Understanding the Aggregation of Model Island and Archipelago Asphaltene Molecules near Kaolinite Surfaces using Molecular Dynamics.

The solubility of asphaltenes in hydrocarbons changes with pressure, composition, and temperature, leading to precipitation and deposition, thereby causing one of the crucial problems that negatively affects oil production, transportation, and processing. Because, in some circumstances, it might be advantageous to promote asphaltene agglomeration into small colloidal particles, molecular dynamics simulations were conducted here to understand the impacts of a chemical additive inspired by cyclohexane on the mechanism of aggregation of model island and archipelago asphaltene molecules in toluene. We compared the results in the presence and absence of a kaolinite surface at 300 and 400 K. Cluster size analyses, radial distribution functions, angles between asphaltenes, radius of gyration, and entropic and energetic calculations were used to provide insights on the behavior of these systems. The results show that the hypothetical additive inspired by cyclohexane promoted the aggregation of both asphaltenes. Structural differences were observed among the aggregates obtained in our simulations. These differences are attributed to the number of aromatic cores and side chains on the asphaltene molecules as well as to that of heteroatoms. For the island structure, aggregation in the bulk phase was less pronounced than that in the proximity of the kaolinite surface, whereas the opposite was observed for the archipelago structure. In both cases, the additive promoted stacking of asphaltenes, yielding more compact aggregates. The results provided insights into the complex nature of asphaltene aggregation, although computational approaches that can access longer time and larger size scales should be chosen for quantifying emergent meso- and macroscale properties of systems containing asphaltenes in larger numbers than those that can currently be sampled via atomistic simulations.

Surface Interactions and Nanoconfinement of Methane and Methane plus CO2 Revealed by High-Pressure Magic Angle Spinning NMR Spectroscopy and Molecular Dynamics.

This study explores the fundamental, molecular- to microscopic-level behavior of methane gas confined into nanoporous silica proxies with different pore diameters and surface-to-volume (S/V) ratios. Surfaces and pore walls of nanoporous silica matrices are decorated with hydroxyl (-OH) groups, resembling natural heterogeneity. High-pressure MAS NMR was utilized to characterize the interactions between methane and the engineered nanoporous silica proxies under various temperature and pressure regimes. There was a change in the chemical shift position of confined methane slightly in the mixtures with nanoporous silica up to 393 K, as shown by high-pressure 13C-NMR. The 13C-NMR chemical shift of methane was changed by pressure, explained by the densification of methane inside the nanoporous silica materials. The influence of pore diameter and S/V of the nanoporous silica materials on the behaviors and dynamics of methane were studied. The presence of CO2 in mixtures of silica and methane needs analysis with caution because CO2 in a supercritical state and gaseous CO2 change the original structure of nanoporous silica and change surface area and pore volume. According to simulation, the picosecond scale dynamics of methane confined in larger pores of amorphous silica is faster. In the 4 nm pore, the diffusivity obtained from MD simulations in the pore with a higher S/V ratio is slower due to the trapping of methane molecules in adsorbed layers close to the corrugated pore surface. In contrast, relaxation measured with NMR for smaller pores (higher S/V) exhibits larger T1, indicating slower relaxation.

Effects of pore connectivity and tortuosity on the dynamics of fluids confined in sub-nanometer pores.

Dynamical behavior of fluids under nano-pore confinement is studied extensively as it has important implications for several industrial as well as geological processes. Pore network in many porous materials exhibits a varied degree of inter connections. The extent of this pore connectivity may affect the structural and dynamical behavior of the confined fluid. However, studies of fluid confinement addressing these effects systematically are lacking. Here, we report molecular dynamics simulation studies addressing the effects of pore connectivity on the dynamics of two representative fluids - CO2 and ethane in silicalite by systematically varying the degree of pore connectivity through selectively blocking some pore space with immobile methane molecules. By selectively turning off the pore spaces in the shape of straight, or tortuous zigzag channels, we also probe the effects of pore tortuosity. In general, pore connectivity is found to facilitate both the translational as well as rotational dynamics of both fluids, while the intermolecular modes of vibration in both fluids remain largely unaffected. The effects of providing connections between a set of straight or zigzag channel-like pores are however more nuanced. Pore tortuosity facilitates the rotational motion, but suppresses the translational motion of CO2, while its effects on the rotational and translational motion of ethane are less pronounced. The intermolecular vibrational modes of both fluids shift to higher energies with an increase in the number of tortuous pores. The results reported here provide a detailed molecular level understanding of the effects of pore connectivity on the dynamics of fluids and thus have implications for applications like fluid separation.

Effects of surface contamination on the interfacial properties of CO2/water/calcite systems.

Understanding the wetting properties of reservoir rocks can be of great benefit for advanced applications such as the effective trapping and geological storage of CO2. Despite their importance, not all mechanisms responsible for wetting mineral surfaces in subsurface environments are well understood. Factors such as temperature, pressure and salinity are often studied, achieving results with little unanimity; other possible factors are left somewhat unexplored. One such factor is the effect of contamination. In the present study, the effects of adding a non-aqueous organic contaminant, ethanol, on the CO2-water interfacial tension (IFT) and the CO2/water/calcite contact angle were investigated using molecular dynamics simulations. Within the conditions studied, relatively small amounts of ethanol cause a significant decrease in the CO2-water IFTs, as well as a pronounced increase in the water-calcite-CO2 three phase contact angle. The latter result is due to the decrease of the IFT between CO2 and water and the strong adsorption of ethanol on the solid substrate. These findings could be helpful for explaining how impurities can affect experimental data and could lead to effective carbon sequestration strategies.

Fluid Behavior in Nanoporous Silica.

We investigate dynamics of water (H2O) and methanol (CH3OH and CH3OD) inside mesoporous silica materials with pore diameters of 4.0, 2.5, and 1.5 nm using low-field (LF) nuclear magnetic resonance (NMR) relaxometry. Experiments were conducted to test the effects of pore size, pore volume, type of fluid, fluid/solid ratio, and temperature on fluid dynamics. Longitudinal relaxation times (T1) and transverse relaxation times (T2) were obtained for the above systems. We observe an increasing deviation in confined fluid behavior compared to that of bulk fluid with decreasing fluid-to-solid ratio. Our results show that the surface area-to-volume ratio is a critical parameter compared to pore diameter in the relaxation dynamics of confined water. An increase in temperature for the range between 25 and 50°C studied did not influence T2 times of confined water significantly. However, when the temperature was increased, T1 times of water confined in both silica-2.5 nm and silica-1.5 nm increased, while those of water in silica-4.0 nm did not change. Reductions in both T1 and T2 values as a function of fluid-to-solid ratio were independent of confined fluid species studied here. The parameter T1/T2 indicates that H2O interacts more strongly with the pore walls of silica-4.0 nm than CH3OH and CH3OD.

Effects of inter-crystalline space on the adsorption of ethane and CO2 in silicalite: implications for enhanced adsorption.

Adsorption of fluids in nanoporous materials is important for a variety of industries including catalysis and is a promising strategy for hydrogen storage and CO2 sequestration. It has therefore been studied extensively. In a typical adsorption experiment, the sorbent sample is usually in powder form which consists of several crystallites separated by an inter-crystalline space. This inter-crystalline space may compete with the nanopores in engineered as well as natural materials for fluid adsorption. While in computer simulations that are used to complement experiments, much attention is focused on the choice of force-field parameters, the effect of inter-crystalline spaces on the properties of adsorbed fluids remains largely ignored. We attempt to study the effects of inter-crystalline space on the simulated adsorption of ethane and CO2 modelled in TraPPE formalism in a silicalite model composed of crystallites separated by different inter-crystalline spaces. The effect of inter-crystalline space is found to be profound and differs for the two sorbates. Presence of quadrupole moment makes CO2 adsorption in the inter-crystalline space more favorable and suggests that increasing surface area of a catalytic substrate for enhanced adsorption might be a relatively more effective strategy for adsorption of a quadrupolar molecule as compared to an apolar molecule. Also, the results imply that in experiments investigating molecules confined in porous media using powder samples, apolar molecules are less likely to give undesired bulk-like contribution from inter-crystalline spaces to the experimental data. CO2 molecules adsorbed on the crystallite surfaces are found to exhibit a high degree of orientational ordering and exhibit a preferred orientation favorable for higher amounts of adsorption. While larger inter-crystalline spacings lead to higher adsorption, the effect of using a larger crystallite is to reduce the amount of adsorption. The mutual negation of these two effects explains the apparent agreement of the experimental data obtained on a powder sample and the simulation data obtained using a perfect crystal model. This work has implications for both simulations of adsorption isotherms in nanoporous materials and the interpretation of experimental data obtained for these systems.

Structure and dynamics of ethane confined in silica nanopores in the presence of CO2.

Fundamental understanding of the subcritical/supercritical behavior of key hydrocarbon species inside nano-porous matrices at elevated pressure and temperature is less developed compared to bulk fluids, but this knowledge is of great importance for chemical and energy engineering industries. This study explores in detail the structure and dynamics of ethane (C2H6) fluid confined in silica nanopores, with a focus on the effects of pressure and different ratios of C2H6 and CO2 at non-ambient temperature. Quasi-elastic neutron scattering (QENS) experiments were carried out for the pure C2H6, C2H6:CO2 = 3:1, and 1:3 mixed fluids confined in 4-nm cylindrical silica pores at three different pressures (30 bars, 65 bars, and 100 bars) at 323 K. Two Lorentzian functions were required to fit the spectra, corresponding to fast and slow translational motions. No localized motions (rotations and vibrations) were detected. Higher pressures resulted in hindrances of the diffusivity of C2H6 molecules in all systems investigated. Pore size was found to be an important factor, i.e., the dynamics of confined C2H6 is more restricted in smaller pores compared to the larger pores used in previous studies. Molecular dynamics simulations were performed to complement the QENS experiment at 65 bars, providing supportive structure information and comparable dynamic information. The simulations indicate that CO2 molecules are more strongly attracted to the pore surface compared to C2H6. The C2H6 molecules interacting with or near the pore surface form a dense first layer (L1) close to the pore surface and a second less dense layer (L2) extending into the pore center. Both the experiments and simulations revealed the role that CO2 molecules play in enhancing C2H6 diffusion ("molecular lubrication") at high CO2:C2H6 ratios. The energy scales of the two dynamic components, fast and slow, quantified by both techniques, are in very good agreement. Herein, the simulations identified the fast component as the main contributor to the dynamics. Molecule motions in the L2 region are mostly responsible for the dynamics (fast and slow) that can be detected by the instrument.

Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface.

Bacteria of the phylum Verrucomicrobia are prevalent and are particularly common in soil and freshwater environments. Their cosmopolitan distribution and reported capacity for polysaccharide degradation suggests members of Verrucomicrobia are important contributors to carbon cycling across Earth's ecosystems. Despite their prevalence, the Verrucomicrobia are underrepresented in isolate collections and genome databases; consequently, their ecophysiological roles may not be fully realized. Here, we expand genomic sampling of the Verrucomicrobia phylum by describing a novel genus, "Candidatus Marcellius," belonging to the order Opitutales "Ca. Marcellius" was recovered from a shale-derived produced fluid metagenome collected 313 days after hydraulic fracturing, the deepest environment from which a member of the Verrucomicrobia has been recovered to date. We uncover genomic attributes that may explain the capacity of this organism to inhabit a shale gas well, including the potential for utilization of organic polymers common in hydraulic fracturing fluids, nitrogen fixation, adaptation to high salinities, and adaptive immunity via CRISPR-Cas. To illuminate the phylogenetic and environmental distribution of these metabolic and adaptive traits across the Verrucomicrobia phylum, we performed a comparative genomic analysis of 31 publicly available, nearly complete Verrucomicrobia genomes. Our genomic findings extend the environmental distribution of the Verrucomicrobia 2.3 kilometers into the terrestrial subsurface. Moreover, we reveal traits widely encoded across members of the Verrucomicrobia, including the capacity to degrade hemicellulose and to adapt to physical and biological environmental perturbations, thereby contributing to the expansive habitat range reported for this phylum.IMPORTANCE The Verrucomicrobia phylum of bacteria is widespread in many different ecosystems; however, its role in microbial communities remains poorly understood. Verrucomicrobia are often low-abundance community members, yet previous research suggests they play a major role in organic carbon degradation. While Verrucomicrobia remain poorly represented in culture collections, numerous genomes have been reconstructed from metagenomic data sets in recent years. The study of genomes from across the phylum allows for an extensive assessment of their potential ecosystem roles. The significance of this work is (i) the recovery of a novel genus of Verrucomicrobia from 2.3 km in the subsurface with the ability to withstand the extreme conditions that characterize this environment, and (ii) the most extensive assessment of ecophysiological traits encoded by Verrucomicrobia genomes to date. We show that members of this phylum are specialist organic polymer degraders that can withstand a wider range of environmental conditions than previously thought.

In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing.

In the last decade, extensive application of hydraulic fracturing technologies to unconventional low-permeability hydrocarbon-rich formations has significantly increased natural-gas production in the United States and abroad. The injection of surface-sourced fluids to generate fractures in the deep subsurface introduces microbial cells and substrates to low-permeability rock. A subset of injected organic additives has been investigated for their ability to support biological growth in shale microbial community members; however, to date, little is known on how complex xenobiotic organic compounds undergo biotransformations in this deep rock ecosystem. Here, high-resolution chemical, metagenomic, and proteomic analyses reveal that widely-used surfactants are degraded by the shale-associated taxa Halanaerobium, both in situ and under laboratory conditions. These halotolerant bacteria exhibit surfactant substrate specificities, preferring polymeric propoxylated glycols (PPGs) and longer alkyl polyethoxylates (AEOs) over polyethylene glycols (PEGs) and shorter AEOs. Enzymatic transformation occurs through repeated terminal-end polyglycol chain shortening during co-metabolic growth through the methylglyoxal bypass. This work provides the first evidence that shale microorganisms can transform xenobiotic surfactants in fracture fluid formulations, potentially affecting the efficiency of hydrocarbon recovery, and demonstrating an important association between injected substrates and microbial growth in an engineered subsurface ecosystem.

Water adsorption on olivine(010) surfaces: Effect of alkali and transition metal cation doping.

Dopants have the potential to locally modify water-olivine interactions, which can impact geological processes, such as weathering, CO2 sequestration, and abiotic hydrocarbon generation. As a first step in understanding the role of dopants on the water structure and chemistry at water-olivine interfaces, water monomer adsorption on alkaline earth (AE) and transition metal (TM) doped forsterite(010) [Mg2SiO4(010)] surfaces was studied using density functional theory (DFT). Dopants that occur in olivine minerals were considered and consisted of Ca, Sr, and Ba for the AE dopants and Cr, Mn, Fe, Co, and Ni for the TM dopants. The water molecule adsorbs on the olivine surface through a metal-water bond (Me-Ow) and a hydrogen bond with an adjacent surface lattice oxygen (Ox-Hw). A frontier orbital analysis reveals that the 1b2, 3a1, and 1b1 (HOMO) of the water molecule are involved in the bonding. All of the TM dopants show strong net Me-Ow covalent bonding between 3a1 and 1b1 water orbitals and TM d states, while the AE dopants except for Mg2SiO4(010) show negligible Me-Ow covalent bonding. Both the AE and TM dopants show similar hydrogen bonding features involving both the 1b2 and 3a1 orbitals. While the AE cations show an overall lower Me-Ow covalent interaction, the AE dopants have strong electrostatic interactions between the positive metal cation and the negatively charged water dipole. A bonding model incorporating a linear combination of the covalent Me-Ow bond, the Ox-Hw hydrogen bond, the electrostatic interaction between the dopant cation and the H2O molecule, and the surface distortion energy is needed to capture the variation in the DFT adsorption energies on the olivine surfaces. The bonding analysis is able to identify the dominant contributions to water-dopant interactions and can serve as a basis for future studies of more realistic water-olivine interfaces.

Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin.

Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted. Here, we report the isolation, genomic and phenotypic characterization of Marinobacter and Arcobacter bacterial species from natural-gas wells in the Utica-Point Pleasant and Marcellus Formations coupled to supporting geochemical and metagenomic analyses of produced fluid samples. These unconventional hydrocarbon system-derived Marinobacter sp. are capable of utilizing a diversity of organic carbon sources including aliphatic and aromatic hydrocarbons, amino acids, and carboxylic acids. Marinobacter and Arcobacter can metabolize organic nitrogen sources and have the capacity for denitrification and dissimilatory nitrate reduction to ammonia (DNRA) respectively; with DNRA and ammonification processes partially explaining high concentrations of ammonia measured in produced fluids. Arcobacter is capable of chemosynthetic sulfur oxidation, which could fuel metabolic processes for other heterotrophic, fermentative, or sulfate-reducing community members. Our analysis revealed mechanisms for growth of these taxa across a broad range of salinities (up to 15% salt), which explains their enrichment during early natural-gas production. These results demonstrate the prevalence of Marinobacter and Arcobacter during a key maturation phase of hydraulically fractured natural-gas wells, and highlight the significant role these genera play in biogeochemical cycling for this economically important energy system.

Structure and dynamics of water on the forsterite surface.

The behavior of water on mineral surfaces is the key to understanding interfacial and chemical reaction processes. Olivine is one of the major rock-forming minerals and its interaction with water is a ubiquitous phenomenon both on Earth's surface and in the subsurface. This work presents a combined study using molecular dynamics (MD) simulations and quasi-elastic neutron scattering (QENS) experiments conducted using three different instruments to study the structure and dynamics of water on the forsterite (Mg-end member of olivine) surface at 270 K. A combination of three different QENS instruments probes dynamical processes occurring across a broad range of time scales (∼1 ps to ∼1 ns in this study). The water structure on the hydroxylated surface is composed of three distinct water layers, transitioning from well-ordered and nearly immobile closest to the surface to a less structured layer. The energies of three motions (including translation and rotation) derived from simulations agree well with the experiments, covering the energy range from a few to hundreds of micro electron volts.

Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale.

About 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic-rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine-scale microdiversity was observed in CRISPR-Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales.

Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth's surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and metabolite findings from the laboratory were then corroborated using regression-based modeling performed on metagenomic and metabolite data from more than 40 produced fluids from five hydraulically fractured shale wells. Collectively, our findings show that Halanaerobium, Geotoga, and Methanohalophilus strain abundances predict a significant fraction of nitrogen and carbon metabolites in the field. Our laboratory findings also exposed cryptic predatory, cooperative, and competitive interactions that impact microorganisms across fractured shales. Scaling these results from the laboratory to the field identified mechanisms underpinning biogeochemical reactions, yielding knowledge that can be harnessed to potentially increase energy yields and inform management practices in hydraulically fractured shales.

Impacts of Methane on Carbon Dioxide Storage in Brine Formations.

In the context of geological carbon sequestration (GCS), carbon dioxide (CO2 ) is often injected into deep formations saturated with a brine that may contain dissolved light hydrocarbons, such as methane (CH4 ). In this multicomponent multiphase displacement process, CO2 competes with CH4 in terms of dissolution, and CH4 tends to exsolve from the aqueous into a gaseous phase. Because CH4 has a lower viscosity than injected CO2 , CH4 is swept up into a 'bank' of CH4 -rich gas ahead of the CO2 displacement front. On the one hand, this may provide a useful tracer signal of an approaching CO2 front. On the other hand, the emergence of gaseous CH4 is undesirable because it poses a leakage risk of a far more potent greenhouse gas than CO2 if the cap rock is compromised. Open fractures or faults and wells could result in CH4 contamination of overlying groundwater aquifers as well as surface emissions. We investigate this process through detailed numerical simulations for a large-scale GCS pilot project (near Cranfield, Mississippi) for which a rich set of field data is available. An accurate cubic-plus-association equation-of-state is used to describe the non-linear phase behavior of multiphase brine-CH4 -CO2 mixtures, and breakthrough curves in two observation wells are used to constrain transport processes. Both field data and simulations indeed show the development of an extensive plume of CH4 -rich (up to 90 mol%) gas as a consequence of CO2 injection, with important implications for the risk assessment of future GCS projects.

Propane-Water Mixtures Confined within Cylindrical Silica Nanopores: Structural and Dynamical Properties Probed by Molecular Dynamics.

Despite the multiple length and time scales over which fluid-mineral interactions occur, interfacial phenomena control the exchange of matter and impact the nature of multiphase flow, as well as the reactivity of C-O-H fluids in geologic systems. In general, the properties of confined fluids, and their influence on porous geologic phenomena are much less well understood compared to those of bulk fluids. We used equilibrium molecular dynamics simulations to study fluid systems composed of propane and water, at different compositions, confined within cylindrical pores of diameter ∼16 Šcarved out of amorphous silica. The simulations are conducted within a single cylindrical pore. In the simulated system all the dangling silicon and oxygen atoms were saturated with hydroxyl groups and hydrogen atoms, respectively, yielding a total surface density of 3.8 -OH/nm2. Simulations were performed at 300 K, at different bulk propane pressures, and varying the composition of the system. The structure of the confined fluids was quantified in terms of the molecular distribution of the various molecules within the pore as well as their orientation. This allowed us to quantify the hydrogen bond network and to observe the segregation of propane near the pore center. Transport properties were quantified in terms of the mean square displacement in the direction parallel to the pore axis, which allows us to extract self-diffusion coefficients. The diffusivity of propane in the cylindrical pore was found to depend on pressure, as well as on the amount of water present. It was found that the propane self-diffusion coefficient decreases with increasing water loading because of the formation of water bridges across the silica pores, at sufficiently high water content, which hinder propane transport. The rotational diffusion, the lifespan of hydrogen bonds, and the residence time of water molecules at contact with the silica substrate were quantified from the simulated trajectories using the appropriate autocorrelation functions. The simulations contribute to a better understanding of the molecular phenomena relevant to the behavior of fluids in the subsurface.

Confinement Effects on Carbon Dioxide Methanation: A Novel Mechanism for Abiotic Methane Formation.

An important scientific debate focuses on the possibility of abiotic synthesis of hydrocarbons during oceanic crust-seawater interactions. While on-site measurements near hydrothermal vents support this possibility, laboratory studies have provided data that are in some cases contradictory. At conditions relevant for sub-surface environments it has been shown that classic thermodynamics favour the production of CO2 from CH4, while abiotic methane synthesis would require the opposite. However, confinement effects are known to alter reaction equilibria. This report shows that indeed thermodynamic equilibrium can be shifted towards methane production, suggesting that thermal hydrocarbon synthesis near hydrothermal vents and deeper in the magma-hydrothermal system is possible. We report reactive ensemble Monte Carlo simulations for the CO2 methanation reaction. We compare the predicted equilibrium composition in the bulk gaseous phase to that expected in the presence of confinement. In the bulk phase we obtain excellent agreement with classic thermodynamic expectations. When the reactants can exchange between bulk and a confined phase our results show strong dependency of the reaction equilibrium conversions, [Formula: see text], on nanopore size, nanopore chemistry, and nanopore morphology. Some physical conditions that could shift significantly the equilibrium composition of the reactive system with respect to bulk observations are discussed.

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales.

Hydraulic fracturing of black shale formations has greatly increased United States oil and natural gas recovery. However, the accumulation of biomass in subsurface reservoirs and pipelines is detrimental because of possible well souring, microbially induced corrosion, and pore clogging. Temporal sampling of produced fluids from a well in the Utica Shale revealed the dominance of Halanaerobium strains within the in situ microbial community and the potential for these microorganisms to catalyze thiosulfate-dependent sulfidogenesis. From these field data, we investigated biogenic sulfide production catalyzed by a Halanaerobium strain isolated from the produced fluids using proteogenomics and laboratory growth experiments. Analysis of Halanaerobium isolate genomes and reconstructed genomes from metagenomic data sets revealed the conserved presence of rhodanese-like proteins and anaerobic sulfite reductase complexes capable of converting thiosulfate to sulfide. Shotgun proteomics measurements using a Halanaerobium isolate verified that these proteins were more abundant when thiosulfate was present in the growth medium, and culture-based assays identified thiosulfate-dependent sulfide production by the same isolate. Increased production of sulfide and organic acids during the stationary growth phase suggests that fermentative Halanaerobium uses thiosulfate to remove excess reductant. These findings emphasize the potential detrimental effects that could arise from thiosulfate-reducing microorganisms in hydraulically fractured shales, which are undetected by current industry-wide corrosion diagnostics. IMPORTANCE Although thousands of wells in deep shale formations across the United States have been hydraulically fractured for oil and gas recovery, the impact of microbial metabolism within these environments is poorly understood. Our research demonstrates that dominant microbial populations in these subsurface ecosystems contain the conserved capacity for the reduction of thiosulfate to sulfide and that this process is likely occurring in the environment. Sulfide generation (also known as "souring") is considered deleterious in the oil and gas industry because of both toxicity issues and impacts on corrosion of the subsurface infrastructure. Critically, the capacity for sulfide generation via reduction of sulfate was not detected in our data sets. Given that current industry wellhead tests for sulfidogenesis target canonical sulfate-reducing microorganisms, these data suggest that new approaches to the detection of sulfide-producing microorganisms may be necessary.

Surface Interactions and Confinement of Methane: A High Pressure Magic Angle Spinning NMR and Computational Chemistry Study.

Characterization and modeling of the molecular-level behavior of simple hydrocarbon gases, such as methane, in the presence of both nonporous and nanoporous mineral matrices allows for predictive understanding of important processes in engineered and natural systems. In this study, changes in local electromagnetic environments of the carbon atoms in methane under conditions of high pressure (up to 130 bar) and moderate temperature (up to 346 K) were observed with 13C magic-angle spinning (MAS) NMR spectroscopy while the methane gas was mixed with two model solid substrates: a fumed nonporous, 12 nm particle size silica and a mesoporous silica with 200 nm particle size and 4 nm average pore diameter. Examination of the interactions between methane and the silica systems over temperatures and pressures that include the supercritical regime was allowed by a novel high pressure MAS sample containment system, which provided high resolution spectra collected under in situ conditions. For pure methane, no significant thermal effects were found for the observed 13C chemical shifts at all pressures studied here (28.2, 32.6, 56.4, 65.1, 112.7, and 130.3 bar). However, the 13C chemical shifts of resonances arising from confined methane changed slightly with changes in temperature in mixtures with mesoporous silica. The chemical shift values of 13C nuclides in methane change measurably as a function of pressure both in the pure state and in mixtures with both silica matrices, with a more pronounced shift when meso-porous silica is present. Molecular-level simulations utilizing GCMC, MD, and DFT confirm qualitatively that the experimentally measured changes are attributed to interactions of methane with the hydroxylated silica surfaces as well as densification of methane within nanopores and on pore surfaces.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.