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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Adaptive management of large-scale ecosystem restoration: increasing certainty of habitat outcomes in the Columbia River Estuary, U.S.A.

Ecological restoration programs in dynamic coastal environments can benefit from adaptive management, including an iterative process for identifying and addressing critical uncertainties. We highlight key developments under the three pillars that have increased the rate of restoration by the Columbia Estuary Ecosystem Restoration Program (CEERP) over 20 years: science, coordination, and management. We show how such programs can be institutionalized to ensure that estuary ecosystems are better understood, conserved, and restored. The principal conservation effort under CEERP is to reconnect historical floodplain wetlands to the mainstem. The program also supports other restoration actions that demonstrate a high potential to benefit ecosystem function and endangered salmon populations, however, there is greater uncertainty regarding these less-utilized techniques. Through adaptive management, we address both technical uncertainty regarding benefits to the environmental resource and programmatic uncertainty pertaining to decision-making. Here, we examine three periods of CEERP growth to establish how complementary research and restoration actions have improved program outcomes over time. We highlight the tools and processes that were developed and integrated into the program to refine program strategy, improve project design, and maximize ecological benefits. CEERP supported 77 restoration projects and reconnected over 7,000 acres of floodplain habitat to the lower Columbia River between 2004 and 2021. Building on these successes, we outline current plans to better engage landowners and local communities, solicit new project types, and maintain enough flexibility within the program to adapt to new priorities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Approaches to investigate crop responses to ozone pollution: from O 3 -FACE to satellite-enabled modeling

Ozone (O 3 ) is a damaging air pollutant to crops. As one of the most reactive oxidants known, O 3 rapidly forms other reactive oxygen species (ROS) once it enters leaves through stomata. Those ROS in turn can cause oxidative stress, reduce photosynthesis, accelerate senescence, and decrease crop yield. To improve and adapt our feed, fuel, and food supply to rising O 3 pollution, a number of Free Air Concentration Enrichment (O 3 -FACE) facilities have been developed around the world and have studied key staple crops. In this review, we provide an overview of the FACE facilities and highlight some of the lessons learned from the last two decades of research. We discuss the differences between C 3 and C 4 crop responses to elevated O 3 , the possible trade-off between productivity and protection, genetic variation in O 3 response within and across species, and how we might leverage this observed variation for crop improvement. We also highlight the need to improve understanding of the interaction between rising O 3 pollution and other aspects of climate change, notably drought. Finally, we propose the use of globally modeled O 3 data that are available at increasing spatial and temporal resolutions to expand upon the research conducted at the limited number of global O 3 -FACE facilities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Tonoplast Sucrose Transporter SUT4-Dependent Sugar Partitioning Modulates Phenological Transitions and Reproductive Success in Poplar

Climate uncertainty is intensifying the need for greater plasticity in carbohydrate reserve utilization to support winter survival and spring growth in woody perennials. In poplar, the single-copy SUT4, which encodes a tonoplast-localized sucrose transporter, and the SUT5/SUT6 genome duplicates, which encode plasma membrane-localized transporters, are expressed year-round, with SUT4 showing the highest expression during cool seasons. Given its role in vacuolar sucrose efflux and winter-predominant expression, SUT4 may play a key role in modulating seasonal carbohydrate dynamics. While SUT4-knockdown and knockout effects have been studied under greenhouse conditions, their impact under field conditions remains unexplored. Here, we report a field-based study comparing CRISPR knockout mutants of winter-expressed SUT4 and SUT5/SUT6 in Populus tremula x alba. We show that sut4, but not sut5/6, mutants exhibited earlier autumn leaf senescence, delayed spring bud flush, reduced stem growth, and altered sugar partitioning in winter xylem and bark relative to controls. After 2 years in the field, all genotypes flowered before leaf flush in early spring; however, sut4 mutants produced sterile ovules despite developing normal-looking catkins. Metabolic profiling revealed disrupted sucrose and raffinose dynamics in elongating sut4 catkins. This was accompanied by transcriptomic signatures of elevated stress and downregulation of proanthocyanidin biosynthesis and circadian clock genes. These findings highlight the critical role of SUT4 in coordinating sugar allocation, stress responses, and seasonal development in poplar.

09 BIOMASS FUELS↗
DOE OSTI2021

Microstructural Evolution During a Solid State Tube Pinch Weld of Type 304l Stainless Steel

Microstructure development is examined for a specialized spot weld that is used as a solid-state closure process for austenitic stainless steel tubing, referred to as pinch welding. In order to elucidate the microstructural evolution of the weld, a series of test welds were made at nominal conditions using tubing and production like components. These pinch welds normally terminate after twelve cycles of a 60 Hz AC weld process. In this study, production tubes were welded from one to twelve cycles and the microstructure and weld variables after each individual weld cycle number were characterized using radiography and optical metallography. Two electrochemical etchants were used to highlight different microstructural features. The study revealed that: (1) this type pinch weld is largely complete after about six cycles of 60 Hz AC current, half the weld time utilized; (2) the resistance, deformation, and closure length approach “steady-state” conditions after six cycles; and (3) both oxalic and nitric acid electrolytic etchants are useful for highlighting specific microstructural attributes of type 304 L stainless steel. Finally, two distinct microstructural regions can be identified for these welds: the edge of the weld, which is driven by concentrated deformation, recrystallization, and grain growth, and the center region, which is more typical of forge welding and micro-asperity breakdown followed by diffusion and grain-growth.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Integrated Sustainable Product Design With Warranty and End-of-Use Considerations

The concept of integrated sustainable product design has recently emerged, aiming to incorporate downstream life cycle performance into the initial product design to enhance sustainability. Various sustainable product design tools based on life cycle assessment or quality function deployment have been established while the impact of reliability on circular practices has received limited attention. Recognizing the critical role of product reliability in post-design performance, this paper develops a product design optimization model that considers the warranty performance and the effect of end-of-use options. The model takes into account the effect of uncertain operating conditions on product reliability. Two optimization goals including the minimization of expected unit life cycle cost and environmental impact are achieved by the model. To demonstrate the benefits of the integrated approach, the model is applied to an electric motor design problem. The results highlight that integrating end-of-use options in the early design phase leads to adjustments in component selection and reliability design. Moreover, the circular utilization of used products enables cost savings throughout the product’s life cycle and contributes to environmental impact reduction. Finally, the study analyzes the effects of operating conditions, warranty policies, and take-back prices for used products on design decisions, providing valuable insights for product designers.

Integrated design↗
DOE OSTI2025

On the Efficacy of Repeat Voltage Holds for Conditioning and Calendar Life Testing of Graphite and Silicon Cells

Voltage-hold (V-hold) protocols have shown promise toward calendar lifetime analysis of cells with graphite (Gr) and silicon (Si) anodes. In this work, repeat V-holds are performed on Gr and Si cells paired with lithium iron phosphate cathodes to delineate their beneficial role in formation and conditioning. We find that V-hold at the top of charge supplements constant current cycling in conditioning the cell to higher capacities for both Gr and Si cells after the first V-hold. A reduced order model provides the irreversible capacity proportions of each V-hold. With each repeat V-hold, parasitic loss of lithium to the solid electrolyte interphase (SEI) decreases on both Gr and Si cells. Gr cells show the square-root-of-time capacity loss behavior within 200 h of V-hold, indicative of its fast relaxation and low impact of reference performance test cycles on the SEI growth. Lifetime estimates from repeat V-holds on Gr can reach years. Si exhibits longer transition times from kinetic to diffusion-limited SEI growth, evidenced by the 400 h and 200 h holds showing square-root-of-time and linear behavior, respectively. Lifetime predictions from repeat V-holds on Si only reach 1–2 months, highlighting its limitations. Recommended duration of V-holds for Si cells should be ≥400 h.

25 ENERGY STORAGE↗
DOE OSTI2026

Tailoring Thermal and Mechanical Performance Through Multimaterial Laser Powder Directed Energy Deposition of Copper and 17-4PH Stainless Steel

This study investigates the additive manufacturing (AM) processing, microstructural evolution, and resulting mechanical and thermal properties of multimaterial components combining 17-4PH stainless steel and pure copper (Cu) fabricated via laser powder directed energy deposition (LP-DED). Conventional tooling steels exhibit limited thermal conductivity, significantly constraining production throughput in high-volume processes. Incorporating Cu, with its superior thermal conductivity, could significantly enhance tool performance, though Cu and steel present metallurgical incompatibilities when processed via AM. A systematic investigation was conducted across compositions ranging from 0 to 100 wt% Cu, revealing critical thresholds influencing solidification behavior, defect formation, microstructure, hardness, and thermal transport. Optical microscopy, electron backscatter diffraction (EBSD), hardness testing, and thermal conductivity measurements provided comprehensive process–structure–property correlations. Severe hot cracking occurred at low-Cu contents (6–25 wt%), aligning generally well with crack susceptibility modeling, with an unexpected discrepancy at 25 wt%. Porosity remained low (≥99% dense) throughout the compositional spectrum. EBSD analysis revealed a transformation from columnar martensitic structures at low-Cu contents to equiaxed FCC Cu-dominated structures at higher Cu concentrations, highlighting the complex microstructural transitions driven by Cu-induced changes in solidification and phase stability. Hardness decreased from 330 HV (pure 17-4PH) to 62 HV (pure Cu), consistent with microstructural changes. Concurrently, thermal conductivity improved substantially from 13.5 W/m K to 367.9 W/m K, emphasizing Cu’s dominant role in thermal transport. The findings highlight the feasibility of leveraging compositional gradients between 17-4PH and Cu to achieve tailored tooling with optimized thermal and mechanical performance.

17-4PH↗
DOE OSTI2020

Accelerating Large-Format Metal Additive Manufacturing: How Controls R&D is Driving Speed, Scale, and Efficiency

This article highlights work at Oak Ridge National Laboratory’s Manufacturing Demonstration Facility to develop closed-loop, feedback control for laser-wire based Directed Energy Deposition, a form of metal Big Area Additive Manufacturing (m-BAAM), a process being developed in partnership with GKN Aerospace specifically for the production of Ti-6Al-4V pre-forms for aerospace components. A large-scale structural demonstrator component is presented as a case-study in which not just control, but the entire 3D printing workflow for m-BAAM is discussed in detail, including design principles for large-format metal AM, toolpath generation, parameter development, process control, and system operation, as well as post-print net-shape geometric analysis and finish machining. In terms of control, a multi-sensor approach has been utilized to measure both layer height and melt pool size, and multiple modes of closed-loop control have been developed to manipulate process parameters (laser power, print speed, deposition rate) to control these variables. Layer height control and melt pool size control have yielded excellent local (intralayer) and global (component-level) geometry control, and the impact of melt pool size control in particular on thermal gradients and material properties is the subject of continuing research. Further, these modes of control have allowed the process to advance to higher deposition rates (exceeding 7.5 lb/hr), larger parts (1-meter scale), shorter build times, and higher overall efficiency. The control modes are examined individually, highlighting their development, demonstration, and lessons learned, and it is shown how they operate concurrently to enable the printing of a large-scale, near net shape Ti-6Al-4V component.

Gibson, Brian↗
DOE OSTI2020

Role of consistent terminology in XPS reproducibility

The use of inconsistent and incorrect terminology in scientific publications contributes to misunderstanding, confusion, and erroneous results in the scientific literature. This issue is of particular importance in x-ray photoelectron spectroscopy (XPS) that is in widespread use for many different purposes by scientists with diverse backgrounds. A set of surface analysis terminology, approved through consensus by international experts, has been developed by International Organization for Standardization Technical Committee TC201 on Surface Chemical Analysis. To encourage wide use, the terminology is accessible at several web sites free of charge. This short overview provides examples to highlight the importance of agreed terminology in eliminating confusion between similar terms. Examples are provided of terms that are commonly misused or confused in the literature. Other examples highlight terminology that provides a common basis for comparing instrument parameters and performance. As science advances, it is important to clarify terminology for describing evolving concepts and developments important to XPS.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

Surface and bulk characterization of reservoir and cap-rocks: Past, present, and future

Geologic formations provide potentially some of the largest volume capacities for CO 2 storage or sequestration. Potential storage sites can be deep saline aquifers, depleted oil reservoirs, and coal seams, surrounded by sealing layers to prevent CO 2 from leaking. It is therefore critical to understand mechanisms contributing to CO 2 trapping and CO 2 leaks. Both phenomena are governed by reactions at the interfaces of the reservoir and cap-rocks and are controlled by the complex chemistry and pore structures of rocks. Mechanisms at the macroscale are affected by the processes occurring at the nanoscale. This review highlights the necessity of multitechnique, multiscale characterization of rocks and points to the importance of surface analysis and surface science studies. Two shale rocks (seals) from Niobrara and Agardhfjellet formations with complex surface chemistry are used as examples throughout the paper. Typically, evaluation of rocks with x-ray diffraction, thermogravimetric analysis, Rock-Eval pyrolysis, gas adsorption, and electron microscopy combined with energy dispersive x-ray spectroscopy is conducted to provide valuable information about the bulk mineralogy, elemental composition, pore volume, and adsorbed species on the sample surface. These studies are necessary prior to designing surface sensitive experiments with x-ray photoelectron spectroscopy (XPS), guiding both sample preparation and sample analysis. XPS has been widely used to study the surface composition of rocks during the investigations of their fine-scale wettability, and the main findings are highlighted here. This paper also reviews the existing literature on ambient-pressure XPS, which provides new opportunities to study in situ chemical alteration due to interactions with CO 2 and offers recommendations for adapting this technique to study rock-fluid interactions, allowing for the identification of fundamental interactions during CO 2 sequestration and guide selection of formation sites for improved storage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota

Methane is a potent greenhouse gas, largely produced by methanogenic archaea, contributing to Earth’s dynamic climate and biogeochemical cycles. In the past decade, metagenomics revealed that lineages outside of the Euryarchaeota superphylum encode genes for methanogenesis. This was recently confirmed through the cultivation of two classes of methanogenic Thermoproteota. Thus far, all methanogens within the Thermoproteota are predicted or were shown to be methylotrophic. The only exception to this are the Nezhaarchaea, for which metagenomic predictions suggest they are CO 2 -reducing methanogens. Here, we demonstrate methanogenic activity in a third class of Thermoproteota, the Methanonezhaarchaeia. Contrary to genomic predictions for this class, we cultivated a methylotrophic species, Candidatus Methanonezhaarchaeum fastidiosum YNP3N, highlighting the importance of testing metagenomic hypotheses through experimentation. We investigate the metabolic diversity of Methanonezhaarchaeia, including metabolic modifications accompanying frequent loss of methanogenesis in this class. This highlights gaps in our understanding of the biochemistry, diversity, and evolution of thermoproteotal methanogens and their contributions to carbon cycling.

Kohtz, Anthony J. [Montana State Univ., Bozeman, M↗
DOE OSTI2020

Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

Science & Technology - Other Topics↗
DOE OSTI2020

Anomalous absorption of electromagnetic waves by 2D transition metal carbonitride Ti 3 CNT x (MXene)

Lightweight, ultrathin, and flexible electromagnetic interference (EMI) shielding materials are needed to protect electronic circuits and portable telecommunication devices and to eliminate cross-talk between devices and device components. Here, we show that a two-dimensional (2D) transition metal carbonitride, Ti 3 CNT x MXene, with a moderate electrical conductivity, provides a higher shielding effectiveness compared with more conductive Ti 3 C 2 T x or metal foils of the same thickness. This exceptional shielding performance of Ti 3 CNT x was achieved by thermal annealing and is attributed to an anomalously high absorption of electromagnetic waves in its layered, metamaterial-like structure. These results provide guidance for designing advanced EMI shielding materials but also highlight the need for exploring fundamental mechanisms behind interaction of electromagnetic waves with 2D materials.

Science & Technology - Other Topics↗
DOE OSTI2020

Using nature’s blueprint to expand catalysis with Earth-abundant metals

Original title changed for publication from; " Using Nature's Blueprint to Enable Catalysis with Earth-Abundant Metals" A diverse array of redox transformations that are essential to life are catalyzed by metalloenzymes that feature an earth-abundant metal. In contrast, platinum-group metals have been the cornerstone of many industrial catalytic reactions for decades, providing high activity, thermal stability and tolerance to chemical poisons. We assert that Nature’s blueprint provides the fundamental principles for vastly expanding the use of abundant metals in catalysis. We highlight the key physical properties of abundant metals that distinguish them from precious metals, and we look to Nature to understand how the inherent attributes of abundant metals can be embraced, leading to unique, highly efficient catalysts, emphasizing reactions crucial to the sustainable production and transformation of fuels and chemicals.

Bullock, Ronald M.↗
DOE OSTI2022

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair’s identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A roadmap to understanding and anticipating microbial gene transfer in soil communities

Engineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. Here, we propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

bioccontainment↗
DOE OSTI2023

Transcriptome architecture of the three main lineages of agrobacteria

ABSTRACT Agrobacteria are a diverse, polyphyletic group of prokaryotes with multipartite genomes capable of transferring DNA into the genomes of host plants, making them an essential tool in plant biotechnology. Despite their utility in plant transformation, genome-wide transcriptional regulation is not well understood across the three main lineages of agrobacteria. Transcription start sites (TSSs) are a necessary component of gene expression and regulation. In this study, we used differential RNA-seq and a TSS identification algorithm optimized on manually annotated TSS, then validated with existing TSS to identify thousands of TSS with nucleotide resolution for representatives of each lineage. We extend upon the 356 TSSs previously reported in Agrobacterium fabrum C58 by identifying 1,916 TSSs. In addition, we completed genomes and phenotyping of Rhizobium rhizogenes C16/80 and Allorhizobium vitis T60/94, identifying 2,650 and 2,432 TSSs, respectively. Parameter optimization was crucial for an accurate, high-resolution view of genome and transcriptional dynamics, highlighting the importance of algorithm optimization in genome-wide TSS identification and genomics at large. The optimized algorithm reduced the number of TSSs identified internal and antisense to the coding sequence on average by 90.5% and 91.9%, respectively. Comparison of TSS conservation between orthologs of the three lineages revealed differences in cell cycle regulation of ctrA as well as divergence of transcriptional regulation of chemotaxis-related genes when grown in conditions that simulate the plant environment. These results provide a framework to elucidate the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. IMPORTANCE Transcription start sites (TSSs) are fundamental for understanding gene expression and regulation. Agrobacteria, a group of prokaryotes with the ability to transfer DNA into the genomes of host plants, are widely used in plant biotechnology. However, the genome-wide transcriptional regulation of agrobacteria is not well understood, especially in less-studied lineages. Differential RNA-seq and an optimized algorithm enabled identification of thousands of TSSs with nucleotide resolution for representatives of each lineage. The results of this study provide a framework for elucidating the mechanistic basis and evolution of pathology across the three main lineages of agrobacteria. The optimized algorithm also highlights the importance of parameter optimization in genome-wide TSS identification and genomics at large.

59 BASIC BIOLOGICAL SCIENCES↗
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.↗