Methanogenic biodegradation of iso-alkanes and cycloalkanes during long-term incubation with oil sands tailings

Uncovering Anaerobic Hydrocarbon Biodegradation Pathways in Oil Sands Tailings from Two Different Tailings Ponds via Metabolite and Functional Gene Analyses

Oil sands tailings, a slurry of alkaline water, silt, clay, unrecovered bitumen, and residual hydrocarbons generated during bitumen extraction, are contained in ponds. Indigenous microbes metabolize hydrocarbons and emit greenhouse gases from the tailings. Metabolism of hydrocarbons in tailings ponds of two operators, namely, Canadian Natural Upgrading Limited (CNUL) and Canadian Natural Resources Limited (CNRL), has not been comprehensively investigated. Previous reports have revealed sequential and preferential hydrocarbon degradation of alkanes in primary cultures established from CNUL and CNRL tailings amended separately with mixtures of hydrocarbons (n-alkanes, iso-alkanes, paraffinic solvent, or naphtha). In this study, activation pathway of hydrocarbon biodegradation in these primary cultures was investigated. The functional gene analysis revealed that fumarate addition was potentially the primary activation pathway of alkanes in all cultures. However, the metabolite analysis only detected transient succinylated 2-methylpentane and 2-methylbutane metabolites during initial methanogenic biodegradation of iso-alkanes and paraffinic solvent in all CNUL and CNRL cultures amended with iso-alkanes and paraffinic solvent. Under sulfidogenic conditions (prepared only with CNUL tailings amended with iso-alkanes), succinylated 2-methylpentane persisted throughout incubation period of ~ 1100 days, implying dead-end nature of the metabolite. Though no metabolite was detected in n-alkanes- and naphtha-amended cultures during incubation, assA/masD genes related to Peptococcaceae were amplified in all CNUL and CNRL primary cultures. The findings of this present study suggest that microbial communities in different tailings ponds can biodegrade hydrocarbons through fumarate addition as activation pathway under methanogenic and sulfidogenic conditions.

Structures and diversities of bacterial communities in oil-contaminated soil at shale gas well site assessed by high-throughput sequencing

Currently, there is limited understanding of the structures and variabilities of bacterial communities in oil-contaminated soil within shale gas development. The Changning shale gas well site in Sichuan province was focused, and high-throughput sequencing was used to investigate the structures of bacterial communities and functions of bacteria in soil with different degrees of oil pollution. Furthermore, the influences of the environmental factors including pH, moisture content, organic matter, total nitrogen, total phosphorus, oil, and the biological toxicity of the soil on the structures of bacterial communities were analyzed. The results revealed that Proteobacteria and Firmicutes predominated in the oil-contaminated soil. α-Proteobacteria and γ-Proteobacteria were the main classes under the Proteobacteria phylum. Bacilli was the main class in the Firmicutes phylum. Notably, more bacteria were only found in CN-5 which was the soil near the storage pond for abandoned drilling mud, including Marinobacter, Balneola, Novispirillum, Castellaniella, and Alishewanella. These bacteria exhibited resilience to higher toxicity and demonstrated proficiency in oil degradation. The functions including carbohydrate transport and metabolism, energy metabolism, replication, recombination and repair replication, signal transduction mechanisms, and amino acid transport and metabolism responded differently to varying concentrations of oil. The disparities in bacterial genus composition across samples stemmed from a complex play of pH, moisture content, organic matter, total nitrogen, total phosphorus, oil concentration, and biological toxicity. Notably, bacterial richness correlated positively with moisture content, while bacterial diversity showed a significant positive correlation with pH. Acidobacteria exhibited a significant positive correlation with moisture content. Litorivivens and Luteimonas displayed a significant negative correlation with pH, while Rhizobium exhibited a significant negative correlation with moisture content. Pseudomonas, Proteiniphilum, and Halomonas exhibited positive correlations not only with organic matter but also with oil concentration. Total nitrogen exhibited a significant positive correlation with Taonella and Sideroxydans. On the other hand, total phosphorus showed a significant negative correlation with Sphingomonas. Furthermore, Sphingomonas, Gp6, and Ramlibacter displayed significant negative correlations with biological toxicity. The differential functions exhibited no significant correlation with environmental factors but displayed a significant positive correlation with the Proteobacteria phylum. Aridibacter demonstrated a significant positive correlation with cell motility and cellular processes and signaling. Conversely, Pseudomonas, Proteiniphilum, and Halomonas were negatively correlated with differential functions, particularly in amino acid metabolism, carbohydrate metabolism, and membrane transport. Compared with previous research, more factors were considered in this research when studying structural changes in bacterial communities, such as physicochemical properties and biological toxicity of soil. In addition, the correlations of differential functions of communities with environmental factors, bacterial phyla, and genera were investigated.

Biodegradation of 2-methylpentane in fluid fine tailings amended with a mixture of iso-alkanes under sulfate-reducing conditions

Anaerobic microorganisms in Canada Natural Upgrading Limited (CNUL) fluid fine tailings (FFT) are sustained by residual solvent hydrocarbons. Although FFT are methanogenic in nature, sulfate-reducing microorganisms represent a significant portion of FFT bacterial community. In this study, we examined biodegradation of three iso-alkanes (2-methylbutane, 2-methylpentane, and 3-methylpentane), representing major iso-alkanes in paraffinic solvent, in CNUL FFT under sulfate-reducing conditions. During ∼1100 days of incubation, only 2-methylpentane was degraded partially, whereas 2-methylbutane and 3-methylpentane were not degraded. During active degradation of 2-methylpentane, the bacterial community was dominated by Anaerolineaceae followed by Syntrophaceae, Peptococcaceae, Desulfobacteraceae, and Desulfobulbaceae. The archaeal community was co-dominated by acetoclastic (Methanosaetaceae) and hydrogenotrophic (Methanobacteriaceae) methanogens. This study underlines the limited capability of the microbial community indigenous to CNUL FFT in degrading recalcitrant iso-alkanes under sulfate-reducing conditions.

Abiotic and biotic constituents of oil sands process-affected waters

The oil sands in Northern Alberta are the largest oil sands in the world, providing an important economic resource for the Canadian energy industry. The extraction of petroleum in the oil sands begins with the addition of hot water to the bituminous sediment, generating oil sands process-affected water (OSPW), which is acutely toxic to organisms. Trillions of litres of OSPW are stored on oil sands mining leased sites in man-made reservoirs called tailings ponds. As the volume of OSPW increases, concerns arise regarding the reclamation and eventual release of this water back into the environment. OSPW is composed of a complex and heterogeneous mix of components that vary based on factors such as company extraction techniques, age of the water, location, and bitumen ore quality. Therefore, the effective remediation of OSPW requires the consideration of abiotic and biotic constituents within it to understand short and long term effects of treatments used. This review summarizes selected chemicals and organisms in these waters and their interactions to provide a holistic perspective on the physiochemical and microbial dynamics underpinning OSPW .

Mitigating methane emission from oil sands tailings using enzymatic and lime treatments

Engineering strategies to reduce greenhouse gases (GHGs) emissions by inhibiting methanogenesis in oil sands tailings have rarely been examined. In this study, we explored the potential impact of chemical treatment (lime) and biological treatment using enzymes (lysozyme and protease) on inhibiting methane emissions from tailings. Overall, treatment with protease 3%, lysozyme 3%, and lime 5000 ppm reduced CH₄ production (by 52%, 28%, and 25%, respectively) and were weakly associated with the archaeal abundance. Enzymes treatment resulted in a higher reduction in CH₄ production compared with lime treatment. A 3% lysozyme treatment suppressed CH₄ production (the change in methane was 0.48 mmol) and reduced the degradation of hexane throughout the experiment. Similarly, 3% protease suppressed CH₄ production throughout the experiment (the change in methane was 0.78 mmol), which could be attributed to the pH reduction to pH 4.9 at week 23 resulting from the formation of volatile fatty acids. Another possible mechanism could be the formation of toxic compounds, such as high nitrogen content, after protease treatment that inhibited the microbial community. The toxicity effect to Vibrio fischeri was greater with lysozyme 3% and protease 3% treatment than with lime treatment (124 TU and 76 TU, respectively). Lime treatment resulted in the highest reduction in 16S rRNA gene copies from 5.7 × 10⁶ cells g^-1 (control) to 2.7 × 10⁵, 1.71 × 10⁵, and 1.4 × 10⁵ cells g^-1 for 1600, 3500, and 5000 ppm treatments, respectively. This study supports further work to examine and determine the optimum conditions (e.g., enzyme and lime dosages) for CH₄ inhibition.

Enhanced biodegradation of oil-contaminated soil oil in shale gas exploitation by biochar immobilization

The enhanced biodegradation of oil-contaminated soil by fixing microorganisms with corn cob biochar was investigated. It was found that the components of oil in the test soil were mainly straight-chain alkanes and branched alkanes. When using corn cob biochar as a carrier to immobilize microorganisms, the best particle size of corn cob biochar as an immobilization carrier was 0.08 mm, and the best immobilization time was 18 h. SEM analysis confirmed that the microorganisms were immobilized on the corn cob biochar. Immobilized microorganisms exhibited high biodegradability under stress to high concentrations of petroleum pollutants, heavy metals, and organic pollutants. Infrared spectroscopy analysis showed that oxygen-containing groups such as hydroxyl, carboxyl, and methoxy on the surface of biochar were involved in the complexation of heavy metals. The mechanism of immobilization promoted microbial degradation of oil contamination was explained by gas chromatography mass. First, alkanes and aromatics were adsorbed by corn cob biochar and passed to immobilized microorganisms to promote their degradation. Their bioavailability increased, especially for aromatics. Second, biochar provided a more suitable environment for microorganisms to degrade. Third, the conversion of ketones to acids was accelerated during the biodegradation of alkanes, and the biodegradation of alkanes was accelerated by immobilization. The biodegradable efficiency of oil by immobilized microorganisms in soil was 70.10% within 60 days, 28.80% higher than that of free microorganisms. The degradation of immobilized microorganisms was highly correlated with the activities of catalase, urease, and polyphenol oxidase.

Insights into removal of sulfonamides in anaerobic activated sludge system: Mechanisms, degradation pathways and stress responses

The fate of antibiotics in activated sludge has attracted increasing interests. However, the focus needs to shift from concerning removal efficiencies to understanding mechanisms and sludge responding to antibiotic toxicity. Herein, we operated two anaerobic sequencing batch reactors (ASBRs) for 200 days with sulfadiazine (SDZ) and sulfamethoxazole (SMX) added. The removal efficiency of SMX was higher than that of SDZ. SDZ was removed via adsorption (9.91-21.18%) and biodegradation (10.20-16.00%), while biodegradation (65.44-86.26%) was dominant for SMX removal. The mechanisms involved in adsorption and biodegradation were investigated, including adsorption strength, adsorption sites and the roles of enzymes. Protein-like substance (tryptophan) functioned vitally in adsorption by forming complexes with sulfonamides. P450 enzymes may catalyze sulfonamides degradation via hydroxylation and desulfurization. Activated sludge showed distinct responses to different sulfonamides, reflected in the changes of microbial communities and functions. These responses were related to sulfonamides removal, corresponding to the stronger adsorption capacity of activated sludge in ASBR-SDZ and degradation capacity in ASBR-SMX. Furthermore, the reasons for different removal efficiencies of sulfonamides were analyzed according to steric and electronic effects. These findings propose insights into antibiotic removal and broaden the knowledge for self-protection mechanisms of activated sludge under chronic toxicities of antibiotics.

Ebullition enhances chemical mass transport across the tailings-water interface of oil sands pit lakes

Base Mine Lake (BML) was the first commercial-scale demonstration oil sands pit lake established in northern Alberta, Canada. Recent studies indicate that ebullition enhances internal mass loading of dissolved constituents during settlement and dewatering of methanogenic fluid fine tailings (FFT) below the overlying water cap. Here, we describe results of integrated field measurements and numerical modelling to (i) determine potential for ebullition and enhanced mixing within BML, and (ii) assess impacts on chemical mass transport across the tailings-water interface. We observed sharp increases in [CH_4(aq)] with depth from <0.1 mg L^-1 immediately above the interface to >60 mg L^-1 over the upper 1.5 to 3.0 m of FTT. Thermodynamic modelling revealed that maximum [CH_4(aq)] values represent 60 to 80% of theoretical saturation, and corresponding total dissolved gas pressures approach or exceed fluid pressures. These findings supported integration of enhanced mixing into one-dimensional (1-D) advective-dispersive transport models, which substantially improved upon previous simulations of conservative tracer (i.e., Cl^-) profiles and chemical mass fluxes. The models revealed a positive relationship between CH_4(aq) saturation and enhanced mixing, showing that ebullition enhances internal mass loading. This information has potential to inform ongoing assessments of pit lake performance and support improved closure and reclamation planning at oil sands mines.

Does Addition of Phosphate and Ammonium Nutrients Affect Microbial Activity in Froth Treatment Affected Tailings?

We examined greenhouse gas (GHG) production upon the addition of ammonium and phosphate to mature fine tailing (MFT) samples from Alberta's Pond 2/3 (at 5 and 15 m) and Pond 7 (12.5 m) in microcosm studies. The methane production rate in unamended Pond 2/3 MFT correlated with sample age; the production rate was higher in the less dense, more recently discharged MFT samples and lower in the denser, deeper sample. Adding small amounts of naphtha increased methane production, but there was no correlation with increasing naphtha, indicating that naphtha may partition into bitumen, reducing its bioavailability. Although non-detectable phosphate and low ammonium in the pore water indicate that these nutrients were potentially limiting microbial activity, their addition did not significantly affect methanogenesis but somewhat enhanced sulphate and nitrate reduction. Neither ammonium nor phosphate were detected in the pore water when added at low concentrations, but when added at high concentrations, 25-35% phosphate and 30-45% ammonium were lost. These ions likely sorbed to MFT minerals such as kaolinite, which have microbial activity governed by phosphate/ammonium desorption. Hence, multiple limitations affected microbial activity. Sulphate was less effective than nitrate was in inhibiting methanogenesis because H₂S may be a less effective inhibitor than NO_x^- intermediates are, and/or H₂S may be more easily abiotically removed. With nitrate reduction, N₂O, a potent GHG was produced but eventually metabolized.

Fugitive Emissions of Volatile Organic Compounds from a Tailings Pond in the Oil Sands Region of Alberta

Tailings ponds in the oil sands (OS) region in Alberta, Canada, have been associated with fugitive emissions of volatile organic compounds (VOCs) and other pollutants to the atmosphere. However, the contribution of tailings ponds to the total fugitive emissions of VOCs from OS operations remains uncertain. To address this knowledge gap, a field study was conducted in the summer of 2017 at Suncor's Pond 2/3 to estimate emissions of a suite of pollutants including 68 VOCs using a combination of micrometeorological methods and measurements from a flux tower. The results indicate that in 2017, Pond 2/3 was an emission source of 3322 ± 727 tons of VOCs including alkanes, aromatics, and oxygenated and sulfur-containing organics. While the total VOC emissions were approximately a factor of 2 higher than those reported by Suncor, the individual VOC species emissions varied by up to a factor of 12. A chemical mass balance (CMB) receptor model was used to estimate the contribution of the tailings pond to VOC pollution events in a nearby First Nations and Metis community in Fort McKay. CMB results indicate that Suncor Pond 2/3 contributed up to 57% to the total mass of VOCs measured at Fort McKay, reinforcing the importance of accurate VOC emission estimation methods for tailings ponds.

Geochemical Stability of Oil Sands Tailings in Mine Closure Landforms

Oil sands surface mining in Alberta has generated over a billion cubic metres of waste, known as tailings, consisting of sands, silts, clays, and process-affected water that contains toxic organic compounds and chemical constituents. All of these tailings will eventually be reclaimed and integrated into one of two types of mine closure landforms: end pit lakes (EPLs) or terrestrial landforms with a wetland feature. In EPLs, tailings deposits are capped with several metres of water while in terrestrial landforms, tailings are capped with solid materials, such as sand or overburden. Because tailings landforms are relatively new, past research has heavily focused on the geotechnical and biogeochemical characteristics of tailings in temporary storage ponds, referred to as tailings ponds. As such, the geochemical stability of tailings landforms remains largely unknown. This review discusses five mechanisms of geochemical change expected in tailings landforms: consolidation, chemical mass loading via pore water fluxes, biogeochemical cycling, polymer degradation, and surface water and groundwater interactions. Key considerations and knowledge gaps with regard to the long-term geochemical stability of tailings landforms are identified, including salt fluxes and subsequent water quality, bioremediation and biogenic greenhouse gas emissions, and the biogeochemical implications of various tailings treatment methods meant to improve geotechnical properties of tailings, such as flocculant (polyacrylamide) and coagulant (gypsum) addition.

Methanogenic Biodegradation of iso-Alkanes by Indigenous Microbes from Two Different Oil Sands Tailings Ponds

iso-Alkanes, a major fraction of the solvents used in bitumen extraction from oil sand ores, are slow to biodegrade in anaerobic tailings ponds. We investigated methanogenic biodegradation of iso-alkane mixtures comprising either three (2-methylbutane, 2-methylpentane, 3-methylpentane) or five (2-methylbutane, 2-methylpentane, 2-methylhexane, 2-methylheptane, 2-methyloctane) iso-alkanes representing paraffinic and naphtha solvents, respectively. Mature fine tailings (MFT) collected from two tailings ponds, having different residual solvents (paraffinic solvent in Canadian Natural Upgrading Limited (CNUL) and naphtha in Canadian Natural Resources Limited (CNRL)), were amended separately with the two mixtures and incubated in microcosms for ~1600 d. The indigenous microbes in CNUL MFT produced methane from the three-iso-alkane mixture after a lag of ~200 d, completely depleting 2-methylpentane while partially depleting 2-methylbutane and 3-methylpentane. CNRL MFT exhibited a similar degradation pattern for the three iso-alkanes after a lag phase of ~700 d, but required 1200 d before beginning to produce methane from the five-iso-alkane mixture, preferentially depleting components in the order of decreasing carbon chain length. Peptococcaceae members were key iso-alkane-degraders in both CNUL and CNRL MFT but were associated with different archaeal partners. Co-dominance of acetoclastic (Methanosaeta) and hydrogenotrophic (Methanolinea and Methanoregula) methanogens was observed in CNUL MFT during biodegradation of three-iso-alkanes whereas CNRL MFT was enriched in Methanoregula during biodegradation of three-iso-alkanes and in Methanosaeta with five-iso-alkanes. This study highlights the different responses of indigenous methanogenic microbial communities in different oil sands tailings ponds to iso-alkanes.

A Deep Look into the Microbiology and Chemistry of Froth Treatment Tailings: A Review

In Alberta’s Athabasca oil sands region (AOSR), over 1.25 billion m³ of tailings waste from the bitumen extraction process are stored in tailings ponds. Fugitive emissions associated with residual hydrocarbons in tailings ponds pose an environmental concern and include greenhouse gases (GHGs), reduced sulphur compounds (RSCs), and volatile organic compounds (VOCs). Froth treatment tailings (FTT) are a specific type of tailings waste stream from the bitumen froth treatment process that contains bioavailable diluent: either naphtha or paraffins. Tailings ponds that receive FTT are associated with the highest levels of biogenic gas production, as diverse microbial communities biodegrade the residual diluent. In this review, current literature regarding the composition, chemical analysis, and microbial degradation of FTT and its constituents is presented in order to provide a more complete understanding of the complex chemistry and biological processes related to fugitive emissions from tailings ponds receiving FTT. Characterizing the composition and biodegradation of FTT is important from an environmental perspective to better predict emissions from tailings ponds and guide tailings pond management decisions.

Anaerobic degradation of xenobiotic organic contaminants (XOCs): The role of electron flow and potential enhancing strategies

In groundwater, deep soil layer, sediment, the widespread of xenobiotic organic contaminants (XOCs) have been leading to the concern of human health and eco-environment safety, which calls for a better understanding on the fate and remediation of XOCs in anoxic matrices. In the absence of oxygen, bacteria utilize various oxidized substances, e.g. nitrate, sulphate, metallic (hydr)oxides, humic substance, as terminal electron acceptors (TEAs) to fuel anaerobic XOCs degradation. Although there have been increasing anaerobic biodegradation studies focusing on species identification, degrading pathways, community dynamics, systematic reviews on the underlying mechanism of anaerobic contaminants removal from the perspective of electron flow are limited. In this review, we provide the insight on anaerobic biodegradation from electrons aspect - electron production, transport, and consumption. The mechanism of the coupling between TEAs reduction and pollutants degradation is deconstructed in the level of community, pure culture, and cellular biochemistry. Hereby, relevant strategies to promote anaerobic biodegradation are proposed for guiding to an efficient XOCs bioremediation.

Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review

Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C₁₀ alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.