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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California

Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains isolated from wild birds in a major agricultural region in California. Shiga toxin genes stx2f were present in all avian strains. Pangenome analyses of 20 complete genomes revealed a total of 11,249 genes, of which nearly 80% were accessory genes. Both core gene-based phylogenetic and accessory gene-based relatedness analyses consistently grouped the three stx2f-positive clinical strains with the five avian strains carrying ST7971. Among the three Stx2f-converting prophage integration sites identified, ssrA was the most common one. Besides the locus of enterocyte effacement and type three secretion system, the high pathogenicity island, OI-122, and type six secretion systems were identified. Substantial strain variation in virulence gene repertoire, Shiga toxin production, and cytotoxicity were revealed. Six avian strains exhibited significantly higher cytotoxicity than that of stx2f-positive E. coli, and three of them exhibited a comparable level of cytotoxicity with that of enterohemorrhagic E. coli outbreak strains, suggesting that wild birds could serve as a reservoir of E. albertii strains with great potential to cause severe diseases in humans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

Abstract Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome‐wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57–.73 and are similar to prediction accuracies obtained with genotyping‐by‐sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low‐coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost‐effective option for genomic selection.

Jensen, Sarah E.↗
DOE OSTI2023

Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression

Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species’ divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species’ pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7±19.1 and 36.5±10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A global phylogenomic analysis of the shiitake genus Lentinula

Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes . We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia–Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase ( lecsl ) and γ-glutamyl transpeptidase ( leggt ), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula . Paralogs of both genes that are unique to Lentinula ( lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes . The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A haplotype-resolved reference genome for Eucalyptus grandis

Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70-90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.

Lötter, Anneri↗
DOE OSTI2024

Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater

Many factors contribute to the ability of a microbial species to persist when encountering complexly contaminated environments, including time of exposure, the nature and concentration of contaminants, availability of nutritional resources, and possession of a combination of appropriate molecular mechanisms needed for survival. Herein we sought to identify genes that are most important for survival of Gram-negative Enterobacteriaceae in contaminated groundwater environments containing high concentrations of nitrate and metals using the metal-tolerant Oak Ridge Reservation isolate, Pantoea sp. MT58 (MT58). Survival fitness experiments in which a randomly barcoded transposon insertion (RB-TnSeq) library of MT58 was exposed directly to contaminated Oak Ridge Reservation groundwater samples from across a nitrate and mixed metal contamination plume were used to identify genes important for survival with increasing exposure times and concentrations of contaminants, and availability of a carbon source. Genes involved in controlling and using carbon, encoding transcriptional regulators, and related to Gram-negative outer membrane processes were among those found to be important for survival in contaminated Oak Ridge Reservation groundwater. A comparative genomics analysis of 75 Pantoea genus strains allowed us to further separate the survival determinants into core and non-core genes in the Pantoea pangenome, revealing insights into the survival of subsurface microorganisms during contaminant plume intrusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology

Extensive microdiversity within Prochlorococcus, the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the Prochlorococcus pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential. Predicted growth rates covaried with observed ecotype abundances, affirming their significance as a measure of fitness and inferring a nonlinear density dependence of mortality. Our study demonstrates the potential to interpret global-scale ecosystem organization in terms of cellular-scale processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Abstract Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Results Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Conclusions Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Fonseca-Garcia, Citlali↗
DOE OSTI2020

KBase Educators Overview

KBase worked with a community of instructors to create a connected workflow that integrates genomics, metagenomics, phylogenetics, and pangenomic concepts in a “choose your own adventure” framework. Each concept is stand alone, while complementing one another as they flow from one topic to another across concepts. The pace of each workflow can be adjusted with the flexibility of modules that are shareable and allow students to copy and interact with data and analyses.

Data science, Education, Training, Genomics, Metag↗
DOE OSTI2021

Genome Extraction from Shotgun Metagenome Sequence Data

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗
DOE OSTI2021

Moab Desert Crust - Sample 4E

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗
DOE OSTI2021

Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform

Over the past year, biology educators and staff at the Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free and easily accessible data science platform that integrates many bioinformatics resources into a graphical user interface built upon reproducible analysis notebooks. KBase held conversations with college and high school instructors to understand how KBase could potentially support their educational goals. These conversations morphed into a working group of biological and data science instructors that adapted the KBase platform to their curriculum needs, specifically around concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. The KBase Educators Working Group developed modular, adaptable, and customizable instructional units. Each instructional module contains teaching resources, publicly available data, analysis tools, and markdown capability to tailor instructions and learning goals for each class. The online user interface enables students to conduct hands-on data science research and analyses without requiring programming skills or their own computational resources (these are provided by KBase). Alongside these resources, KBase continues to work with instructors, supporting the development of additional curriculum modules. For anyone new to the platform, KBase, and the growing KBase Educators Organization, provides a community network, accompanied by community-sourced guidelines, instructional templates, and peer support to use KBase within a classroom whether virtual or in-person.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform

Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Genomic Analysis of the Natural Variation of Fatty Acid Composition in Seed Oils of Camelina sativa

Camelina sativa is an oilseed crop that has shown strong promise as a biofuel feedstock. The profile of fatty acids greatly influences the oil quality; however, genetic mechanisms that determine the natural variation of fatty acid composition in camelina are not fully understood. A genome wide association study (GWAS) was performed to uncover genetic loci that may contribute to the contents of major fatty acids such as oleic and linolenic acids in camelina seed. Two approaches were taken to improve the GWAS efficiency. First, growing a diversity panel of 212 accessions in four locations and two nitrogen fertilization conditions revealed great variation in fatty acid contents in seeds. Second, using an improved reference genome, abundant markers, including 203,320 single nucleotide polymorphisms (SNPs) and 99,067 insertions/deletions (indels), were developed, which refined the population structure of the diversity panel. GWAS resulted in 118 genetic markers across 31 trait/treatment conditions. Closely linked markers were determined based on linkage decay and by comparing secondarily associated markers when highly associated ones were removed. Candidate genes were examined by comparing the pangenomes of 12 high-quality reference genomes. This study provides new resources to understand seed lipid metabolism and improve camelina oils through molecular breeding.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2025

Status on Genetic Resistance to Rice Blast Disease in the Post-Genomic Era

Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production, necessitating the development of resistant cultivars through genetic improvement. Breakthroughs in rice genomics, including the complete genome sequencing of japonica and indica subspecies and the availability of various sequence-based molecular markers, have greatly advanced the genetic analysis of blast resistance. To date, approximately 122 blast-resistance genes have been identified, with 39 of these genes cloned and molecularly characterized. The application of these findings in marker-assisted selection (MAS) has significantly improved rice breeding, allowing for the efficient integration of multiple resistance genes into elite cultivars, enhancing both the durability and spectrum of resistance. Pangenomic studies, along with AI-driven tools like AlphaFold2, RoseTTAFold, and AlphaFold3, have further accelerated the identification and functional characterization of resistance genes, expediting the breeding process. Future rice blast disease management will depend on leveraging these advanced genomic and computational technologies. Emphasis should be placed on enhancing computational tools for the large-scale screening of resistance genes and utilizing gene editing technologies such as CRISPR-Cas9 for functional validation and targeted resistance enhancement and deployment. These approaches will be crucial for advancing rice blast resistance, ensuring food security, and promoting agricultural sustainability.

Pedrozo, Rodrigo↗