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      Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters.

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          Abstract

          The methanogenic biodegradation of crude oil is an important process occurring in petroleum reservoirs and other oil-containing environments such as contaminated aquifers. In this process, syntrophic bacteria degrade hydrocarbon substrates to products such as acetate, and/or H2 and CO2 that are then used by methanogens to produce methane in a thermodynamically dependent manner. We enriched a methanogenic crude oil-degrading consortium from production waters sampled from a low temperature heavy oil reservoir. Alkylsuccinates indicative of fumarate addition to C5 and C6 n-alkanes were identified in the culture (above levels found in controls), corresponding to the detection of an alkyl succinate synthase encoding gene (assA/masA) in the culture. In addition, the enrichment culture was tested for its ability to produce methane from residual oil in a sandstone-packed column system simulating a mature field. Methane production rates of up to 5.8 μmol CH4/g of oil/day were measured in the column system. Amounts of produced methane were in relatively good agreement with hydrocarbon loss showing depletion of more than 50% of saturate and aromatic hydrocarbons. Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. Here, Methanobacterium sp. were most abundant, as were bacterial members of the genus Pseudomonas and other known biofilm forming organisms. Our findings show that microorganisms enriched from petroleum reservoir waters can bioconvert crude oil components to methane both planktonically and in sandstone-packed columns as test systems. Further, the results suggest that different organisms may contribute to oil biodegradation within different phases (e.g., planktonic vs. sessile) within a subsurface crude oil reservoir.

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          The quantitative significance of Syntrophaceae and syntrophic partnerships in methanogenic degradation of crude oil alkanes

          Libraries of 16S rRNA genes cloned from methanogenic oil degrading microcosms amended with North Sea crude oil and inoculated with estuarine sediment indicated that bacteria from the genera Smithella (Deltaproteobacteria, Syntrophaceace) and Marinobacter sp. (Gammaproteobacteria) were enriched during degradation. Growth yields and doubling times (36 days for both Smithella and Marinobacter) were determined using qPCR and quantitative data on alkanes, which were the predominant hydrocarbons degraded. The growth yield of the Smithella sp. [0.020 g(cell-C)/g(alkane-C)], assuming it utilized all alkanes removed was consistent with yields of bacteria that degrade hydrocarbons and other organic compounds in methanogenic consortia. Over 450 days of incubation predominance and exponential growth of Smithella was coincident with alkane removal and exponential accumulation of methane. This growth is consistent with Smithella's occurrence in near surface anoxic hydrocarbon degrading systems and their complete oxidation of crude oil alkanes to acetate and/or hydrogen in syntrophic partnership with methanogens in such systems. The calculated growth yield of the Marinobacter sp., assuming it grew on alkanes, was [0.0005 g(cell-C)/g(alkane-C)] suggesting that it played a minor role in alkane degradation. The dominant methanogens were hydrogenotrophs (Methanocalculus spp. from the Methanomicrobiales). Enrichment of hydrogen-oxidizing methanogens relative to acetoclastic methanogens was consistent with syntrophic acetate oxidation measured in methanogenic crude oil degrading enrichment cultures. qPCR of the Methanomicrobiales indicated growth characteristics consistent with measured rates of methane production and growth in partnership with Smithella.
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            Thermodynamic constraints on methanogenic crude oil biodegradation.

            Methanogenic degradation of crude oil hydrocarbons is an important process in subsurface petroleum reservoirs and anoxic environments contaminated with petroleum. There are several possible routes whereby hydrocarbons may be converted to methane: (i) complete oxidation of alkanes to H2 and CO2, linked to methanogenesis from CO2 reduction; (ii) oxidation of alkanes to acetate and H2, linked to acetoclastic methanogenesis and CO2 reduction; (iii) oxidation of alkanes to acetate and H2, linked to syntrophic acetate oxidation and methanogenesis from CO2 reduction; (iv) oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis and (v) oxidation of alkanes to acetate alone, linked to syntrophic acetate oxidation and methanogenesis from CO2 reduction. We have developed the concept of a 'window of opportunity' to evaluate the range of conditions under which each route is thermodynamically feasible. On this basis the largest window of opportunity is presented by the oxidation of alkanes to acetate alone, linked to acetoclastic methanogenesis. This contradicts field-based evidence that indicates that in petroleum rich environments acetoclastic methanogenesis is inhibited and that methanogenic CO2 reduction is the predominant methanogenic process. Our analysis demonstrates that under those biological constraints oxidation of alkanes to acetate and H2, linked to syntrophic acetate oxidation and methanogenesis from CO2 reduction offers a greater window of opportunity than complete oxidation of alkanes to H2 and CO2 linked to methanogenic CO2 reduction, and hence is the process most likely to occur.
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              Role of Bacterial Exopolysaccharides (EPS) in the Fate of the Oil Released during the Deepwater Horizon Oil Spill

              Halomonas species are recognized for producing exopolysaccharides (EPS) exhibiting amphiphilic properties that allow these macromolecules to interface with hydrophobic substrates, such as hydrocarbons. There remains a paucity of knowledge, however, on the potential of Halomonas EPS to influence the biodegradation of hydrocarbons. In this study, the well-characterized amphiphilic EPS produced by Halomonas species strain TG39 was shown to effectively increase the solubilization of aromatic hydrocarbons and enhance their biodegradation by an indigenous microbial community from oil-contaminated surface waters collected during the active phase of the Deepwater Horizon oil spill. Three Halomonas strains were isolated from the Deepwater Horizon site, all of which produced EPS with excellent emulsifying qualities and shared high (97-100%) 16S rRNA sequence identity with strain TG39 and other EPS-producing Halomonas strains. Analysis of pyrosequence data from surface water samples collected during the spill revealed several distinct Halomonas phylotypes, of which some shared a high sequence identity (≥97%) to strain TG39 and the Gulf spill isolates. Other bacterial groups comprising members with well-characterized EPS-producing qualities, such as Alteromonas, Colwellia and Pseudoalteromonas, were also found enriched in surface waters, suggesting that the total pool of EPS in the Gulf during the spill may have been supplemented by these organisms. Roller bottle incubations with one of the Halomonas isolates from the Deepwater Horizon spill site demonstrated its ability to effectively produce oil aggregates and emulsify the oil. The enrichment of EPS-producing bacteria during the spill coupled with their capacity to produce amphiphilic EPS is likely to have contributed to the ultimate removal of the oil and to the formation of oil aggregates, which were a dominant feature observed in contaminated surface waters.
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                Author and article information

                Journal
                Front Microbiol
                Frontiers in microbiology
                Frontiers Media SA
                1664-302X
                1664-302X
                2014
                : 5
                Affiliations
                [1 ] Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada.
                Article
                10.3389/fmicb.2014.00197
                4017130
                24829563
                7575ee38-89de-41e5-b58e-8d6c6ff0679a
                History

                alkylsuccinates,crude oil,crude oil reservoir,hydrocarbon methanogenesis,pyrotag sequencing

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