Biogenic methane production in formation waters from a large gas field in the North Sea

Perspective on the use of methanogens in lithium recovery from brines

Methanogenic archaea stand out as multipurpose biocatalysts for different applications in wide-ranging industrial sectors due to their crucial role in the methane (CH4) cycle and ubiquity in natural environments. The increasing demand for raw materials required by the manufacturing sector (i.e., metals-, concrete-, chemicals-, plastic- and lubricants-based industries) represents a milestone for the global economy and one of the main sources of CO2 emissions. Recovery of critical raw materials (CRMs) from byproducts generated along their supply chain, rather than massive mining operations for mineral extraction and metal smelting, represents a sustainable choice. Demand for lithium (Li), included among CRMs in 2023, grew by 17.1% in the last decades, mostly due to its application in rechargeable lithium-ion batteries. In addition to mineral deposits, the natural resources of Li comprise water, ranging from low Li concentrations (seawater and freshwater) to higher ones (salt lakes and artificial brines). Brines from water desalination can be high in Li content which can be recovered. However, biological brine treatment is not a popular methodology. The methanogenic community has already demonstrated its ability to recover several CRMs which are not essential to their metabolism. Here, we attempt to interconnect the well-established biomethanation process with Li recovery from brines, by analyzing the methanogenic species which may be suitable to grow in brine-like environments and the corresponding mechanism of recovery. Moreover, key factors which should be considered to establish the techno-economic feasibility of this process are here discussed.

Investigation of the Critical Biomass of Acclimated Microbial Communities to High Ammonia Concentrations for a Successful Bioaugmentation of Biogas Anaerobic Reactors with Ammonia Inhibition

This study aimed to investigate the role of the bioaugmented critical biomass that should be injected for successful bioaugmentation for addressing ammonia inhibition in anaerobic reactors used for biogas production. Cattle manure was used as a feedstock for anaerobic digestion (AD). A mixed microbial culture was acclimated to high concentrations of ammonia and used as a bioaugmented culture. Different volumes of bioaugmented culture were injected in batch anaerobic reactors under ammonia toxicity levels i.e., 4 g of NH₄⁺-N L^-1. The results showed that injecting a volume equal to 65.62% of the total working reactor volume yielded the best methane production. Specifically, this volume of bioaugmented culture resulted in methane production rates of 196.18 mL g^-1 Volatile Solids (VS) and 245.88 mL g^-1 VS after 30 and 60 days of AD, respectively. These rates were not significantly different from the control reactors (30d: 205.94 mL CH₄ g^-1 VS and 60d: 230.26 mL CH₄ g^-1 VS) operating without ammonia toxicity. Analysis of the microbial community using 16S rRNA gene sequencing revealed the dominance of acetoclastic methanogen members from the genus Methanosaeta in all reactors.

Identifying and Understanding Microbial Methanogenesis in CO2 Storage

Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO₂ can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO₂, yet there has been little consideration of the subsurface microbial impact on CO₂ storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO₂ that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO₂ storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H₂ generation. We expect that the bioavailability of H₂ (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO₂ storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO₂ storage sites and its potential impact.

Geological processes mediate a microbial dispersal loop in the deep biosphere

The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.

Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir

Oil reservoirs can represent extreme environments for microbial life due to low water availability, high salinity, high pressure and naturally occurring radionuclides. This study investigated the microbiome of saline formation water samples from a Gulf of Mexico oil reservoir. Metagenomic analysis and associated anaerobic enrichment cultures enabled investigations into metabolic potential for microbial activity and persistence in this environment given its high salinity (4.5%) and low nutrient availability. Preliminary 16S rRNA gene amplicon sequencing revealed very low microbial diversity. Accordingly, deep shotgun sequencing resulted in nine metagenome-assembled genomes (MAGs), including members of novel lineages QPJE01 (genus level) within the Halanaerobiaceae, and BM520 (family level) within the Bacteroidales. Genomes of the nine organisms included respiratory pathways such as nitrate reduction (in Arhodomonas, Flexistipes, Geotoga and Marinobacter MAGs) and thiosulfate reduction (in Arhodomonas, Flexistipes and Geotoga MAGs). Genomic evidence for adaptation to high salinity, withstanding radioactivity, and metal acquisition was also observed in different MAGs, possibly explaining their occurrence in this extreme habitat. Other metabolic features included the potential for quorum sensing and biofilm formation, and genes for forming endospores in some cases. Understanding the microbiomes of deep biosphere environments sheds light on the capabilities of uncultivated subsurface microorganisms and their potential roles in subsurface settings, including during oil recovery operations.

Rapid microbial methanogenesis during CO2 storage in hydrocarbon reservoirs

Carbon capture and storage (CCS) is a key technology to mitigate the environmental impact of carbon dioxide (CO₂) emissions. An understanding of the potential trapping and storage mechanisms is required to provide confidence in safe and secure CO₂ geological sequestration^1,2. Depleted hydrocarbon reservoirs have substantial CO₂ storage potential¹,³, and numerous hydrocarbon reservoirs have undergone CO₂ injection as a means of enhanced oil recovery (CO₂-EOR), providing an opportunity to evaluate the (bio)geochemical behaviour of injected carbon. Here we present noble gas, stable isotope, clumped isotope and gene-sequencing analyses from a CO₂-EOR project in the Olla Field (Louisiana, USA). We show that microbial methanogenesis converted as much as 13-19% of the injected CO₂ to methane (CH₄) and up to an additional 74% of CO₂ was dissolved in the groundwater. We calculate an in situ microbial methanogenesis rate from within a natural system of 73-109 millimoles of CH₄ per cubic metre (standard temperature and pressure) per year for the Olla Field. Similar geochemical trends in both injected and natural CO₂ fields suggest that microbial methanogenesis may be an important subsurface sink of CO₂ globally. For CO₂ sequestration sites within the environmental window for microbial methanogenesis, conversion to CH₄ should be considered in site selection.

Water Salinity as Potential Aid for Improving the Carbon Dioxide Replacement Process’ Effectiveness in Natural Gas Hydrate Reservoirs

Natural gas hydrates represent a valid opportunity to counteract two of the most serious issues that are affecting humanity this century: climate change and the need for new energy sources, due to the fast and constant increase in the population worldwide. The energy that might be produced with methane contained in hydrates is greater than any amount of energy producible with known conventional energy sources; being widespread in all oceans, they would greatly reduce problems and conflicts associated with the monopoly of energy sources. The possibility of extracting methane and simultaneously performing the permanent storage of carbon dioxide makes hydrate an almost carbon-neutral energy source. The main topic of scientific research is to improve the recovery of technologies and guest species replacement strategies in order to make the use of gas hydrates economically advantageous. In the present paper, an experimental study on how salt can alter the formation process of both methane and carbon dioxide hydrate was carried out. The pressure–temperature conditions existing between the two respective equilibrium curves are directly proportional to the effectiveness of the replacement process and thus its feasibility. Eighteen formation tests were realized at three different salinity values: 0, 30 and 37 g/L. Results show that, as the salinity degree increases, the space between CO2 and CH4 formation curves grows. A further aspect highlighted by the tests is how the carbon dioxide formation process tends to assume a very similar trend in all experiments, while curves obtained during methane tests show a similar trend but with some significant differences. Moreover, this tendency became more pronounced with the increase in the salinity degree.

An Unexpectedly Broad Thermal and Salinity-Tolerant Estuarine Methanogen Community

Moderately thermophilic (T_max, ~55 °C) methanogens are identified after extended enrichments from temperate, tropical and low-temperature environments. However, thermophilic methanogens with higher growth temperatures (T_opt ≥ 60 °C) are only reported from high-temperature environments. A microcosm-based approach was used to measure the rate of methane production and methanogen community structure over a range of temperatures and salinities in sediment from a temperate estuary. We report short-term incubations (<48 h) revealing methanogens with optimal activity reaching 70 °C in a temperate estuary sediment (in situ temperature 4–5 °C). While 30 °C enrichments amended with acetate, H₂ or methanol selected for corresponding mesophilic trophic groups, at 60 °C, only hydrogenotrophs (genus Methanothermobacter) were observed. Since these methanogens are not known to be active under in situ temperatures, we conclude constant dispersal from high temperature habitats. The likely provenance of the thermophilic methanogens was studied by enrichments covering a range of temperatures and salinities. These enrichments indicated that the estuarine sediment hosted methanogens encompassing the global activity envelope of most cultured species. We suggest that estuaries are fascinating sink and source environments for microbial function study.

16s rRNA gene sequencing and radioisotopic analysis reveal the composition of ammonia acclimatized methanogenic consortia

Different mesophilic and thermophilic methanogenic consortia were acclimatised and enriched to extreme total ammonia (9.0 and 5.0 g NH₄⁺-N L^-1, respectively) and free ammonia (1.0 and 1.4 g NH₃-N L^-1, respectively) levels in this study. [2-¹⁴C] acetate radioisotopic analyses showed the dominance of aceticlastic methanogenesis in all enriched consortia. According to 16S rRNA gene sequencing result, in mesophilic consortia, methylotrophic Methanomassiliicoccus luminyensis was predominant, followed by aceticlastic Methanosarcina soligelidi. A possible scenario explaining the dominance of M. luminyensis includes the use of methylamine produced by Tissierella spp. and biomass build-up by metabolizing acetate. Nevertheless, further studies are needed to pinpoint the exact metabolic pathway of M. luminyensis. In thermophilic consortia, aceticlastic Methanosarcina thermophila was the sole dominant methanogen. Overall, results derived from this study demonstrated the efficient biomethanation ability of these ammonia-tolerant methanogenic consortia, indicating a potential application of these consortia to solve ammonia toxicity problems in future full-scale reactors.

Oil reservoirs, an exceptional habitat for microorganisms

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Water-containing parts within oil reservoirs extend the zone of biodegradation.

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Biodegradation is controlled by environmental factors.

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Proteobacteria and Euryarchaeota are ubiquitous in oil reservoirs over all temperature ranges.

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Biofilms as microbial adaption in oil reservoirs.

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Viruses as potential control for microbial activity and function.

Microorganisms are present in oil reservoirs around the world where they degrade oil and lead to changes in oil quality. Unfortunately, our knowledge about processes in deep oil reservoirs is limited due to the lack of undisturbed samples. In this review, we discuss the distribution of microorganisms at the oil-water transition zone as well as in water saturated parts of the oil leg and their possible physiological adaptations to abiotic and biotic ecological factors such as temperature, salinity and viruses. We show the importance of studying the water phase within the oil, because small water inclusions and pockets within the oil leg provide an exceptional habitat for microorganisms within a natural oil reservoir and concurrently enlarge the zone of oil biodegradation. Environmental factors such as temperature and salinity control oil biodegradation. Temperature determines the type of microorganisms which are able to inhabit the reservoir. Proteobacteria and Euryarchaeota, are ubiquitous in oil reservoirs over all temperature ranges, whereas some others are tied to specific temperatures. It is proposed that biofilm formation is the dominant way of life within oil reservoirs, enhancing nutrient uptake, syntrophic interactions and protection against environmental stress. Literature shows that viruses are abundant in oil reservoirs and the possible impact on microbial community composition due to control of microbial activity and function is discussed.

Different Diversity and Distribution of Archaeal Community in the Aqueous and Oil Phases of Production Fluid From High-Temperature Petroleum Reservoirs

To get a better knowledge on how archaeal communities differ between the oil and aqueous phases and whether environmental factors promote substantial differences on microbial distributions among production wells, we analyzed archaeal communities in oil and aqueous phases from four high-temperature petroleum reservoirs (55–65°C) by using 16S rRNA gene based 454 pyrosequencing. Obvious dissimilarity of the archaeal composition between aqueous and oil phases in each independent production wells was observed, especially in production wells with higher water cut, and diversity in the oil phase was much higher than that in the corresponding aqueous phase. Statistical analysis further showed that archaeal communities in oil phases from different petroleum reservoirs tended to be more similar, but those in aqueous phases were the opposite. In the high-temperature ecosystems, temperature as an environmental factor could have significantly affected archaeal distribution, and archaeal diversity raised with the increase of temperature (p < 0.05). Our results suggest that to get a comprehensive understanding of petroleum reservoirs microbial information both in aqueous and oil phases should be taken into consideration. The microscopic habitats of oil phase, technically the dispersed minuscule water droplets in the oil could be a better habitat that containing the indigenous microorganisms.

Effect of different ammonia sources on aceticlastic and hydrogenotrophic methanogens

Ammonium chloride (NH₄Cl) was usually used as a model ammonia source to simulate ammonia inhibition during anaerobic digestion (AD) of nitrogen-rich feedstocks. However, ammonia in AD originates mainly from degradation of proteins, urea and nucleic acids, which is distinct from NH₄Cl. Thus, in this study, the inhibitory effect of a "natural" ammonia source (urea) and NH₄Cl, on four pure methanogenic strains (aceticlastic: Methanosarcina thermophila, Methanosarcina barkeri; hydrogenotrophic: Methanoculleus bourgensis, Methanoculleus thermophilus), was assessed under mesophilic (37 °C) and thermophilic (55 °C) conditions. The results showed that urea hydrolysis increased pH significantly to unsuitable levels for methanogenic growth, while NH₄Cl had a negligible effect on pH. After adjusting initial pH to 7 and 8, urea was significantly stronger inhibitor with longer lag phases to methanogenesis compared to NH₄Cl. Overall, urea seems to be more toxic on both aceticlastic and hydrogenotrophic methanogens compared to NH₄Cl under the same total and free ammonia levels.

Study on distribution of reservoir endogenous microbe and oil displacement mechanism

In order to research oil displacement mechanism by indigenous microbial communities under reservoir conditions, indigenous microbial flooding experiments using the endogenous mixed bacterium from Shengli Oilfield were carried out. Through microscopic simulation visual model, observation and analysis of distribution and flow of the remaining oil in the process of water flooding and microbial oil displacement were conducted under high temperature and high pressure conditions. Research has shown that compared with atmospheric conditions, the growth of the microorganism metabolism and attenuation is slowly under high pressure conditions, and the existence of the porous medium for microbial provides good adhesion, also makes its growth cycle extension. The microbial activities can effectively launch all kinds of residual oil, and can together with metabolites, enter the blind holes off which water flooding, polymer flooding and gas flooding can't sweep, then swap out remaining oil, increase liquidity of the crude oil and remarkably improve oil displacement effect.

Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica

A strictly anaerobic, mesophilic, syntrophic, alkane-degrading strain, L81T, was isolated from a biofilm sampled from a black smoker chimney at the Loki's Castle vent field. Cells were straight, rod-shaped, Gram-positive-staining and motile. Growth was observed at pH 6.2-9.5, 14-42 °C and 0.5-6 % (w/w) NaCl, with optima at pH 7.0-8.2, 37 °C and 3% (w/w) NaCl. Proteinaceous substrates, sugars, organic acids and hydrocarbons were utilized for growth. Thiosulfate was used as an external electron acceptor during growth on crude oil. Strain L81T was capable of syntrophic hydrocarbon degradation when co-cultured with a methanogenic archaeon, designated strain LG6, isolated from the same enrichment. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain L81T is affiliated with the family Lachnospiraceae, and is most closely related to the type strains of Natranaerovirga pectinivora (92 % sequence similarity) and Natranaerovirga hydrolytica (90%). The major cellular fatty acids of strain L81T were C15 : 0, anteiso-C15 : 0 and C16 : 0, and the profile was distinct from those of the species of the genus Natranaerovirga. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, four unidentified glycolipids and two unidentified phosphoglycolipids. The G+C content of genomic DNA was determined to be 31.7 mol%. Based on our phenotypic, phylogenetic and chemotaxonomic results, strain L81T is considered to represent a novel species of a new genus of the family Lachnospiraceae, for which we propose the name Abyssivirga alkaniphila gen. nov., sp. nov. The type strain of Abyssivirga alkaniphila is L81T (=DSM 29592T=JCM 30920T). We also provide emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.

Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA

Microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4–1.1 m) coalbeds with marginal thermal maturities (0.5–0.7% R_o) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na–Cl type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L⁻¹. Gas dryness values [C₁/(C₂ + C₃)] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183‰. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales, an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.

Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management

Our understanding of the processes underlying the formation of heavy oil has been transformed in the last decade. The process was once thought to be driven by oxygen delivered to deep petroleum reservoirs by meteoric water. This paradigm has been replaced by a view that the process is anaerobic and frequently associated with methanogenic hydrocarbon degradation. The thermal history of a reservoir exerts a fundamental control on the occurrence of biodegraded petroleum, and microbial activity is focused at the base of the oil column in the oil water transition zone, that represents a hotspot in the petroleum reservoir biome. Here we present a synthesis of new and existing microbiological, geochemical, and biogeochemical data that expands our view of the processes that regulate deep life in petroleum reservoir ecosystems and highlights interactions of a range of biotic and abiotic factors that determine whether petroleum is likely to be biodegraded in situ, with important consequences for oil exploration and production. Specifically we propose that the salinity of reservoir formation waters exerts a key control on the occurrence of biodegraded heavy oil reservoirs and introduce the concept of palaeopickling. We also evaluate the interaction between temperature and salinity to explain the occurrence of non-degraded oil in reservoirs where the temperature has not reached the 80-90°C required for palaeopasteurization. In addition we evaluate several hypotheses that might explain the occurrence of organisms conventionally considered to be aerobic, in nominally anoxic petroleum reservoir habitats. Finally we discuss the role of microbial processes for energy recovery as we make the transition from fossil fuel reliance, and how these fit within the broader socioeconomic landscape of energy futures.

Physicochemical impacts associated with natural gas development on methanogenesis in deep sand aquifers

The Minami-Kanto gas field, where gases are dissolved in formation water, is a potential analogue for a marine gas hydrate area because both areas are characterized by the accumulation of microbial methane in marine turbidite sand layers interbedded with mud layers. This study examined the physicochemical impacts associated with natural gas production and well drilling on the methanogenic activity and composition in this gas field. Twenty-four gas-associated formation water samples were collected from confined sand aquifers through production wells. The stable isotopic compositions of methane in the gases indicated their origin to be biogenic via the carbonate reduction pathway. Consistent with this classification, methanogenic activity measurements using radiotracers, culturing experiments and molecular analysis of formation water samples indicated the predominance of hydrogenotrophic methanogenesis. The cultivation of water samples amended only with methanogenic substrates resulted in significant increases in microbial cells along with high-yield methane production, indicating the restricted availability of substrates in the aquifers. Hydrogenotrophic methanogenic activity increased with increasing natural gas production from the corresponding wells, suggesting that the flux of substrates from organic-rich mudstones to adjacent sand aquifers is enhanced by the decrease in fluid pressure in sand layers associated with natural gas/water production. The transient predominance of methylotrophic methanogens, observed for a few years after well drilling, also suggested the stimulation of the methanogens by the exposure of unutilized organic matter through well drilling. These results provide an insight into the physicochemical impacts on the methanogenic activity in biogenic gas deposits including marine gas hydrates.

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

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.

Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field

A thermophilic and hydrogenotrophic methanogen, strain RMAST, was isolated from gas-associated formation water of a gas-producing well in a natural gas field in Japan. Strain RMAST grew solely on H2/CO2 but required Casamino acids, tryptone, yeast extract or vitamins for growth. Growth of strain RMAST was stimulated by acetate. Cells were non-motile, straight rods (0.5×3.5–10.5 µm) and occurred singly or in pairs. Bundles of fimbriae occurred at both poles of cells and the cell wall was thick (approximately 21 nm, as revealed by ultrathin section electron microscopy). Strain RMAST grew at 45–80 °C (optimum, 70 °C), at pH 5.8–8.7 (optimum, pH 6.9–7.7) and with 0.001–20 g NaCl l−1 (optimum, 2.5 g NaCl l−1). Phylogenetic analysis revealed that Methanothermobacter thermautotrophicus ΔHT was most closely related to the isolate (95.7 % 16S rRNA gene sequence similarity). On the basis of morphological, phenotypic and phylogenetic characteristics, it is clear that strain RMAST represents a novel species of the genus Methanothermobacter , for which we propose the name Methanothermobacter tenebrarum sp. nov. The type strain is RMAST ( = DSM 23052T = JCM 16532T = NBRC 106236T).

Characterization of the relationship between microbial degradation processes at a hydrocarbon contaminated site using isotopic methods

Decisions to employ monitored natural attenuation (MNA) as a remediation strategy at contaminated field sites require a comprehensive characterization of the site-specific biodegradation processes. In the present study, compound-specific carbon and hydrogen isotope analysis (CSIA) was used to investigate intrinsic biodegradation of benzene and ethylbenzene in an aquifer with high levels of aromatic and aliphatic hydrocarbon contamination. Hydrochemical data and isotope fractionation analysis of sulfate and methane was used complementarily to elucidate microbial degradation processes over the course of a three year period, consisting of six sampling campaigns, in the industrial area of Weißandt-Gölzau (Saxony-Anhalt, Germany). Enrichment of (13)C and (2)H isotopes in the residual benzene and ethylbenzene pool downgradient from the pollution sources provided evidence of biodegradation of BTEX compounds at this site, targeting both compounds as the key contaminants of concern. The enrichment of heavy sulfur isotopes accompanied by decreasing sulfate concentrations and the accumulation of isotopically light methane suggested that sulfate-reducing and methanogenic processes are the major contributors to overall biodegradation in this aquifer. Along the contaminant plume, the oxidation of methane with δ(13)C(CH4) values of up to +17.5‰ was detected. This demonstrates that methane formed in the contaminant source can be transported along groundwater flow paths and be oxidized in areas with higher redox potentials, thereby competing directly with the pollutants for electron acceptors. Hydrochemical and isotope data was summarized in a conceptual model to assess whether MNA can be used as viable remediation strategy in Weißandt-Gölzau. The presented results demonstrate the benefits of combining different isotopic methods and hydrochemical approaches to evaluate the fate of organic pollutants in contaminated aquifers.

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.

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

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 CO(2) -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.

Microbial life in a liquid asphalt desert

Pitch Lake in Trinidad and Tobago is a natural asphalt reservoir nourished by pitch seepage, a form of petroleum that consists of mostly asphaltines, from the surrounding oil-rich region. During upward seepage, pitch mixes with mud and gases under high pressure, and the lighter portion evaporates or is volatilized, which produces a liquid asphalt residue characterized by low water activity, recalcitrant carbon substrates, and noxious chemical compounds. An active microbial community of archaea and bacteria, many of them novel strains (particularly from the new Tar ARC groups), totaling a biomass of up to 10(7) cells per gram, was found to inhabit the liquid hydrocarbon matrix of Pitch Lake. Geochemical and molecular taxonomic approaches revealed diverse, novel, and deeply branching microbial lineages with the potential to mediate anaerobic hydrocarbon degradation processes in different parts of the asphalt column. In addition, we found markers for archaeal methane metabolism and specific gene sequences affiliated with facultative and obligate anaerobic sulfur- and nitrite-oxidizing bacteria. The microbial diversity at Pitch Lake was found to be unique when compared to microbial communities analyzed at other hydrocarbon-rich environments, which included Rancho Le Brea, a natural asphalt environment in California, USA, and an oil well and a mud volcano in Trinidad and Tobago, among other sites. These results open a window into the microbial ecology and biogeochemistry of recalcitrant hydrocarbon matrices and establish the site as a terrestrial analogue for modeling the biotic potential of hydrocarbon lakes such as those found on Saturn's largest moon Titan.

Methanogenic degradation of petroleum hydrocarbons in subsurface environments remediation, heavy oil formation, and energy recovery

Hydrocarbons are common constituents of surface, shallow, and deep-subsurface environments. Under anaerobic conditions, hydrocarbons can be degraded to methane by methanogenic microbial consortia. This degradation process is widespread in the geosphere. In comparison with other anaerobic processes, methanogenic hydrocarbon degradation is more sustainable over geological time scales because replenishment of an exogenous electron acceptor is not required. As a consequence, this process has been responsible for the formation of the world's vast deposits of heavy oil, which far exceed conventional oil assets such as those found in the Middle East. Methanogenic degradation is also a potentially important component of attenuation in hydrocarbon contamination plumes. Studies of the organisms, syntrophic partnerships, mechanisms, and geochemical signatures associated with methanogenic hydrocarbon degradation have identified common themes and diagnostic markers for this process in the subsurface. These studies have also identified the potential to engineer methanogenic processes to enhance the recovery of energy assets as biogenic methane from residual oils stranded in petroleum systems.