Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales

Interactions between microbial communities and polymers in hydraulic fracturing water cycle: A review

Hydraulic fracturing (HF) has substantially boosted global unconventional hydrocarbon production but has also introduced various environmental and operational challenges. Understanding the interactions between abundant and diverse microbial communities and chemicals, particularly polymers used for proppant delivery, thickening, and friction reduction, in HF water cycles is crucial for addressing these challenges. This review primarily examined the recent studies conducted in China, an emerging area for HF activities, and comparatively examined studies from other regions. In China, polyacrylamide (PAM) and its derivatives products became key components in hydraulic fracturing fluid (HFF) for unconventional hydrocarbon development. The microbial diversity of unconventional HF water cycles in China was higher compared to North America, with frequent detection of taxa such as Shewanella, Marinobacter, and Desulfobacter. While biodegradation, biocorrosion, and biofouling were common issues across regions, the mechanisms underlying these microbe-polymer interactions differed substantially. Notably, in HF sites in the Sichuan Basin, the use of biocides gradually decreased its efficiency to mitigate adverse microbial activities. High-throughput sequencing proved to be a robust tool that could identify key bioindicators and biodegradation pathways, and help select optimal polymers and biocides, leading to more efficient HFF systems. The primary aim of this study is to raise awareness about the interactions between microorganisms and polymers, providing fresh insights that can inform decisions related to enhanced chemical use and biological control measures at HF sites.

Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin

Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a "shut-in" period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.

Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential

Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.

Illegal dumping of oil and gas wastewater alters arid soil microbial communities

The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.

Changes in environmental and engineered conditions alter the plasma membrane lipidome of fractured shale bacteria

IMPORTANCE

Microorganisms inadvertently introduced into the shale reservoir during fracturing face multiple stressors including brine-level salinities and starvation. However, some anaerobic halotolerant bacteria adapt and persist for long periods of time. They produce hydrogen sulfide, which sours the reservoir and corrodes engineering infrastructure. In addition, they form biofilms on rock matrices, which decrease shale permeability and clog fracture networks. These reduce well productivity and increase extraction costs. Under stress, microbes remodel their plasma membrane to optimize its roles in protection and mediating cellular processes such as signaling, transport, and energy metabolism. Hence, by observing changes in the membrane lipidome of model shale bacteria, Halanaerobium congolense WG10, and mixed consortia enriched from produced fluids under varying subsurface conditions and growth modes, we provide insight that advances our knowledge of the fractured shale biosystem. We also offer data-driven recommendations for improving biocontrol efficacy and the efficiency of energy recovery from unconventional formations.

Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs

Hydraulic fracturing has unlocked vast amounts of hydrocarbons trapped within unconventional shale formations. This large-scale engineering approach inadvertently introduces microorganisms into the hydrocarbon reservoir, allowing them to inhabit a new physical space and thrive in the unique biogeochemical resources present in the environment. Advancing our fundamental understanding of microbial growth and physiology in this extreme subsurface environment is critical to improving biofouling control efficacy and maximizing opportunities for beneficial natural resource exploitation. Here, we used metaproteomics and exometabolomics to investigate the biochemical mechanisms underpinning the adaptation of model bacterium Halanaerobium congolense WG10 and mixed microbial consortia enriched from shale-produced fluids to hypersalinity and very low reservoir flow rates (metabolic stress). We also queried the metabolic foundation for biofilm formation in this system, a major impediment to subsurface energy exploration. For the first time, we report that H. congolense WG10 accumulates tyrosine for osmoprotection, an indication of the flexible robustness of stress tolerance that enables its long-term persistence in fractured shale environments. We also identified aromatic amino acid synthesis and cell wall maintenance as critical to biofilm formation. Finally, regulation of transmembrane transport is key to metabolic stress adaptation in shale bacteria under very low well flow rates. These results provide unique insights that enable better management of hydraulically fractured shale systems, for more efficient and sustainable energy extraction.

Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential

The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.

Microbial communities in freshwater used for hydraulic fracturing are unable to withstand the high temperatures and pressures characteristic of fractured shales

Natural gas is recovered from shale formations by hydraulic fracturing, a process known to create microbial ecosystems in the deep subsurface. Microbial communities that emerge in fractured shales include organisms known to degrade fracturing fluid additives and contribute to corrosion of well infrastructure. In order to limit these negative microbial processes, it is essential to constrain the source of the responsible micro-organisms. Previous studies have identified a number of potential sources, including fracturing fluids and drilling muds, yet these sources remain largely untested. Here, we apply high-pressure experimental approaches to assess whether the microbial community in synthetic fracturing fluid made from freshwater reservoir water can withstand the temperature and pressure conditions of hydraulic fracturing and the fractured shale environment. Using cell enumerations, DNA extraction and culturing, we show that the community can withstand high pressure or high temperature alone, but the combination of both is fatal. These results suggest that initial freshwater-based fracturing fluids are an unlikely source of micro-organisms in fractured shales. These findings indicate that potentially problematic lineages, such as sulfidogenic strains of Halanaerobium that have been found to dominate fractured shale microbial communities, likely derive from other input sources into the downwell environment, such as drilling muds.

Factors affecting bacterial community dynamics and volatile metabolite profiles of Thai traditional salt fermented fish

Bacterial diversity of the Thai traditional salt fermented fish with roasted rice bran (Pla-ra) was investigated using classical and molecular approaches. Bacterial population of Pla-ra ranged from 10²-10⁶ in solid-state (SSF) and 10⁶-10⁹ CFU/g in submerged (SMF) fermentation types. Halanaerobium spp. and Lentibacillus spp. were the main genera particularly detected when rRNA analysis was applied. Tetragenococcus halophillus were dominant during the final stage in sea salt-recipe samples while Bacillus spp. were found in those rock salt recipes. In contrast, cultural plating demonstrated that Bacillus spp., generally B. amyloliquefaciens, were the dominant genera. In addition, B. pumilus, B. autrophaeus, B.subtilis and B. velezensis shown some relations with rock salt-recipe samples. The main volatile metabolites in all samples were butanoic acid and its derivatives. Key factors affected bacterial profiles and volatile compounds of salt fermented fish were type of salt, addition of roasted rice bran, and fermenting conditions.

New microbiological insights from the Bowland shale highlight heterogeneity of the hydraulically fractured shale microbiome

BACKGROUND

Hydraulically fractured shales offer a window into the deep biosphere, where hydraulic fracturing creates new microbial ecosystems kilometers beneath the surface of the Earth. Studying the microbial communities from flowback fluids that are assumed to inhabit these environments provides insights into their ecophysiology, and in particular their ability to survive in these extreme environments as well as their influence on site operation e.g. via problematic biofouling processes and/or biocorrosion. Over the past decade, research on fractured shale microbiology has focused on wells in North America, with a few additional reported studies conducted in China. To extend the knowledge in this area, we characterized the geochemistry and microbial ecology of two exploratory shale gas wells in the Bowland Shale, UK. We then employed a meta-analysis approach to compare geochemical and 16S rRNA gene sequencing data from our study site with previously published research from geographically distinct formations spanning China, Canada and the USA.

RESULTS

Our findings revealed that fluids recovered from exploratory wells in the Bowland are characterized by moderate salinity and high microbial diversity. The microbial community was dominated by lineages known to degrade hydrocarbons, including members of Shewanellaceae, Marinobacteraceae, Halomonadaceae and Pseudomonadaceae. Moreover, UK fractured shale communities lacked the usually dominant Halanaerobium lineages. From our meta-analysis, we infer that chloride concentrations play a dominant role in controlling microbial community composition. Spatio-temporal trends were also apparent, with different shale formations giving rise to communities of distinct diversity and composition.

CONCLUSIONS

These findings highlight an unexpected level of compositional heterogeneity across fractured shale formations, which is not only relevant to inform management practices but also provides insight into the ability of diverse microbial consortia to tolerate the extreme conditions characteristic of the engineered deep subsurface.

Guar Gum Stimulates Biogenic Sulfide Production in Microbial Communities Derived from UK Fractured Shale Production Fluids

Shale gas production fluids offer a window into the engineered deep biosphere. Here, for the first time, we report on the geochemistry and microbiology of production fluids from a UK shale gas well in the Bowland shale formation. The composition of input fluids used to fracture this well were comparatively lean, consisting only of water, sand, and polyacrylamide. This formation therefore represents an interesting comparison to previously explored fractured shales in which more additives were used in the input fluids. Here, we combine cultivation and molecular ecology techniques to explore the microbial community composition of hydraulic fracturing production fluids, with a focus on the potential for common viscosity modifiers to stimulate microbial growth and biogenic sulfide production. Production fluids from a Bowland Shale exploratory well were used as inocula in substrate utilization experiments to test the potential for polyacrylamide and guar gum to stimulate microbial metabolism. We identified a consortium of thiosulfate-reducing bacteria capable of utilizing guar gum (but not polyacrylamide), resulting in the production of corrosive and toxic hydrogen sulfide. Results from this study indicate polyacrylamide is less likely than guar gum to stimulate biogenic sulfide production during shale gas extraction and may guide planning of future hydraulic fracturing operations. IMPORTANCE Shale gas exploitation relies on hydraulic fracturing, which often involves a range of chemical additives in the injection fluid. However, relatively little is known about how these additives influence fractured shale microbial communities. This work offers a first look into the microbial community composition of shale gas production fluids obtained from an exploratory well in the Bowland Shale, United Kingdom. It also seeks to establish the impact of two commonly used viscosity modifiers, polyacrylamide and guar gum, on microbial community dynamics and the potential for microbial sulfide production. Not only does this work offer fascinating insights into the engineered deep biosphere, it could also help guide future hydraulic fracturing operations that seek to minimize the risk of biogenic sulfide production, which could reduce efficiency and increase environmental impacts of shale gas extraction.

Salinity and hydraulic retention time induce membrane phospholipid acyl chain remodeling in Halanaerobium congolense WG10 and mixed cultures from hydraulically fractured shale wells

Bacteria remodel their plasma membrane lipidome to maintain key biophysical attributes in response to ecological disturbances. For Halanaerobium and other anaerobic halotolerant taxa that persist in hydraulically fractured deep subsurface shale reservoirs, salinity, and hydraulic retention time (HRT) are important perturbants of cell membrane structure, yet their effects remain poorly understood. Membrane-linked activities underlie in situ microbial growth kinetics and physiologies which drive biogeochemical reactions in engineered subsurface systems. Hence, we used gas chromatography-mass spectrometry (GC-MS) to investigate the effects of salinity and HRT on the phospholipid fatty acid composition of H. congolense WG10 and mixed enrichment cultures from hydraulically fractured shale wells. We also coupled acyl chain remodeling to membrane mechanics by measuring bilayer elasticity using atomic force microscopy (AFM). For these experiments, cultures were grown in a chemostat vessel operated in continuous flow mode under strict anoxia and constant stirring. Our findings show that salinity and HRT induce significant changes in membrane fatty acid chemistry of H. congolense WG10 in distinct and complementary ways. Notably, under nonoptimal salt concentrations (7% and 20% NaCl), H. congolense WG10 elevates the portion of polyunsaturated fatty acids (PUFAs) in its membrane, and this results in an apparent increase in fluidity (homeoviscous adaptation principle) and thickness. Double bond index (DBI) and mean chain length (MCL) were used as proxies for membrane fluidity and thickness, respectively. These results provide new insight into our understanding of how environmental and engineered factors might disrupt the physical and biogeochemical equilibria of fractured shale by inducing physiologically relevant changes in the membrane fatty acid chemistry of persistent microbial taxa. GRAPHICAL ABSTRACTSalinity significantly alters membrane bilayer fluidity and thickness in Halanaerobium congolense WG10.

Dissolved organic matter within oil and gas associated wastewaters from U.S. unconventional petroleum plays: Comparisons and consequences for disposal and reuse

Wastewater generated during petroleum extraction (produced water) may contain high concentrations of dissolved organics due to their intimate association with organic-rich source rocks, expelled petroleum, and organic additives to fluids used for hydraulic fracturing of unconventional (e.g., shale) reservoirs. Dissolved organic matter (DOM) within produced water represents a challenge for treatment prior to beneficial reuse. High salinities characteristic of produced water, often 10× greater than seawater, coupled to the complex DOM ensemble create analytical obstacles with typical methods. Excitation-emission matrix spectroscopy (EEMS) can rapidly characterize the fluorescent component of DOM with little impact from matrix effects. We applied EEMS to evaluate DOM composition in 18 produced water samples from six North American unconventional petroleum plays. Represented reservoirs include the Eagle Ford Shale (Gulf Coast Basin), Wolfcamp/Cline Shales (Permian Basin), Marcellus Shale and Utica/Point Pleasant (Appalachian Basin), Niobrara Chalk (Denver-Julesburg Basin), and the Bakken Formation (Williston Basin). Results indicate that the relative chromophoric DOM composition in unconventional produced water may distinguish different lithologies, thermal maturity of resource types (e.g., heavy oil vs. dry gas), and fracturing fluid compositions, but is generally insensitive to salinity and DOM concentration. These results are discussed with perspective toward DOM influence on geochemical processes and the potential for targeted organic compound treatment for the reuse of produced water.

The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms

The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry. IMPORTANCE The Permian Basin is the largest producing oil and gas region in the United States and plays a critical role supplying national energy needs. Previous work in other basins has demonstrated that the geochemistry and microbiology of hydrocarbon regions can have a major impact on well infrastructure and production. Despite that, little work has been done to understand the complex dynamics present in the Permian Basin. This study characterizes and analyzes 10 unique wells and one groundwater sample in the Permian Basin using geochemical and microbial techniques. Across all wells we found a high number of classic and thiosulfate reducers, suggesting that hydrogen sulfide production may be especially prevalent in the Permian Basin. Additionally, our analysis revealed a biogeochemical signal impacted by the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. This information can be utilized by the oil and gas industry to improve oil recovery efforts and minimize commercial and environmental costs.

Community Vertical Composition of the Laguna Negra Hypersaline Microbial Mat, Puna Region (Argentinean Andes)

The Altiplano-Puna region is a high-altitude plateau in South America characterized by extreme conditions, including the highest UV incidence on Earth. The Laguna Negra is a hypersaline lake located in the Catamarca Province, northwestern Argentina, where stromatolites and other microbialites are found, and where life is mostly restricted to microbial mats. In this study, a particular microbial mat that covers the shore of the lake was explored, to unravel its layer-by-layer vertical structure in response to the environmental stressors therein. Microbial community composition was assessed by high-throughput 16S rRNA gene sequencing and pigment content analyses, complemented with microscopy tools to characterize its spatial arrangement within the mat. The top layer of the mat has a remarkable UV-tolerance feature, characterized by the presence of Deinococcus-Thermus and deinoxanthin, which might reflect a shielding strategy to cope with high UV radiation. Chloroflexi and Deltaproteobacteria were abundant in the second and third underlying layers, respectively. The bottom layer harbors copious Halanaerobiaeota. Subspherical aggregates composed of calcite, extracellular polymeric substances, abundant diatoms, and other microorganisms were observed all along the mat as the main structural component. This detailed study provides insights into the strategies of microbial communities to thrive under high UV radiation and hypersalinity in high-altitude lakes in the Altiplano-Puna region.

Pre-incubation conditions determine the fermentation pattern and microbial community structure in fermenters at mild hydrostatic pressure

Fermentation at elevated hydrostatic pressure is a novel strategy targeting product selectivity. However, the role of inoculum history and cross-resistance, that is, acquired tolerance from incubation under distinctive environmental stress, remains unclear in high-pressure operation. In our here presented work, we studied fermentation and microbial community responses of halotolerant marine sediment inoculum (MSI) and anaerobic digester inoculum (ADI), pre-incubated in serum bottles at different temperatures and subsequently exposed to mild hydrostatic pressure (MHP; < 10 MPa) in stainless steel reactors. Results showed that MHP effects on microbial growth, activity, and community structure were strongly temperature-dependent. At moderate temperature (20°C), biomass yield and fermentation were not limited by MHP; suggesting a cross-resistance effect from incubation temperature and halotolerance. Low temperatures (10°C) and MHP imposed kinetic and bioenergetic limitations, constraining growth and product formation. Fermentation remained favorable in MSI at 28°C and ADI at 37°C, despite reduced biomass yield resulting from maintenance and decay proportionally increasing with temperature. Microbial community structure was modified by temperature during the enrichment, and slight differences observed after MHP-exposure did not compromise functionality. Results showed that the relation incubation temperature-halotolerance proved to be a modifier of microbial responses to MHP and could be potentially exploited in fermentations to modulate product/biomass ratio.

Membrane Bioreactors for Produced Water Treatment: A Mini-Review

Environmentalists are prioritizing reuse, recycling, and recovery systems to meet rising water demand. Diving into produced water treatment to enable compliance by the petroleum industry to meet discharge limits has increased research into advanced treatment technologies. The integration of biological degradation of pollutants and membrane separation has been recognized as a versatile technology in dealing with produced water with strength of salts, minerals, and oils being produced during crude refining operation. This review article presents highlights on produced water, fundamental principles of membrane bioreactors (MBRs), advantages of MBRs over conventional technologies, and research progress in the application of MBRs in treating produced water. Having limited literature that specifically addresses MBRs for PW treatment, this review also attempts to elucidate the treatment efficiency of MBRs PW treatment, integrated MBR systems, general fouling, and fouling mitigation strategies.

Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation

BACKGROUND

Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation.

RESULTS

We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems.

CONCLUSIONS

These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.

Effect of biochar combined with a biotrickling filter on deodorization, nitrogen retention, and microbial community succession during chicken manure composting

The high-nitrogen content and dense structure of poultry manure compost cause volatilization of N to ammonia (NH₃). This study evaluated the combined application of biochar and biotrickling filtration (BTF) to remove of odor in chicken manure mixed straw compost (w/w, 2.5:1). Adding of 10% biochar reduced NH₃, hydrogen sulfide (H₂S), and total volatile organic compounds (TVOCs) contents by 20.04%, 16.18%, and 17.55% respectively, and decreased the N loss rate by 8.27%, compared with those observed in control. The organic matter content decreased by 28.11% and germination index reached 97.36% in the experimental group. Meanwhile, the N-cycling microorganisms such as Pusillimonas and Pseudomonas became more active, and the relative abundance of sulfur-cycling microorganisms Hydrogenispora decreased in the experimental group. Following BTF application, the NH₃, H₂S, and TVOCs removal rates reached 95%, 97%, and 53%, respectively.

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.

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm^TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N₂ fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

Comparison of the Hydraulic Fracturing Water Cycle in China and North America: A Critical Review

There is considerable debate about the sustainability of the hydraulic fracturing (HF) water cycle in North America. Recently, this debate has expanded to China, where HF activities continue to grow. Here, we provide a critical review of the HF water cycle in China, including water withdrawal practices and flowback and produced water (FPW) management and their environmental impacts, with a comprehensive comparison to the U.S. and Canada (North America). Water stress in arid regions, as well as water management challenges, FPW contamination of aquatic and soil systems, and induced seismicity are all impacts of the HF water cycle in China, the U.S., and Canada. In light of experience gained in North America, standardized practices for analyzing and reporting FPW chemistry and microbiology in China are needed to inform its efficient and safe treatment, discharge and reuse, and identification of potential contaminants. Additionally, conducting ecotoxicological studies is an essential next step to fully reveal the impacts of accidental FPW releases into aquatic and soil ecosystems in China. From a policy perspective, the development of China's unconventional resources lags behind North America's in terms of overall regulation, especially with regard to water withdrawal, FPW management, and routine monitoring. Our study suggests that common environmental risks exist within the world's two largest HF regions, and practices used in North America may help prevent or mitigate adverse effects in China.

The oil spill and the use of chemical surfactant reduce microbial corrosion on API 5L steel buried in saline soil

In order to evaluate the biocorrosion of API 5L metal buried in saline soils, three different conditions in microcosms were evaluated. The control microcosm contained only saline soil, the second had the addition of petroleum, and the third contained the addition of both petroleum and surfactant. The corrosion rate of the metals was measured by loss of mass after 30 days, and the microbial communities were delineated using 16S rRNA gene sequencing techniques. The species were dominated by halophiles in all samples analyzed. Among the bacteria, the predominant group was Proteobacteria, with emphasis on the Alphaproteobacteria and Gammaproteobacteria. Betaproteobacteria and Deltaproteobacteria members were also identified in a smaller number in all conditions. Firmicutes were especially abundant in the control system, although it was persistently present in other conditions evaluated. Bacteroidetes and Actinobacteria were also present in a considerable number of OTUs in the three microcosms. Halobacteria were predominant among archaea and were present in all conditions. The analysis pointed to a conclusion that in the control microcosm, the corrosion rate was higher, while the microcosm containing only oil had the lowest corrosion rate. These results suggest that, under these conditions, the entry of other carbon sources favors the presence of petroleum degraders, rather than samples involved in the corrosion of metals.

Emerging Trends in Biological Treatment of Wastewater From Unconventional Oil and Gas Extraction

Unconventional oil and gas exploration generates an enormous quantity of wastewater, commonly referred to as flowback and produced water (FPW). Limited freshwater resources and stringent disposal regulations have provided impetus for FPW reuse. Organic and inorganic compounds released from the shale/brine formation, microbial activity, and residual chemicals added during hydraulic fracturing bestow a unique as well as temporally varying chemical composition to this wastewater. Studies indicate that many of the compounds found in FPW are amenable to biological degradation, indicating biological treatment may be a viable option for FPW processing and reuse. This review discusses commonly characterized contaminants and current knowledge on their biodegradability, including the enzymes and organisms involved. Further, a perspective on recent novel hybrid biological treatments and application of knowledge gained from omics studies in improving these treatments is explored.

Carbonate facies-specific stable isotope data record climate, hydrology, and microbial communities in Great Salt Lake, UT

Organic and inorganic stable isotopes of lacustrine carbonate sediments are commonly used in reconstructions of ancient terrestrial ecosystems and environments. Microbial activity and local hydrological inputs can alter porewater chemistry (e.g., pH, alkalinity) and isotopic composition (e.g., δ¹⁸ O_water , δ¹³ C_DIC ), which in turn has the potential to impact the stable isotopic compositions recorded and preserved in lithified carbonate. The fingerprint these syngenetic processes have on lacustrine carbonate facies is yet unknown, however, and thus, reconstructions based on stable isotopes may misinterpret diagenetic records as broader climate signals. Here, we characterize geochemical and stable isotopic variability of carbonate minerals, organic matter, and water within one modern lake that has known microbial influences (e.g., microbial mats and microbialite carbonate) and combine these data with the context provided by 16S rRNA amplicon sequencing community profiles. Specifically, we measure oxygen, carbon, and clumped isotopic compositions of carbonate sediments (δ¹⁸ O_carb , δ¹³ C_carb , ∆₄₇ ), as well as carbon isotopic compositions of bulk organic matter (δ¹³ C_org ) and dissolved inorganic carbon (DIC; δ¹³ C_DIC ) of lake and porewater in Great Salt Lake, Utah from five sites and three seasons. We find that facies equivalent to ooid grainstones provide time-averaged records of lake chemistry that reflect minimal alteration by microbial activity, whereas microbialite, intraclasts, and carbonate mud show greater alteration by local microbial influence and hydrology. Further, we find at least one occurrence of ∆₄₇ isotopic disequilibrium likely driven by local microbial metabolism during authigenic carbonate precipitation. The remainder of the carbonate materials (primarily ooids, grain coatings, mud, and intraclasts) yield clumped isotope temperatures (T(∆₄₇ )), δ¹⁸ O_carb , and calculated δ¹⁸ O_water in isotopic equilibrium with ambient water and temperature at the time and site of carbonate precipitation. Our findings suggest that it is possible and necessary to leverage diverse carbonate facies across one sedimentary horizon to reconstruct regional hydroclimate and evaporation-precipitation balance, as well as identify microbially mediated carbonate formation.

Geochemistry and Microbiology Predict Environmental Niches With Conditions Favoring Potential Microbial Activity in the Bakken Shale

The Bakken Shale and underlying Three Forks Formation is an important oil and gas reservoir in the United States. The hydrocarbon resources in this region are accessible using unconventional oil and gas extraction methods, including horizontal drilling and hydraulic fracturing. However, the geochemistry and microbiology of this region are not well understood, although they are known to have major implications for productivity and water management. In this study, we analyzed the produced water from 14 unconventional wells in the Bakken Shale using geochemical measurements, quantitative PCR (qPCR), and 16S rRNA gene sequencing with the overall goal of understanding the complex dynamics present in hydraulically fractured wells. Bakken Shale produced waters from this study exhibit high measurements of total dissolved solids (TDS). These conditions inhibit microbial growth, such that all samples had low microbial loads except for one sample (well 11), which had lower TDS concentrations and higher 16S rRNA gene copies. Our produced water samples had elevated chloride concentrations typical of other Bakken waters. However, they also contained a sulfate concentration trend that suggested higher occurrence of sulfate reduction, especially in wells 11 and 18. The unique geochemistry and microbial loads recorded for wells 11 and 18 suggest that the heterogeneous nature of the producing formation can provide environmental niches with conditions conducive for microbial growth. This was supported by strong correlations between the produced water microbial community and the associated geochemical parameters including sodium, chloride, and sulfate concentrations. The produced water microbial community was dominated by 19 bacterial families, all of which have previously been associated with hydrocarbon-reservoirs. These families include Halanaerobiaceae, Pseudomonadaceae, and Desulfohalobiaceae which are often associated with thiosulfate reduction, biofilm production, and sulfate reduction, respectively. Notably, well 11 was dominated by sulfate reducers. Our findings expand the current understanding of microbial life in the Bakken region and provide new insights into how the unique produced water conditions shape microbial communities. Finally, our analysis suggests that produced water chemistry is tightly linked with microbiota in the Bakken Shale and shows that additional research efforts that incorporate coupled microbial and geochemical datasets are necessary to understand this ecosystem.

Water Treatment: Are Membranes the Panacea?

Alongside the rising global water demand, continued stress on current water supplies has sparked interest in using nontraditional source waters for energy, agriculture, industry, and domestic needs. Membrane technologies have emerged as one of the most promising approaches to achieve water security, but implementation of membrane processes for increasingly complex waters remains a challenge. The technical feasibility of membrane processes replacing conventional treatment of alternative water supplies (e.g., wastewater, seawater, and produced water) is considered in the context of typical and emerging water quality goals. This review considers the effectiveness of current technologies (both conventional and membrane based), as well as the potential for recent advancements in membrane research to achieve these water quality goals. We envision the future of water treatment to integrate advanced membranes (e.g., mixed-matrix membranes, block copolymers) into smart treatment trains that achieve several goals, including fit-for-purpose water generation, resource recovery, and energy conservation.

Identification of Persistent Sulfidogenic Bacteria in Shale Gas Produced Waters

Produced waters from hydraulically fractured shale formations give insight into the microbial ecology and biogeochemical conditions down-well. This study explores the potential for sulfide production by persistent microorganisms recovered from produced water samples collected from the Marcellus shale formation. Hydrogen sulfide is highly toxic and corrosive, and can lead to the formation of “sour gas” which is costly to refine. Furthermore, microbial colonization of hydraulically fractured shale could result in formation plugging and a reduction in well productivity. It is vital to assess the potential for sulfide production in persistent microbial taxa, especially when considering the trend of reusing produced waters as input fluids, potentially enriching for problematic microorganisms. Using most probable number (MPN) counts and 16S rRNA gene sequencing, multiple viable strains of bacteria were identified from stored produced waters, mostly belonging to the Genus Halanaerobium, that were capable of growth via fermentation, and produced sulfide when supplied with thiosulfate. No sulfate-reducing bacteria (SRB) were detected through culturing, despite the detection of relatively low numbers of sulfate-reducing lineages by high-throughput 16S rRNA gene sequencing. These results demonstrate that sulfidogenic produced water populations remain viable for years post production and, if left unchecked, have the potential to lead to natural gas souring during shale gas extraction.

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

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.

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.

Geochemical and microbial characterizations of flowback and produced water in three shale oil and gas plays in the central and western United States

Limited understanding of wastewater streams produced from shale oil and gas wells impedes best practices of wastewater treatment and reuse. This study provides a comprehensive and comparative analysis of flowback and produced water from three major and newly developed shale plays (the Bakken shale, North Dakota; the Barnett shale, Texas; and the Denver-Julesburg (DJ) basin, Colorado) in central and western United States. Geochemical features that included more than 10 water quality parameters, dissolved organic matter, as well as microbial community structures were characterized and compared. Results showed that wastewater from Bakken and Barnett shales has extremely high salinity (∼295 g/L total dissolved solids (TDS)) and low organic concentration (80-252 mg/L dissolved organic carbon (DOC)). In contrast, DJ basin showed an opposite trend with low TDS (∼30 g/L) and high organic content (644 mg/L DOC). Excitation-emission matrix (EEM) fluorescence spectra demonstrated that more humic acid and fluvic acid-like organics with higher aromaticity existed in Bakken wastewater than that in Barnett and DJ basin. Microbial communities of Bakken samples were dominated by Fe (III)-reducing bacteria Geobacter, lactic acid bacteria Lactococcus and Enterococcus, and Bradyrhizobium, while DJ basin water showed higher abundance of Rhodococcus, Thermovirga, and sulfate reducing bacteria Thermotoga and Petrotoga. All these bacteria are capable of hydrocarbon degradation. Hydrogenotrophic methanogens dominated the archaeal communities in all samples.

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.

Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering

Bacterial cells have long been thought to be simple cells with little spatial organization, but recent research has shown that they exhibit a remarkable degree of subcellular differentiation. Indeed, bacteria even have organelles such as magnetosomes for sensing magnetic fields or gas vesicles controlling cell buoyancy. A functionally diverse group of bacterial organelles are the bacterial microcompartments (BMCs) that fulfill specialized metabolic needs. Modification and reengineering of these BMCs enable innovative approaches for metabolic engineering and nanomedicine.

Deep-Subsurface Pressure Stimulates Metabolic Plasticity in Shale-Colonizing Halanaerobium spp

Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48 MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.IMPORTANCE The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause "clumping" of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.

Culturing the Uncultured: Risk versus Reward

Isolation of new microorganisms is challenging, but cultures are invaluable resources for experimental validation of phenotype, ecology, and evolutionary processes. Although the number of new isolates continues to grow, the majority of cultivars still come from a limited number of phylogenetic groups and environments, necessitating investment in new cultivation efforts.

Isolation of new microorganisms is challenging, but cultures are invaluable resources for experimental validation of phenotype, ecology, and evolutionary processes. Although the number of new isolates continues to grow, the majority of cultivars still come from a limited number of phylogenetic groups and environments, necessitating investment in new cultivation efforts. While most microbiologists probably agree that axenic cultures have great value, we need to collectively put our money where our mouth is. I propose that we examine cultivation from the perspective of expected value to rationally incorporate risks and rewards of isolating new microbes. If we can even broadly constrain the cultivation probability and relative values of isolates, we can use this information to evaluate and improve experimental design. There are numerous scenarios for which isolation projects have positive expectations and therefore represent a sound investment.

Microbial Metabolism and Community Dynamics in Hydraulic Fracturing Fluids Recovered From Deep Hydrocarbon-Rich Shale

Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion of a well, the fluid returns to the surface (produced water) and contains natural gas, subsurface constituents, and microorganisms (Barbot et al., 2013; Daly et al., 2016). While the microbial community of the produced fluids has been studied in multiple gas wells, the activity of these microorganisms and their relation to biogeochemical activity is not well understood. In this experiment, we supplemented produced fluid with ¹³C-labeled carbon sources (glucose, acetate, bicarbonate, methanol, or methane), and ¹⁵N-labeled ammonium chloride in order to isotopically trace microbial activity over multiple day in anoxic incubations. Nanoscale secondary ion mass spectrometry (NanoSIMS) was used to generate isotopic images of ¹³C and ¹⁵N incorporation in individual cells, while isotope ratio monitoring–gas chromatography–mass spectrometry (IRM–GC–MS) was used to measure ¹³CO₂, and ¹³CH₄ as metabolic byproducts. Glucose, acetate, and methanol were all assimilated by microorganisms under anoxic conditions. ¹³CO₂ production was only observed with glucose as a substrate indicating that catabolic activity was limited to this condition. The microbial communities observed at 0, 19, and 32 days of incubation did not vary between different carbon sources, were low in diversity, and composed primarily of the class Clostridia. The primary genera detected in the incubations, Halanaerobium and Fusibacter, are known to be adapted to harsh physical and chemical conditions consistent with those that occur in the hydrofracturing environment. This study provides evidence that microorganisms in produced fluid are revivable in laboratory incubations and retained the ability to metabolize added carbon and nitrogen substrates.

Organic sulfur fingerprint indicates continued injection fluid signature 10 months after hydraulic fracturing

Hydraulic fracturing requires the injection of large volumes of fluid to extract oil and gas from low permeability unconventional resources (e.g., shale, coalbed methane), resulting in the production of large volumes of highly complex and variable waste fluids. Shale gas fluid samples were collected from two hydraulically fractured wells in Morgantown, WV, USA at the Marcellus Shale Energy and Environment Laboratory (MSEEL) and analyzed using ultrahigh resolution mass spectrometry to investigate the dissolved organic sulfur (DOS) pool. Using a non-targeted approach, ions assigned DOS formulas were analyzed to identify dominant DOS classes, describe their temporal trends and their implications, and describe the molecular characteristics of the larger DOS pool. The average molecular weight of organic sulfur compounds in flowback decreased and was lowest in produced waters. The dominant DOS classes were putatively assigned to alcohol sulfate and alcohol ethoxysulfate surfactants, likely injected as fracturing fluid additives, on the basis of exact mass and homolog distribution matching. This DOS signature was identifiable 10 months after the initial injection of hydraulic fracturing fluid, and an absence of genes that code for alcohol ethoxysulfate degrading proteins (e.g., sulfatases) in the shale well genomes and metagenomes support that these additives are not readily degraded biologically and may continue to act as a chemical signature of the injected fluid. Understanding the diversity, lability, and fate of organic sulfur compounds in shale wells is important for engineering productive wells and preventing gas souring as well as understanding the consequences of unintended fluid release to the environment. The diversity of DOS, particularly more polar compounds, needs further investigation to determine if the identified characteristics and temporal patterns are unique to the analyzed wells or represent broader patterns found in other formations and under other operating conditions.

Characterization and implications of solids associated with hydraulic fracturing flowback and produced water from the Duvernay Formation, Alberta, Canada

Public concern is heightened around flowback and produced water (FPW) generated by the hydraulic fracturing process. FPW is a complex mix of organic and inorganic solutes derived from both the injected hydraulic fracturing fluid and interactions with the subsurface lithology. Few studies to date have systematically investigated the composition of FPW or its individual components. Here, we provide the first systematic characterization of the composition of the solids associated with FPW by analyzing samples from three wells drilled into the Duvernay Formation in Alberta, Canada. The FPW initially returned to the surface with high total dissolved solids (greater than 170 000 mg L-1) and enriched with Fe(ii), silica, sulfate, barium, and strontium. The solids form two distinct phases once the FPW reached the surface: (1) silica-enriched Fe(iii) oxyhydroxides, and (2) a barite-celestine solid solution. We hypothesize that the precipitation of the amorphous silica-enriched Fe(iii) oxyhydroxide is a two-step process, where first the silica precipitates as a function of the cooling of the FPW from elevated subsurface temperatures to ambient surface temperatures. Next, the silica acts as a template for the precipitation of Fe(iii) oxyhydroxide as the diffusion of oxygen into the subsurface causes oxidation of aqueous Fe(ii). The barite-celestine solid solution precipitates solely as a function of cooling. Elevated dissolved Fe concentrations in FPW and modeled saturation indices from five North American shale plays (Marcellus, Fayetteville, Barnett, Bakken, and Denver-Julesburg) indicate that solids similar to those found in Duvernay FPW, specifically Fe(iii) oxyhydroxides, barite and quartz, are likely to occur. With the solids known to carry a significant portion of FPW's toxicity and organic contaminant load, the development of new treatment technologies, such as the oxidation of the Fe(ii) in FPW, may increase FPW reuse and reduce the environmental risk posed by FPW.

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.

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.

Draft Genome Sequences of Two Chemosynthetic Arcobacter Strains Isolated from Hydraulically Fractured Wells in Marcellus and Utica Shales

Genome sequences were obtained for two isolates of the genus Arcobacter from saline fluids produced from hydraulically fractured shale gas wells in the Marcellus and Utica formations. These genomes provide insight into microbial sulfur cycles occurring in a high-salt deep terrestrial shale environment.