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The Microbiology of Oil Sands Tailings

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 26382

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Dr. Julia M. Foght

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Guest Editor

Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
Interests: Metagenomics of hydrocarbon-degrading microbial communities, especially under anaerobic conditions; microbiology of oil sands tailings ponds; biodegradation of petroleum hydrocarbons, particularly under adverse environmental conditions in fuel-contaminated Antarctic soils, cold groundwater and subsurface soils; fundamental studies on mechanisms of hydrocarbon transport across bacterial membranes

Dr. Tariq Siddique

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Guest Editor

Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2G7, Canada
Interests: biodegradation of hydrocarbons under different redox conditions; exploring microbial metabolic pathways through molecular characterization of microbial communities; modeling greenhouse gas emissions from tailings ponds; understanding biogeochemical processes responsible for tailings consolidation and contaminant flux from underlying tailings to surface cap water in end-pit lakes; biotransformation of clay minerals in tailings; and biotransformation of metals and their speciation in the environment.

Special Issue Information

Dear Colleagues:

The study of microbes associated with surface-mined oil sands tailings and reclamation of disturbed mine sites is relatively new, but the magnitude of this resource development has highlighted the environmental and industrial importance of microbial activities in situ. Early studies described diverse microbiota in process-affected water and anaerobic strata of tailings ponds. Subsequent research revealed the impact of microbial activity on aspects of tailings generation and management, including during reclamation of sites disturbed by surface mining of oil sands ores. Areas of interest include:

Sources, diversity, and roles of microbes in the native ore formations;
Generation or mitigation of chronic toxicity of formation water and process waters (e.g., naphthenic acid production or biodegradation);
Aerobic and anaerobic biodegradation of diluent and bitumen hydrocarbons;
Mobilization and immobilization of trace elements in tailings;
Biogeneration and release of greenhouse gases (e.g., methane) from tailings ponds, and mitigation via methanotrophy;
Accelerated settling of suspended fine materials in processed waters;
Accelerated densification and de-watering of mature fine tailings;
Biogeochemical element cycling at the water–sediment interface;
Production of hydrogen sulfide from tailings;
Mitigation of volatile organic carbon emissions;
Acidification potential of treated tailings exposed to air;
Effects on remediation and reclamation strategies such as end-pit lakes and wetlands;
Reclamation of disturbed mine sites and establishment of microbial communities as indices of soil productivity (e.g., carbon and nitrogen transformations);
Soil microbiome changes associated with establishing sustainable boreal landscape
Microbiome of process affected water during reclamation;
Soil microbiome in reconstructed soils after oil sands exploitation.

For this Special Issue, we invite manuscripts that provide novel insights into understanding microbial biodiversity, biogeochemical activities, and environmental impacts associated with oil sands tailings from native ore formations, to processing and tailings deposition, to remediation and reclamation. Papers describing new and emerging areas of oil sand microbiology are encouraged.

Dr. Julia M. Foght
Dr. Tariq Siddique
Guest Editors

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Keywords

Biogeochemistry
Hydrocarbon biodegradation
Naphthenic acids
Trace element mobilization
Sediment densification
Anaerobic sediments
Bitumen
Tailings ponds
End pit lakes
Oil sands tailings reclamation

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Published Papers (9 papers)

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16 pages, 2475 KiB

Open AccessArticle

Alum Addition Triggers Hypoxia in an Engineered Pit Lake

by Gerdhard L. Jessen, Lin-Xing Chen, Jiro F. Mori, Tara E. Colenbrander Nelson, Gregory F. Slater, Matthew B. J. Lindsay, Jillian F. Banfield and Lesley A. Warren

Microorganisms 2022, 10(3), 510; https://doi.org/10.3390/microorganisms10030510 - 26 Feb 2022

Cited by 6 | Viewed by 3340

Abstract

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. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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9 pages, 771 KiB

Open AccessCommunication

High Potential for Anaerobic Microbial Sulfur Oxidation in Oil Sands Tailings Ponds

by Sebastian Stasik, Juliane Schmidt and Katrin Wendt-Potthoff

Microorganisms 2021, 9(12), 2529; https://doi.org/10.3390/microorganisms9122529 - 7 Dec 2021

Cited by 4 | Viewed by 2253

Abstract

The biogenic production of toxic H₂S gas in sulfate-rich oil sands tailings ponds is associated with strong environmental concerns. Beside precipitation into sulfide minerals and chemical re-oxidation, microbial sulfur oxidation may catalyze sulfide re-cycling but potentially contributes to acid rock drainage (ARD) generation. To evaluate the microbial potential for sulfur oxidation, we conducted a microcosm-based pilot study with tailings of an active pond. Incubations were performed under oxic and anoxic conditions, with and without KNO₃ as an electron acceptor and thiosulfate as a common substrate for microbial sulfur oxidation. The highest potentials of sulfur oxidation occurred in oxic assays (1.21 mmol L⁻¹ day⁻¹). Under anoxic conditions, rates were significantly lower and dominated by chemical transformation (0.09 mmol L⁻¹ day⁻¹; p < 0.0001). The addition of KNO₃ to anoxic incubations increased microbial thiosulfate oxidation 2.5-fold (0.23 mmol L⁻¹ day⁻¹; p = 0.0474), with complete transformation to SO₄²⁻ coupled to NO₃⁻ consumption, pointing to the activity of sulfur-oxidizing bacteria (SOB) under nitrate-reducing conditions. Importantly, in the presence of KNO₃, a decrease in sedimentary sulfides was associated with an increase in S⁰, which indicates the potential for microbially mediated oxidation of sulfide minerals and ARD generation. Furthermore, the comparative analysis of sediments from other anthropogenic aquatic habitats demonstrated high similarities with respect to viable SOB counts and corresponding activity rates. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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22 pages, 2872 KiB

Open AccessArticle

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

by Greg F. Slater, Corey A. Goad, Matthew B. J. Lindsay, Kevin G. Mumford, Tara E. Colenbrander Nelson, Allyson L. Brady, Gerdhard L. Jessen and Lesley A. Warren

Microorganisms 2021, 9(12), 2509; https://doi.org/10.3390/microorganisms9122509 - 3 Dec 2021

Cited by 6 | Viewed by 2706

Abstract

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. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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15 pages, 1228 KiB

Open AccessArticle

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

by Juliana A. Ramsay, Mara R. de Lima e Silva, Michael A. R. Tawadrous and Bruce A. Ramsay

Microorganisms 2021, 9(11), 2224; https://doi.org/10.3390/microorganisms9112224 - 26 Oct 2021

Viewed by 1853

Abstract

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. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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17 pages, 2917 KiB

Open AccessArticle

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

by Parisa Chegounian, Stephane Flibotte, Kerry Peru, John Headley, Dena McMartin, Bryne Gramlich and Vikramaditya G. Yadav

Microorganisms 2021, 9(10), 2124; https://doi.org/10.3390/microorganisms9102124 - 9 Oct 2021

Cited by 3 | Viewed by 2624

Abstract

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. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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14 pages, 4697 KiB

Open AccessArticle

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

by Mohd Faidz Mohamad Shahimin, Julia M. Foght and Tariq Siddique

Microorganisms 2021, 9(8), 1569; https://doi.org/10.3390/microorganisms9081569 - 23 Jul 2021

Cited by 7 | Viewed by 2506

Abstract

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. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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22 pages, 3938 KiB

Open AccessArticle

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

by Amy-lynne Balaberda and Ania C. Ulrich

Microorganisms 2021, 9(7), 1502; https://doi.org/10.3390/microorganisms9071502 - 14 Jul 2021

Cited by 10 | Viewed by 2355

Abstract

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. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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19 pages, 1534 KiB

Open AccessArticle

Biofilms for Turbidity Mitigation in Oil Sands End Pit Lakes

by Heidi L. Cossey, Mian Nabeel Anwar, Petr V. Kuznetsov and Ania C. Ulrich

Microorganisms 2021, 9(7), 1443; https://doi.org/10.3390/microorganisms9071443 - 4 Jul 2021

Cited by 7 | Viewed by 2745

Abstract

End pit lakes (EPLs) have been proposed as a method of reclaiming oil sands fluid fine tailings (FFT), which consist primarily of process-affected water and clay- and silt-sized particles. Base Mine Lake (BML) is the first full-scale demonstration EPL and contains thick deposits of FFT capped with water. Because of the fine-grained nature of FFT, turbidity generation and mitigation in BML are issues that may be detrimental to the development of an aquatic ecosystem in the water cap. Laboratory mixing experiments were conducted to investigate the effect of mudline biofilms made up of microbial communities indigenous to FFT on mitigating turbidity in EPLs. Four mixing speeds were tested (80, 120, 160, and 200 rpm), all of which are above the threshold velocity required to initiate erosion of FFT in BML. These mixing speeds were selected to evaluate (i) the effectiveness of biofilms in mitigating turbidity and (ii) the mixing speed required to ‘break’ the biofilms. The impact of biofilm age (10 weeks versus 20 weeks old) on turbidity mitigation was also evaluated. Diverse microbial communities in the biofilms included photoautotrophs, namely cyanobacteria and Chlorophyta (green algae), as well as a number of heterotrophs such as Gammaproteobacteria, Desulfobulbia, and Anaerolineae. Biofilms reduced surface water turbidity by up to 99%, depending on the biofilm age and mixing speed. Lifting and layering in the older biofilms resulted in weaker attachment to the FFT; as such, younger biofilms performed better than older biofilms. However, older biofilms still reduced turbidity by 69% to 95%, depending on the mixing speed. These results indicate that biostabilization is a promising mechanism for turbidity mitigation in EPLs. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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Review

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18 pages, 976 KiB

Open AccessReview

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

by Angeline Van Dongen, Abdul Samad, Nicole E. Heshka, Kara Rathie, Christine Martineau, Guillaume Bruant and Dani Degenhardt

Microorganisms 2021, 9(5), 1091; https://doi.org/10.3390/microorganisms9051091 - 19 May 2021

Cited by 4 | Viewed by 4113

Abstract

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. Full article

(This article belongs to the Special Issue The Microbiology of Oil Sands Tailings)

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