifying succession in response to hydrocarbon degradation and biostimulation. The Labrador Sea sediment community was found to be more responsive to oil spills and biostimulation mitigation strategies, which could be tied to historical exposures of the community to natural oil seepages in the region. Porticoccus and Oleispira are suggested as robust bioindicators for cold seawater environments contaminated by diesel or crude oil, respectively. A comparison of three PCR primer pairs for HCB detection found 341F/806R was the preferred choice for detecting HCB taxa and assessing environmental baselines in areas at risk of oil spills. Microbial biodiversity baselines and in situ rates of microbial degradation should be included in future environment assessments by industry. Overall, this study provided a first account of key crude oil- and diesel-degrading bacteria among marine sediments in this subarctic region.
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    Genetics of Ribitol Catabolism in Rhizobium leguminosarum
    (2019-09-20) Buhlers, Deborah; Hynes, Michael F.; Gieg, Lisa M.; Wong, Sui-Lam; Oresnik, Ivan; Niu, Dongyan
    Rhizobium leguminosarum bv. viciae strain VF39SM contains six plasmids; a strain cured of both pRleVF39c and pRleVF39d is unable to grow on ribitol, whereas strains cured of only one of the plasmids can grow on this substrate. BLAST database searches and previous work show that the pRleVF39d plasmid ribitol catabolic genes are widely distributed among many R. leguminosarum strains. The less common pRleVF39c plasmid locus contains genes encoding a DeoR transcriptional regulator (rlcR), an ATPase component of an ABC transporter (rlcB), a periplasmic binding protein of an ABC transporter (rlcA), two ABC transporter permease components (rlcC, rlcF), a glycerophosphoryl diester phosphodiesterase (rlcG), a hydrolase (rlcH), a ribitol dehydrogenase (rlcD) and a ribulokinase (rlcK). The pRleVF39d locus contains genes encoding a reductase (rldE), a ribitol-2-dehydrogenase (rldD), an ABC transporter permease (rldC), the ATPase of an ABC transporter (rldB), the periplasmic binding protein of an ABC transporter (rldA), and an AraC-like regulator (rldR). Mutagenesis of the genes of these two loci showed that rlcK, rlcD, rldD, rldA, and rldR are required for the catabolism of ribitol. Three c and d plasmid double mutants, rlcK-rldA, rlcK-rldD and rlcK-rldR, were also unable to grow in the presence of ribitol as sole carbon and energy source. The d plasmid ribitol catabolic genes comprise as single operon, while the c plasmid ribitol catabolic genes are in multiple operons, with rlcR and rlcB comprising a divergently transcribed operon, and the remaining c plasmid ribitol catabolic genes making up additional transcripts. The c plasmid ribitol catabolic genes are induced by ribitol and seed exudates of peas, beans and lentils. Nodulation competition assays using ribitol catabolic gene single and double mutants, demonstrated that ribitol catabolism is required for nodulation competitiveness on peas (cv. Little Marvel) and lentils (cv. Marble), but not for vetch or faba beans (cv. Windsor). Ribitol catabolic gene induction during interaction of R. leguminosarum VF39SM with lentils and vetch seedlings also showed that rldR, but not rlcA was induced during early stages of interaction with the roots of lentil seedlings, and that rlcA is induced within the nodules of vetch.
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    In situ detection of an aerobic alkane metabolites in subsurface environments
    (Frontiers, 2013-06-04) Agrawal, Akhil; Gieg, Lisa M.
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    Physiology and Molecular Characterization of Microbial Communities in Oil Sands Tailings Ponds
    (2013-01-25) Ramos Padron, Esther; Gieg, Lisa M.
    In northern Alberta, mining operations to obtain bitumen from the oil sands generates large volumes of tailings. These are a mixture of sand, clay, water, organic solvents and residual bitumen that are deposited into old open pits, creating tailings ponds, where they are allowed to settle with the final goal of land reclamation. To speed up the sedimentation process, the addition of gypsum (CaSO4 ∙ 2H2O) is currently a management approach used bysome companies. This creates a deep watery mud line with very low oxygen permeability and enough sulfate to support the growth of anaerobic microbial communities. In this thesis work, the microbial physiology and communities associated with oil sands tailings ponds were assessed. Chemical, physiological, and molecular biology approaches were used to determine the key microbial processes (methanogenesis, sulfate reduction/oxidation), identify key substrates, and determine the dominant microbial community members in the anaerobic and aerobic zones of tailings ponds. Microbial community analysis showed that in the anaerobic zone of tailings, the sulfate-reducing/disproportionating bacterium Desulfocapsa. and the sulfide oxidizer/iron reducer Thiobacillus sp. are among the most prevalent organisms when sulfate is present. After sulfate is depleted, methanogenic Archaea become predominantly active and Methanosaeta and Methanolinea in association with Syntrophus dominate in the ponds, presumably interacting to biodegrade the available organic compounds. The residual naphtha components that constitute part of the tailings composition are the preferred electron donors in anaerobic zones (in comparison to naphthenic acids) based on enrichment culture studies. In naphtha-amended laboratory cultures, a variety of methanogens in association with Thauera sp. and Desulfocapsa sp. became enriched as the dominant organisms. Overall, microbial community composition as a function of depth in tailings ponds paralleled key iii microbial processes that were measured (sulfate reduction and methanogenesis). In the aerobic surface water, other microbes with known metabolic capabilities to degrade hydrocarbon-derived compounds such as naphthenic acids were found. The results of this work also showed that operational changes to tailings ponds shift the microbial community structure and functions. For example, pond closure resulted in a shift from a predominantly methanogenic and sulfate-reducing environment to one dominated by putative hydrocarbon degraders, indicating a positive management outcome in microbial activity associated with pond closure.
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    Spectrometric analysis of the metabolism and adsorption of naphthenic acid fraction compounds in a phytoremediation treatment system
    (2024-08-14) Charriere, Camryn; Muench, Douglas G.; O'Sullivan, Gwen; Gieg, Lisa M.
    Bitumen mining in northern Alberta produces large volumes of oil sands process-affected water (OSPW) that require treatment before being released into the environment. Naphthenic acid fraction compounds (NAFCs) are considered primary contributors to OSPW toxicity; therefore, remediation efforts often target these compounds. Phytoremediation is proposed as a feasible treatment for OSPW using a constructed wetland treatment system (CWTS) strategy due to the cost-effective and low-maintenance nature of this technology. A CWTS uses plants and their associated microorganisms to take advantage of natural metabolic processes for the uptake and biotransformation of environmental contaminants. While CWTSs for OSPW treatment have demonstrated success in attenuating NAFCs and reducing toxicity in mesocosm and pilot-scale studies, the fate of NAFCs in a CWTS is not well understood. This thesis research aimed to gain insight into NAFC fate in CWTSs by exploring NAFC biotransformation processes in plant tissues and the adsorption characteristics of NAFCs onto sediment substrates. A method for extracting NAFCs and their metabolites from plant tissues was developed and used to extract the isotopically labelled model compound 1-adamantanecarboxylic acid (¹³C-AdCA) and NAFCs from OSPW. This method, in combination with high-resolution Orbitrap mass spectrometry, was used to track the uptake, translocation, and biotransformation within plant roots and shoots. These experiments showed a general decrease in compound abundance over time, indicative of transformation events. The OSPW treatments further demonstrated that the majority of NAFCs were completely transformed in root and shoot tissues. Additionally, incubation studies were conducted to test parameters associated with NAFC adsorption onto various sediments. The adsorption of NAFCs from OSPW onto a sediment substrate from the oil sands region appeared to be impacted by the properties of the OSPW itself, including NAFC concentration, class differences, or shifts in carbon number and double bond equivalents. Other factors, such as water quality characteristics, may also impact adsorption. Overall, the results of this research provide insight into the fate of NAFCs in phytoremediation systems, guiding future metabolomics studies and considerations for the large-scale implementation of plant-based technologies in OSPW treatment strategies.
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    Syntrophic hydrocarbon metabolism under methanogenic conditions
    (2014-04-30) Fowler, Susan Jane; Gieg, Lisa M.; Voordouw, Gerrit
    Methanogenic metabolism of organic matter is a key process in both natural and engineered systems. Methanogenic hydrocarbon degradation is an important biogeochemical process in the deep subsurface, and subsurface hydrocarbon contamination is frequently remediated by methanogenic processes. Despite the importance of methanogenic processes in hydrocarbon-impacted systems, we currently have an incomplete understanding of the hydrocarbon activation and degradation pathways used by the syntrophic bacteria, the roles of the non-hydrocarbon degrading syntrophs, which are often present in high abundance, and the ways in which syntrophic bacteria and methanogenic archaea establish and maintain relationships that allow them to coordinate their metabolism. By studying methanogenic hydrocarbon degrading enrichment cultures, we remove many complicating features of natural systems and can gain a basic understanding of the primary factors governing hydrocarbon metabolism under methanogenic conditions. In this dissertation, we describe several methanogenic hydrocarbon degrading enrichment cultures with a major focus on a toluene degrading methanogenic enrichment culture. Methanogenic hydrocarbon degrading communities consist of a diverse assemblage of Archaea and Bacteria dominated by members of the Methanomicrobia, Firmicutes, Deltaproteobacteria, Chloroflexi, Spirochaetes and other bacterial phyla in smaller proportions. Using stable isotope probing, key organisms involved in the degradation of toluene were identified, including Desulfosporosinus sp., which is associated with toluene activation as well as Syntrophus- like organisms and Desulfovibrio sp. Metabolite and metagenomic analysis indicate that fumarate addition is involved in toluene activation in this culture and results from this and other cultures suggest that fumarate addition is a key mechanism involved in the activation of alkanes, monoaromatic and polyaromatic hydrocarbons under methanogenic conditions. Comparative metagenomic analysis suggests that key functional features that distinguish methanogenic hydrocarbon degrading cultures include enrichment of archaeal and bacterial hydrogenases, as well as functions related to the regulation of redox conditions, energy conservation and methanogenesis. Hydrogen and/or formate transfer appears to play a major role in metabolite and electron transfer in these cultures. A better understanding of the processes involved in methanogenic hydrocarbon metabolism may provide us with the knowledge to develop new tools to monitor, control and harness these technologies to the benefit of ourselves and our environment.