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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Preliminary Simulations of Commercial Drying Cycles Using the Advanced Drying Cycle Simulator

The purpose of this report is to document updates on the apparatus to simulate commercial vacuum drying procedures at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system during subsequent storage and disposal. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates well-designed investigations of drying process efficacy and water retention. Scaled tests that incorporate relevant physics and well-controlled boundary conditions are essential to provide insight and guidance to the simulation of prototypic systems undergoing drying processes. This report documents fiscal year 2023 (FY23) updates on the Advanced Drying Cycle Simulator (ADCS). This apparatus was built to simulate commercial drying procedures and quantify the amount of residual water remaining in a pressurized water reactor (PWR) fuel assembly after drying. The ADCS was constructed with a prototypic 17×17 PWR fuel skeleton and waterproof heater rods to simulate decay heat. These waterproof heaters are the next generation design to heater rods developed and tested at Sandia National Laboratories in FY20. In FY23, a series of four simulated commercial drying tests was completed. This report presents the temperature and pressure histories of the drying tests as well as axial temperature profiles that can be compared to data from the Electric Power Research Institute (EPRI) High Burnup Demonstration TN-32B cask. Water content measurements and dew point calculations from a Hiden Analytical HPR-30 mass spectrometer are also presented in this report. Due to familiarization with this first-of-a-kind system, refinements to equipment calibration and test procedures have been identified to better match commercial drying cycles for future simulated tests. However, the presented data demonstrate the successful construction and operation of a viable research platform for quantifying residual water content closely approaching that expected in dry storage canisters during commercial drying procedures.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Separation of protactinium from uranium-niobium alloys for 231 Pa– 235 U radiochronometry in nuclear forensic investigations

The isolation and purification of protactinium from uranium materials is essential for 231 Pa– 235 U radiochronometry, but separating Pa from uranium-niobium alloys, a common material in the nuclear fuel cycle, is challenging due to the chemical similarity of Pa and Nb. Here, in this work, we present three resin chromatography separation techniques for isolating Pa from U and Nb which were independently developed by three different laboratories through ad hoc adaptations of standard operating procedures. Our results underscore the need for and value of purification methods suitable for a diversity of uranium-based materials to ensure the operational readiness of nuclear forensics laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Implementation of ASHRAE Guideline 36 Control Logic into Oak Ridge National Laboratory (ORNL)’s Flexible Research Platform (FRP)

This report presents the initial field test procedure and results for ASHRAE Guideline 36 control logic. The US Department of Energy’s Oak Ridge National Laboratory’s (ORNL’s) two-story Flexible Research Platform (FRP-2) was selected as a test building. The rooftop unit (RTU) system serves as the building’s primary cooling system, and each variable air volume (VAV) box with an electric reheat coil serves as the building’s heating system along with RTU gas furnace. In this study, the control for the RTU and VAV box adopted the practical control sequences from ASHRAE Guideline 36-2018: High-Performance Sequences of Operation. Each story of the FRP-2 building has 5 office zones (thermal zones), for a total of 10 zones.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Measurement of Convective Heat Transfer Coefficients with Supercritical CO2 in Novel Additively Manufactured Helically Patterned Pin Fin Tubes Using the Wilson Plot Technique

This paper describes the measurement of convective heat transfer coefficients and friction factors for sCO2 flowing in pin-fin patterned pipes in the Heat Exchange and Experimental Testing (HEET) facility at the US DoE’s National Energy Technology Laboratory (NETL) in Morgantown, WV. The measurement procedures in the HEET rig were validated by conducting benchmark tests with smooth stainless-steel tube and comparing the results with published correlations for Nusselt number (Nu) and friction factor. Over typical Reynolds number range in sCO2, the measured Nu and friction factors were within 7% of classical correlations for smooth tube flow.The candidate pin fin patterned pipes were additively manufactured (AM) at the Oak Ridge National Laboratory. The pins were circular or elliptical in cross-section. Pin length to diameter aspect ratios were 1.33 and 2, while the pin diameter to tube diameter ratio was 0.188 and 0.125. Tests were performed for ReD varying from 6.9×104 to 2.2×105 and at conditions equivalent to the low pressure outlet (8.69 MPa, 361 K) of the low temperature recuperator (LTR) in an indirect sCO2 power cycle. The Wilson plot technique was utilized to measure the bulk heat transfer coefficients.For the better performing design (tube A, pin length to tube diameter ratio: 1.33, pin diameter to tube diameter ratio: 0.188), the local heat transfer coefficient increased by 112% relative to the Dittus-Boelter correlation at the LTR low pressure outlet. This corresponded to a 282% increase in the product of the heat transfer coefficient and the surface area. Large pressure drops across the test articles were observed.

Searle, Matthew↗
DOE OSTI2021

Update on the Simulation of Commercial Drying of Spent Nuclear Fuel

The purpose of this report is to document improvements in the simulation of commercial vacuum drying procedures at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates additional, well-designed investigations of drying process efficacy and water retention. Scaled tests that incorporate relevant physics and well-controlled boundary conditions are essential to provide insight and guidance to the simulation of prototypic systems undergoing drying processes.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Response of a Pressurized Water Reactor Dashpot Region to Commercial Drying Cycles

The purpose of this report is to document updates to the simulation of commercial vacuum drying procedures at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates additional, well-designed investigations of drying process efficacy and water retention. Scaled tests that incorporate relevant physics and well-controlled boundary conditions are essential to provide insight and guidance to the simulation of prototypic systems undergoing drying processes. This report documents testing updates for the Dashpot Drying Apparatus (DDA), an apparatus constructed at a reduced scale with multiple Pressurized Water Reactor (PWR) fuel rod surrogates and a single guide tube dashpot. This apparatus is fashioned from a truncated 5×5 section of a prototypic 17×17 PWR fuel skeleton and includes the lowest segment of a single guide tube, often referred to as the dashpot region. The guide tube in this assembly is open and allows for insertion of a poison rod (neutron absorber) surrogate.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Quantification of Residual Water in Spent Fuel Dry Storage Canisters Using Mass Spectrometry

The purpose of this report is to document updates on the apparatus to simulate commercial vacuum drying procedures at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system during subsequent storage and disposal, such as fuel degradation; cladding corrosion, embrittlement, or breaching; and the creation of a flammable environment via radiolysis of water. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates well-designed investigations of drying process efficacy and water retention. Scaled tests that incorporate relevant physics and well-controlled boundary conditions are essential to provide insight and guidance to the simulation of prototypic systems undergoing drying processes. This report documents details on the quantification of residual water in the Advanced Drying Cycle Simulator (ADCS), an apparatus built to simulate commercial drying procedures and quantify the amount of residual water remaining in a pressurized water reactor (PWR) fuel assembly after drying. The ADCS was constructed with a prototypic 17×17 PWR fuel skeleton and waterproof heater rods to simulate decay heat. The ADCS is outfitted with thermocouples to measure the thermal response of the ADCS to simulated decay heats and internal helium fill pressures relevant to commercial drying procedures. The ADCS is also instrumented with pressure transducers to measure the pressures and vacuum levels observed during simulated commercial drying. The most unique instrumentation used for quantifying residual water in the ADCS is a Hiden Analytical HPR-30 mass spectrometer (MS), which measures gas compositions of the ADCS internal free volume, based on partial pressures calculated from relative proportions of gas molecules detected by the MS. This report details the methodology used to implement MS measurements in quantifying residual water in the ADCS. This methodology includes the calibration of the HPR-30 MS to a Buck Research Instruments CR-4 chilled mirror hygrometer, which itself is calibrated to a NIST-traceable standard. Data collected by both the MS and the chilled mirror hygrometer from water/helium mixtures ranging from 150 to 500,000 ppmv water in helium were used to generate calibration curves, establishing a source of verification of MS measured water contents. Details regarding water content measurement uncertainties are included in this report, defining the accuracy and verifiability of the HPR-30 MS in measuring residual water content in simulated dry storage canister environments.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

Ammonia Fiber Expansion (AFEX) Pretreatment of Lignocellulosic Biomass

Lignocellulosic materials are plant-derived feedstocks, such as crop residues (e.g., corn stover, rice straw, and sugar cane bagasse) and purpose-grown energy crops (e.g., miscanthus, and switchgrass) that are available in large quantities to produce biofuels, biochemicals, and animal feed. Plant polysaccharides (i.e., cellulose, hemicellulose, and pectin) embedded within cell walls are highly recalcitrant towards conversion into useful products. Ammonia fiber expansion (AFEX) is a thermochemical pretreatment that increases accessibility of polysaccharides to enzymes for hydrolysis into fermentable sugars. These released sugars can be converted into fuels and chemicals in a biorefinery. Here, we describe a laboratory-scale batch AFEX process to produce pretreated biomass on the gram-scale without any ammonia recycling. The laboratory-scale process can be used to identify optimal pretreatment conditions (e.g., ammonia loading, water loading, biomass loading, temperature, pressure, residence time, etc.) and generates sufficient quantities of pretreated samples for detailed physicochemical characterization and enzymatic/microbial analysis. The yield of fermentable sugars from enzymatic hydrolysis of corn stover pretreated using the laboratory-scale AFEX process is comparable to pilot-scale AFEX process under similar pretreatment conditions. This paper is intended to provide a detailed standard operating procedure for the safe and consistent operation of laboratory-scale reactors for performing AFEX pretreatment of lignocellulosic biomass.

09 BIOMASS FUELS↗
DOE OSTI2021

Saltstone First Quarter Calendar Year 2021 (1QCY21) Toxicity Characteristic Leaching Procedure (TCLP) Results

The aqueous waste from Tank 50 (salt solution) is sampled quarterly for transfers to the Saltstone Production Facility (SPF). Salt solution is treated at SPF and disposed of in the Saltstone Disposal Facility (SDF). Per request of customer, X-TTR-Z00023, Revision 0, two SDF waste form (saltstone) samples were prepared in the Savannah River National Laboratory (SRNL) from the Tank 50 Waste Acceptance Criteria (WAC) sample and Z-Area premix material for the first quarter of calendar year 2021(1QCY21). One sample contained a Full Premix which included 10:45:45 (by weight) of cement, slag and fly ash. The second sample contained 60:40 (by weight) of slag and fly ash only referred to as the “Cement-Free grout sample”. Results from this technical report support Task 2: ‘Grout Leaching Analyses’ of the Task Technical Request (TTR) prepared by Savannah River Remediation (SRR). After at least 28 days cured, a sample of each of the SDF waste forms was collected and shipped to a certified laboratory for analysis using the Toxicity Characteristic Leaching Procedure (TCLP). The 1QCY21 saltstone (Full Premix) and the Cement-Free grout samples met the South Carolina (SC) Code of Regulations for Hazardous Waste Management Regulations (HWMR) 61-79.261.24 and 61-79-268.48 requirements for a non-hazardous waste form with respect to Resource Conservation and Recovery Act (RCRA) metals and Underlying Hazardous Constituents (UHCs), and also met the SPF WAC that was in effect at the time of the tank sampling.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Saltstone third quarter calendar year 2019 (3QCY19) toxicity characteristic leaching procedure (TCLP) results

The aqueous waste from Tank 50 (salt solution) is sampled quarterly for transfers to the Saltstone Production Facility (SPF). Salt solution is treated at SPF and disposed of in the Saltstone Disposal Facility (SDF). Per request of customer, X-TAR-Z-00008, Revision 01, two SDF waste form (saltstone) samples were prepared in the Savannah River National Laboratory (SRNL) from the Tank 50 Waste Acceptance Criteria (WAC) sample and Z-Area premix material for the third quarter of calendar year 2019 (3QCY19). One sample contained a Full Premix which included 10:45:45 (by weight) of cement, slag and fly ash. The second sample contained 60:40 (by weight) of slag and fly ash only referred to as the “Cement-Free grout sample”. Results from this technical report support Task 2: ‘Grout Leaching Analyses’ of the Task Technical Request (TTR) prepared by Savannah River Remediation (SRR). After a 28 day cure, a sample of each of the SDF waste forms was collected and shipped to a certified laboratory for analysis using the Toxicity Characteristic Leaching Procedure (TCLP). The 3QCY19 saltstone (Full Premix) and the Cement-Free grout samples met the South Carolina (SC) Code of Regulations for Hazardous Waste Management Regulations (HWMR) 61-79.261.24 and 61-79-268.48 requirements for a non-hazardous waste form with respect to Resource Conservation and Recovery Act (RCRA) metals and Underlying Hazardous Constituents (UHCs), and also met the SPF WAC.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Saltstone Third Quarter Calendar Year 2021 (3QCY21) Toxicity Characteristic Leading Procedure (TCLP) Results

The aqueous waste from Tank 50 (salt solution) is sampled quarterly for transfers to the Saltstone Production Facility (SPF). Salt solution is treated at SPF and disposed of in the Saltstone Disposal Facility (SDF). Per request of customer, X-TTR-Z-00023, Revision 0, two SDF waste form (saltstone) samples were prepared in the Savannah River National Laboratory (SRNL) from the Tank 50 Waste Acceptance Criteria (WAC) sample and Z-Area premix material for the third quarter of calendar year 2021(3QCY21). One sample contained a Full Premix which included 10:45:45 (by weight) of cement, slag and fly ash. The second sample contained 60:40 (by weight) of slag and fly ash only referred to as the “Cement-Free grout sample”. Results from this technical report support Task 2: ‘Grout Leaching Analyses’ of the Task Technical Request (TTR) prepared by Savannah River Remediation (SRR). After at least 28 days cured, a sample of each of the SDF waste forms was collected and shipped to a certified laboratory for analysis using the Toxicity Characteristic Leaching Procedure (TCLP). The 3QCY21 saltstone (Full Premix) and the Cement-Free grout samples met the South Carolina (SC) Code of Regulations for Hazardous Waste Management Regulations (HWMR) 61-79.261.24 and 61-79-268.48 requirements for a non-hazardous waste form with respect to Resource Conservation and Recovery Act (RCRA) metals and Underlying Hazardous Constituents (UHCs), and also met the SPF WAC that was in effect at the time of the tank sampling.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

October 2025 Semiannual Composite Salt Waste Processing Facility Decontaminated Salt Solution Toxicity Characteristic Leaching Procedure Results

The aqueous waste from the Salt Waste Processing Facility is sampled semiannually for transfers to the Saltstone Disposal Facility. Salt solution is treated at the Saltstone Production Facility and disposed of in the Saltstone Disposal Facility. Per request of customer, X-TTR-Z-00027, Revision 0, one Saltstone Processing Facility Decontaminated Salt Solution and Z area premix material for the October 2025 semiannual Toxicity Characteristic Leaching Procedure sample. The sample contained 60:40 (by weight) of slag and fly ash (referred to as the “Cement-Free grout sample”). Results from the technical report support Task 2: ‘Grout Leaching Analyses’ of the Task Technical Request prepared by Savannah River Mission Completion. At 51 days cured, the Saltstone sample was collected and shipped to a certified laboratory for analysis using the Toxicity Characteristic Leaching Procedure. The October 2025 Semiannual Cement-Free grout sample met 61 79.268.48 requirements for a non-hazardous waste form with respect to the Resource Conservation and Recovery Act metals and Underlying Hazardous Constituents and met the Saltstone Production Facility Waste Acceptance Criteria that was in effect at the time of the sample collection at the Salt Waste Processing Facility.

Hsieh, Madison [Savannah River National Laboratory↗
DOE OSTI2020

Measuring Heat Transfer Coefficients for Supercritical Carbon Dioxide Cycle Recuperators

This paper describes the measurement of convective heat transfer coefficients and friction factors for sCO 2 flowing in pin-fin patterned pipes at the US DoE’s National Energy Technology Laboratory (NETL) in Morgantown, WV. The measurement procedures were validated by conducting benchmark tests with smooth stainless-steel tube and comparing the results with published correlations for Nusselt number (𝑁𝑢) and friction factor. Over Reynolds numbers (Re D ) ranging from 5×104 to 2.5×105 , measured 𝑁𝑢 was within 5% of the Dittus-Boelter correlation and measured friction factors were within 5% of the McAdams correlation for smooth tube flow.

42 ENGINEERING↗
DOE OSTI2023

Status Report of Joint RPI/ORNL NCSP Task for Thermal Neutron Total Cross Section Measurements

A new cold neutron moderator system was developed and constructed at the Rensselaer Polytechnic Institute (RPI) Gaerttner Linear Accelerator. This system was then used to measure the neutron total cross section in the thermal energy range for polyethylene, polystyrene, Lucite, and yttrium hydride. In tandem with these measurements, a fitting procedure was developed at Oak Ridge National Laboratory to vary computationally simulated phonon density of states until a fit with differential and integral data was achieved. This model, combined with the new RPI total cross section data, was used to generate thermal scattering law files for the materials measured at RPI.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Thermal Performance of Spandrel Assemblies in Glazed Wall Systems: Laboratory Test Design – Challenges and Test Results

Accurate thermal performance calculation procedures for opaque spandrel areas in curtain wall and window wall systems are essential for rating systems when comparing spandrel systems. However, there is a lack of consensus in thermal modeling needed for accurately characterizing heat transfer through spandrel assemblies due to the complex arrangement of materials and structural components. Several studies indicate that conventional 2D thermal simulations may overestimate R-values by 30% compared to physical testing and 3D simulations. Detailed simulations and well-curated laboratory test data are necessary to build confidence in simulation models, which will later be used to develop correlations to improve widely used conventional 2D thermal simulations. This study aims to experimentally test heat transfer through various spandrel assemblies to validate 3D simulation models. Also, the challenges of conducting a thorough testing design along with the solutions would be documented. The team developed a design for testing spandrel assemblies, making appropriate modifications to the existing heat, air, and moisture (HAM) chamber to accommodate the testing needs. Two moveable baffles were designed and fabricated to guide airflow direction parallel to the test article surface. The data acquisition capabilities in the chamber were upgraded to add more than two hundred sensors to the climate and indoor side of the chamber. The goal is to provide a quality dataset for validating complex 3D modeling simulations, which will be used to develop improved thermal simulation techniques that more accurately represent the thermal behavior of spandrel assemblies and their integration within the building envelope. This paper will summarize the results for the boundary conditions of the testing and the temperature variation across different locations of the spandrel assemblies.

Kunwar, Niraj [ORNL] (ORCID:0000000263457652)↗
DOE OSTI2025

Interlaboratory comparison of secondary ion mass spectrometry analysis results from the 7th international technical nuclear forensics working group collaborative material exercise

A review and interlaboratory comparison of secondary ion mass spectrometry (SIMS) data obtained by laboratories participating in the International Technical Nuclear Forensics Working Group (ITWG) 7th Collaborative Material Exercise (CMX-7) has been conducted. The analyzed materials were two uranium compounds in powder form and two pieces of uranium metal. The instruments used in this comparison were a small-geometry (SG) SIMS, CAMECA IMS 7f from the Research Centre Rez, and a large-geometry (LG) SIMS, CAMECA IMS 1280 from Los Alamos National Laboratory. Despite the differences in instruments and analytical procedures, e.g., sample preparation, SIMS setups, and data post-processing, there was good agreement for the 234 U/ 238 U, 235 U/ 238 U, and 236 U/ 238 U ratios in the analyzed materials. The main difference was in the precision, which was, as expected, higher for the LG-SIMS. In addition, a comparison between the laboratories was also made for the image processing algorithms applied to raw data acquired in automated particle measurement (APM) mode. In conclusion, the result of this comparison has led to identification of best practices for setting up parameters of the APM software.

and nuclear chemistry↗
DOE OSTI2023

Advanced Drying Cycle Simulator Thermal Response to Commercial Drying Conditions

The purpose of this report is to document updates on testing of the apparatus built to simulate commercial drying procedures for spent nuclear fuel at the Nuclear Energy Work Complex at Sandia National Laboratories. Validation of the extent of water removal in a dry spent nuclear fuel storage system based on drying procedures used at nuclear power plants is needed to close existing technical gaps. Operational conditions leading to incomplete drying may have potential impacts on the fuel, cladding, and other components in the system during subsequent storage and disposal. A general lack of data suitable for model validation of commercial nuclear canister drying processes necessitates well-designed investigations of drying process efficacy and water retention that incorporate relevant physics and well-controlled boundary conditions. This report documents testing updates for the Advanced Drying Cycle Simulator (ADCS). This apparatus was built to simulate commercial drying procedures and quantify the amount of residual water remaining in a pressurized water reactor (PWR) fuel assembly after drying. The ADCS was constructed with a prototypic 17×17 PWR fuel skeleton and waterproof heater rods to simulate decay heat. These waterproof heaters are the next generation design to heater rods developed and tested at Sandia National Laboratories in FY20. This report describes preliminary testing of the ADCS through measurement and analysis of the thermal response of the system to a subset of commercial drying conditions that exclude the introduction of water, namely simulated decay heats and pressures relevant to commercial drying. This test series, referred to as a “dry” test series in this report, spans three uniform waterproof heater rod powers (representing spent fuel decay heats), four helium fill pressures, and six vacuum levels. This test series was conducted to cover the range of expected ADCS testing conditions for upcoming “wet” testing, where water will be introduced and a simulated commercial drying cycle will be performed. The dry test conditions were derived from the commercial drying conditions seen in the High Burnup Demonstration and the vacuum drying conditions chosen for a smaller scale Dashpot Drying Apparatus tested at Sandia National Laboratories in FY22. For a given uniform power and pressure/vacuum level, the ADCS was operated at constant power and pressure and allowed to reach steady state conditions. The thermal data obtained from these tests were analyzed, and the results can inform computational models built to simulate commercial drying processes by providing baseline thermal data prior to the introduction of water. Following the preliminary dry tests, a test plan for the ADCS will be developed to implement a drying procedure that begins with the introduction of water to the system and is based on measurements from the drying process used for the High Burnup Demonstration Project. While applying power to the simulated fuel rods, this procedure is expected to consist of filling the ADCS vessel with water, draining the water with applied pressure and multiple helium blowdowns, evacuating additional water with a vacuum drying sequence at successively lower pressures, and backfilling the vessel with helium. Additional investigations are expected to feature failed fuel rod simulators with engineered cladding defects and guide tubes with obstructed dashpots to challenge the drying system with multiple water retention sites. The data from these investigations is expected to inform the efficacy of commercial drying operations through the quantification of residual water in a prototypic-length dry storage canister.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
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↗