Browsing by Author "Voordouw, Gerrit"

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    Acetic acid formation by acetogens from hydrogen and CO2:dissolution of carbonates and competition by methanogens
    (2014-07-11) Rollick, Lindsay; Voordouw, Gerrit
    Methane-producing archea (methanogens) and bacteria that produce acetic acid from H2 and CO2 (acetogens) exist in many low nutrient environments where other electron acceptors are absent. Methanogens usually outcompete acetogens because of a more powerful energy production but recent evidence suggests that acetogens may be able to compete through greater substrate diversity and energy efficiency (Lever 2012). Acetogenesis could be adapted as a biotechnology to induce carbonate dissolution in carbonate oil reservoirs. Enrichments were conducted on the subsurface production waters from a conventional oil field. Variations in medium composition were tested to promote acetogenesis over methanogenesis. High levels of acetic acid of up to 2400 μmol or 28 mM were produced and the consumed along with various levels of methane. Analysis of 16S rRNA gene sequences show a progression from dominance of acetogenesis to methanogenesis and then a shift to a group of microbes that consume acetate to create biopolymers like polyhydroxybutyrate for storage of carbon in nutrient-limited environments. Factors that increase acetic acid production include ultra-low nutrient environments, sufficient pH buffering, not adding bicarbonate, and possibly increased surface area. Dissolution via microbial acetic acid was tested for powdered CaCO3, crushed and solid carbon rock but results are inconclusive. Acetogens can be competitive with methanogens under the lowest nutrient conditions. The excess of the H2/CO2 energy and carbon substrates used in these experiments along with differences seen in nutrient variation suggest that conditions other than substrate availability can influence this competition. Sampling loss, re-precipitation and other experimental factors make carbonate dissolution mediated by microbial acetic acid difficult to track.
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    Aerobic Hydrocarbon-degrading Microbial Communities in Oilsands Tailings Ponds
    (2016) Rochman, Fauziah; Dunfield, Peter F.; Voordouw, Gerrit; Gieg, Lisa; Hettiaratchi, Patrick
    Oilsands process-affected water (OSPW), produced by the surface-mining oilsands industry in Alberta, Canada, is alkaline and contains salts, various metals, and hydrocarbon compounds. In this thesis, aerobic communities involved in several key biogeochemical processes in OSPW were studied. Degradation of several key hydrocarbons was analyzed in depth. Benzene and naphthalene were used as models for aromatic hydrocarbons, in which their oxidation rates, degrading communities, and degradation pathways in OSPW were researched. The potential oxidation rates were 36.7 μmol L-1 day-1 for benzene and 85.4 μmol L-1 day-1 for naphthalene. Via stable isotope probing (SIP), and high-throughput sequencing of 16S rRNA gene amplicons, it was discovered that strains of the genera Methyloversatilis and Zavarzinia were the main benzene degraders, while Thiococcus and Pseudomonas were the main naphthalene degraders. Cultivated strains of Zavarzinia and Pseudomonas were shown to be growing on benzene and naphthalene. Metagenomics analysis revealed genes encoding oxygenases active against aromatic compounds, as well as catechol oxidases. Although these belonged to many phylogenetically diverse bacteria, only few bacteria were predominant in the SIP experiments. A highly divergent pmoA-like gene was also detected in the metagenome data. Here, the possibility of this gene allowing growth on short alkanes (C1 to C3) was examined. This gene was investigated via SIP and quantitative PCR. Results showed that the monooxygenase encoded by the gene has high affinity toward ethane and mostly propane. For the study of lighter hydrocarbons, methane, ethane, and propane were chosen as model compounds. OSPW was capable of supporting methane oxidation with a rate of 108.2 μmol of CH4 L−1 OSPW d−1, ethane oxidation with a rate of 83.2 μmol of C2H6 L−1 OSPW d−1, and propane oxidation with a rate of 58.6 μmol of C3H8 L−1 OSPW d−1. SIP analysis uncovered Methyloparacoccus to be predominant in methane-incubated samples, whereas Methyloversatilis was predominant in ethane and propane-incubated samples. SIP technique was also employed to study photosynthetic bacterial communities and indigenous aerobic bacterial communities that assimilate methanol, acetate, and protein extracts. All OSPW photosynthetic ‘heavy-DNA’ samples were dominated by unidentified Planctomycetes. Predominant groups in methanol, acetate, and protein extract-SIPs were Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes. Finally, via a modified cultivation technique, a novel Verrucomicrobia was isolated from OSPW. The aerobic bacterium was named Oleiharenicola alkalitolerans gen. nov., sp. nov., and it was studied in depth via phylogenetic, chemotaxonomic and whole-genome sequencing techniques.
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    Calcium nitrate treatment of oil sand tailings for improved densification and reduced greenhouse gas emissions
    (2013-12-19) Brown, Damon Craig; Voordouw, Gerrit
    Canada contains one of the world’s largest bitumen reservoirs, the mining of which produces huge volumes of tailings stored in ponds where they persist as mature fine tailings (MFT) for decades, releasing up to 43,000 m3 d-1 biogenic methane from a single pond. MFT are typically treated with gypsum or polyacrylamide (PAM) to accelerate densification. Microbial reduction of sulfate and methane formation have been associated with improved densification through an unknown mechanism. Here, calcium nitrate treatment balanced with a carbon and energy source (molasses) was found to inhibit methanogenesis and reduced the number of syntrophs and methanogens present. Nitrous oxide emissions were found to be transient while the microbial cell counts increased suggesting biomass has a stronger influence on enhanced microbial densification than biogenic gas. Microbes associated with PAM treated tailings were found to remove amide groups and in the presence of oxygen create a nitrogen cycle while maintaining PAM flocs integrity.
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    Characterization and Control of Halophilic Sulfate-Reducing and Methanogenic Microbial Communities in Shale Oil and Gas Systems
    (2017) An, Biwen Annie; Voordouw, Gerrit; Gieg, Lisa; Harrison, Joe; Mayer, Bernhard; Mouser, Paula
    In recent years, the oil and gas industry has been revolutionized by the expansion of shale oil and shale gas operations due to the advancement of hydraulic fracturing and high economic benefits compared to other unconventional resources. Several mechanisms have been proposed for the possible roles of microorganisms in shale gas fields. However, there remains a lack of knowledge regarding the key microbial players shared by all shale reservoirs and their involvements in the operations. Three case studies were conducted using samples obtained from various shale oil and shale gas reservoirs on the possibility of reservoir souring, microbiologically influenced corrosion (MIC) and microbially enhanced oil recovery (MEOR) through both culture-dependent and independent approaches. Case study I, for the Bakken shale oil field in Saskatchewan Canada, showed that continuous injection of low salinity source water can alter the microbial and geochemical conditions of the reservoir. There is a dominance of halophilic microbial community in the saline shale formations, in which Halanaerobium can synthesize the substrates used by halophilic sulfate-reducing bacteria (SRB) for sulfate-reduction, and halophilic nitrate-reducing bacteria (NRB) can inhibit the growth of SRB through nitrite production. At low salinity, the microbial community is much more diverse involving Halanaerobium, Desulfovibrio, Thiomicrospira, Dethiosulfatibacter and Arcobacter, with high potential for souring and MIC. In addition, at low salinity, nitrate-mediated souring control cannot be as easily achieved as nitrite is further reduced to N2. Case studies II and III were for the Duvernay shale gas field and Montney shale oil field in Alberta, Canada, which showed high MIC potential involving similar halophilic taxa as found in the Bakken field. Finally, samples from all three case studies indicated higher salinities were associated with higher ammonium concentrations, which is a product of methylotrophic methanogenesis using methylamines. The addition of methylamines in the hydraulic fracturing process can facilitate the possible interactions between the key players identified in all three case studies. Through this work, mitigation and monitoring technologies targeting recurring taxa involved in shale reservoirs on souring and MIC can be developed, which is highly beneficial for the environment and the economy.
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    Characterization of thermophilic microorganism in oil reservoirs
    (2005) Kaster, Krista; Voordouw, Gerrit
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    Characterizing and Accelerating Methanogenic Hydrocarbon Biodegradation
    (2017) Toth, Courtney; Gieg, Lisa; Dunfield, Peter; Voordouw, Gerrit
    Microbial transformation of hydrocarbons to methane is an environmentally relevant but slow process taking place in a wide variety of electron acceptor-depleted environments, from oil reservoirs and coal deposits, to contaminated groundwater and deep sediments. Despite the prevalence of chemical evidence demonstrating methanogenic hydrocarbon metabolism in field investigations, there are significant gaps in our understanding of the anaerobic activation mechanisms of model substrates (particularly monoaromatic and polycyclic aromatic hydrocarbons, PAHs) and whole crude oil, as well as the degradation pathways and microorganisms governing oil transformation to methane. By studying the chemical and functional responses of methanogenic consortia to enrichment on model and mixed hydrocarbon substrates, we can gain a more complete understanding of the fate of hydrocarbon components in electron acceptor-depleted environments. In this dissertation, we sought to characterize the biodegradation of an expanded range of hydrocarbon substrates using a series of chemical and molecular approaches. We also explored cultivation-based strategies for optimizing rates of methanogenic hydrocarbon utilization, of which the most successful methods were adopted for future cultivation studies described here. Members of the Desulfosporosinus genus, known to catalyze methanogenic toluene biodegradation, were also found to co-metabolize other alkylbenzene substrates. Other members of the Firmicutes phylum, such as Desulfotomaculum, were shown to be functionally capable of activating toluene by addition to fumarate in a crude oil-degrading produced water consortium, and are proposed to play a key role in the formation of heavy oil in petroleum reservoirs. Microbial community sequencing, DNA-based stable isotope probing, and metagenomic surveys of previously established and novel methanogenic PAH-degrading cultures suggest that Clostridium may be important for degrading larger aromatic structures by an unknown mechanism. Experimental evidence of a hypothetical energy conservation mechanism in Syntrophus was detected during alkylbenzene biodegradation, suggesting this organism plays a vital role in coordinating syntrophic hydrocarbon biodegradation in a bioenergetically favourable manner. In all, this research has gleaned new insights into the microorganisms and metabolic processes regulating methanogenic hydrocarbon biodegradation, and has produced a wealth of new research questions to be explored in future investigations.
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    Composition and activities of microbial communities in Alberta’s oil sands
    (2013-01-09) Wong, Man Ling; Voordouw, Gerrit
    Fossil fuels will probably be our main source of energy in the foreseeable future. The fossil fuel that is currently receiving the most attention is oil sands. A focus of many companies with oil sands operations is to look for more environmentally friendly and still economically feasible methods to produce this resource. This thesis focuses on determining the microbial communities in Alberta’s oil sands and their activities with the intention of eventually utilizing this information for improved production strategies. The microbial communities from oil sands outcrops, mined oil sands and oil sands cores were assessed in detail. Oil sands at different depths had diverse microbial communities, while the subsamples obtained from the same environment also displayed varied populations. All oil sands microbial communities have thermophilic genera with enhanced potential in bitumen biodegradation. The combination of oxygen, high temperatures and the absence of light was shown to greatly stimulate bitumen biodegradation.
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    Control of hydrogen sulfide production in oil fields by managing microbial communities through nitrate or nitrite addition
    (2004) Hubert, Casey R.J.; Voordouw, Gerrit
    Nitrate or nitrite injection into oil reservoirs during water flooding has the potential to control biological souring, the production of hydrogen sulfide (H2S) by sulfate-reducing bacteria (SRB). Souring control is essential because sulfide is toxic, sulfide precipitates can plug reservoir formations, souring lowers crude oil value, and SRB induce corrosion. Nitrate and nitrite can stimulate heterotrophic nitrate- or nitrite­reducing bacteria (hNRB) and nitrate- or nitrite-reducing, sulfide oxidizing bacteria (NR­SOB). Nitrite also inhibits SRB activity by blocking the sulfate reduction pathway. Continuous up-flow packed-bed bioreactors were inoculated with produced water from the Coleville oil field to establish sulfide-producing biofilms similar to those found in sour reservoirs. Nitrate or nitrite addition to bioreactors indicated that the dose required for hNRB or NR-SOB to control souring depended on the concentration of oil organics. Either mechanism mediates the net removal of oil organics (lactate) with nitrate or nitrite, with lower doses of nitrate required due to its greater oxidative power. Microbial community analysis by reverse sample genome probing (RSGP) revealed that NR-SOB mediated sulfide removal at low nitrate or nitrite concentrations when lactate was still available to SRB and the redox potential was low. At high nitrate doses hNRB oxidized lactate directly, produced nitrite and maintained a high redox potential, thus excluding SRB activity. Facultatively chemolithotrophic Campylobacter sp. strains were isolated from the bioreactors and incorporated into RSGP analyses, revealing their dominance in both NR-SOB- and hNRB-containing communities. The metabolic flexibility of these strains may confer a competitive advantage over obligate chemolithotrophs like Thiomicrospira sp. strain CVO or hNRB that do not have NR-SOB activity like newly isolated Thauera sp. and Rhodobacter sp. strains. A single high dose of nitrite resulted in immediate inhibition of SRB that was independent of hNRB or NR-SOB. Examination of corrosion coupons following bioreactor experiments revealed that nitrite inhibition was the only mechanism that prevented both souring and corrosion. Sulfide elimination by hNRB or NR-SOB resulted in increased pitting corrosion in the region of greatest microbial activity. These findings are instructive for designing souring control treatments and improve understanding of oil field microbial communities.
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    Control of Microbial Sulfide Production in Low and High Temperature Oil Field with Nitrate and Perchlorate
    (2017) Okpala, Gloria; Voordouw, Gerrit; Coates, John; Ryan, Cathryn; Gieg, Lisa; Hubert, Casey
    The activity of sulfate reducing bacteria (SRB), which produce sulfide, in low and high temperature oilfields, poses a severe challenge for oil and gas industries. Nitrate injection is used to limit the growth of SRB, through stimulation of nitrate reducing bacteria (NRB) that reduce nitrate to nitrite and subsequently to N2. Data from temperature dependent studies done in this work reveal thermophilic nitrate reducing bacteria (tNRB) isolated from low and high temperature oilfields reduce nitrate to nitrite and not further at 50°C or above. This observation is especially important for nitrate-mediated control of sulfide production in high temperature oil fields, because nitrite is a strong SRB inhibitor. To better understand how nitrate injection works in a seawater flooded high temperature reservoir, dual temperature bioreactors and multi-temperature microcosms were used in monitoring sulfate reduction by mesophilic and thermophilic NRB and SRB. The results indicated that nitrate may be ineffective when injected into a cold zone (<45°C) and that preventing emergence of such a zone by injecting hot produced water may be an effective way to control souring with nitrate. Control of souring with perchlorate under low temperature conditions in batch incubations and bioreactors containing heavy oil was also tested. Perchlorate caused a delay in the onset of sulfate reduction in batch incubations. However, its reduction with oil was not seen in batch culture incubations or bioreactors. Chlorite was more effective at inhibiting SRB activity under these conditions. The research in this thesis thus contributes to improved management of sulfide production in oil fields.
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    Control of Microbial Sulfide Production with Nitrate and Biocide in Oilfield-Simulating Bioreators
    (2015-01-28) Xue, Yuan (Fiona); Voordouw, Gerrit
    Souring, the production of sulfide by sulfate-reducing bacteria in oil fields, can be remediated by nitrate injection. However, continuous amendment of sulfate-containing injection water with nitrate leads to microbial zonation. The combination of nitrate and biocide that may break this zonation and control souring more effectively was investigated here using bioreactors injected with excess volatile fatty acids and 2 mM sulfate or 2 mM sulfate and 2 mM nitrate. Biocide was pulsed with long duration (5 days) at low concentrations or short duration (1 h) at high concentrations. The success of these strategies was determined by the time needed for sulfide recovery. The results indicated that pulsed biocide can be synergistic with continuous nitrate. However, it depends on the type of biocide, its concentration, and the length of the pulse. Hence, pulsed biocide can improve souring control with continuous nitrate injections, if the appropriate product and injection strategy are chosen.
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    Control of SRB – Mediated Microbially Influenced Corrosion in Flowing Systems
    (2016) Pinnock, Tijan; Voordouw, Gerrit; Hubert, Casey; Gieg, Lisa
    Corrosion is the major threat to oil and gas production and transportation infrastructure around the world. It is now accepted that microorganisms, especially sulfate-reducing bacteria, may play a significant role in the corrosion mechanism in many of the corrosion scenarios in the oil and gas industry. Therefore, an understanding of how to control sulfate-reducing bacteria mediated microbially influenced corrosion is key to controlling microbially influenced corrosion in the oil and gas industry. The biocorrosion threat to a steam-assisted gravity drainage operation was assessed and found to be low. The control of sulfate-reducing bacteria mediated microbially influenced corrosion in model systems involving carbon steel beads under flow was accomplished with biocides and corrosion inhibitors. While significant corrosion control was observed with biocides, oil soluble corrosion inhibitors reduced the corrosion rate by as much ninety-nine percent. These control methods had different effects on the microbial communities involved in the corrosion process.
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    Diversity of methane and short chain hydrocarbon degrading bacteria with an emphasis on methane biofilter systems
    (2018-10-03) Khadka, Roshan; Dunfield, Peter F.; Voordouw, Gerrit; Hubert, Casey R. J.
    Methanotrophs house enzymes capable of methane oxidation, act as a sink for atmospheric methane and play a key role in the global carbon cycle. This study conducted multiple studies on methanotrophs, including: examination of the evolutionary history of copper membrane monooxygenases (CuMMOs), application of methanotrophic communities in protocol design for monitoring methane biofilter systems, and the analyses of single cell genomes containing new CuMMO-encoding genes. CuMMOs are encoded by three genes, usually in an operon of xmoCAB, and oxidize ammonia, methane, and short chain alkanes and alkenes. To examine the evolutionary history of CuMMOs, phylogenetic inferences and compositional genome analyses were applied to a set of 66 genomes. Individual phylogeny of all genes xmoA, xmoB, and xmoC closely matched in almost all genomes, indicating this operon evolved as a unit. However in Verrucomicrobia pmoB has a distinct phylogeny from pmoA and pmoC. The gammaproteobacteria AMO (Nitrosococcus spp.), the gammaproteobacterial Pxm, the thaumarcheotal AMO and the NC10 pMMO showed little or no compositional bias in the xmo operon indicating similar compositional biases to its genome. Based on the analysis, possible lateral gene transfer events of xmoCAB genes were predicted. The nitrifying bacterium Nitrosococcus postulated as the donor of pmoCAB to both the alpha- and gammaproteobacterial methanotrophs. To design a monitoring protocol that would allow a simple, cost effective and accurate estimation of whether a methane biofilter is operating efficiently, microcosms using compost as a biofilter material were tested via growth and starvation experiments for long periods. Analysis of 16S rRNA gene sequences suggested that non-methanotrophic methylotrophic bacteria belonging the family Methylophilaceae showed a rapid response to biofilter methane oxidation activity and may be a good monitoring target. A monitoring system based on these “methanotroph-associated methylotrophs” is proposed and a ratio of Methylophilaceae to Methylococcaceae of 0.35 was related to high methane activity and 0.1 to low activity. Novel copper membrane monooxygenase encoding operons (xmoCAB) were detected while screening metagenomes obtained from oil sands environments. Quantitative PCR assays were developed for detection of xmoCAB genes in methane, ethane and propane enrichment cultures from environmental samples. Single cell genomes were sequenced from the xmoCAB positive sorted cells of a propane enrichment culture. Screening the genomes identified Polaromonas and Rhodoferax as containing multiple xmoCAB operons. Potential propane oxidation pathways were predicted based on enzymes present in single cell genomes of these two genera.
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    Fate of dicyclopentadiene in the environment
    (1997) Stehmeier, Lester G.; Voordouw, Gerrit
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