Results for “data needs” — Page 70

DOE OSTI2021

Reliability Prediction using FMEA, FTA, and Related Techniques [Slides]

Summary: We presented a reliability analysis framework. We made point estimates of reliability using reliability block diagrams, fault trees, success trees and estimates with uncertainty using expert elicitation, Monte Carlo simulation, Bayesian analysis. Expert elicitation of failure modes and probabilities is labor-intensive, but critical. Bayesian analysis updates information from expert elicitation with data from reliability and aging tests (aging/compatibility data are needed to estimate lower-bound reliabilities at end of life). Estimation by more than one method helps insure consistency and accuracy.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Survey of Available Information on U.S. Manufacturing Wastewater and Energy Requirements for Reuse

This report seeks to inform an improved understanding of the energy tradeoff associated with manufacturing water reuse in the United States, in part by developing an analytical framework for understanding when this tradeoff for reuse is beneficial. In order to apply this approach, existing literature and publicly available information on typical contaminants in industrial effluent and available treatment technologies are reviewed and summarized. An existing case study is then discussed in light of how the analytical framework could be applied if sufficient data were available. We conclude that the shortcomings of the available data severely restrict our ability to apply this framework. These limitations are highlighted with the intent of providing the broader research community information on where data gaps need to be filled.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

2021 Results for Avian Monitoring of Inorganic and Organic Element Concentrations in Passerine Eggs and Nestlings Collected from Technical Area 16 Burn Grounds, Technical Area 36 Minie, and Technical Area 39 Point 6 at Los Alamos National Laboratory (Rev. 2)

In 2021, non-viable avian eggs and one nestling were opportunistically collected at Los Alamos National Laboratory (LANL) near open detonation sites located at Technical Area (TA) 16 burn grounds and TA-36 Minie. Similar to previous years, nestboxes were monitored at TA-39 Point 6, however, no avian samples were available for opportunistic collection. Samples were evaluated for inorganic elements (mostly metals), dioxins, and furans. One ash-throated flycatcher (Myiarchus cinerascens) egg sample was collected from TA-16 burn grounds. One ash-throated flycatcher and one mountain bluebird (Sialia currucoides) egg sample and one deceased western bluebird (Sialia mexicana) nestling sample were collected from TA-36 Minie. Concentrations of inorganic elements observed in this study were compared with the regional statistical reference level (RSRL) which is the upper-level bounds of background concentrations (mean + three standard deviations = 99% confidence interval). Several inorganic elements were not detected in avian eggs. Most inorganic elements detected were below the RSRL and all were the lowest observable adverse effect level (LOAEL), when available. The nestling collected from TA-36 did not contain detectable concentrations of dioxin or furan congeners. These data suggest that inorganic and organic element concentrations in eggs and nestlings are not of ecological concern. More data are needed to make a robust assessment and to evaluate trends over time.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Affordable Solid Panel "Perfect Wall" System

The SPS is an innovative interpretation of the “perfect wall” concept, in which environmental control layers are located on the exterior side of the structural components, as opposed to traditional cavity insulated, stud-framed walls. The primary objective of this study is to validate the SPS technology in terms of its constructability, cost, and performance. Specifically for this project, we partnered with two affordable housing nonprofits in Minnesota—Twin Cities Habitat for Humanity and Urban Homeworks—to build five new houses using SPS walls, as well as two high-performance stud-framed comparison homes. We also reviewed cost and performance data from 13 SPS homes built prior to this project by MonoPath and Spero Environmental Builders. Reviewing the outcomes of these 20 homes total, we find promising results in terms of constructability, cost, and performance, although more structural performance data are needed before this new technology can see widespread adoption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2022

Processing Particle Data Flows with SmartNICs

Many distributed applications implement complex data flows and need a flexible mechanism for routing data between producers and consumers. Recent advances in programmable network interface cards, or SmartNICs, represent an opportunity to offload data-flow tasks into the network fabric, thereby freeing the hosts to perform other work. System architects in this space face multiple questions about the best way to leverage SmartNICs as processing elements in data flows. In this paper, we advocate the use of Apache Arrow as a foundation for implementing data-flow tasks on SmartNICs. We report on our experiences adapting a partitioning algorithm for particle data to Apache Arrow and measure the on-card processing performance for the BlueField-2 SmartNIC. Our experiments confirm that the BlueField-2’s (de)compression hardware can have a significant impact on in-transit workflows where data must be unpacked, processed, and repacked.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Perspectives on Nuclear Data on Nuclear Criticality Safety Needs [Slides]

Abstract not provided.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

2022 Results for Avian Monitoring of Inorganic Elements and Organic Chemical Concentrations in Passerine Eggs and Nestlings Collected from Technical Area 16 Burn Grounds, Technical Area 36 Minie, and Technical Area 39 Point 6 at Los Alamos National Laboratory

In 2022, nonviable avian eggs and one nestling were opportunistically collected at Los Alamos National Laboratory (LANL) near open detonation sites located at Technical Area (TA) 16 burn grounds, TA-36 Minie, and TA-39 Point 6. Samples were evaluated for inorganic elements (mostly metals) or per- and polyfluoroalkyl substances (PFAS). Three western bluebird (Sialia mexicana) egg samples were collected from TA-16 burn grounds. One deceased mountain bluebird (Sialia currucoides) nestling sample was collected from TA-36 Minie. One ash-throated flycatcher (Myiarchus cinerascens) egg sample was collected from TA-39 Point 6. Concentrations of inorganic elements (i.e., mostly metals) observed in this study were compared with the regional statistical reference level (RSRL), which is the upper-level bounds of background concentrations (mean + three standard deviations = 99% confidence interval). Several inorganic elements were not detected in avian eggs. All of the inorganic elements that were detected were below the RSRL and the lowest observable adverse effect level (LOAEL), when available. No PFAS compounds were detected in the mountain bluebird nestling sample collected from TA-36, and the majority of PFAS compounds were not detected in the western bluebird egg sample from TA-16. These data suggest that inorganic element and PFAS concentrations in eggs and nestlings are not of ecological concern. More data are needed to make a robust assessment and to evaluate trends over time.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Summary of Methodology for Mitigating Risks Associated with Licensing and Qualifying AM Nuclear Materials

The US Department of Energy’s Advanced Materials and Manufacturing Technologies (AMMT) program focuses on accelerating the development, qualification, demonstration, and deployment of advanced materials and manufacturing technologies to enable reliable and economical nuclear energy. Laser powder bed fusion (LPBF) is one of the most popular additive manufacturing (AM) processes for fabricating components with intrinsically complex geometries. LPBF was extensively explored for nuclear applications under the previous Transformational Challenge Reactor program. Additionally, Oak Ridge National Laboratory developed and licensed the Peregrine software and larger digital platform that couples machine learning and in situ data collection during AM to detect anomalies and any evolved defects. The digital platform will be critical to (1) the qualification of AM components for nuclear applications that link location-specific data to macroscopic properties and (2) predict final component performance. Current in situ process monitoring tools are valuable for observing the formation of stochastic flaws, but additional data are needed to predict the resulting microstructures and associated material performance. Rapid cooling rates and large thermal gradients have caused large heterogeneities in the microstructure, which cause anisotropy in mechanical performance. The AMMT program is evaluating the best approaches for addressing these heterogeneities and their effect on component performance using a combination of multiscale modeling, enhanced in situ process monitoring, and high throughput experimental testing. This report summarizes strategies for mitigating the risks associated with qualifying AM components, including developing new sensing capabilities for in situ process monitoring and characterizing melt pool solidification and residual stresses to inform multiscale modeling efforts.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Building a better framework for evaluating human well-being impacts in global change analysis: The example of energy security

Human well-being can be greatly impacted by the global environmental and socio-economic change captured in Integrated Models of Global Change (IMGCs). Though most IMGCs address some aspects of well-being, their underlying modeling approach and ‘philosophy’ differ widely, and some key elements – like energy security – are omitted. In this report, we describe a project in which we set out to a create a framework through which the well-being dimensions of the household are connected to key drivers of socio-economic and environmental change – and how the needed metrics, data and modeling methods can be brought to bear. We focus on the well-being dimensions of energy, and lay out the necessary elements to capturing household energy security – using household energy burden as the relevant metric. We begin by showing the conceptual linkage of energy burden to environmental drivers like temperature change, using a simple and straightforward conceptual framework. We then go further to use the example of GCAM-USA to show how some key analytical features of the model can provide insight into how energy security across different groups can change along alternative pathways to sustainability. We compare our preliminary assessment of household energy burden to existing data and suggest further steps to improve and refine this analysis in future research.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

Hydrodynamic Test Requirements Process Improvements

Hydrodynamic testing at Los Alamos National Laboratory would benefit from a process improvement for the requirements process. Cameo was used as a digital solution for requirements management to allow Lead Engineers to track requirements more effectively. This was identified as a process improvement throughout this Capstone project. This report includes a project proposal, business case, literature review, methodology, project plan, data analysis, decision-making report, financial analysis report, discussion, and conclusion. Initially, this project focused on figuring out a solution for the hydrotest requirement process improvements. The scope narrowed to focus on the use of Cameo for requirement capture and management. During this Capstone, four tests had digital models produced for requirements management in Cameo. The initial model was the baseline, with core requirements used across the tests. Commonalities in tests were used and the core requirements allowed for process efficiencies. In the data analysis, it was seen that overall, the implementation of using Cameo for requirements resulted in a decreasing trend for both schedule and normalized cost. Tests have different complexity levels which is also a factor in how long the requirements process will take. Additional data is needed to continue analyzing process improvements. Through decisionmaking and financial analysis, the recommendation was to use Cameo for requirements process improvement. Multiple experts provided feedback for requirements that were then captured within models. Numerous tangible and intangible benefits were identified with this process improvement. For return on investment, the metric of success was schedule reduction, which was overall seen. Four tests were analyzed, so future analysis will be needed. There is also not a great financial risk because the main cost would be purchasing more licenses. Individuals must generate requirements whether using this software or not. Overall, training is needed to help improve the skillsets of Lead Engineers but is already being supported on a regular frequency. A desktop guide was started associated with explaining the process, however, it is a work in progress. The team plans on adding additional information in the digital models to help status when requirements are met using verification methods and artifacts. From working on this project an improved understanding of Cameo and requirements was the result. There are future opportunities to extend the usage for requirements management and progress will continue after this project.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2024

Williston Basin CORE-CM Initiative Final Report

The University of North Dakota Energy & Environmental Research Center (EERC) is leading the Williston Basin Carbon Ore, Rare Earth, and Critical Minerals (CORE-CM) Initiative to drive the expansion and transformation of coal and coal-based resource usage within the Williston Basin to produce rare-earth elements (REEs), CMs, and nonfuel carbon-based products (CBPs). This project is the first phase in a long-term program and set the stage for future work by assessing resource, market, technology, and infrastructure knowledge; identifying knowledge gaps; developing a series of plans to be carried out in future work; and initiating stakeholder engagement. Composed of several tasks, the project sought to identify, characterize, and assess several necessary aspects vital to make this future work a reality. The project’s fundamental task was to characterize the Williston Basin CORE-CM resources. Over 2500 samples from multiple sources were utilized to begin the assessment. Several locations were identified in western North Dakota where sample analysis identified the total REE (TREE) concentration as being over 500 parts per million (ppm), which is at a concentration level that would be suitable to consider for mining and extraction. Current operating coal mines have sufficient concentrations of TREEs for consideration. However, the current data across the basin are still not adequate to fully characterize REE and CM content nor give reliable estimates of the total resource potential. Waste stream reuse was also considered, and several streams were identified which ranged from potential energy sources to chemicals to material wastes. This includes streams that result from oil and gas production. These streams are not fully characterized, and further data are needed before they can be accurately assessed. Infrastructure within the Williston Basin is suitable for expansion of a new industry to mine, extract, and concentrate REEs and CMs. The development of this industry will not only preserve many existing jobs in the coal-mining industry but produce many new jobs. The supply chain for REEs and CMs is currently controlled outside of the United States in nations such as China, but the potential to develop the supply chain within the basin is considered possible. Processing of the mined materials for REEs and CMs needs further research. The technology and knowhow exist outside of the United States, and within the country much of the knowledge has been lost and must be regained. To develop the supply chain and regain lost processing technology, the creation of technology innovation centers (TICs) is crucial. The Williston Basin contains several similar centers and entrepreneurial assistance for other industries that can be applied in the development of REE and CM innovation centers. Education to develop the new skill sets required is also needed. Outreach is important for the development of the REE and CM industry within the basin. Understanding throughout federal and state governments, state agencies, industry, and resource end users is vital for the industry to form and grow. Through this project these groups have been contacted through bulletins, presentations, webinars, and annual symposiums. The report is a summary of the work conducted and throughout refers to a series of appendixes which contain more thorough and specific information about each section.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2024

Time-Temperature-Transformation (TTT) Diagram for a Sludge Batch 9 Glass Composition Based on Coupled-Operation with the Salt Waste Processing Facility

The amorphous structure of a glass waste form has the potential to rearrange into crystalline phases at temperatures between the liquidus temperature and the glass transition temperature (Tg). Certain phases that can form will be detrimental to the durability of the glass and it is important to know the conditions that promote devitrification. The canister-centerline-cooling (CCC) profile is used to replicate the area within the center of the Defense Waste Processing Facility (DWPF) canister with the slowest cooling during the initial cool down after pouring, which has the greatest potential for crystallization. Other time-temperature conditions that cause significant changes in either phase structure or phase composition are identified by a time-temperature-transformation (TTT) study. The phase stability of a waste form must be determined as a part of the Waste Acceptance Product Specifications (WAPS) if it is to eventually be stored in a geologic repository. This requires the creation of a TTT diagram and analysis of the Tg, as defined by the Department of Energy (DOE). The previous TTT study for a DWPF glass waste form was completed in 2010 prior to coupled operation with the Salt Waste Processing Facility (SWPF). SWPF transfers two high activity waste streams to DWPF for vitrification: a cesium-containing strip effluent and a stream containing monosodium titanate/sludge solids. These SWPF streams were first transferred to DWPF for vitrification during Sludge Batch 9 (SB9) in 2021. The impact of these SWPF streams on crystallization behavior was not determined in previous studies and the need for data to satisfy WAPS Specification 1.4 for SB9 was identified.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

From Silos to Synergy: Identifying a Roadmap for Cross-Sector Research to Accelerate the Clean Energy Transition

The U.S. Department of Energy's blueprints for the transportation, buildings, and electricity sectors call for substantial reductions in greenhouse gas (GHG) emissions by 2050. These plans focus on zero-emission vehicles, investments in transit, energy-efficient buildings, and the widespread adoption and deployment of renewable energy technologies like solar photovoltaics (PV), energy storage and energy-efficient appliances. However, these sectors are often studied and modeled in isolation, overlooking how household decisions to adopt clean technologies in one sector influence others. This study, led by an interdisciplinary team at the National Renewable Energy Laboratory (NREL), explores opportunities for cross-sector collaboration to drive more effective and equitable decarbonization. Through discussions with 22 NREL researchers across transportation, building, solar, and grid sectors, the study highlights the need for integrated tools and models that capture interactions between these sectors. Key insights include the need for data standardization and interoperability to enable cross-sector analysis and decision-making. Strengthening utility partnerships is also critical to align energy policies with decarbonization goals and manage the increased demand for renewable energy. The study also emphasizes the importance of equity in the clean energy transition, calling for targeted incentives and support to ensure that low-income and underserved communities benefit from clean technologies like electric vehicles and energy-efficient appliances. To support these efforts, innovative funding mechanisms must be expanded to facilitate interdisciplinary research, such as city-specific decarbonization plans and federal projects like DOE"s Standard Scenarios. By encouraging collaboration and integrating cross-sector insights, this study aims to provide a roadmap to accelerate the clean energy transition and ensure it is both sustainable and inclusive.

14 SOLAR ENERGY↗

DOE OSTI2024

U.S. Department of Energy-National Lab Equity Summit: Grid Planning and Operations (Workshop Report)

This report summarizes the U.S. DOE and national laboratories equity summit that was held on February 5, 2024, and focused on grid planning and operations. The objectives of the summit were to connect DOE and lab researchers working on grid-related equity issues, share information on current and planned grid-related equity projects and initiatives, and inspire and educate participants by hearing from our panelists about solutions and challenges to integrating equity in grid planning and operations. The summit included two panels of industry leaders. The first was a state and community perspectives panel that included representatives from a state public utility commission (Oregon Public Utility Commission), a state energy office (Washington Department of Commerce), a state utility consumer advocate (Connecticut Consumer Counsel), and industry consultants (Elevated Engagement and ArkSpring Consulting). Panelists shared successes they have seen, critical challenges related to equity and grid planning and operations, and other considerations. The second panel addressed utility perspectives and included representatives from two utilities (Commonwealth Edison and Tacoma Power), the National Rural Electric Cooperative (NRECA), and a former utility employee and legal consultant. Panelists discussed the role of the utility concerning equity, the most significant technical and data modeling needs and opportunities, and the role the labs could help advance equity in grid planning and operations. There was also a session on partner organization presentations. Argonne National Laboratory made a short presentation on the Grid Modernization Laboratory Consortium (GMLC) project they are leading on equity-informed power system planning. NARUC, NASEO, and the Clean Energy States Alliance, as partners of the GMLC project also shared updates on relevant activities and resources. During the summit, there were two rounds of lightning presentations by national labs and DOE highlighting research that addresses equity and grid planning and operations (Tables 5 and 6 and slides in the Appendix). The goal of the lightning rounds was to share information between participants to encourage collaboration and leverage ongoing research at labs and DOE. The summit included two interactive exercises where summit participants shared their perspectives on relevant equity projects and initiatives (Table 2), key challenges regarding equity and grid planning and operations (Table 3), and promising innovations or progress (Table 4). At the end of the session, participants were asked to share essential insights from the event (Table 7) and an action they plan to take as a result of the event. Participants agreed that the event was useful in helping them share and learn from each other. The project team plans to use the information from the summit as a starting point to help inform future research and technical assistance. In 2026, another Equity Summit will be held (virtually or in person) as part of the same project to help raise awareness and disseminate research and resources completed during the project's duration.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Loss of Flow Conditions in a Modern Pool-type SFR and In-Pile Experiment Design

The metallic fuel safety performance under unprotected design-basis transients is a key consideration for the deployment of advanced sodium fast reactors (SFRs). Reliable data are needed to validate advanced safety codes, reduce uncertainty in cladding failure thresholds, and strengthen confidence in licensing approaches. To address this need, this report develops blueprints for a conceptual sodium loss-of-flow (LOF) experiment in the Mk-IIIR loop at the Transient Reactor Test Facility (TREAT), providing the technical foundation for future integral testing.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Audible Noise Modeling of Hydrogen Release Sonic Hazards in Rail Maintenance Facilities

This study implemented validated literature models to predict audible noise due to pressurized gaseous hydrogen releases through a thermally-activated pressure relief device (TPRD) and attached vent stack. A literature survey discovered limited hydrogen-specific noise prediction models validated by experiments. However, empirical noise prediction models for air flowing through pipes and valves were identified. These empirical models were used to predict noise levels and compared against hydrogen noise data reported in two studies: one experimental study of noise from hydrogen leaking through a pipe and another which modeled hydrogen flowing through a solenoid valve during a fuel cell vehicle refueling. The valve flow model was then applied to predict noise for hydrogen releases through a TPRD. Results show that hydrogen releases through a TPRD can produce harmful noise levels varying from 134 to 150 dB. However, further model validation and additional experimental data are needed to improve prediction confidence and accuracy.

08 HYDROGEN↗

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↗

DOE OSTI2024

KBase Narrative - Lachnospiraceae sp. C1.1 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↗