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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Development of High-Fidelity and Efficient Modeling Capabilities for Enabling Co-Optimization of Fuels and Multi-Mode Engines

The objective of this closely coordinated research project is to develop improved physical sub-models and innovative numerical algorithms to enable accurate and efficient predictions of multi-mode combustion to support EERE’s Co-Optima program. To this end, a research pro-gram is proposed that seeks • to develop accurate submodels for predicting multi-mode combustion regimes, wall-heat transfer, non-equilibrium plasma ignition, and combustion-mode transition, • to develop dynamic load-rebalancing algorithms and efficient semi-implicit time-integration schemes for enabling exascale computing, • to validate the computational submodels against experiments and direct numerical simulation (DNS) data in conjunction with sensitivity analysis, and • to support the direct transition of the resulting sub-models into other engine-simulation tools through the development of self-contained modules. All sub-models will be integrated into the open-source exascale engine-simulation platform Nek5000.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Conceptual Design of Integrated Energy Systems with Market Interaction Surrogate Models

Most integrated energy system (IES) optimization frameworks employ the price-taker approximation, which ignores important interactions with market and can result in overestimated economic values. In this work, we pro-pose a machine learning surrogate-assisted optimization framework to quantify the IES/market interactions and thus go beyond price taker. We use time series clustering to generate representative IES operation profiles for the IES optimization problem and use machine learning surrogate models to predict the IES/market interaction. We quantify the accuracy of the time series clustering and surrogate models in a case study to optimally retrofit a nuclear power plant with polymer electrolyte membrane electrolyzer to co-produce electricity and hydrogen.

Chen, Xinhe↗
DOE OSTI2024

Considerations in Proliferation Resistance Optimization of Medical Isotope Facilities

The U.S. Proliferation Resistance and Optimization (PRO-X) program provides a framework for design optimization of a system, component, or feature of a nuclear facility to minimize potential Special Nuclear Material production and diversion pathways while optimizing system performance for peaceful, asintended missions.

Groden, Nicholas D.↗
DOE OSTI2025

Report for the 2024 ASCR Workshop on Energy-Efficient Computing for Science

In September 2024, the US Department of Energy’s Advanced Scientific Computing Research pro gram convened a Workshop on Energy-Efficient Computing for Science to address the critical research challenges and opportunities in this field. The workshop brought together experts from academia, government, and industry to explore innovative approaches to improve energy efficiency across the computing stack over the next two decades. Participants identified five priority research directions (PRDs) that emphasize the need for a holistic approach.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Analog Computing for Science

Conventional digital computing faces fundamental physical limits: large scale computing systems already con sume tens of Megawatts of power, Dennard scaling has ended, and data movement costs dominate application performance. Next generation experimental facilities generate data at rates that overwhelm conventional pro cessing and demand real-time analysis at the source. Analog computing, which exploits the continuous dynamics of physical systems to perform computation, promises a transformative path toward orders-of-magnitude gains in energy efficiency and time-to-solution for scientific workloads.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Coupled Aerodynamic and Hydrodynamic Hybrid Simulation of Floating Offshore Wind Turbines

The development and innovation of floating offshore wind energy in the U.S. requires detailed high-fidelity observations and measurements of turbine and platform loading due to wind, waves, and currents. However, full-scale and quasi-full-scale experiments require significant financial and temporal investments for construction, experimental testing, and long-term field campaigns. To support the commercial advancement of the offshore wind energy industry, specialized wind tunnel and wave basin experimental facilities are critical to be able to test FOWT designs at small scale under controlled conditions prior to full-scale deployment. Oregon State University (OSU) is internationally known as a leader in water and energy research, development, and testing. The O.H. Hinsdale Wave Research Laboratory (HWRL) and the Wallace Energy Systems and Renewables Facility (WESRF) at OSU have extensive experience building, modeling, monitoring, controlling, and actuating scaled systems. Experiments on wave-structure interaction have been performed at the HWRL since its establishment in 1972. Studies have included the interaction of waves with coastal structures (breakwaters, seawalls, buildings, cylinders, bridges, fixed foundations of offshore wind turbines, etc.) and with floating structures (e.g., wave energy converters, maneuvering of vessels, etc.). Hinsdale is actively used by marine energy technology developers, both for private testing and OSU-collaborative research projects. However, despite the availability of several large-scale facilities for hydrodynamic testing (at OSU and elsewhere in the U.S.), existing experimental laboratories are generally limited in their ability to accurately generate combined wind and wave conditions. The simulation of both wind and waves in experimental testing is complicated due to a number of constraints, including: [i] incompatible similitude laws governing the wind and waves for scaled experiments, [ii] producing accurate wind over a large enough control volume via fans, and [iii] generating wind that reasonably represents the atmospheric boundary layer in existing wave basins/flumes. Hence, physical test data providing insight into the simultaneous wave- and wind-structure response of floating offshore wind components can be difficult to generate. Given the aforementioned challenges in classic hydrodynamic experiments, the motivation of this project is to establish a real-time hybrid simulation (RTHS) approach that can apply aero- and hydro-dynamic loading by augmenting wave-only experimental facilities with virtual aerodynamic forces through numerical models representing the remaining dynamic forces. RTHS is a physical-numerical approach that partitions a prototype system into physical and numerical sub-assemblies that interact with each other through actuators and sensors in real time. In coupling physical and numerical models, the hybrid simulation approach applied herein is ideal for problems with: (1) structures subjected to different scaling laws, such as floating offshore wind turbines subjected to combined aero/hydro-dynamic loading, (2) structures that are too large or complex to be tested entirely in a laboratory setting, such as deep-water mooring applications, and (3) component testing, where the behavior of a portion of the assembly is uncertain but still interacts with other portions of the structure, such as testing the fatigue life of turbine blades. Few U.S. experimental facilities are able to test simultaneous aero- and hydro-dynamic loading and none can accurately produce aero/hydro-dynamic response on scaled FOWT models due to conflicting similitude laws between the wind (commonly Reynolds) and the waves (commonly Froude). To aid in accelerating the development of the U.S. floating offshore industry, there is a significant need to develop a flexible, modular framework that can expand the capacities of existing wave-only laboratories. The project goal is to demonstrate a hydrodynamic real-time hybrid simulation (hydro-RTHS) framework that couples numerical wind and physical waves acting on a FOWT, thus representing simultaneous aero/hydro-dynamic loading. The FOWT is partitioned into a full-scale numerical sub-assembly associated with the aerodynamics and a model-scale physical sub-assembly associated with the hydrodynamics. The numerical-physical partition associated with hydro-RTHS mitigates scaling constraints by supplying different scaling laws to the physical and numerical sub-assemblies. Herein, length, force, and time are scaled and exchanged between the sub-assemblies using Froude scaling to represent the open-channel flow in the physical sub-assembly. Other similitude laws could also be utilized depending on the problem definition. It is envisioned that the ability to model FOWTs under waves and wind, with mitigation of similitude distortions, would result in reduced development costs (currently, FOWT concept development is performed with full-size pro- totypes at enormous expense and risk) and increase the reliability of the FOWT industry (since extreme wave and wind conditions and contingency events can be tested safely in a controlled environment).

16 TIDAL AND WAVE POWER↗
DOE OSTI2024

Automating the Analysis of Large Language Models Responses through Zero-Shot Question Answering

Recent advancements in Large Language Models (LLMs) have shown significant potential in various applications, yet their evaluation, particularly in zero-shot question answering scenarios, remains a challenging task. In this study, our objective was to explore precision metrics for Large Language Models (LLM) and design and implement a software pipeline to automatically evaluate LLMs' outputs under zero-shot question answering. Zero-shot question answering involves a model providing answers to questions about topics it hasn't seen during training. It leverages the principles of zero-shot learning by relying on semantic understanding and generalization from related knowledge. The data used was metadata from medical databases on congenital heart disease. We explored eleven LLM metrics and selected three for our evaluation: BLEU, BERTScore, and MoverScore. BLEU calculates a score based on the overlap of n-grams (contiguous sequences of n items, typically words) between the machine-generated translation and the reference translations. Higher BLEU scores indicate better correspondence between the machine-generated and human-generated translations. BERTScore is a metric used to evaluate the quality of machine-generated text by measuring the similarity of token embeddings produced by BERT (Bidirectional Encoder Representations from Transformers) between the generated text and reference text. MoverScore is a metric that quantifies the dissimilarity between the distributions of word embeddings from machine-generated text and reference text, emphasizing semantic similarity over exact token overlap. We also introduced HBKI, a composite metric summarizing these approaches. We tested five models —GPT-3, Llama-2, Gemini 1.5 Pro, Solar 10.7B, and Mixtral-8x7b. Our software pipeline, designed and implemented using Object-Oriented Programming principles, allows users to customize the selection and extraction of features for topics of interest in their own research. Our results show that MoverScore delivered the most precise evaluation of the LLM's outputs, while Mixtral-8x7b achieved the best overall performance in extracting metadata from the databases.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

GEANT3 simulations for a beryllium Moderator for the Neutron Target Demonstrator (NTD)

Measurements of neutron-induced reactions, particularly on short-lived nuclei, are crucial for nuclear astrophysics and applications. The Neutron Target Demonstrator (NTD) aims to address this by using a strong mod erated spallation neutron source coupled with an ion storage ring. This work investigates the potential of improving the neutron moderator, a key component of the NTD. Using GEANT3 simulations, we compare the performance of the existing 80 cm carbon moderator with a new moder ator design, which utilizes beryllium pieces available at LANL to form a core surrounded by carbon. Simulations were performed 800 MeV pro tons incident on a tungsten target. The results demonstrate that the beryllium-core moderator increases the density of moderated neutrons within the central beam pipe by roughly a factor 4 compared to the pure carbon moderator. This enhancement makes the beryllium-core design a very promising option for future experiments focused on neutron-induced measurements in inverse kinematics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

C136A and C138A Report of Analysis

In this work the isotopic ratios and weight percentages of 238 Pu, 239 Pu, 240 Pu, 241 Pu and 242 Pu were determined using Isotope Dilution Mass Spectrometry. Two samples of C136A and C138A were sent to the Analytical Research laboratories by the National Nuclear Security Administration Nuclear Reference Material Program. The four samples were dissolved in concentrated hydrochloric acid. From the parent solutions, eight aliquots were taken, diluted, spiked with 244 Pu and submitted to separations. After the samples were separated, they were analyzed using Multicollector Inductively Coupled Plasma Mass Spectrometry. Along with the samples, two C126A Quality Control Samples were analyzed each day. Mass bias standards were also analyzed at the beginning, during and at the end of the analysis. GUM Workbench Pro software Version 2.4.1.406 was used to calculate the isotopic ratios relative to 239 Pu, and total Pu mass and the correlated expanded uncertainties.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗
DOE OSTI2025

Fermilab PIP-II Master Oscillator and Precision Reference Line Design and Construction

The phase averaging reference line system pro- vides the RF phase reference, LO and clock sig- nals to the LLRF and other accelerator sub- systems. The PIP-II linac has RF systems at three frequencies – 162.5 MHz, 325 MHz and 650 MHz. A temperature-stabilized, low-phase- noise oscillator is used as the master oscil- lator. Phase reference signals at 162.5 MHz, 325 MHz, and 650 MHz, along with LO signals at 182.5 MHz, 345 MHz, 670 MHz and LLRF clocks at 1320 MHz and 1300 MHz, are generated in temperature-controlled RF modules at each fre- quency section. A phase reference from each module travels to the next section, where it is doubled to produce required frequencies. The reference also travels alongside the accelerating cavities in the tunnel, allowing cavity probe and reference cables to temperature track and reduce measurement errors from temperature changes or phase drift.

Syed, Ahmed [Fermilab]↗
DOE OSTI2025

EV Stock and Load Forecasting for HECO [Slides]

This presentation covers the work completed for the HECO Forecasting Department for the Electric Vehicle Stock and Load Forecast for Integrated Grid Planning project. This project uses a suite of detailed analytical tools developed by the National Laboratory of the Rockies, including TEMPO and EVI-Pro, to develop future scenarios to 2050 of county-level electric vehicle adoption and associated annual hourly charging load profiles for the state of Hawaii.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2025

Systems Analysis of Biomass and Coal Co-firing Power Plants with Deep Carbon Capture Toward Net-zero Emissions

Achieving a net-zero emission economy in the United States requires integrating diverse low-carbon and negative-emission technologies into the existing fossil fuel-dominant power fleet. Potential technologies from the low-carbon portfolio include renewable power, fossil power with carbon capture and storage (CCS), bioenergy with CCS (BECCS), and direct air capture (DAC). Renewable power is a clean energy source but has to pair with costly battery storage to provide dispatchable electricity. Fossil power with CCS offers dispatchable electricity yet still relies on DAC to offset residual emissions, even when deploying deep CCS with more than 90% CO2 capture. Coal-biomass co-firing with CCS, a subset of BECCS, is a reliable energy production technology that can be retrofitted from existing electricity generation units (EGUs). Power plant retrofit maximizes the use of the current U.S. coal power fleet without the need for large-scale deployment of new renewable power, battery storage, or DAC. Retrofitting coal-biomass co-firing with deep CCS in EGUs is a promising option, but not a universal solution. Biomass co-firing at a power plant introduces economic challenges and indirectly poses pressure on land and water resources. Meanwhile, retrofitting deep CCS affects plant efficiency and raises electricity generation costs. Overall, the technical feasibility and economic viability of plant retrofits vary across EGUs, as they are contingent upon the regional availability of biomass, unit-specific characteristics, site-specific fuel supply costs, and adjacent CO2 storage potential. Government incentives like 45Q can improve the retrofit viability, though the impact requires further quantification. A comprehensive analysis at the unit level is essential to address the question regarding the fate of the U.S. coal-fired electricity generation fleet toward the net-zero emission goal. This study conducts a systematic techno-economic-environmental assessment of EGUs to identify the viability of biomass co-firing and deep CCS retrofits in the U.S. coal-fired power fleet. Specifically, it characterizes the techno-economic performance of deep carbon capture, estimates life cycle greenhouse gas (GHG) emissions, and conducts a fleet-level assessment on retrofit viability. The key objectives are (1) to estimate the unit-specific performance and retrofitted cost under various biomass co-firing levels and CO2 capture rates; (2) to determine the possibility of reaching net-zero emission at the fleet level; (3) to quantify the cumulative capacities that are suitable for plant retrofits under current and future biomass supply scenarios; and (4) to improve the understanding of policy impacts on such retrofits to help the power sector’s transition to a net-zero economy. Techno-economic Model of Deep Carbon Capture. This study develops the performance and economic models for Monoethanolamine-based post-combustion CO2 capture at 95–99% capture rates. The process is simulated in Aspen Plus, analyzing the performance of carbon capture technology by varying the plant sizes, solvent lean loading, CO2 concentrations, and flue gas inlet temperature. Based on the key inputs and output parameters of CO2 capture, a reduced-order performance model of deep carbon capture is formulated. In addition, an engineering-economic model integrating the performance metrics is developed to estimate the capital as well as operation and maintenance (O&M) costs. Capital cost estimations follow the framework of the Integrated Environmental Control Model (IECM) and incorporate data regressions from three technical reports by IECM, the National Energy Technology Laboratory (NETL), and the National Renewable Energy Laboratory. The O&M cost estimation utilizes the actual inventory consumption rate and labor requirements. Both performance and cost models are embedded into IECM v13.0-beta, a fossil-fuel power plant modeling tool. Life Cycle Assessment of Power Plants. This study estimates the GHG emissions of power plants through life cycle assessment (LCA). The LCA scope includes fuel supply, combustion-based power generation, and CO2 transport and storage. The fuel-based life cycle module is designed following the framework of the NETL Unit Process Library and CO2U LCA Guidance Toolkit. The module is then incorporated into IECM v13.0-beta. The process-based LCA is applied to estimate the GHG emissions of coal and biomass supply, coal- and coal-biomass co-firing power plant operation, as well as CO2 pipeline transport and geographical sequestration. An uncertainty analysis is conducted to quantify the variability and uncertainty associated with the LCA using the Latin Hypercube Sampling (LHS) method. Fleet-level Assessment. This study evaluates the technical and economic feasibility of selected coal-fired EGUs, examines the role of tax credits in retrofit viability, and assesses the competitiveness of retrofitted units against other low-carbon options. Unit screening identifies EGUs for the study, focusing on new, efficient baseload units with air pollution controls. The power plant databases are then established to organize unit-specific information on performance and operating conditions from the relevant public databases. Biomass for co-firing retrofits is selected based on home and neighboring county availability, ensuring sustained operation with at least a 5% co-firing level. The CO2 storage site is determined by state-level storage potential, with ArcGIS Pro and NETL CO2 Saline Storage Cost Model used to identify the optimal balance between the nearest transport distances and affordable storage costs. The latest IECM v13.0-beta is then employed to configure and evaluate the eligible EGUs with or without the deployment of deep CCS and biomass co-firing. A supply curve is established to illustrate the cumulative installed capacity suitable for retrofits at different cost levels. A sensitivity analysis on tax credits for carbon sequestration is performed. Finally, a unit-level cost comparison is conducted among retrofitted plants, renewable power with battery storage, and abated fossil fuels with DAC. Expected Results. This study evaluates the technical, economic, and environmental metrics of each EGU across an array of CO2 capture rates and biomass co-firing level scenarios. Unit-level comparisons will identify critical factors influencing technical performance. The supply curves with and without tax incentives will provide insights into the impact of tax credits on biomass co-firing and CCS deployment. The cost comparisons with renewables and DAC-retrofit will assess the competitiveness of the retrofitted units. Life cycle emissions from each unit will be assessed to identify the scenarios under which net-zero emissions can be achieved. These analyses are expected to determine the total coal-fired capacity suitable for serving as a low-carbon energy source with or without tax incentives. The study results are novel in identifying optimal unit-specific strategies for producing carbon-neutral power, whether through retrofitting EGUs with deep CCS, biomass co-firing, DAC, or installing renewable power with battery. The findings will provide insight into nationwide efforts to ensure reliable, affordable, and low-carbon electricity. It also will inform investment decisions and policies in the deployment of deep carbon capture and negative emission technologies for a net-zero energy future.

Biomass Co-firing↗
DOE OSTI2024

Quantum surrogate models for uncertainty quantification

Surrogate models are a critical ingredient to computation-based design and validation of many DOE mission-relevant physical systems. When first-principles computation of properties of a physical systems becomes pro hibitive, surrogate models are the only path towards achieving tasks such as uncertainty quantification (UQ), exploration of design space, and validation of design choices. In this project we have developed and demonstrated a new surro gate modeling paradigm for complex models that is data-driven, non-intrusive, and has the potential to be versatile and equipped with performance guaran tees. This combination of features is absent in existing surrogate modeling tools. The framework we have developed in this project exploits a quantum-classical correspondence to establish a quantum system that mimics the dynamics of the classical Hamiltonian system from which data in the form of temporal snapshots is provided. Since quantum dynamics propagates distributions over observables, the framework is naturally suited to propagation of epistemic uncertainties in the form of distributions over initial state and parametric uncertainties. In this project, we take the first step in establishing this novel framework by deriving a quantization and de-quantization procedure, demonstrating the accuracy of the quantum surrogate models these define using two model systems, and defining the next steps in maturing the framework towards a tool applicable to Sandia mission-relevant problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

High-Power Amplifier Considerations for testing the LAMP RFQ and first DTL Cavity

As part of the LANSCE Accelerator Modernization Pro ject (LAMP), critical portions of the proposed accelerator will be tested as proof of concept and aid in planning the installation of LAMP at Los Alamos Neutron Science Cen ter. As part of this demonstration, the radio frequency quadrupole (RFQ) and the first drift-tube linac (DTL) cav ity will be tested with beam. For this purpose, high-power RF amplifiers are being designed to meet the testing de mands. This is a description of the requirements of these amplifiers and how the design is intended to meet them.

42 ENGINEERING↗
DOE OSTI2026

Reducing Deferrals by Integrating Health Homes with Weatherization

The U.S. Department of Energy’s Weatherization Assistance Program (WAP) improves energy efficiency and household health for low-income families, yet a substantial number of otherwise eligible homes are deferred from due to health and safety concerns in their homes, including mold, moisture damage, or structural deficiencies. These deferred homes are often occupied by marginalized or otherwise vulnerable residents who may be exposed to elevated indoor air pollutant concentration. Integrating Healthy Homes (HH) interventions with weatherization has been proposed as a strategy to reduce deferrals, address environmental justice concerns, and improve health outcomes. However, limited data on the health and economic implications of such integration exist. This study aimed to assess the potential health benefits and savings-to-investment ratio (SIR) associated with integrating Healthy Homes interventions into weatherization programs for homes typically deferred from WAP services. We collected indoor air pollutant data from homes undergoing health home renovations, including fine particulate matter (PM 2.5 ), nitrogen dioxide (NO 2 ), carbon monoxide (CO), and formaldehyde, with sampling times up to one month. Except for fomaldehyde, which was measured using passive UMEx badges, the other metrics were measured using the airQ Pro indoor air quality monitor.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Baseline Hypothetical Facility for the Production of 131 I and 99 Mo using Activation Targets

This report describes a hypothetical facility for production of medical radioisotopes via activation under the Proliferation Resistance and Optimization (PRO-X) program. The facility uses neutron activation of non-special nuclear material (SNM) to produce the medical isotopes 131 I and 99 Mo at a throughput of 60 Ci/week of 131 I and 5 Ci/week of 99 Mo. The hypothetical design was carried out using a 10 MWt research reactor. The precursors used for the activation process were TeO2 for 131 I and MoO 3 for 99 Mo. The processes are performed in 3 hot cells used for target receipt, extraction, purification low specific activity (LSA) generator introduction, and packaging. A fourth hotcell is used for waste processing. The hot cell processing area takes up a footprint of 15.4 m 2 with the total footprint of the facility, including space for administrative offices, non-rad labs, quality assurance, and radiation buffer areas set at 763 m 2 . Waste is produced at a weekly rate of 257.8 g low activity solid waste and 8032.7 mL of low activity liquid waste, 8032 mL of which is water. This baseline hypothetical facility for production of medical isotopes via activation was then compared and contrasted to the hypothetical facility for production of medical isotopes via fission products to show the differences in approach for the two production modes. The two production modes had several highlighted differences including the overall facility and hot cell layout, the type and amount of waste produced by the respective facilities, and economic factors impacting production mode. Finally, a decision tree for which production mode might be more beneficial for an entrant into medical isotope production was developed based on the differences examined and the desired output of medical isotopes desired by the entrant.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Electron polarimetry at EIC

The Electron-Ion Collider will be the first collider to use both polarized electron beams and polarized protons and light ions . This will offer unique opportunities to study the structure of protons and nuclei and answer fundamental questions in QCD. The uncertainties on the polarization measurement translate directly into the uncertainties of final physics observables. Hence, a precise measurement of the hadron beam polarization and a good control of the uncertainties are critical for the success of the spin program at the EIC. The requirements for beam polarimetry are non-destructive with uncertainty less than 1%. At the Electron Storage Ring (ESR) and the Rapid Cycling Synchrotron (RCS), the electron beam polarization will be measured using wellestablished Compton polarimetry techniques. However, the EIC Compton polarimeter will face unique challenges, demanding further developments. A Mott polarimeter will also be employed at the source for initial polarization measurements. Both longitudinal and transverse polarization will be measured, with the capability to monitor polarization on a bunch-by-bunch basis. Achieving these precise measurements will be critical to controlling systematic uncertainties and ensuring the overall success of the EIC’s physics objectives.

Zhang, Zhengqiao (ORCID:0009000742521735)↗
DOE OSTI2024

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗