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

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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Metagenome-assembled genomes from Wind River Basin floodplain sediments Riverton, Wyoming site (August 2015)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken August 29, 2015 at a location (KB1) close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site in the Wind River Basin (WRB). The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Sediment samples from a deep soil pit were collected from 0 to 234 cm depth below surface at discrete depths every ~10-20 cm for microbial analyses. 13 metagenomes were sequenced through JGI and can be found under Gold sequencing project: Gs0131241. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores).This dataset includes a zip file of 2216 MAG fasta files and a csv file with quality, taxonomic classification (GTDB RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled genomes from Wind River Basin floodplain sediments Riverton, Wyoming site (June to October 2019)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken at three time points from June 12, 2019 to October 23,2019 at a location (PTT1) close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site in the Wind River Basin (WRB). The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Sediment samples were collected from 60 to 180 cm below surface every 30cm for microbial analyses through metagenomic sequencing. 15 metagenomes were sequenced through JGI and can be found under Gold sequencing project: Gs0131241. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 780 MAG fasta files and a csv file with quality, taxonomic classification (GTDB RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. A sample metadata file (samples.csv) that contains site information has also been included.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled genomes from Wind River Basin floodplain sediments Riverton, Wyoming site (May to September 2017)

Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken roughly every month in the period May 18 to September 13 in 2017 at a location (Pit2) close to DOE Legacy Management well 855 at the Riverton, Wyoming floodplain site in the Wind River Basin (WRB). The groundwater at this site exhibits persistent U, Mo, and sulfate plumes and is one of the field sites in focus for the SLAC Groundwater Quality SFA program. Cores were taken with a hand-auger and separated into 5-20 cm segments based on soil horizonation down to 150 cm depth below surface. Each segment was subsampled for microbial analyses. Corresponding 16S rRNA gene amplicon data is available at the NCBI Single Read Archive (SRA) Database BioProject ID PRJNA626616, and soil geochemistry data at doi:10.15485/1631972. 40 metagenomes were sequenced through JGI and can be found under Gold sequencing project: Gs0142591. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 6993 MAG fasta files and a csv file with quality, taxonomic classification (GTDB RS220), and metagenome accessions for MAGs generated from the Wind River Basin (WRB). This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling

Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Potential applications of microbial genomics in nuclear non-proliferation

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as “characteristic communities of microorganisms” found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Hamptons Road Sanitation District (HRSD) with High and Low Dissolved Oxygen Conditions

In this study, we aimed to evaluate Biological Nutrient Removal (BNR) and investigate microbial community changes as the dissolved oxygen is reduced in the aerated portions of wastewater treatment trains. We present a dataset of Metagenome-Assembled Genomes (MAGs) obtained from activated sludge collected from the Hamptons Road Sanitation District (HRSD) BNR plant at the beginning of operation, when the DO was high, and at the end of operation, when the DO was low.

Genomics↗
DOE OSTI2025

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Los Angeles County Sanitation District (LACSD) with High and Low Dissolved Oxygen Conditions

In this study, we aimed to evaluate Biological Nutrient Removal (BNR) and investigate microbial community changes as the dissolved oxygen is reduced in the aerated portions of wastewater treatment trains. We present a dataset of Metagenome-Assembled Genomes (MAGs) obtained from activated sludge collected from the Los Angeles County Sanitation District (LACSD) BNR plant at the beginning of operation, when the DO was high, and at the end of operation, when the DO was low.

Genomics↗
DOE OSTI2025

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

We compared the genomes of 12 plant-pathogenic Saccharomycotina strains to 360 plant-associated strains to identify features unique to the phytopathogens. Characterization of the oxylipin synthesis genes, a compound believed to be involved in Eremothecium pathogenicity, did not reveal any differences in gene presence within or between the plant-pathogenic and plant-associated strains. A reverse-ecological approach, however, revealed that plant pathogens lack several metabolic enzymes known to assist other phytopathogens in overcoming plant defenses.

phytopathogen↗
NASA NTRS2002

A genomic regulatory network for development

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

Non-NASA Center↗
NASA NTRS2001

Radiation induces genomic instability and mammary ductal dysplasia in Atm heterozygous mice

Ataxia-telangiectasia (AT) is a genetic syndrome resulting from the inheritance of two defective copies of the ATM gene that includes among its stigmata radiosensitivity and cancer susceptibility. Epidemiological studies have demonstrated that although women with a single defective copy of ATM (AT heterozygotes) appear clinically normal, they may never the less have an increased relative risk of developing breast cancer. Whether they are at increased risk for radiation-induced breast cancer from medical exposures to ionizing radiation is unknown. We have used a murine model of AT to investigate the effect of a single defective Atm allele, the murine homologue of ATM, on the susceptibility of mammary epithelial cells to radiation-induced transformation. Here we report that mammary epithelial cells from irradiated mice with one copy of Atm truncated in the PI-3 kinase domain were susceptible to radiation-induced genomic instability and generated a 10% incidence of dysplastic mammary ducts when transplanted into syngenic recipients, whereas cells from Atm(+/+) mice were stable and formed only normal ducts. Since radiation-induced ductal dysplasia is a precursor to mammary cancer, the results indicate that AT heterozygosity increases susceptibility to radiogenic breast cancer in this murine model system.

Non-NASA Center↗
NASA NTRS2004

A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

BACKGROUND: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. RESULTS: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5-3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1-4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8-4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8-3.1 Ga, and an origin of aerobic methanotrophy 2.5-2.8 Ga. CONCLUSIONS: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8-2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations.

Methane/metabolism↗
NASA NTRSDate not supplied

Bionutrients-1: Utilizing Genomics and Transcriptomics to Assess the Reliability of Microorganisms for In Situ Nutrient Production on Long Duration Missions

The resupply of current long-duration crewed missions to the ISS relies on ground-launched supplies. As NASA looks toward Mars, ground-based resupply will no longer be an option. Critical nutrients, including vitamin C, vitamin K, folate, and thiamin, degrade during long-term storage, and regular consumption of these nutrients is essential for astronaut health. Another challenge of current food systems is the difficulty of consuming sufficient calories when subsisting on the limited flavors of freeze-dried food, which can lead to weight loss. The inclusion of microorganism-based food systems could alleviate both concerns. For example, the fermentation of rehydrated milk into yogurt with microorganisms genetically incorporating genes to produce critical vitamins would allow for both in situ production of nutrients and a fresh food product with additional flavor profiles. In comparison to plant food production, microorganisms require less flight infrastructure. The BioNutrients-1 mission is demonstrating viability of microbial fermentation food production in microgravity and testing the reliability of this approach for long-duration missions lacking resupply. While the BioNutrients-1 mission includes the collection of multiple phenotypic measurements, this status update will focus on the processing of samples for genomics and transcriptomics analyses as well as the planned analysis pipelines. First, the BioNutrients-1 mission seeks to identify microorganisms capable of surviving long-duration storage at ambient temperatures while maintaining genetic fidelity. To achieve this, nine commonly employed microbial species were stored at ambient temperatures in Stasis Packs on the ISS for five years. The viability and mutation rates will be measured at multiple time points for both flown and ground control samples. From an omics perspective, the changes in the bulk rates of point mutations and genetic rearrangements across the Stasis Pack species during the five years of storage will be determined, providing valuable insights into the potential of these microorganisms for long-duration space missions. Second, the BioNutrients-1 mission is characterizing the impact of microgravity on fermentation. Two strains of the yeast Saccharomyces cerevisiae, each encoding antioxidants (β-carotene or zeaxanthin) were flown to ISS for storage and fermentation within simplified bioreactors (Production Packs). The impact of microgravity on the expression of the antioxidant production genes and general metabolic genes will be determined using RNA sequencing. Ultimately, the transcriptome data will be compared to phenotypic measurements, such as the antioxidant yield, end-state biomass, and the production of EtOH, to determine the impacts of microgravity and long-term storage on microbial fermentation. The findings from this research will be instrumental in understanding the challenges and opportunities of microorganism-based food systems in space missions.

BioNutrients↗
DOE OSTI2024

The Defects Genome of Janus Transition Metal Dichalcogenides

2D Janus Transition Metal Dichalcogenides (TMDs) have attracted much interest due to their exciting quantum properties arising from their unique two-faced structure, broken-mirror symmetry, and consequent colossal polarization field within the monolayer. While efforts are made to achieve high-quality Janus monolayers, the existing methods rely on highly energetic processes that introduce unwanted grain-boundary and point defects with still unexplored effects on the material's structural and excitonic properties Through high-resolution scanning transmission electron microscopy (HRSTEM), density functional theory (DFT), and optical spectroscopy measurements; this work introduces the most encountered and energetically stable point defects. It establishes their impact on the material's optical properties. HRSTEM studies show that the most energetically stable point defects are single (V S and V Se ) and double chalcogen vacancy (V S −V Se ), interstitial defects (Mi), and metal impurities (MW) and establish their structural characteristics. DFT further establishes their formation energies and related localized bands within the forbidden band. Cryogenic excitonic studies on h-BN-encapsulated Janus monolayers offer a clear correlation between these structural defects and observed emission features, which closely align with the results of the theory. Finally, the overall results introduce the defect genome of Janus TMDs as an essential guideline for assessing their structural quality and device properties.

2D materials↗
DOE OSTI2024

Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat

Abstract Powdery mildew, caused by the fungal pathogenBlumeria graminis(DC.) E. O. Speer f. sp.triticiEm. Marchal (Bgt), is a constant threat to global wheat (Triticum aestivumL.) production. Although ∼100 powdery mildew (Pm) resistance genes and alleles have been identified in wheat and its relatives, more is needed to minimizeBgt’s fast evolving virulence. In tetraploid wheat (Triticum turgidumL.), wild emmer wheat [T. turgidumssp.dicoccoides(Körn. ex Asch. & Graebn.) Thell.] accessions from Israel have contributed manyPmresistance genes. However, the diverse genetic reservoirs of cultivated emmer wheat [T. turgidumssp.dicoccum(Schrank ex Schübl.) Thell.] have not been fully exploited. In the present study, we evaluated a diverse panel of 174 cultivated emmer accessions for their reaction toBgtisolateOKS(14)‐B‐3‐1and found that 66% of accessions, particularly those of Ethiopian (30.5%) and Indian (6.3%) origins, exhibited high resistance. To determine the genetic basis ofBgtresistance in the panel, genome‐wide association studies were performed using 46,383 single nucleotide polymorphisms (SNPs) from genotype‐by‐sequencing and 4331 SNPs from the 9K SNP Infinium array. Twenty‐five significant SNP markers were identified to be associated withBgtresistance, of which 21 SNPs are likely novel loci, whereas four possibly represent emmer derivedPm4a,Pm5a,PmG16, andPm64. Most novel loci exhibited minor effects, whereas three novel loci on chromosome arms 2AS, 3BS, and 5AL had major effect on the phenotypic variance. This study demonstrates cultivated emmer as a rich source of powdery mildew resistance, and the resistant accessions and novel loci found herein can be utilized in wheat breeding programs to enhanceBgtresistance in wheat.

Genetics & Heredity↗
DOE OSTI2025

Zymomonas mobilis : bringing an ancient human tool into the genomic era

Zymomonas mobilis is an ethanologenic bacterium that has been used for over 1500 years to produce alcoholic beverages. Recently, this microbe has become a top candidate for biofuel production due to its efficient metabolism. Z. mobilis is being developed to utilize lignocellulosic biomass as a feedstock and synthesize a range of valuable chemicals and fuels. Genetic and metabolic engineering strategies are crucial to reach these goals. Recent advances include genome engineering, CRISPR editing, and CRISPRi knockdown of genes. Metabolic engineering has enabled redirection of carbon from the natural product ethanol to chemicals such as 2,3-butanediol and polyhydroxybutyrate. Finally, the approaches summarized here will streamline the development of Z. mobilis as an industrial chassis for sustainable liquid fuels and chemicals.

Boismier, Emma C. [Michigan State Univ., East Lans↗
DOE OSTI2024

Genome-scale analysis of interactions between genetic perturbations and natural variation

Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 8046 CRISPRi perturbations targeting 1721 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual’s response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genome-guided isolation of the hyperthermophilic aerobe Fervidibacter sacchari reveals conserved polysaccharide metabolism in the Armatimonadota

Few aerobic hyperthermophilic microorganisms degrade polysaccharides. Here, we describe the genome-enabled enrichment and optical tweezer-based isolation of an aerobic polysaccharide-degrading hyperthermophile, Fervidibacter sacchari, previously ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides for growth at 65–87.5°C and expresses 191 carbohydrate-active enzymes (CAZymes) according to RNA-Seq and proteomics, including 31 with unusual glycoside hydrolase domains (GH109, GH177, GH179). Fluorescence in-situ hybridization and nanoscale secondary ion mass spectrometry confirmed rapid assimilation of 13 C-starch in spring sediments. Purified GHs were optimally active at 80–100°C on ten different polysaccharides. Finally, we propose reassigning Fervidibacteria as a class within phylum Armatimonadota, along with 18 other species, and show that a high number and diversity of CAZymes is a hallmark of the phylum, in both aerobic and anaerobic lineages. Our study establishes Fervidibacteria as hyperthermophilic polysaccharide degraders in terrestrial geothermal springs and suggests a broad role for Armatimonadota in polysaccharide catabolism.

59 BASIC BIOLOGICAL SCIENCES↗