Anaerobic alkane biodegradation by cultures enriched from oil sands tailings ponds involves multiple species capable of fumarate addition

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.

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%.

Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions

This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.

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.

Simultaneous detection of transcribed functional assA gene and the corresponding metabolites of linear alkanes (C4, C5, and C7) in production water of a low-temperature oil reservoir

Methanogenic hydrocarbon degradation is an important biogeochemical process in oil reservoirs; however, genomic DNA-based analysis of microorganisms and metabolite detection are not conclusive for identification of the ongoing nature of this bioprocess. In this study, a suite of analyses, involving the study of microbial community and selective gene quantification of both genomic DNA and RNA together with signature metabolites, were performed to comprehensively advance the understanding of the methanogenic biodegradation of hydrocarbons in a low-temperature oilfield. The fumarate addition products for alkanes-C₄, C₅, and C₇-alkylsuccinates-and transcribed assA and mcrA genes were simultaneously detected in the production water sample, providing robust and convincing evidence for both the initial activation of n-alkanes and methane metabolism in this oilfield. The clone library of assA gene transcripts showed that Smithella was active and most likely responsible for the addition of fumarate to n-alkanes, whereas Methanoculleus and Methanothrix were the dominant and active methane-producers via CO₂ reduction and acetoclastic pathways, respectively. Additionally, qPCR results of assA and mcrA genes and their transcribed gene copy numbers revealed a roughly similar transcriptional activity in both n-alkanes-degraders and methane producers, implying that they were the major participants in the methanogenic degradation of n-alkanes in this oilfield. To the best of our knowledge, this is the first report presenting sufficient speculation, through detection of signature intermediates, corresponding gene quantification at transcriptional levels, and microbial community analysis, of methanogenic degradation of n-alkanes in production water of an oil reservoir.

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.

Methanogenic biodegradation of C9 to C12n-alkanes initiated by Smithella via fumarate addition mechanism

In the present study, a methanogenic alkane-degrading (a mixture of C₉ to C₁₂n-alkanes) culture enriched from production water of a low-temperature oil reservoir was established and assessed. Significant methane production was detected in the alkane-amended enrichment cultures compared with alkane-free controls over an incubation period of 1 year. At the end of the incubation, fumarate addition metabolites (C₉ to C₁₂ alkylsuccinates) and assA genes (encoding the alpha subunit of alkylsuccinate synthase) were detected only in the alkane-amended enrichment cultures. Microbial community analysis showed that putative syntrophic n-alkane degraders (Smithella) capable of initiating n-alkanes by fumarate addition mechanism were enriched in the alkane-amended enrichment cultures. In addition, both hydrogenotrophic (Methanocalculus) and acetoclastic (Methanothrix) methanogens were also observed. Our results provide further evidence that alkanes can be activated by addition to fumarate under methanogenic conditions.

Analysis of petroleum biodegradation by a bacterial consortium isolated from worms of the polychaeta class (Annelida): Implications for NPK fertilizer supplementation

Degradation of petroleum hydrocarbons using bacterial consortia may be a means of optimizing bioremediation techniques. In this study, bacterial strains were isolated from the digestive tract of polychaete worms and evaluated concerning the potential of the bacteria to degrade petroleum compounds (Acinetobacter sp., Bacillus sp., Pantoea sp. and Enterobacter sp.). The strains were separately screened regarding their potential to degrade oil after 24 h. The main experiment was carried out for 30 days with the addition of nitrogen, phosphorus and potassium (NPK) after 15 days (Bact-NPK15) and 28 days (Bact-NPK28) and without NPK (Bact). The Bact treatment biomass remained stable until the 20th day of the experiment. C13-C40 n-alkanes were degraded with all treatments in the following order: Bact>Bact-NPK28>Bact-NPK15. Significant differences were observed between the controls and all treatments (p = 0.00031). Measurement of polycyclic aromatic hydrocarbons (PAHs) indicates a lower contribution of these compounds in the Bact-NPK28 treatment, although no significant difference between groups was observed. Bact-NPK28 was able to remove 40% of naphthalene, while Bact-NPK15 removed 20%; this effect was not observed in Bact. Higher hopane degradation levels were observed in Bact and, to a lesser extent, in Bact-NPK28. NPK application for 28 days mainly favored PAH degradation. The evaluated consortium thus exhibits potential in the bioremediation of petroleum-contaminated areas.

Survival and Energy Producing Strategies of Alkane Degraders Under Extreme Conditions and Their Biotechnological Potential

Many petroleum-polluted areas are considered as extreme environments because of co-occurrence of low and high temperatures, high salt, and acidic and anaerobic conditions. Alkanes, which are major constituents of crude oils, can be degraded under extreme conditions, both aerobically and anaerobically by bacteria and archaea of different phyla. Alkane degraders possess exclusive metabolic pathways and survival strategies, which involve the use of protein and RNA chaperones, compatible solutes, biosurfactants, and exopolysaccharide production for self-protection during harsh environmental conditions such as oxidative and osmotic stress, and ionic nutrient-shortage. Recent findings suggest that the thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus uses a novel alkylsuccinate synthase for long-chain alkane degradation, and the thermophilic Candidatus Syntrophoarchaeum butanivorans anaerobically oxidizes butane via alkyl-coenzyme M formation. In addition, gene expression data suggest that extremophiles produce energy via the glyoxylate shunt and the Pta-AckA pathway when grown on a diverse range of alkanes under stress conditions. Alkane degraders possess biotechnological potential for bioremediation because of their unusual characteristics. This review will provide genomic and molecular insights on alkane degraders under extreme conditions.

Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.

Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH₄ and CO₂. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H₂ metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H₂-producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation.

IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an understanding of public good dynamics could result in new ways to improve microbial pollutant degradation in anaerobic systems.

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth’s surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system. Analysis of the entire Halfdan oil field in the North Sea (32 producing wells in production for 1–15 years) using quantitative PCR, multigenic sequencing, comparative metagenomic and genomic bins reconstruction revealed systematic shifts in microbial community composition and metabolic potential, as well as changing ecological strategies in response to anthropogenic perturbation of the oil field ecosystem, related to length of time in production. The microbial communities were initially dominated by slow growing anaerobes such as members of the Thermotogales and Clostridiales adapted to living on hydrocarbons and complex refractory organic matter. However, as seawater and nitrate injection (used for secondary oil production) delivered oxidants, the microbial community composition progressively changed to fast growing opportunists such as members of the Deferribacteres, Delta-, Epsilon- and Gammaproteobacteria, with energetically more favorable metabolism (for example, nitrate reduction, H₂S, sulfide and sulfur oxidation). This perturbation has profound consequences for understanding the microbial ecology of the system and is of considerable practical importance as it promotes detrimental processes such as reservoir souring and metal corrosion. These findings provide a new conceptual framework for understanding the petroleum reservoir biosphere and have consequences for developing strategies to manage microbiological problems in the oil industry.

Methanogenic biodegradation of paraffinic solvent hydrocarbons in two different oil sands tailings

Microbial communities drive many biogeochemical processes in oil sands tailings and cause greenhouse gas emissions from tailings ponds. Paraffinic solvent (primarily C₅-C₆; n- and iso-alkanes) is used by some oil sands companies to aid bitumen extraction from oil sands ores. Residues of unrecovered solvent escape to tailings ponds during tailings deposition and sustain microbial metabolism. To investigate biodegradation of hydrocarbons in paraffinic solvent, mature fine tailings (MFT) collected from Albian and CNRL ponds were amended with paraffinic solvent at ~0.1wt% (final concentration: ~1000mgL^-1) and incubated under methanogenic conditions for ~1600d. Albian and CNRL MFTs exhibited ~400 and ~800d lag phases, respectively after which n-alkanes (n-pentane and n-hexane) in the solvent were preferentially metabolized to methane over iso-alkanes in both MFTs. Among iso-alkanes, only 2-methylpentane was completely biodegraded whereas 2-methylbutane and 3-methylpentane were partially biodegraded probably through cometabolism. 16S rRNA gene pyrosequencing showed dominance of Anaerolineaceae and Methanosaetaceae in Albian MFT and Peptococcaceae and co-domination of "Candidatus Methanoregula" and Methanosaetaceae in CNRL MFT bacterial and archaeal communities, respectively, during active biodegradation of paraffinic solvent. The results are important for developing future strategies for tailings reclamation and management of greenhouse gas emissions.

Sequential biodegradation of complex naphtha hydrocarbons under methanogenic conditions in two different oil sands tailings

Methane emissions in oil sands tailings ponds are sustained by anaerobic biodegradation of unrecovered hydrocarbons. Naphtha (primarily C₆-C₁₀; n- iso- and cycloalkanes) is commonly used as a solvent during bitumen extraction process and its residue escapes to tailings ponds during tailings deposition. To investigate biodegradability of hydrocarbons in naphtha, mature fine tailings (MFT) collected from Albian and CNRL tailings ponds were amended with CNRL naphtha at ∼0.2 wt% (∼2000 mg L^-1) and incubated under methanogenic conditions for ∼1600 d. Microbial communities in both MFTs started metabolizing naphtha after a lag phase of ∼100 d. Complete biodegradation/biotransformation of all n-alkanes (except partial biodegradation of n-octane in CNRL MFT) followed by major iso-alkanes (2-methylpentane, 3-methylhexane, 2- and 4-methylheptane, iso-nonanes and 2-methylnonane) and a few cycloalkanes (derivatives of cyclopentane and cyclohexane) was observed during the incubation. 16S rRNA gene pyrosequencing showed dominance of Peptococcaceae and Anaerolineaceae in Albian MFT and Anaerolineaceae and Syntrophaceae in CNRL MFT bacterial communities with co-domination of Methanosaetaceae and "Candidatus Methanoregula" in archaeal populations during active biodegradation of hydrocarbons. The findings extend the known range of hydrocarbons susceptible to methanogenic biodegradation in petroleum-impacted anaerobic environments and help refine existing kinetic model to predict greenhouse gas emissions from tailings ponds.

Vertical gradients in carbon flow and methane production in a sulfate-rich oil sands tailings pond

Oil sands tailings ponds are primary storage basins for tailings produced during oil sands processing in Alberta (Canada). Due to microbial metabolism, methane production contributes to greenhouse gas emissions, but positively affects tailings densification, which is relevant for operational water re-use. Depending on the age and depth of tailings, the activity of sulfate-reducing bacteria (SRB) may control methanogenesis due to the competition for substrates. To assess the depth-related impact of sulfate reduction on CH₄ emissions, original tailings of two vicinal pond profiles were incubated in anoxic microcosms with/without molybdate as selective inhibitor of microbial sulfate reduction. Integrating methane production rates, considerable volumes of CH₄ emissions (∼5.37 million L d^-1) may be effectively prevented by the activity of SRB in sulfidic tailings between 3.5 and 7.5 m. To infer metabolic potentials controlling methanogenic pathways, a set of relevant organic acids (acetate, formate, propionate, butyrate, lactate) was added to part of the microcosms. Generally, organic acid transformation shifted with depth, with highest rates (305-446 μmol L^-1 d^-1) measured in fresh tailings at 5.5-7.5 m. In all depths, a transient accumulation of acetate revealed its importance as key intermediate during organic matter decomposition. SRB dominated the transformation of acetate, butyrate and propionate, but were not essential for lactate and formate turnover. Acetate as methanogenic substrate was important only at 13.5 m. At 1-7.5 m, methanogenesis significantly increased in presence of organic acids, most likely due to the syntrophic oxidation of acetate to CO₂ by SRB and subsequent conversion to CH₄.

Co-occurrence of methanogenesis and N2 fixation in oil sands tailings

Oil sands tailings ponds in northern Alberta, Canada have been producing biogenic gases via microbial metabolism of hydrocarbons for decades. Persistent methanogenic activity in tailings ponds without any known replenishment of nutrients such as fixed nitrogen (N) persuaded us to investigate whether N2 fixation or polyacrylamide (PAM; used as a tailings flocculant) could serve as N sources. Cultures comprising mature fine tailings (MFT) plus methanogenic medium supplemented with or deficient in fixed N were incubated under an N2 headspace. Some cultures were further amended with citrate, which is used in oil sands processing, as a relevant carbon source, and/or with PAM. After an initial delay, N-deficient cultures with or without PAM produced methane (CH4) at the same rate as N-containing cultures, indicating a mechanism of overcoming apparent N-deficiency. Acetylene reduction and (15)N2 incorporation in all N-deficient cultures (with or without PAM) suggested active N2 fixation concurrently with methanogenesis but inability to use PAM as a N source. 16S rRNA gene pyrosequencing revealed little difference between archaeal populations regardless of N content. However, bacterial sequences in N-deficient cultures showed enrichment of Hyphomicrobiaceae and Clostridium members that might contain N2-fixing species. The results are important in understanding long-term production of biogenic greenhouse gases in oil sands tailings.

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds

Oil sands tailings ponds harbor diverse anaerobic microbial communities capable of methanogenic biodegradation of solvent hydrocarbons entrained in the tailings. Mature fine tailings (MFT) from two operators (Albian and CNRL) that use different extraction solvents were incubated with mixtures of either two (n-pentane and n-hexane) or four (n-pentane, n-hexane, n-octane and n-decane) n-alkanes under methanogenic conditions for ~600 d. Microbes in Albian MFT began methane production by ~80 d, achieving complete depletion of n-pentane and n-hexane in the two-alkane mixture and their preferential biodegradation in the four-alkane mixture. Microbes in CNRL MFT preferentially metabolized n-octane and n-decane in the four-alkane mixture after a ~80 d lag but exhibited a lag of ~360 d before commencing biodegradation of n-pentane and n-hexane in the two-alkane mixture. 16S rRNA gene pyrosequencing revealed Peptococcaceae members as key bacterial n-alkane degraders in all treatments except CNRL MFT amended with the four-alkane mixture, in which Anaerolineaceae, Desulfobacteraceae (Desulfobacterium) and Syntrophaceae (Smithella) dominated during n-octane and n-decane biodegradation. Anaerolineaceae sequences increased only in cultures amended with the four-alkane mixture and only during n-octane and n-decane biodegradation. The dominant methanogens were acetoclastic Methanosaetaceae. These results highlight preferential n-alkane biodegradation by microbes in oil sands tailings from different producers, with implications for tailings management and reclamation.

Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon-enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands.

Community Structure in Methanogenic Enrichments Provides Insight into Syntrophic Interactions in Hydrocarbon-Impacted Environments

The methanogenic biodegradation of crude oil involves the conversion of hydrocarbons to methanogenic substrates by syntrophic bacteria and subsequent methane production by methanogens. Assessing the metabolic roles played by various microbial species in syntrophic communities remains a challenge, but such information has important implications for bioremediation and microbial enhanced energy recovery technologies. Many factors such as changing environmental conditions or substrate variations can influence the composition and biodegradation capabilities of syntrophic microbial communities in hydrocarbon-impacted environments. In this study, a methanogenic crude oil-degrading enrichment culture was successively transferred onto the single long chain fatty acids palmitate or stearate followed by their parent alkanes, hexadecane or octadecane, respectively, in order to assess the impact of different substrates on microbial community composition and retention of hydrocarbon biodegradation genes. 16S rRNA gene sequencing showed that a reduction in substrate diversity resulted in a corresponding loss of microbial diversity, but that hydrocarbon biodegradation genes (such as assA/masD encoding alkylsuccinate synthase) could be retained within a community even in the absence of hydrocarbon substrates. Despite substrate-related diversity changes, all communities were dominated by hydrogenotrophic and acetotrophic methanogens along with bacteria including Clostridium sp., members of the Deltaproteobacteria, and a number of other phyla. Microbial co-occurrence network analysis revealed a dense network of interactions amongst syntrophic bacteria and methanogens that were maintained despite changes in the substrates for methanogenesis. Our results reveal the effect of substrate diversity loss on microbial community diversity, indicate that many syntrophic interactions are stable over time despite changes in substrate pressure, and show that syntrophic interactions amongst bacteria themselves are as important as interactions between bacteria and methanogens in complex methanogenic communities.

Methanogenic Hydrocarbon Degradation: Evidence from Field and Laboratory Studies

Microbial transformation of hydrocarbons to methane is an environmentally relevant process taking place in a wide variety of electron acceptor-depleted habitats, from oil reservoirs and coal deposits to contaminated groundwater and deep sediments. Methanogenic hydrocarbon degradation is considered to be a major process in reservoir degradation and one of the main processes responsible for the formation of heavy oil deposits and oil sands. In the absence of external electron acceptors such as oxygen, nitrate, sulfate or Fe(III), fermentation and methanogenesis become the dominant microbial metabolisms. The major end product under these conditions is methane, and the only electron acceptor necessary to sustain the intermediate steps in this process is CO2, which is itself a net product of the overall reaction. We are summarizing the state of the art and recent advances in methanogenic hydrocarbon degradation research. Both the key microbial groups involved as well as metabolic pathways are described, and we discuss the novel insights into methanogenic hydrocarbon-degrading populations studied in laboratory as well as environmental systems enabled by novel cultivation-based and molecular approaches. Their possible implications on energy resources, bioremediation of contaminated sites, deep-biosphere research, and consequences for atmospheric composition and ultimately climate change are also addressed.

Metabolism of Hydrocarbons in n-Alkane-Utilizing Anaerobic Bacteria

The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from n-hexane activation by the n-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2S,1'R) and (2R,1'R). Experiments with stereospecifically deuterated n-(2,5-2H2)hexanes revealed that exclusively the pro-S hydrogen atom is abstracted from C2 of the n-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the n-alkane forming the new C-C-bond, and thus stereochemically resembles a SN2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of n-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for n-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various n-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms n-alkylsuccinates during growth with n-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of n-alkanes.

Long-Term Incubation Reveals Methanogenic Biodegradation of C5 and C6 iso-Alkanes in Oil Sands Tailings

iso-Alkanes are major components of petroleum and have been considered recalcitrant to biodegradation under methanogenic conditions. However, indigenous microbes in oil sands tailings ponds exposed to solvents rich in 2-methylbutane, 2-methylpentane, 3-methylpentane, n-pentane, and n-hexane produce methane in situ. We incubated defined mixtures of iso- or n-alkanes with mature fine tailings from two tailings ponds of different ages historically exposed to different solvents: one, ~10 years old, receiving C5-C6 paraffins and the other, ~35 years old, receiving naphtha. A lengthy incubation (>6 years) revealed iso-alkane biodegradation after lag phases of 900-1800 and ~280 days, respectively, before the onset of methanogenesis, although lag phases were shorter with n-alkanes (~650-1675 and ~170 days, respectively). 2-Methylpentane and both n-alkanes were completely depleted during ~2400 days of incubation, whereas 2-methylbutane and 3-methylpentane were partially depleted only during active degradation of 2-methylpentane, suggesting co-metabolism. In both cases, pyrotag sequencing of 16S rRNA genes showed codominance of Peptococcaceae with acetoclastic (Methanosaeta) and hydrogenotrophic (Methanoregula and Methanolinea) methanogens. These observations are important for predicting long-term greenhouse-gas emissions from oil sands tailings ponds and extend the known range of hydrocarbons susceptible to methanogenic biodegradation in petroleum-impacted anaerobic environments.