Thomas B.P. Oldenburg

Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely affected the majority of the world’s oil, making recovery and refining of that oil more costly. The prevalent occurrence of biodegradation in shallow subsurface petroleum reservoirs has been attributed to aerobic bacterial hydrocarbon degradation stimulated by surface recharge of oxygen-bearing meteoric waters. This hypothesis is empirically supported by the likelihood of encountering biodegraded oils at higher levels of degradation in reservoirs near the surface. More recent findings, however, suggest that anaerobic degradation processes dominate subsurface sedimentary environments, despite slow reaction kinetics and uncertainty as to the actual degradation pathways occurring in oil reservoirs. Here we use laboratory experiments in microcosms monitoring the hydrocarbon composition of degraded oils and generated gases, together with the carbon isotopic compositions of gas and oil samples taken at wellheads and a Rayleigh isotope fractionation box model, to elucidate the probable mechanisms of hydrocarbon degradation in reservoirs. We find that crude-oil hydrocarbon degradation under methanogenic conditions in the laboratory mimics the characteristic sequential removal of compound classes seen in reservoir-degraded petroleum. The initial preferential removal of n-alkanes generates close to stoichiometric amounts of methane, principally by hydrogenotrophic methanogenesis. Our data imply a common methanogenic biodegradation mechanism in subsurface degraded oil reservoirs, resulting in consistent patterns of hydrocarbon alteration, and the common association of dry gas with severely degraded oils observed worldwide. Energy recovery from oilfields in the form of methane, based on accelerating natural methanogenic biodegradation, may offer a route to economic production of difficult-to-recover energy from oilfields.

The controls on the composition of biodegraded oils in the deep subsurface: Part II - Geological controls on subsurface biodegradation fluxes and constraints on reservoir-fluid property prediction

The principal controls on the fluid properties of biodegraded oil systems have been determined by a combination of petroleum geochemistry, numerical modeling of oil biodegradation in reservoirs, and analysis of oil property data sets from a variety of geological settings. Petroleum biodegradation proceeds under anaerobic conditions in any reservoir that has a water leg and has not been heated to temperatures more than 80C. In most reservoirs with low concentrations of aqueous sulfate, methanogenic degradation is a primary mechanism of petroleum degradation, whereas in waters containing abundant sulfate, sulfate reduction and sulfide production may dominate. Net degradation of petroleum fractions in reservoirs is primarily controlled by the reservoir temperature, the chemical compounds being degraded, and relationships between the oil-water contact (OWC) area and oil volume. The relative volumes of water leg to oil leg, prior level of oil biodegradation, and reservoir water salinity act as second-order controls on the process. Typically, degradation fluxes (kilograms of petroleum destroyed per square meter of oil-water contact area per year or kg petroleum m2 OWC yr1) for fresh petroleum in clastic reservoirs are in the range of 103–104 kg petroleum m2 OWC yr1 and increase with decreasing reservoir temperature, from zero near 80C, to a maximum flux at the OWC of less than 103 kg petroleum m2 OWC yr1 at a temperature less than 40C. At very low reservoir temperatures and with severely degraded oils, such as are seen in the near-surface Canadian tar sands at the present day, the net degradation fluxes are much less than maximum values. Nutrient supply from the aquifer and adjacent shales, mostly buffered by mineral dissolution, probably provides the ultimate control on the range of degradation flux values. Oil compositional gradients and resulting oil viscosity variations are common on both reservoir thickness and field scales in biodegraded oil reservoirs and are a defining characteristic of heavy oil fields produced by crude-oil biodegradation. Continuous vertical gradients in the oil columns document episodic degradation for many millions of years, suggesting that the time scales of oil-field degradation and petroleum charging are similar. The flux-temperature relationship we have derived, coupled with typical reservoir charge histories, defines the range of variation of fluid properties seen in many biodegraded oil provinces and identifies oil charge, mixing of biodegraded and fresh oils, and reservoir-temperature history as the primary controls on fluid properties. These flux-temperature relationships are easily integrated into prospect charge modeling procedures; sensitivity analyses show that the limiting factor in fluid property predictions, using even this first-level approach, are ultimately constrained by the accuracy of current oil-charge modeling estimates. The absence today of any functional geochemical proxies for assessing oil-residence time in oil fields and the substantial uncertainty in petroleum-charging times estimated by forward basin modeling is a major obstacle to more accurate fluid-property predictions that needs to be addressed.

Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common

Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed by syntrophic bacteria and methanogenic archaea, is thought to be one of the dominant processes. We compared 160 microbial community compositions in ten hydrocarbon resource environments (HREs) and sequenced twelve metagenomes to characterize their metabolic potential. Although anaerobic communities were common, cores from oil sands and coal beds had unexpectedly high proportions of aerobic hydrocarbon-degrading bacteria. Likewise, most metagenomes had high proportions of genes for enzymes involved in aerobic hydrocarbon metabolism. Hence, although HREs may have been strictly anaerobic and typically methanogenic for much of their history, this may not hold today for coal beds and for the Alberta oil sands, one of the largest remaining oil reservoirs in the world. This finding may influence strategies to recover energy or chemicals from these HREs by in situ microbial processes.

Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

Summary The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense – an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems.

Influence of biodegradation on carbazole and benzocarbazole distributions in oil columns from the Liaohe basin, NE China

Abstract Alkylcarbazoles and benzocarbazoles in petroleum reservoir core extracts isolated from several oil columns within the Lengdong oilfield, Liaohe basin, China were studied to investigate their occurrence and the effect of biodegradation on their concentrations and distributions. Bulk petroleum composition and molecular data indicate the occurrence of systematic biodegradation gradients within the oil columns, the extent of biodegradation ranging from light (level 1) to moderate (level 4-5) in Es3 columns, and from moderate (level 5) to heavy (level 8) in Es1 columns [all ‘levels’ in this paper refer to the Peters and Moldowan biodegradation scale (Peters, K.E., Moldowan, J.M., 1993. The Biomarker Guide: Interpreting Molecular Fossils in Petroleum and Ancient Sediments. Prentice Hall, Englewood Cliffs, NJ.)]. Whereas carbazoles and benzocarbazoles can be useful as migration markers in certain geological situations, the results presented here indicate that biodegradation also plays a significant role in controlling the distribution of carbazole compounds in reservoired oils. Alkylcarbazoles are generally regarded as resistant to biodegradation at low to moderate levels of biodegradation but at biodegradation levels greater than level 4 they may be microbially altered in a way similar to that observed for aliphatic and aromatic hydrocarbons. The concentrations of carbazole compounds in the oils increase slightly during the early stages of biodegradation and then sharply decrease after level 4, when preferential depletion of alkylated carbazoles compared to benzocarbazoles and dibenzocarbazoles or naphthocarbazoles is observed. The susceptibility of alkylated carbazole isomers to biodegradation decreases with increasing carbon number of the alkyl substituents. Furthermore, nitrogen (N–H) shielded or partially shielded compounds substituted in the 1 and/or 8 positions seem more susceptible to biodegradation than their nitrogen-exposed counterparts. For example, biodegradation resulted in the preferential removal of 1-methylcarbazole relative to the other methylcarbazole isomers and among the dimethylcarbazoles; 1,8-dimethylcarbazole seems more susceptible to biodegradation than other isomers, even though some exceptions do occur in our sample set. The benzocarbazole ratio [Nature 383 (1996) 593] decreased with increasing degree of biodegradation. Benzo[b]carbazole has the highest apparent ability to resist biodegradation among the benzocarbazole isomers.

Influence of maturity on carbazole and benzocarbazole distributions in crude oils and source rocks from the Sonda de Campeche, Gulf of Mexico

Carbazole geochemistry has been studied fo a petroleum system in which vertical migration is prominent and where reservoirs are locally sourced. An essentially uniform organofacies of organicrich Tithonian source rocks from the Sonda de Campeche (Gulf of Mexico), covering a well defined maturity sequence (0.36 1 29% R 1 ) and associated crude oils (0.49 0.92% R c ) from Palaeocene reservoirs formed the sampling base. Comparison of the distribution of alkylcarbazoles and benzocarbazoles in rock bitumens and oils revealed that fractionation due to primary expulsion had no effect on the distribution of shielded exposed carbazoles within crude oils. Perhaps more importantly, the benzocarbazole ratio in both rock extracts and crude oils increased with maturity, indicating that this parameter cannot be directly used as a migration indicator in petroleum systems where vertical migration through faults and fissures represents the main avenues of oil migration.

Xanthones-novel aromatic oxygen-containing compounds in crude oils

Abstract Xanthone and its alkylated homologues were determined to be present in 64 of 69 investigated oils from offshore Norway (Central Graben, Viking Graben, Haltenbanken). This is the first description of xanthones in crude oils. These compounds were identified by comparison with authentic standards by coinjection, based on mass spectra and relative retention times on two different GC columns. The elution order of the four methylxanthones was established as 1-4-2-3 by using a BPX-5 column. About 2/3 of the oils contain concentrations of xanthone lower than 5 μg/g oil, but some oils are clearly enriched in the parent compound. The highest amount of xanthone in the sample set was 38 μg/g oil. The relative abundance of xanthone, the sum of the methylxanthones and the sum of the C 2 -xanthones is mainly controlled by maturity. Partitioning processes may effect changes in the distribution of methylxanthones as observed for a biodegradation sequence from the Gullfaks field. Molecular dynamics calculations support the observation of a better preservation of the shielded isomers (1- and to a lesser extent 4-methylxanthone) in the oil phase compared to the non-shielded isomers (2- and 3-methylxanthone). The ratio of these two different isomer groups may be useful as an indicator of secondary migration distances, as demonstrated for an oil sequence from the Tampen Spur and Haltenbanken oils. However, biodegradation could also cause an increase of the shielded isomers relative to the non-shielded isomers due to sterical hindrance by the methyl groups restricting access to the oxygen functionalities. The origin of xanthones in crude oils and source rocks is not known but they could be generated as diagenetic products, formed by oxidation of xanthenes in the reservoir, or originate by geosynthesis from aromatic precursors.

Geological Controls on the Origin of Heavy Oil and Oil Sands and Their Impacts on In Situ Recovery

Biodegradation of crude oil in subsurface petroleum reservoirs is an important alteration process affecting most of the worlds oil deposits. The process preferentially removes light components from conventional oil to form heavy oil and oil sand, which are more difficult to produce and are more costly to refine. Although reservoir temperature is a key control on biodegradation, large variations in oil properties have been documented in accumulations from similar depths within a play area. Data from the Liaohe Basin, NE China and other basins in China and elsewhere, indicate that biodegradation is most active in a narrow zone at or near the base of the oil column in contact with the water leg. The availability of nutrients from mineral dissolution within the water leg is also thought to have a significant impact upon the degree of biodegradation. Thus, the level of biodegradation increases with water leg thickness. Charge history and in-reservoir mixing of continuously charged oil with residual biodegraded oil also have a significant impact on oil physical properties. The conceptual biodegradation model proposed combines geochemical and geological factors to provide a coherent approach to estimate the impact of degradation on petroleum and to help reliably predict biodegradation risk at the prospect level. Our geochemical approach can be used to locate sweet spots (areas of less degraded oil), optimize the placement of new wells and completion intervals and help with production allocation from long production wells.

Biostimulation of Oil Sands Process-Affected Water with Phosphate Yields Removal of Sulfur-Containing Organics and Detoxification

The ability to mitigate toxicity of oil sands process-affected water (OSPW) for return into the environment is an important issue for effective tailings management in Alberta, Canada. OSPW toxicity has been linked to classical naphthenic acids (NAs), but the toxic contribution of other acid-extractable organics (AEOs) remains unknown. Here, we examine the potential for in situ bioremediation of OSPW AEOs by indigenous algae. Phosphate biostimulation was performed in OSPW to promote the growth of indigenous photosynthetic microorganisms and subsequent toxicity and chemical changes were determined. After 12 weeks, the AEO fraction of phosphate-biostimulated OSPW was significantly less toxic to the fission yeast Schizosaccharomyces pombe than unstimulated OSPW. Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analysis of the AEO fraction in phosphate-biostimulated OSPW showed decreased levels of SO3 class compounds, including a subset that may represent linear arylsulfonates. A screen with S. pombe transcription factor mutant strains for growth sensitivity to the AEO fraction or sodium dodecylbenzenesulfonate revealed a mode of toxic action consistent with oxidative stress and detrimental effects on cellular membranes. These findings demonstrate a potential algal-based in situ bioremediation strategy for OSPW AEOs and uncover a link between toxicity and AEOs other than classical NAs.

Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops

ABSTRACT Oil sands are surface exposed in river valley outcrops in northeastern Alberta, where flat slabs (tablets) of weathered, bitumen-saturated sandstone can be retrieved from outcrop cliffs or from riverbeds. Although the average yearly surface temperature of this region is low (0.7°C), we found that the temperatures of the exposed surfaces of outcrop cliffs reached 55 to 60°C on sunny summer days, with daily maxima being 27 to 31°C. Analysis of the cooccurrence of taxa derived from pyrosequencing of 16S/18S rRNA genes indicated that an aerobic microbial network of fungi and hydrocarbon-, methane-, or acetate-oxidizing heterotrophic bacteria was present in all cliff tablets. Metagenomic analyses indicated an elevated presence of fungal cytochrome P450 monooxygenases in these samples. This network was distinct from the heterotrophic community found in riverbeds, which included fewer fungi. A subset of cliff tablets had a network of anaerobic and/or thermophilic taxa, including methanogens, Firmicutes, and Thermotogae, in the center. Long-term aerobic incubation of outcrop samples at 55°C gave a thermophilic microbial community. Analysis of residual bitumen with a Fourier transform ion cyclotron resonance mass spectrometer indicated that aerobic degradation proceeded at 55°C but not at 4°C. Little anaerobic degradation was observed. These results indicate that bitumen degradation on outcrop surfaces is a largely aerobic process with a minor anaerobic contribution and is catalyzed by a consortium of bacteria and fungi. Bitumen degradation is stimulated by periodic high temperatures on outcrop cliffs, which cause significant decreases in bitumen viscosity.