The microbiology of oil sands tailings: past, present, future

A multi-step approach: Coupling of biodegradation and UV photocatalytic oxidation TiO2 for the treatment of naphthenic acid fraction compounds in oil sands process-affected water

Bitumen extraction in Alberta's oil sands region uses large volumes of water, leading to an abundance of oil sands process-affected water (OSPW). OSPW contains naphthenic acid fraction compounds (NAFCs) which have been found to contribute to OSPW toxicity. This study utilized a multistep treatment, coupling biological degradation with UV photocatalytic oxidation, and nutrient addition to boost the native microbial community's degradation capacity. OSPW initially contained 40-42 mg/L NAFCs with a toxicity of 3.8-3.9 TU. Initial biodegradation (Step 1) was used to remove the easily biodegradable NAFCs (11-25% removal), followed by a light or heavy dose of oxidation (Step 2) to breakdown the recalcitrant NAFCs (66-82% removal). Lastly, post-oxidation biodegradation with nutrients (Step 3) removed the residual bioavailable NAFCs (16-31% removal). By the end of the multistep treatment, the final NAFC concentrations and toxicity ranged from 5.3 to 6.8 mg/L and 1.1-1.2 TU. Analysis showed that OPSW was limited in phosphorus (below detection limit), and the addition of nutrients improved the degradation of NAFCs. Two treatments throughout the multistep treatment never received nutrients and showed minimal NAFC degradation post-oxidation. The native microbial community survived the stress from UV photocatalytic oxidation as seen by the post-oxidation NAFC biodegradation. Microbial community diversity was reduced considerably following oxidation, but increased with nutrient addition. The microbial community consisted predominately of Proteobacteria (Gammaproteobacteria and Alphaproteobacteria), and the composition shifted depending on the level of oxidation received. Possible NAFC-degrading microbes identified after a light oxidation dose included Pseudomonas, Acinetobacter and Xanthomonadales, while Xanthobacteracea and Rhodococcus were the dominant microbes after heavy oxidation. This experiment confirms that the microbial community is capable of degrading NAFCs and withstanding oxidative stress, and that degradation is further enhanced with the addition of nutrients.

Phytoplankton ecology in the early years of a boreal oil sands end pit lake

BACKGROUND

Base Mine Lake (BML) is the first full-scale end pit lake for the oil sands mining industry in Canada. BML sequesters oil sands tailings under a freshwater cap and is intended to develop into a functional ecosystem that can be integrated into the local watershed. The first stage of successful reclamation requires the development of a phytoplankton community supporting a typical boreal lake food web. To assess the diversity and dynamics of the phytoplankton community in BML at this reclamation stage and to set a baseline for future monitoring, we examined the phytoplankton community in BML from 2016 through 2021 using molecular methods (targeting the 23S, 18S, and 16S rRNA genes) and microscopic methods. Nearby water bodies were used as controls for a freshwater environment and an active tailings pond.

RESULTS

The phytoplankton community was made up of diverse bacteria and eukaryotes typical of a boreal lake. Microscopy and molecular data both identified a phytoplankton community comparable at the phylum level to that of natural boreal lakes, dominated by Chlorophyta, Cryptophyta, and Cyanophyta, with some Bacillariophyta, Ochrophyta, and Euglenophyta. Although many of the same genera were prominent in both BML and the control freshwater reservoir, there were differences at the species or ASV level. Total diversity in BML was also consistently lower than the control freshwater site, but consistently higher than the control tailings pond. The phytoplankton community composition in BML changed over the 5-year study period. Some taxa present in 2016-2019 (e.g., Choricystis) were no longer detected in 2021, while some dinophytes and haptophytes became detectable in small quantities starting in 2019-2021. Different quantification methods (qPCR analysis of 23S rRNA genes, and microscopic estimates of populations and total biomass) did not show a consistent directional trend in total phytoplankton over the 5-year study, nor was there any consistent increase in phytoplankton species diversity. The 5-year period was likely an insufficient time frame for detecting community trends, as phytoplankton communities are highly variable at the genus and species level.

CONCLUSIONS

BML supports a phytoplankton community composition somewhat unique from control sites (active tailings and freshwater lake) and is still changing over time. However, the most abundant genera are typical of natural boreal lakes and have the potential to support a complex aquatic food web, with many of its identified major phytoplankton constituents known to be primary producers in boreal lake environments.

Complete genome sequence of Pseudomonas veronii strain OST1911 isolated from oil sand tailing pond water in Alberta, Canada

Here, we report the complete genome sequence of Pseudomonas veronii strain OST1911, recovered from oil sand process-affected water accumulated in tailing ponds. This water contains numerous organic and inorganic compounds of environmental significance. The genome size is 6,435,955 bp with a G+C content of 61.21%.

An optimized extraction and gas chromatography analysis method for the quantification of diluent hydrocarbons in froth treatment tailings

Froth treatment tailings are one type of waste stream generated during the extraction of surface-mined oil sands bitumen. To remove water and solids from bitumen froth recovered during the water-based extraction process, hydrocarbon diluent is added, and settling and/or centrifugation are applied to the diluted bitumen froth, producing diluted bitumen and froth treatment tailings. While recovery processes are in place to remove and recycle the diluent from froth treatment tailings, some residual diluent can remain. Since tailings are stored in outdoor ponds, the residual diluent can have implications for methanogenic microbial processes and resulting greenhouse gas emissions. This work presents a methodology to accurately extract and quantify diluent hydrocarbons from froth treatment tailings using gas chromatography. A cold-start temperature program is used to separate diluent hydrocarbons from any residual bitumen in the sample, and diluent is quantified using commercial standards as well as unprocessed diluent. A series of extraction parameters were tested and results from multiple conditions are shown with a rationale for the selected optimized parameters. Quantification of diluent in tailings samples is demonstrated from 60 to 5329 μg/g, and results from quality control standards show an average diluent recovery of 100 ± 10%.

Microbial communities inhabiting shallow hydrothermal vents as sentinels of acidification processes

Introduction

Shallow hydrothermal vents are considered natural laboratories to study the effects of acidification on biota, due to the consistent CO2 emissions with a consequent decrease in the local pH.

Methods

Here the microbial communities of water and sediment samples from Levante Bay (Vulcano Island) with different pH and redox conditions were explored by Next Generation Sequencing techniques. The taxonomic structure was elucidated and compared with previous studies from the same area in the last decades.

Results and discussion

The results revealed substantial shifts in the taxonomic structure of both bacterial and archaeal communities, with special relevance in the sediment samples, where the effects of external parameters probably act for a long time. The study demonstrates that microbial communities could be used as indicators of acidification processes, by shaping the entire biogeochemical balance of the ecosystem in response to stress factors. The study contributes to understanding how much these communities can tell us about future changes in marine ecosystems.

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.

Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species

The oil sands mining operations in Alberta have produced billions of m³ of tailings which must be reclaimed and integrated into various mine closure landforms, including terrestrial landforms. Microorganisms play a central role in nutrient cycling during the reclamation of disturbed landscapes, contributing to successful vegetation restoration and long-term sustainability. However, microbial community succession and response in reconstructed and revegetated tailings remain largely unexplored. This study aimed to monitor the structural and functional responses of microbial communities in tailings subjected to different capping and vegetation strategies over two growing seasons (GS). To achieve this, a column-based greenhouse experiment was conducted to investigate microbial communities in tailings that were capped with a layer (10 or 30 cm) of peat-mineral mix (PMM) and planted with either upland or wetland communities. DNA metabarcoding analysis of the bacterial 16S rRNA gene and fungal ITS2 region as well as shotgun metagenomics were used to asses the impact of treatments on microbial taxonomy and functions, respectively. Results showed that tailings microbial diversity and community composition changed considerably after two GS compared to baseline samples, while communities in the PMM capping layer were much more stable. Likewise, several microbial functions were significantly enriched in tailings after two GS. Interestingly, the impact of capping on bacterial communities in tailings varied depending on the plant community, leading to a higher number of differentially abundant taxa and to a decrease in Shannon diversity and evenness in the upland treatment but not in the wetland treatment. Moreover, while capping in the presence of wetland vegetation increased the energy-related metabolic functions (carbon, nitrogen, and sulfur), these functions were depleted by capping in the upland treatment. Fungi represented a small proportion of the microbial community in tailings, but the relative abundance of several taxa changed over time, while the capping treatments favored the growth of some beneficial taxa, notably the root endophyte Serendipita, in both upland and wetland columns. The results suggest that selecting the right combination of capping material and vegetation type may contribute to improve below-ground microbial processes and sustain plant growth in harsh environments such as oil sands tailings.

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 .

Alum Addition Triggers Hypoxia in an Engineered Pit Lake

Here, we examine the geobiological response to a whole-lake alum (aluminum sulfate) treatment (2016) of Base Mine Lake (BML), the first pilot-scale pit lake established in the Alberta oil sands region. The rationale for trialing this management amendment was based on its successful use to reduce internal phosphorus loading to eutrophying lakes. Modest increases in water cap epilimnetic oxygen concentrations, associated with increased Secchi depths and chlorophyll-a concentrations, were co-incident with anoxic waters immediately above the fluid fine tailings (FFT) layer post alum. Decreased water cap nitrate and detectable sulfide concentrations, as well as increased hypolimnetic phospholipid fatty acid abundances, signaled greater anaerobic heterotrophic activity. Shifts in microbial community to groups associated with greater organic carbon degradation (i.e., SAR11-LD12 subclade) and the SRB group Desulfuromonodales emerged post alum and the loss of specialist groups associated with carbon-limited, ammonia-rich restricted niches (i.e., MBAE14) also occurred. Alum treatment resulted in additional oxygen consumption associated with increased autochthonous carbon production, watercap anoxia and sulfide generation, which further exacerbate oxygen consumption associated with on-going FFT mobilized reductants. The results illustrate the importance of understanding the broader biogeochemical implications of adaptive management interventions to avoid unanticipated outcomes that pose greater risks and improve tailings reclamation for oil sands operations and, more broadly, the global mining sector.

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.

Isotopic and Chemical Assessment of the Dynamics of Methane Sources and Microbial Cycling during Early Development of an Oil Sands Pit Lake

Water-capped tailings technology (WCTT) is a key component of the reclamation strategies in the Athabasca oil sands region (AOSR) of northeastern Alberta, Canada. The release of microbial methane from tailings emplaced within oil sands pit lakes, and its subsequent microbial oxidation, could inhibit the development of persistent oxygen concentrations within the water column, which are critical to the success of this reclamation approach. Here, we describe the results of a four-year (2015-2018) chemical and isotopic (δ¹³C) investigation into the dynamics of microbial methane cycling within Base Mine Lake (BML), the first full-scale pit lake commissioned in the AOSR. Overall, the water-column methane concentrations decreased over the course of the study, though this was dynamic both seasonally and annually. Phospholipid fatty acid (PLFA) distributions and δ¹³C demonstrated that dissolved methane, primarily input via fluid fine tailings (FFT) porewater advection, was oxidized by the water column microbial community at all sampling times. Modeling and under-ice observations indicated that the dissolution of methane from bubbles during ebullition, or when trapped beneath ice, was also an important source of dissolved methane. The addition of alum to BML in the fall of 2016 impacted the microbial cycling in BML, leading to decreased methane oxidation rates, the short-term dominance of a phototrophic community, and longer-term shifts in the microbial community metabolism. Overall, our results highlight a need to understand the dynamic nature of these microbial communities and the impact of perturbations on the associated biogeochemical cycling within oil sands pit lakes.

Seasonal dynamics of methanotrophic bacteria in a boreal oil sands end-pit lake

Base Mine Lake (BML) is the first full-scale demonstration end pit lake for the oil sands mining industry in Canada. We examined aerobic methanotrophic bacteria over all seasons for five years in this dimictic lake. Methanotrophs comprised up to 58% of all bacterial reads in 16S rRNA gene amplicon sequencing analyses (median 2.8%), and up to 2.7 × 10⁴ cells mL^-1 of water (median 0.5 × 10³) based on qPCR of pmoA genes. Methanotrophic activity and populations in the lake water were highest during fall turnover, and remained high through the winter ice-covered period into spring turnover. They declined during summer stratification, especially in the epilimnion. Three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus) cycled seasonally, based on both relative and absolute abundance measurements. Methylobacter and Methylovulum populations peaked in winter/spring, when methane oxidation activity was psychrophilic. Methyloparacoccus populations increased in the water column through summer and fall, when methane oxidation was mesophilic, and also predominated in the underlying tailings sediment. Other, less abundant genera grew primarily during summer, possibly due to distinct CH₄/O₂ microniches created during thermal stratification. These data are consistent with temporal and spatial niche differentiation based on temperature, CH₄ and O₂. This pit lake displays methane cycling and methanotroph population dynamics similar to natural boreal lakes. Importance statement: The study examined methanotrophic bacteria in an industrial end pit lake, combining molecular DNA methods (both quantitative and descriptive) with biogeochemical measurements. The lake was sampled over 5 years, in all four seasons, as often as weekly, and included sub-ice samples. The resulting multi-season and multi-year dataset is unique in its size and intensity, and allowed us to document clear and consistent seasonal patterns of growth and decline of three methanotroph genera (Methylobacter, Methylovulum, and Methyloparacoccus). Laboratory experiments suggested that one major control of this succession was niche partitioning based on temperature. The study helps to understand microbial dynamics in engineered end-pit lakes, but we propose that the dynamics are typical of boreal stratified lakes, and widely applicable in microbial ecology and limnology. Methane oxidising bacteria are important model organisms in microbial ecology, and have implications for global climate change.

Transcriptome Analysis of Environmental Pseudomonas Isolates Reveals Mechanisms of Biodegradation of Naphthenic Acid Fraction Compounds (NAFCs) in Oil Sands Tailings

Naphthenic acid fraction compounds (NAFCs) are highly recalcitrant constituents of oil sands tailings. Although some microorganisms in the tailings can individually and synergistically metabolize NAFCs, the biochemical mechanisms that underpin these processes are hitherto unknown. To this end, we isolated two microorganisms, Pseudomonas protegens and Pseudomonas putida, from oils sands tailings and analyzed their transcriptomes to shed light on the metabolic processes employed by them to degrade and detoxify NAFCs. We identified 1048, 521 and 1434 genes that are upregulated in P. protegens, P. putida and a 1:1 co-culture of the strains, respectively. We subsequently enumerated the biochemical activities of enriched genes and gene products to reveal the identities of the enzymes that are associated with NAFC degradation. Separately, we analyzed the NAFCs that are degraded by the two pseudomonads and their 1:1 co-culture and determined the composition of the molecules using mass spectrometry. We then compared these molecular formulas to those of the cognate substrates of the enriched enzymes to chart the metabolic network and understand the mechanisms of degradation that are employed by the microbial cultures. Not only does the consortium behave differently than the pure cultures, but our analysis also revealed the mechanisms responsible for accelerated rate of degradation of NAFCs by the co-culture. Our findings provide new directions for engineering or evolving microorganisms and their consortia for degrading NAFCs more stably and aggressively.

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.

Salt selected for hydrocarbon-degrading bacteria and enhanced hydrocarbon biodegradation in slurry bioreactors

Hydrocarbon and salt contamination of surface and groundwater resources often co-occur from oil production activities. However, salt is often considered as a potential inhibitor of microbial activity. The feasibility of microbiome-based biotechnologies to treat the hydrocarbon contamination is contingent on the ability of the indigenous community to adapt to saline conditions. Here, we demonstrate enhanced hydrocarbon biodegradation in soil slurries under saline conditions of up to ~1 M (5%) compared to non-saline systems and the underlying causes. The mineralization extent of hexadecane was enhanced by salinity in the absence of nutrients. Salinity, similar to nutrients, enhanced the mineralization but through ecological selection. Microbial community analysis indicated a significant enrichment of Actinobacteria phylum and an increase in the absolute abundance of the hydrocarbon-degrading Dietzia genus, but a decrease in the total population size with salinity. Moreover, the in situ expression of alkane hydroxylases genes of Dietzia was generally increased with salinity. The data demonstrate that indigenous halotolerant hydrocarbon degraders were enriched, and their hydrocarbon degradation genes upregulated under saline conditions. These findings have positive implications for engineered biotreatment approaches for hydrocarbons in saline environments such as those affected with produced waters and oil sands tailing ponds.

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing

Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.

Bacterial diversity in petroleum coke based biofilters treating oil sands process water

Adopting nature-based solutions for the bioremediation of oil sands process water (OSPW) is of significant interest, which requires a thorough understanding of how bacterial communities behave within treatment systems operated under natural conditions. This study investigates the OSPW remediation potential of delayed petroleum-coke (PC), which is a byproduct of bitumen upgrading process and is readily available at oil refining sites, in fixed-bed biofilters particularly for the degradation of naphthenic acids (NAs) and aromatics. The biofilters were operated continuously and total and active bacterial communities were studied by DNA and RNA-based amplicon sequencing in a metataxonomic fashion to extrapolate the underlying degradation mechanisms. The results of total community structure indicated a high abundance of aerobic bacteria at all depths of the biofilter, e.g., Porphyrobacter, Legionella, Pseudomonas, Planctomyces. However, redox conditions within the biofilters were anoxic (-153 to -182 mV) that selected anaerobic bacteria to actively participate in the remediation of OSPW, i.e., Ruminicoccus, Eubacterium, Faecalibacterium, Dorea. After 15 days of operation, the removal of classical NAs was recorded up to 20% whereas oxidized NAs species were poorly removed, i.e., O₃-NAs: 4.8%, O₄-NAs: 1.2%, O₅-NAs: 1.7%, and O₆-NAs: 0.5%. Accordingly, monoaromatics, diaromatics, and triaromatics were removed up to 16%, 22%, and 15%, respectively. The physiology of the identified genera suggested that the degradation in the PC-based biofilters was most likely proceeded in a scheme similar to beta-oxidation during anaerobic digestion process. The presence of hydrogenotrophic methanogens namely Methanobrevibacter and Methanomassiliicoccus and quantification of mcrA gene (2.4 × 10² to 8.7 × 10² copies/mg of PC) revealed that methane production was likely occurring in a syntrophic mechanism during the OSPW remediation. A slight reduction in toxicity was also observed. This study suggests that PC-based biofilters may offer some advantages in the remediation of OSPW; however, the production of methane could be of future concerns if operated at field-scale.

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.

Persulfate Oxidation Coupled with Biodegradation by Pseudomonas fluorescens Enhances Naphthenic Acid Remediation and Toxicity Reduction

The extraction of bitumen from the Albertan oilsands produces large amounts of oil sands process-affected water (OSPW) that requires remediation. Classical naphthenic acids (NAs), a complex mixture of organic compounds containing O₂^- species, are present in the acid extractable organic fraction of OSPW and are a primary cause of acute toxicity. A potential remediation strategy is combining chemical oxidation and biodegradation. Persulfate as an oxidant is advantageous, as it is powerful, economical, and less harmful towards microorganisms. This is the first study to examine persulfate oxidation coupled to biodegradation for NA remediation. Merichem NAs were reacted with 100, 250, 500, and 1000 mg/L of unactivated persulfate at 21 °C and 500 and 1000 mg/L of activated persulfate at 30 °C, then inoculated with Pseudomonas fluorescens LP6a after 2 months. At 21 °C, the coupled treatment removed 52.8-98.9% of Merichem NAs, while 30 °C saw increased removals of 99.4-99.7%. Coupling persulfate oxidation with biodegradation improved removal of Merichem NAs and chemical oxidation demand by up to 1.8× and 6.7×, respectively, and microbial viability was enhanced up to 4.6×. Acute toxicity towards Vibrio fischeri was negatively impacted by synergistic interactions between the persulfate and Merichem NAs; however, it was ultimately reduced by 74.5-100%. This study supports that persulfate oxidation coupled to biodegradation is an effective and feasible treatment to remove NAs and reduce toxicity.

Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River

Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilm, suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the level of phyla, different niche communities were highly similar to one another and across locations. However, there were significant differences in the abundance of specific genera amongst different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though "suspended load" communities collected by any means remained stably diverse across locations. Though there was influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.

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.

Energy and carbon fluxes from an oil sands pit lake

Currently, post-mining landscape plans in the Athabasca Oil Sand Region include large watersheds terminating in pit lakes. In 2012, Base Mine Lake (BML), was constructed with the aim of demonstrating technologies associated with lake reclamation in the region. This paper examines the first 6.5 years of lake-atmosphere energy and carbon exchange. Energetically, BML behaved similar to other northern lakes, storing large quantities of heat in the spring and releasing it in the fall as sensible and latent heat fluxes. At various times a hydrocarbon sheen formed on the lake, which may have suppressed evaporation. However, simple linear relationships failed to statistically quantify the impacts and more comprehensive modelling of the variability may be required. At daily scales, variability in evaporation was well explained by the product of vapour pressure deficit and wind speed as well as the available energy (R² = 0.74), while sensible heat was explained by the product of wind speed and the difference in air and surface temperature as well as available energy (R² = 0.85). Spring CH₄ fluxes were high, particularly around ice melt, with a maximum flux of 3.3 g m^-2 day^-1. Otherwise fluxes were low, except during irregular periods. The peak flux of these periods occurred following ~58 h of continuously falling pressure, relating cyclone activity to these large periods of methane emissions. Annually, CO₂ and CH₄ fluxes were initially high, with median fluxes of 231 mg CO₂ m^-2 h^-1 and 23 mg CH₄ m^-2 h^-1 in 2014. However, the median fluxes reduced quickly and over the least three years of the study (2017 through 2019) the median fluxes declined to 36 mg CO₂ m^-2 h^-1 and 10 mg CH₄ m^-2 h^-1. Overall, BML behaves similar to other boreal lake ecosystems with above average carbon fluxes compared to other constructed reservoirs.

Oil sands process affected water sourced Trichoderma harzianum demonstrates capacity for mycoremediation of naphthenic acid fraction compounds

Development of Alberta's oil sands requires large volumes of water, leading to the abundance of oil sands process affected water (OSPW) that must be remediated prior to discharge or reuse. OSPW contains a variety of dissolved organic compounds, however naphthenic acids (NAs) have been found to contribute significantly to the toxicity of OSPW. A fungus, Trichoderma harzianum, isolated directly from OSPW, has previously demonstrated a high tolerance and capacity for growth in the presence of commercial NAs. This study conducted microcosm experiments to elucidate and characterize the capacity of T. harzianum to degrade labile commercial NAs (Merichem), and OSPW-sourced naphthenic acid fraction compounds (NAFCs). Additionally, two model NA compounds, the simple single ring cyclohexane carboxylic acid (CHCA) and complex diamondoid 1-adamanatane carboxylic acid (ADA), were utilized to determine the influence of NA structure on degradation. T. harzianum degraded 14% of CHCA, 13% of ADA, and 23-47% of Merichem NAs. Additionally, Orbitrap mass spectrometry revealed a large change in Z-series within NAFCs. This removal and shift in composition correlated to a 59% and 52% drop in toxicity as per Microtox, for Merichem NAs and NAFCs respectively. This proof of concept experiment confirms that the fungal species T. harzianum can contribute to the biodegradation of complex dissolved organics found in OSPW, including cyclic and diamondoid structures.

Waste Containment Ponds Are a Major Source of Secondary Organic Aerosol Precursors from Oil Sands Operations

The surface mining and bitumen extraction of oil sands (OS) generates over one million barrels of heavy oil each day in the Alberta Oil Sands Region of Canada. Recent observations suggest that emissions from OS development contribute to secondary organic aerosol (SOA) formation, but the chemical composition, mass fluxes, and sources of those emissions are poorly delineated. Here, we simulated OS extraction and used comprehensive two-dimensional gas chromatography to quantify and characterize direct air emissions, bitumen froth, residual wastewater, and tailings components, ultimately enabling fate modeling of over 1500 chromatographic features simultaneously. During the non-ice cover season, tailings ponds emissions contributed 15 000-72 000 metric tonnes of hydrocarbon SOA precursors, translating to 3000-13 000 tonnes of SOA, whereas direct emissions during the extraction process itself were notably smaller (960 ± 500 tonnes SOA yr^-1). These results suggest that tailings pond waste management practices should be targeted to reduce environmental emissions.

Engineering Microbes for Remediation of Oil Sands Tailings

Synthetic biology and adaptive laboratory evolution are key tools for developing biotechnology platforms for the remediation of oil sands tailings. However, field deployment and subsequent regulation of engineered and/or evolved strains is rife with uncertainties and risks. Here, we detail an innovation strategy to derisk and deploy engineered bioremediation platforms.

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

Microbes indigenous to oil sands tailings ponds methanogenically biodegrade certain hydrocarbons, including n-alkanes and monoaromatics, whereas other hydrocarbons such as iso- and cycloalkanes are more recalcitrant. We tested the susceptibility of iso- and cycloalkanes to methanogenic biodegradation by incubating them with mature fine tailings (MFT) collected from two depths (6 and 31 m below surface) of a tailings pond, representing different lengths of exposure to hydrocarbons. A mixture of five iso-alkanes and three cycloalkanes was incubated with MFT for 1700 d. Iso-alkanes were completely biodegraded in the order 3-methylhexane > 4-methylheptane > 2-methyloctane > 2-methylheptane, whereas 3-ethylhexane and ethylcyclopentane were only partially depleted and methylcyclohexane and ethylcyclohexane were not degraded during incubation. Pyrosequencing of 16S rRNA genes showed enrichment of Peptococcaceae (Desulfotomaculum) and Smithella in amended cultures with acetoclastic (Methanosaeta) and hydrogenotrophic methanogens (Methanoregula and Methanoculleus). Bioaugmentation of MFT by inoculation with MFT-derived enrichment cultures reduced the lag phase before onset of iso-alkane and cycloalkane degradation. However, the same enrichment culture incubated without MFT exhibited slower biodegradation kinetics and less CH₄ production, implying that the MFT solid phase (clay minerals) enhanced methanogenesis. These results help explain and predict continued emissions of CH₄ from oil sands tailings repositories in situ.

Diagnostic Ratio Analysis: A New Concept for the Tracking of Oil Sands Process-Affected Water Naphthenic Acids and Other Water-Soluble Organics in Surface Waters

A diagnostic ratio forensics tool, similar to that recognized internationally for oil spill source identification, is proposed for use in conjunction with existing LC/QToF quantitative methodology for bitumen-derived water-soluble organics (WSOs). The concept recognizes that bitumen WSOs bear a chemical skeletal relationship to stearane and hopane oil biomarkers. The method uses response ratios for 50 selected WSOs compared between samples by their relative percent difference and adopted acceptance criteria. Oil sands process-affected water (OSPW) samples from different locations within a single tailings pond were shown to match, while those from different industrial sites did not. Acid extractable organic samples collected over 3 weeks from the same location within a single tailings pond matched with each other; as did temporal OSPW samples a year apart. Blind quality assurance samples of OSPW diluted in surface waters were positively identified to their corresponding OSPW source. No interferences were observed from surface waters, and there was no match between bitumen-influenced groundwater and OSPW samples, as expected for different sources. Proof of concept for OSPW source identification using diagnostic ratios was demonstrated, with anticipated application in the tracking of OSPW plumes in surface receiving waters, together with the potential for confirmation of source.

Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria

Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. This study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.

Second-generation stoichiometric mathematical model to predict methane emissions from oil sands tailings

Microbial metabolism of fugitive hydrocarbons produces greenhouse gas (GHG) emissions from oil sands tailings ponds (OSTP) and end pit lakes (EPL) that retain fluid tailings from surface mining of oil sands ores. Predicting GHG production, particularly methane (CH₄), would help oil sands operators mitigate tailings emissions and may assist regulators evaluating the trajectory of reclamation scenarios. Using empirical datasets from laboratory incubation of OSTP sediments with pertinent hydrocarbons, we developed a stoichiometric model for CH₄ generation by indigenous microbes. This model improved on previous first-approximation models by considering long-term biodegradation kinetics for 18 relevant hydrocarbons from three different oil sands operations, lag times, nutrient limitations, and microbial growth and death rates. Laboratory measurements were used to estimate model parameter values and to validate the new model. Goodness of fit analysis showed that the stoichiometric model predicted CH₄ production well; normalized mean square error analysis revealed that it surpassed previous models. Comparison of model predictions with field measurements of CH₄ emissions further validated the new model. Importantly, the model also identified in-situ parameters that are currently lacking but are needed to enable future robust modeling of CH₄ production from OSTP and EPL in-situ.

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake

Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria “MBAE14.” While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO₂-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

Phylogenetic Estimation of Community Composition and Novel Eukaryotic Lineages in Base Mine Lake: An Oil Sands Tailings Reclamation Site in Northern Alberta

Reclamation of anthropogenically impacted environments is a critical issue worldwide. In the oil sands extraction industry of Alberta, reclamation of mining-impacted areas, especially areas affected by tailings waste, is an important aspect of the mining life cycle. A reclamation technique currently under study is water-capping, where tailings are capped by water to create an end-pit lake (EPL). Base Mine Lake (BML) is the first full-scale end-pit lake in the Alberta oil sands region. In this study, we sequenced eukaryotic 18S rRNA genes recovered from 92 samples of Base Mine Lake water in a comprehensive sampling programme covering the ice-free period of 2015. The 565 operational taxonomic units (OTUs) generated revealed a dynamic and diverse community including abundant Microsporidia, Ciliata and Cercozoa, though 41% of OTUs were not classifiable below the phylum level by comparison to 18S rRNA databases. Phylogenetic analysis of five heterotrophic phyla (Cercozoa, Fungi, Ciliata, Amoebozoa and Excavata) revealed substantial novel diversity, with many clusters of OTUs that were more similar to each other than to any reference sequence. All of these groups are entirely or mostly heterotrophic, as a relatively small number of definitively photosynthetic clades were amplified from the BML samples.

Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight

Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world’s largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.

Indigenous microorganisms residing in oil sands tailings biodegrade residual bitumen

The purpose of this study was to determine the capacity of indigenous microbes in tailings to degrade bitumen aerobically, and if acetate biostimulation further improved degradation. Fluid fine tailings, from Base Mine Lake (BML), were used as microbial inocula, and bitumen in the tailings served as a potential carbon source during the experiment. The tailings were capped with 0.22 μm-filtered BML surface water with or without BML bitumen and acetate addition and incubated for 100 days at 20 °C. CO₂ production and petroleum hydrocarbon reductions (50-70% for the biostimulation treatment) in the tailings were observed. DNA was extracted directly from the tailings, and increased bacterial density was observed by qPCR targeting the rpoB gene in the biostimulated group. 16 S rRNA sequencing was used to determine microbial composition profiles in each treatment group. The microbial communities indigenous to the tailings shifted after the bitumen was added. Acidovorax, Rhodoferax, Pseudomonas and Pseudoxanthomonas spp. significantly increased compared to the original microbial community and demonstrated tolerance to bitumen-based toxicity. The first three genera showed more potential for biostimulation treatment with acetate and may be important bitumen/hydrocarbon-degraders in an oil sands end pit lake environment.

Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond

Oil sands process-affected water (OSPW), produced by surface-mining of oil sands in Canada, is alkaline and contains high concentrations of salts, metals, naphthenic acids, and polycyclic aromatic compounds (PAHs). Residual hydrocarbon biodegradation occurs naturally, but little is known about the hydrocarbon-degrading microbial communities present in OSPW. In this study, aerobic oxidation of benzene and naphthalene in the surface layer of an oil sands tailings pond were measured. The potential oxidation rates were 4.3 μmol L^-1 OSPW d^-1 for benzene and 21.4 μmol L^-1 OSPW d^-1 for naphthalene. To identify benzene and naphthalene-degrading microbial communities, metagenomics was combined with stable isotope probing (SIP), high-throughput sequencing of 16S rRNA gene amplicons, and isolation of microbial strains. SIP using ¹³C-benzene and ¹³C-naphthalene detected strains of the genera Methyloversatilis and Zavarzinia as the main benzene degraders, while strains belonging to the family Chromatiaceae and the genus Thauera were the main naphthalene degraders. Metagenomic analysis revealed a diversity of genes encoding oxygenases active against aromatic compounds. Although these genes apparently belonged to many phylogenetically diverse taxa, only a few of these taxa were predominant in the SIP experiments. This suggested that many members of the community are adapted to consuming other aromatic compounds, or are active only under specific conditions. 16S rRNA gene sequence datasets have been submitted to the Sequence Read Archive (SRA) under accession number SRP109130. The Gold Study and Project submission ID number in Joint Genome Institute IMG/M for the metagenome is Gs0047444 and Gp0055765.