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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Systems Level Understanding of Interconnected Methane and Nitrogen Cycles Using Complex Synthetic Communities

The main goal of this project was to follow up on prior discovery of the communal nature of methane utilization by the aerobic methanotrophic bacteria, resulting in carbon transfer along a food chain. This goal was approached via manipulation of specially designed, synthetic bacterial communities, fed exclusively by methane, under a variety of simulated environmental conditions. Using (meta)genomics, metatranscriptomics, stable isotope probing and mutant generation, we obtained solid evidence for the nature of the core microbiota involved in collaborative methane consumption, the major players (true methanotrophs) being the members of the family Methylococcaceae, their major partners (non-methanotrophic methylotrophs) being members of the family Methylophilaceae, and minor but persistent partners in the communities being members of the orders Burkholderiales and Bacteroidetes. Metabolic reconstruction from single genomes and metagenome-assembled genomes (MAGs), along with metatranscriptomics results delineated major pathways for carbon metabolism, suggesting that the methanotrophs share different organic compounds with different functional guilds: methanol with Methylophilaceae, acetate with Burkholderiales, and polymeric substances with Bacteroidetes. Overall, the results of this project expand our understanding of microbial metabolism of methane and, thus, provide basis for strategies for microbial methane mitigation, with obvious benefits to the society of the United States and worldwide.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Upgrade of Gamma Spectrometry Systems for ORNL TRISO Fuel PIE

Gamma spectrometry is a key element in much of the post-irradiation examination (PIE) work performed under the Advanced Gas Reactor Fuel Development and Qualification (AGR) Program (Demkowicz et al. 2015; Stempien et al. 2021). Gamma spectrometers are integrated into three major capabilities used at the Oak Ridge National Laboratory (ORNL) Irradiated Fuels Examination Laboratory (IFEL) for PIE of tristructural-isotropic (TRISO) coated particles and fuel compacts: the Core Conduction Cooldown Test Facility (CCCTF), the Vertical Counting System (VCS), and the Irradiated Microsphere Gamma Analyzer (IMGA). The CCCTF includes liquid-nitrogen-cooled traps to extract 85 Kr out of the He sweep gas that passes through the furnace in which the fuel compacts are heated during safety testing. Analysis of the 85 Kr activity in the traps is the primary indicator for TRISO failure during safety testing. The VCS is a system used to accurately measure gamma emission from components placed in a lead-shielded chamber. It is used to count the CCCTF deposition cups after removal from furnace. Each cup resides in the CCCTF furnace for typically 12–24 h and is periodically replaced with a fresh cup throughout the safety test. Metallic fission products collect on the water-cooled cups and several gamma-emitting isotopes ( 110 mAg, 134 Cs, 137 Cs, 154 Eu, and 155 Eu) are often measured and provide indication of the retention performance of the TRISO coatings. The VCS is also used to measure the presence of these isotopes on the CCCTF tantalum liner and sweep gas inlet tube for the determination of cup collection efficiency, as well as support other gamma spectrometry needs related to calibration of the 85 Kr fission gas traps and various other special PIE tasks. The IMGA uses gamma spectrometry to measure the inventory of gamma-emitting isotopes in individual TRISO particles. An automated particle handling system within the IMGA hot cell removes each particle from a source vial and positions it in front of a gamma detector, and output from the gamma spectrometer is used by the IMGA software to determine a destination vial such that particles are sorted according to their inventory and retention characteristics. At the conclusion of the AGR-1 and AGR-2 PIE campaigns, the gamma spectrometer systems used at ORNL to support that PIE had reached the end of its life cycle due to gradual obsolescence of the hardware and software. Upgrade of the Canberra Genie 2000 software used by these systems to a Windows 10 version was not a viable option, because the newest Windows 10 version offered by Mirion (the new owner of the Canberra technology) did not include the dynamic-link libraries (DLLs) needed for integration with the custom PIE software used with the CCCTF and IMGA, and Mirion had no current plans for development and release of Windows 10 versions of these DLLs with the Model S560 Genie 2000 Programming Library. Ultimately a switch was made to ORTEC gamma spectrometry systems, which appeared to be a more sustainable solution due to more proactive vendor support. The ORTEC conversion involved replacing the aging detector preamplifier and multichannel analyzer (MCA) hardware, upgrading the obsolete Windows 7 computers to Windows 10 compatible models, adopting ORTEC GammaVision software, and extensive modification of the ORNL-developed Visual Basic .NET (VB.NET) programs that provide the CCCTF and IMGA user interfaces.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

The Dark Energy Survey Six-Year Calibration Star Catalog

This Technical Note presents a catalog of calibrated reference stars that was generated by the Forward Calibration Method (FGCM) pipeline (arXiv:1706.01542) as part of the FGCM photometric calibration of the full Dark Energy Survey (DES) 6-Year data set (Y6). This catalog provides DES grizY magnitudes for 17 million stars with i-band magnitudes mostly in the range 16 < i < 21 spread over the full DES footprint covering 5000 square degrees over the Southern Galactic Cap at galactic latitudes b < -20 degrees (plus a few outlying fields disconnected from the main survey footprint). These stars are calibrated to a uniformity of better than 1.8 milli-mag (0.18%) RMS over the survey area. The absolute calibration of the catalog is computed with reference to the STISNIC.007 spectrum of the Hubble Space Telescope CalSpec standard star C26202; including systematic errors, the absolute flux system is known at the approximately 1% level. As such, these stars provide a useful reference catalog for calibrating grizY-band or grizY-like band photometry in the Southern Hemisphere, particularly for observations within the DES footprint.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Eddy Current Shielding of the Magnetic Field Ripple in the EIC Electron Storage Ring Vacuum Chambers

The EIC electron storage ring (ESR) has very tight tolerances for the beam position and size stability at the interaction point. The oscillations at the proton betatron frequency and its harmonics are the most dangerous because, for instance, they could lead to unacceptable proton emittance growth from the oscillating beam-beam kick from the electrons at the amplitude of the positional oscillations as low as 10 -4 of the beam size. Even at much lower frequencies, down to the single Hz range, the position oscillations at a few percent level of the nominal beam size were found to be dangerous. These oscillations could have different causes including magnet power supply ripple, mag net vibration, noise in the main and crab RF systems, and some collective instabilities. To specify the acceptable level of the current ripple and noise of the magnet power supplies we need to accurately account for the eddy current shielding by the vacuum chamber, as well as, potentially, by the laminated magnet yokes (considered elsewhere). With some ap proximations, the chamber shielding can be described analytically. The main objective of this note is to derive these analytical expressions and to document the resulting shielding performance of the ESR chamber.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Characterization of Microbial Consortia and the Products Associated with Selenium Reduction in Real Flue Gas Desulfurization (FGD) Wastewater

Biological treatment is a recognized approach for removing toxic selenate and selenite oxyanions present in flue gas desulfurization (FGD) wastewater. However, the knowledge on the specific microbial species or communities responsible for reducing water-soluble selenium oxyanions to insoluble elemental selenium remains limited. In addition, the selenium oxyanion reduction genes and pathways have yet to be understood in these wastewaters. This study characterizes selenium oxyanion reducing bacteria (SeRB) native to FGD wastewater, and the resulting elemental selenium particles formed. By selecting for native SeRB microbes in a defined media, a novel resolution of these organisms has been achieved. This research identifies previously unrecognized selenium oxyanion reducing capabilities in Anaerosolibacter, alongside predominant SeRB from Mesobacillus and Tepidibacillus genera. This work encompasses both 16S and metagenomic techniques to recover novel metagenome assembled genomes (MAGs), distinct to this environment. The biogenic selenium produced by these organisms were predominantly of elemental selenium, in either amorphous or with a hexagonal structure. In addition, the elemental selenium particles formed where shown to increase in purity as the microbes were enriched. This study identifies the SeRB present in FGD wastewater and characterizes their selenium products, offering crucial insights to enhance the efficiency of biological treatment strategies and the potential of selenium recovery from this industrial waste.

microbiology↗
DOE OSTI2020

SPRUCE: Sphagnum Carbon, Nitrogen and Phosphorus Concentrations in the SPRUCE Experimental Plots

This data set reports the concentrations of carbon (C), nitrogen (N), and phosphorus (P) in capitula, current year stems, and one-year old stem tissue of Sphagnum from 2016-2018. Measurements are continuing and new data will be appended as they become available. Three types of Sphagnum were sampled -- S. angustifolium/fallax from hummocks (AngFal_Hum), S. angustifolium/fallax from hollows (AngFal_Hol), and S. magellanicum from hummocks (Mag_Hum) from SPRUCE experimental study plots. Measurements were made in 10 enclosures comprising five levels of temperature elevation in ambient CO2 and five levels in elevated CO2. Measurements also were made in two ambient (no enclosure) plots. Nutrient concentrations were analyzed in conjunction with assessment of Sphagnum growth, which was measured in 3.79-cm diameter mesh columns collected every October and are described in the related dataset (https://doi.org/10.25581/spruce.049/1426474). The SPRUCE experiment is being conducted at the 8.1-ha S1 bog forest site in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

SPRUCE Quantitative PCR (qPCR) of Microbial Gene Copy Numbers, 2021-2022

This dataset provides the results for quantitative polymerase chain reaction (qPCR) of peat samples collected from ambient and experimental plots in the Spruce and Peatland Responses Under Climatic and Environmental Change (SPRUCE) experiment site in June and August of 2021, and June of 2022. SPRUCE is located within the Marcell Experimental Forest in northern Minnesota, USA. The dataset includes bacterial, archaeal, fungal gene copy numbers, along with corresponding logarithmic values, at 11 depth increments of two-meter deep peat cores taken from 12 sampling sites locations inside SPRUCE plots (10 chambered and 2 ambient plots). The sampling, sample prep and analysis followed standard methods outlined in prior publications (Wilson et al. 2016; Kluber et al. 2020) except that a higher yielding Omega Bio-Tek Mag-Bind Environmental DNA 96 Kit was used for extractions and DNA was quantified using Qubit dsDNA High Sensitivity Assay Kit. qPCR subsamples of peat cores from the SPRUCE plots characterize changes in the abundance and composition of microbial communities of peat seasonally showing how composition varies under multiple levels of experimental peat warming and atmospheric CO2 concentrations. This dataset contains one data file in comma-separated values (.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma-separated values (.csv) format and a user guide in PDF (*.pdf) format. On 2026-07-07 this dataset was updated to add three columns to the data file: ‘Fungal_copy_dry’, ‘Log_fungal_copy_dry’, ‘Fungal_copy_wet’. No previously released data values were altered. Additionally, the abstract, data dictionary, and user guide were updated, and a file-level metadata file was added.

Archaea↗
DOE OSTI2023

HiC manuscript: bulk metagenomic data_MG_raw Upload

The raw bulk metagenomic data were trimmed and de-novo assembled. The assemblies were screened for viral contigs (by virsorter2, Deepvirfinder, VIBRANT, checkV) and binned to generate MAGs that were further refined by Hi-C read links.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

KBase Narrative - Mse_Genome_Assembly

Upon investigating the gut microbiome of mice for microbes related to Polycystic Ovary Syndrome (PCOS), our team found 2 metagenomes that could not be classified using alignment based methods. To further investigate microbial species from these samples, we used common MAGs workflow to create draft genomes which were then later taxonomically classified using GTDB-tk app.

Rastegar, Kiarash↗
DOE OSTI2024

KBase Narrative - Timberlake Metagenomes

This narrative contains the MAG Analysis from: Clifton P Bueno de Mesquita, Wyatt H Hartman, Marcelo Ardón, Susannah G Tringe, Disentangling the effects of sulfate and other seawater ions on microbial communities and greenhouse gas emissions in a coastal forested wetland, ISME Communications, 2024; ycae040, https://doi.org/10.1093/ismeco/ycae040 Metagenomes were uploaded to IMG/M for other analyses.

de Mesquita, Clifton Bueno↗
DOE OSTI2024

KBase Narrative - Metabolic_reconstruction_ETDI_mangrove

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

Laux, Marcele↗
DOE OSTI2025

Predictions for the Detectability of Milky Way Satellite Galaxies and Outer-Halo Star Clusters with the Vera C. Rubin Observatory

We predict the sensitivity of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) to faint, resolved Milky Way satellite galaxies and outer-halo star clusters. We characterize the expected sensitivity using simulated LSST data from the LSST Dark Energy Science Collaboration (DESC) Data Challenge 2 (DC2) accessed and analyzed with the Rubin Science Platform as part of the Rubin Early Science Program. We simulate resolved stellar populations of Milky Way satellite galaxies and outer-halo star clusters over a wide range of sizes, luminosities, and heliocentric distances, which are broadly consistent with expectations for the Milky Way satellite system. We inject simulated stars into the DC2 catalog with realistic photometric uncertainties and star/galaxy separation derived from the DC2 data itself. We assess the probability that each simulated system would be detected by LSST using a conventional isochrone matched-filter technique. We find that assuming perfect star/galaxy separation enables the detection of resolved stellar systems with $M_V$ = 0 mag and $r_{1/2}$ = 10 pc with >50% efficiency out to a heliocentric distance of ~250 kpc. Similar detection efficiency is possible with a simple star/galaxy separation criterion based on measured quantities, although the false positive rate is higher due to leakage of background galaxies into the stellar sample. When assuming perfect star/galaxy classification and a model for the galaxy-halo connection fit to current data, we predict that 89 +/- 20 Milky Way satellite galaxies will be detectable with a simple matched-filter algorithm applied to the LSST wide-fast-deep data set. Different assumptions about the performance of star/galaxy classification efficiency can decrease this estimate by ~7%-25%, which emphasizes the importance of high-quality star/galaxy separation for studies of the Milky Way satellite population with LSST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ~75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan

Thermoflexus hugenholtzii JAD2 T , the only cultured representative of the Chloroflexota order Thermoflexales, is abundant in Great Boiling Spring (GBS), NV, United States, and close relatives inhabit geothermal systems globally. However, no defined medium exists for T. hugenholtzii JAD2 T and no single carbon source is known to support its growth, leaving key knowledge gaps in its metabolism and nutritional needs. Here, we report comparative genomic analysis of the draft genome of T. hugenholtzii JAD2 T and eight closely related metagenome-assembled genomes (MAGs) from geothermal sites in China, Japan, and the United States, representing “Candidatus Thermoflexus japonica,” “Candidatus Thermoflexus tengchongensis,” and “Candidatus Thermoflexus sinensis.” Genomics was integrated with targeted exometabolomics and 13 C metabolic probing of T. hugenholtzii. The Thermoflexus genomes each code for complete central carbon metabolic pathways and an unusually high abundance and diversity of peptidases, particularly Metallo- and Serine peptidase families, along with ABC transporters for peptides and some amino acids. The T. hugenholtzii JAD2 T exometabolome provided evidence of extracellular proteolytic activity based on the accumulation of free amino acids. However, several neutral and polar amino acids appear not to be utilized, based on their accumulation in the medium and the lack of annotated transporters. Adenine and adenosine were scavenged, and thymine and nicotinic acid were released, suggesting interdependency with other organisms in situ. Metabolic probing of T. hugenholtzii JAD2 T using 13 C-labeled compounds provided evidence of oxidation of glucose, pyruvate, cysteine, and citrate, and functioning glycolytic, tricarboxylic acid (TCA), and oxidative pentose-phosphate pathways (PPPs). However, differential use of position-specific 13 C-labeled compounds showed that glycolysis and the TCA cycle were uncoupled. Thus, despite the high abundance of Thermoflexus in sediments of some geothermal systems, they appear to be highly focused on chemoorganotrophy, particularly protein degradation, and may interact extensively with other microorganisms in situ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH 4 + :NO 2 - , where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH 4 + :NO 2 - ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH 4 + :NO 2 - ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89–202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169–200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0–89, compared to 85.49 ± 0.01% from day 89–169, and 83.04 ± 0.01% from day 169–200). When the ratio was slightly increased to 1:1.17–1:1.2 (day 202–253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH 4 + :NO 2 - ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

59 BASIC BIOLOGICAL SCIENCES↗