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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study

ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.

Kulyashov, M. A.↗
DOE OSTI2025

Theoretical and Experimental Insights into CO 2 Capture and Methanation over Amine-Grafted Ru-Based Catalysts

Carbon capture and storage (CCS) technologies, along with CO 2 capture and conversion methods, have emerged as crucial research areas to address rising CO 2 emissions. In this study, we seek to understand the mechanistic role of amines in enabling lower-energy pathways for CO 2 conversion. Our research focuses on the development and analysis of dual-functional materials (DFMs) engineered for the reactive capture and conversion (RCC) of CO 2 into methane, utilizing Ru catalysts grafted with amine groups. We employ Density Functional Theory (DFT) calculations using methylamine as a model amine to investigate the impact of amine groups on CO 2 methanation on a Ru(0001) surface, both in the presence and absence of amine groups. The amine ligand alters the carbon coordination environment, promoting direct C–O dissociation and potentially destabilizing the CO* adsorbate, thereby reducing the risk of CO poisoning. Additionally, we observe a preference for hydrogenation, although it becomes more energetically uphill in the amine-bound scenario. Our experiments, however, report similar CO 2 conversion and CH 4 production rates over the synthesized catalysts “Ru/TiO 2 ” and the amine (N-(2-aminoethyl)-3-aminoproplytrimethoxysilane (“diaminosilane”)) deposited catalyst “Diamine−Ru/TiO 2 ”. By constructing comparative reaction-free energy diagrams and performing microkinetic modeling (MKM) simulations, we link our theoretical findings with experimentally observed CO 2 uptake, conversion, and methane production rates. A microkinetic model was employed to investigate the anomaly, showing reduced amine–carbon complex coverage and increased CO 2 coverage at all temperatures. The MKM simulations consistently confirmed these trends. In conclusion, this comprehensive approach offers key insights into the role of the amine-CO 2 bond in methanation, highlighting a pathway toward lower-energy, more efficient CO 2 capture and conversion processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Noble-Metal-Free, Nickel-Based Dual Functional Materials for Improved Methane Production from In Situ Carbon Dioxide Capture and Conversion

Promoters for dual functional materials have not been well explored, but promoters could improve the efficiency of the process by improving the selectivity of the CO 2 methanation process. Utilizing integrated capture and conversion, where CO 2 is captured and converted to useful products, would allow for a useful avenue to control CO 2 emissions. One such way to accomplish this would be to utilize materials that can both capture and convert CO 2 to useful products. However, these materials are often based on costly noble metals, like ruthenium and platinum, decreasing their viability on an industrial scale. Less expensive metals, for example, nickel, would allow for dual functional materials to be more readily utilized in industrial settings. Nickel-based dual functional materials often do not react with the captured CO 2 and merely desorb the CO 2 rather than form a useful product. However, promoters have not been well explored for these types of materials to improve the catalytic properties, which would be beneficial to improve nickel-based materials. Herein, we report the addition of ytterbium on a nickel-based dual functional material and the improvements to the production of methane from captured CO 2 with the incorporated ytterbium promoter. The ytterbium promoter improves the selectivity of the catalysts for the hydrogenation of captured CO 2 to methane and increases the ability for the material to capture CO 2 due to additional basic sites being formed on the surface of alumina. As a result, the 12%Ni/4%Yb/6%Na 2 O/Al 2 O 3 catalyst was utilized to capture carbon dioxide and then convert the captured CO 2 to methane over five cycles, where both the amount captured and the amount converted remained stable, indicating the stability of the material over long-term use.

Catalysts↗
DOE OSTI2025

Methane pyrolysis by Joule heating for graphitic carbon and hydrogen production

The global energy transition toward sustainability requires technologies that can decarbonize energy carriers and fuels while producing valuable materials. Methane, a primary component of natural gas, is both a high-energy-density fuel and a significant greenhouse gas. This study reports an approach for methane pyrolysis utilizing Joule heating within the deposition substrate to drive the endothermic reaction. With electric current passing through a resistive porous carbon cloth, heat is generated to break C-H bonds of methane molecules. Here, the decomposition of methane as it flows through the cloth results in hydrogen production and the formation of conformally layered graphite around the carbon fibers. The effects of input power, chamber pressure, feedstock flow rate, and process duration on hydrogen and graphite production are characterized via in situ mass spectrometry and laser absorption spectroscopy, resulting in methane conversion rates up to 88%, with hydrogen and carbon yields of 82% and 72%, respectively. Material characterization verifies uniform high-quality graphite deposition, with a Raman I D /I G ratio of 0.1 and 3.38 Å d-spacing. This Joule heating method for catalyst-free methane pyrolysis offers the potential for advancing hydrogen production technology by simultaneously producing valuable materials such as solid graphite, thus enhancing the economic viability of the fuel decarbonization process.

Energy Resources↗
DOE OSTI2025

G2CFX Final Technical Report - Release

The primary objective of this project is to develop a process for production of high-performance, high-value carbon derived from wellhead natural gas. This will be done either by direct graphitization of pyrolysis carbon produced at the wellhead, or through precipitation of the carbon from a molten metal solution to form high-value graphite.

03 NATURAL GAS↗
DOE OSTI2025

Sorbent Mediated Electrocatalytic Reduction of Dilute CO 2 to Methane

Efficient CO 2 utilization is a critical component of closing the anthropogenic carbon cycle. Most studies have focused on the use of pure streams of CO 2 . However, CO 2 is generally available only in dilute streams, which requires capture by sorbents followed by energy-intensive regeneration to release concentrated CO 2 . Direct utilization of sorbed-CO 2 avoids the costly regeneration step, and the sorbent-CO 2 interaction can kinetically activate CO 2 to tune its reactivity toward products that could otherwise be inaccessible with direct CO 2 reduction. We demonstrate that an N-heterocyclic carbene, 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (DPIy), quantitatively reacts with CO 2 from dilute streams (0.04 and 10%) to form the sorbent-CO 2 substrate 1,3-bis(2,6-diisopropylphenyl)imidazolium-2-carboxylate (DPICx). Electrocatalyst iron tetraphenylporphyrin chloride (Fe(TPP)Cl) typically reduces CO 2 to CO; however, with DPICx as the substrate, the eight-electron reduced product methane (CH 4 ) is produced with a high Faradaic efficiency (>85%) and regeneration of the sorbent DPIy. In addition to the overall energy and capital advantages of integrated CO 2 capture and conversion, this result illustrates how sorbents can serve a dual purpose for both CO 2 capture and chemical auxiliary purposes to access unique products. CO 2 has a spectrum of reactivity with different types of sorbents; thus, these studies demonstrate how sorbent-CO 2 interactions can be leveraged for integrated capture and utilization platforms to access a wider range of CO 2 -derived products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Slow-Light Mid-IR Silicon Photonic Chips for NO 2 and CH 4 Gas Detection

A compact, chip-scale mid-infrared gas sensor is demonstrated, leveraging a two-dimensional photonic crystal waveguide (PCW) fabricated on a silicon-on-insulator (SOI) platform. The PCW comprises a hexagonal lattice with lattice constant a = 860 nm and hole radius r = 0.22a, incorporating a central line defect of reduced-radius holes (r s = 0.7r) to induce slow-light propagation near the photonic band edge with a group index of approximately 73, thereby enhancing light-matter interaction. The sensor operates at fundamental absorption wavelengths of 3.42 μm for nitrogen dioxide (NO 2 ) and 3.40 μm for methane (CH 4 ), utilizing the strongest molecular vibrational transitions for maximum sensitivity. Experimental validation was conducted using dynamically diluted gas mixtures generated by mass flow controllers, with signal acquisition performed by a liquid nitrogen-cooled InSb detector. For NO 2 , the sensor exhibited excellent linear response over 5–25 ppm (part per million) with coefficient of determination R 2 = 0.9934, achieving a detection limit of 210 ppb (part per billion)─representing the first reported silicon photonic-based NO 2 detection. For CH 4 , exposure to 25 ppm resulted in a 6.4% decrease in transmitted intensity, demonstrating multigas sensing capability. The CMOS-compatible fabrication process and compact 3 mm device footprint establish this SOI-PCW platform as a scalable, low-power solution for integrated mid-infrared gas sensing, with significant potential for environmental monitoring and industrial safety applications.

Crystals↗
DOE OSTI2025

Common practices for quantifying methane emissions from plumes detected by remote sensing

This document provides a set of community-accepted practices for quantifying methane emissions based on plumes detected via spectroscopic remote sensing. Its primary goal is to promote consistency in the generation, validation, reporting, and quality assessment of methane emission estimates derived from remote sensing radiances. Developed by subject matter experts with deep experience across all stages of the measurement process, this guidance reflects a critical evaluation of current methodologies and highlights key practices needed to produce reliable, interoperable, and traceable products. The focus is specifically on methane emissions quantified from distinct plumes originating from localized sources, rather than diffuse emissions spread over large regions, which are beyond the scope of this work. This document is intended to serve both data producers and users. For producers, it offers a framework for aligning with field-recognized standards to ensure their outputs meet rigorous quality and transparency criteria. For users, it provides a reference to assess dataset fitness-for-purpose by highlighting essential metadata, assumptions, and methodological choices that underpin emission estimates. By fostering a shared understanding of best practices, this work aims to enhance comparability, confidence, and utility of remotely sensed methane emission products.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Integrated CO 2 capture and hydrogenation in presence of Ru–Na 2 ZrO 3 : An in-situ study

Integrated CO 2 capture and conversion (ICCC) by hydrogenation is a promising strategy to utilize carbon dioxide and this work add to the effort to elucidate the catalytic hydrogenation mechanism using Ru based dual functional materials (DFM). Ru-Na 2 ZrO 3 DFMs, obtained through different wet methods, were evaluated for the first time and the relationship between Ru and support systematically investigated. The thermally stable and cyclable Ru-Na 2 ZrO 3 -a (obtained without filtration step) exhibited CO 2 conversion of 80% and a higher yield of CO at 400°C compared to previously tested DFM, while the Na depleted/Zr rich Ru-Na 2 ZrO 3 -b resulted in 90% selectivity to CH 4 with yield of 1.11 mmol/g at the same temperature. The in-situ experiments have provided conclusive evidence showing that CO 2 hydrogenation on the two Ru DFMs is fundamentally different. In Ru-Na 2 ZrO 3 -a, the monoclinic Na 2 ZrO 3 support acted as the active centre (not as promoter) for CO 2 bridging binding and hydrogenation to CH 4 at the metal-support interface through associative formate pathway with limited further reduction to methane due to lack of H 2 spillover from the small and well dispersed Ru NPs, which results in CO desorption. Conversely, abundant clusters of larger Ru NPs in Ru-Na 2 ZrO 3 -b, led to CH 4 production due to co-existent Ru on-top direct dissociation of CO 2 (preferential) and monodentate formate adsorption and further methanation. Alkali zirconates doped metals, and their synthesis method could thus play a crucial role in designing tuneable heterogeneous catalysis in C 1 chemistry, which could significantly benefit the environment by lowering CO 2 levels, encouraging cleaner industrial practices, supporting a circular economy, and converting waste CO 2 into valuable products.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Polyphenol rewiring of the microbiome reduces methane emissions

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, ~40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens—either through direct toxic effects or by diverting their substrates and energy—to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72%–84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from Days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Potential Challenges of HyBlend Storage in a Methane Reservoir Located in Southwestern United States

Hydrogen has been identified as a flexible energy carrier with zero or negative emissions across multiple energy systems. It is possible to utilize hydrogen by storing Hyblend, or hydrogen gas blended with methane, in existing natural gas infrastructure. However, the compatibility of adapting the current CH4 storage strategies to include H2 injection has not been fully demonstrated. It is essential that we understand the impact of H2 gas on the naturally occurring microbial community of subsurface storage reservoirs before deploying large-scale H2-CH4 storage. We designed a series of experiments that allowed us to identify potential geochemical and microbial challenges of HyBlend Storage in existing methane reservoirs. First, we collected and characterized field fluid samples from a methane reservoir located in southwestern United States. Next, we used these field fluid samples to complete a series of short-term reactor experiments at reservoir conditions (80 °C and ~1,000 psi) for a natural gas (100% CH4) and HyBlend(80% CH4/20% H2) storage environment to measure the transformation of gas content. We conducted both biotic and abiotic (sterilized) measurements to accurately understand and decouple abiotic and microbially driven processes. Overall, we found that our field sample was characterized by a diverse microbial community with the metabolic capacity for sulfur reduction, iron reduction, and acetogenesis. Across our reactors, there was minimal change in geochemistry.

hydrogen storage↗
DOE OSTI2026

Methane Mitigation Using Linear Motor Leak Recovery Compressor

GTI Energy (GTI), in collaboration with The University of Texas at Austin - Center for Electromechanics (UT‑CEM), designed, fabricated, and tested a linear motor–driven compressor intended to mitigate methane emissions at natural gas facilities across transmission, storage, gathering, and processing sectors of the gas value chain.

02 PETROLEUM↗
DOE OSTI2026

Low-Temperature Non-Oxidative Coupling of Methane on Atomically Dispersed Titanium–Aluminum–Boron Nanopowder

Nonoxidative coupling of methane represents a long-standing challenge in heterogeneous catalysis, as it requires activation of the carbon–hydrogen (C–H) bond, controlled carbon–carbon (C–C) bond formation, and effective hydrogen management without relying on oxidants. Here, we report a low-temperature C–H activation and nonoxidative C–C coupling of methane over atomically dispersed titanium–aluminum–boron nanopowder (Ti–Al–B NP) utilizing a catalytic microreactor coupled to synchrotron single-photon photoionization reflectron time-of-flight mass spectrometry. The soft-ionization, in situ probing method detects the nascent reaction products and radical intermediates under operando conditions, including methyl radical, C2 hydrocarbons, and molecular hydrogen. Methane activation is initiated at 800 K, approximately 700 K below the gas-phase decomposition threshold, leading predominantly to ethylene formation with selectivity reaching up to 78% among the C–C coupled products. Electronic structure calculations on model Ti–Al–B clusters elucidate a cooperative catalytic mechanism in which titanium enables methane adsorption and C–H activation, boron acts as a reversible hydrogen reservoir, and aluminum stabilizes methylene intermediates, thereby facilitating selective C–C coupling and dehydrogenation. These findings establish a distinct catalyst architecture for nonoxidative methane coupling based on earth abundant elements alternative to expensive platinum and other noble metal-containing conventional catalysts and provide molecular-level design principles for controlling dehydrogenation and subsequent C–C bond formation in challenging light alkane conversions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Identifying microbial functional guilds performing cryptic organotrophic and lithotrophic redox cycles in anaerobic granular biofilms

Granular biofilms used in anaerobic digester systems contain diverse microbial populations that interact to hydrolyze organic matter and produce methane within controlled environments. Prior research investigated the feasibility of utilizing granular biofilms obtained from an anaerobic digester to remove nitrate without the addition of exogenous electron donors. These granules possessed a unique structure of alternating light and dark iron sulfide and pyrite rich layers that potentially served as both an electron source and sink, linking carbon, nitrogen, sulfur, and iron cycles. To characterize the functional roles of diverse microbial populations enriched within these layered biofilms, we analyzed metagenomes obtained from three different granules. Comparisons between the functional gene content of forty metagenome assembled genomes (MAGs) identified phylogenetically cohesive functional guilds. Each of these functional MAG clusters was assigned to specific steps in anaerobic digestion (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) and anaerobic respiration (denitrification and sulfate reduction). Comparisons with metagenomes derived from a variety of natural and engineered ecosystems confirmed that the enriched denitrifying bacteria were similar to populations typically found in wetlands and biological nitrogen removal systems. Analysis of read alignments to individual genes within the forty MAGs identified conserved genomic features that were representative of the functions that distinguished functional guilds. Overall, this research illustrates the utility of functional based classification of microorganisms for characterizing ecosystem functions and highlights the potential application of engineered ecosystems to serve as experimental models for complex natural ecosystems.

Ecosystem engineering↗
DOE OSTI2025

Microwave-Assisted Activation of Mo/HZSM5 in Methane Dehydroaromatization

Natural gas flaring is a significant challenge for oil and gas producers. One viable option to mitigate flaring is the conversion of natural gas into valuable chemicals. Applying microwave energy to heterogenous catalyst materials offers advantages in terms of higher rates and product selectivities in comparison to traditional thermal systems which can be designed for on-demand chemical production in modular reactor systems. Methane dehydroaromatization (MDHA) produces transportable, liquid aromatic products directly from natural gas, which is ideal for remote production but is hindered by low thermodynamic yields and rapid deactivation. The stability and performance of the Mo/ZSM5 catalyst is often determined by the state and nature of Mo in the catalyst, which in turn is dictated by the temperature and gaseous environment during catalyst activation. In this study, the Mo/HZSM5 catalyst was activated under three different heating modes (thermal, microwave E-field, and microwave H-field) and four different gas environments (CO, He, CH4+H2, and H2). All the activated catalysts were characterized using different tools and performance evaluated in MDHA.

methane dehydroaromatization↗
DOE OSTI2025

Potential Risks Associated with Short-Term Hydrogen Storage in Methane Reservoirs

Hydrogen (H2) has been identified as a flexible energy carrier with zero emissions. It is possible to utilize H2 by storing Hyblend, or H2 blended with CH4, in existing natural gas infrastructure. However, the compatibility of adapting the current CH4 storage strategies to include H2 injection has not been fully demonstrated. It is essential that we understand the impact of H2 gas on the naturally occurring microbial community of subsurface storage reservoirs before deploying large-scale H2-CH4 storage. We designed a series of experiments that allowed us to identify potential challenges of HyBlend Storage in existing methane reservoirs (Figure 1). First, we characterized two field fluid samples from a methane reservoir located in Western United States. Next, we used these samples to complete a series of short-term reactor experiments at reservoir conditions for a natural gas (100% CH4) and HyBlend (80% CH4/20% H2) storage environment.

geomicrobiology↗
DOE OSTI2025

Efficient Synthetic Natural Gas Production from Direct Air Capture Using Titania-Based Dual Function Materials

Converting atmospheric CO2 into methane offers a compelling pathway to store intermittent renewable electricity and enhance energy security using existing natural gas infrastructure. However, current CO2 utilization approaches remain energy- and capital-intensive, largely due to the need for separate capture, purification, and conversion steps. Integrating CO2 capture with catalytic methanation represents a transformative strategy for process intensification on both the unit operation and molecular levels. We report a series of Ru-Na/TiO2 dual function materials (DFMs) for a reactive carbon capture (RCC) process consisting of simulated direct air capture and subsequent CO2 methanation (DACM). Superior methane desorption purity was observed on TiO2-based DFMs (>94 %) relative to state-of-the-art Al2O3-supported DFMs (77 %). Modifying the process to begin CO2 adsorption immediately following the methanation stage, rather than beginning adsorption near ambient temperature, resulted in >97 % methane desorption purity, suitable for injection into the natural gas pipeline without additional CO2 separation steps.

organic↗