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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Strontium isoscape of sub-Saharan Africa allows tracing origins of victims of the transatlantic slave trade

Abstract Strontium isotope ( 87 Sr/ 86 Sr) analysis with reference to strontium isotope landscapes (Sr isoscapes) allows reconstructing mobility and migration in archaeology, ecology, and forensics. However, despite the vast potential of research involving 87 Sr/ 86 Sr analysis particularly in Africa, Sr isoscapes remain unavailable for the largest parts of the continent. Here, we measure the 87 Sr/ 86 Sr ratios in 778 environmental samples from 24 African countries and combine this data with published data to model a bioavailable Sr isoscape for sub-Saharan Africa using random forest regression. We demonstrate the efficacy of this Sr isoscape, in combination with other lines of evidence, to trace the African roots of individuals from historic slavery contexts, particularly those with highly radiogenic 87 Sr/ 86 Sr ratios uncommon in the African Diaspora. Our study provides an extensive African 87 Sr/ 86 Sr dataset which includes scientifically marginalized regions of Africa, with significant implications for the archaeology of the transatlantic slave trade, wildlife ecology, conservation, and forensics.

Science & Technology - Other Topics↗
DOE OSTI2025

A genomic view of Earth’s biomes

Microorganisms are essential to all life on Earth through critical roles in key biological processes and diverse interactions with other organisms that shape ecosystems, drive biogeochemical cycles and influence both human health and environmental health. High-throughput sequencing from environmental samples has revolutionized the understanding of microbial diversity and functions. With vast amounts of genomes now available across Earth’s biomes, these data provide a blueprint of microbial life that can be harnessed for a more holistic understanding of microbiome structure and function across the various ecosystems on Earth. Here we review the application of genome-centric approaches, including recent advances in single-cell sequencing and functional profiling, to survey microbial and viral diversity. Furthermore, we highlight some of the most impactful evolutionary and functional discoveries, explore the spatial diversity and temporal dynamics of microorganisms across diverse environments, and discuss genome-enabled insights into host-associated microorganisms.

Ecology↗
DOE OSTI2025

Interpretable machine learning models classify minerals via spectroscopy

Developing methods to identify mineral species confidently and rapidly from Raman spectral analysis is critical to numerous fields. Traditionally, analysis relies on pattern matching the Raman spectrum of an unknown dataset with a supporting library of well-characterized spectral data, which may prove difficult for environmental samples that are poorly crystalline or phase mixtures. Here, we developed interpretable machine learning models that can classify uranium minerals by secondary oxyanion chemistry and other physicochemical properties based solely on Raman spectra. This new ML method produces a mineral profile of physical and chemical properties for an unknown sample and can rapidly classify or identify unknown minerals from Raman data, without the need for an exact pattern match in a spectral library. Training models are validated by 1. Strong correlation of high confidence model regions with published spectroscopic assignments and 2. Correct classification of a mineral not present in training data. Training data are from the Compendium of Uranium Raman and Infrared Experimental Spectra and available crystallographic information files within the open-source Smart Spectral Matching scientific framework. Physically meaningful classifier models can rapidly identify key structural and chemical information about unknown uranium minerals and the overall methodology is broadly applicable for mineral phases.

Machine learning↗
DOE OSTI2020

Experimental and computational study of particle formation kinetics in UF6 hydrolysis

The formation and growth of UO 2 F 2 particles by gas-phase UF 6 hydrolysis remains of interest to actinide chemistry researchers. The total number concentration of the UO 2 F 2 aerosol particles that can be produced in the reaction is regulated primarily by the availability of water molecules under our reactor conditions. An increase in water molecule concentration corresponds with a higher amount and larger size of UO 2 F 2 aerosol particles produced. The growth rates of aerosol particles appear to approach a single number in the range of [0.05 ± 0.03–0.08 ± 0.04] (nm s -1 ), as the molar ratio of water to UF 6 decreases below 1. The size of primary particles produced from the UF 6 hydrolysis under water-deprived conditions was estimated to be 3.6 ± 0.4 nm. As the molar ratio became greater than 1.7, the size of primary particles increased with increased availability of water molecules. The primary particle model developed in this work predicted a size range for the UO 2 F 2 primary particles similar to that estimated based on the data from gas-phase UF 6 hydrolysis experiments. This result suggests that the volume-driven coalescence process assumption used in the derivation of the primary particle model was reasonable. The ability to precisely control the availability of water molecules and reaction time could lead to the production of nearly monodispersed aerosol particles. This finding has significant implications in the engineering and manufacturing of fuel powder materials and possibly the future development and deployment of environmental sampling apparatus.

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

Direct analysis of cotton swipes for plutonium isotope determination by microextraction-ICP-MS

This study demonstrates a method for determining the isotopic composition of low-level (sub-pg) plutonium (Pu) directly from a cotton swipe. Environmental sample (ES) swipes are routinely employed as a tool for monitoring activities in nuclear facilities. Traditional ES swipe analysis, as employed in nuclear safeguards, utilizes laborious ashing, digestion, and chemical separation procedures prior to mass spectrometric (MS) analysis. Here, an innovative sample introduction technique employing a microextraction probe to extract Pu directly from the swipe surface is described. The microextraction probe lowers onto the swipe surface, seals on a small area (8 mm 2 ), and delivers solvent (2% HNO 3 ) to extract actinide material that may be present. The extracted analyte is subsequently directed into a sector field inductively coupled plasma (ICP)-MS for isotope ratio determination. This microextraction-ICP-MS method successfully determined the isotopic composition ( 240 Pu/ 239 Pu and 242 Pu/ 239 Pu) of three Pu certified reference materials (CRM 136, 137, and 138) that were deposited (1 pg) onto ES swipes. The percent relative difference from the certified value, uncorrected for instrumental fractionation, was <2% for the 240 Pu/ 239 Pu ratio on all three CRMs and <10% for the 242 Pu/ 239 Pu ratio on CRM 136 and 138. Here, the percent relative standard deviation, an estimate of the sample-to-sample isotopic precision, was <4% for the 240 Pu/ 239 Pu and <15% for the 242 Pu/ 239 Pu. Method limits of detection were determined, based on measurements of an enriched 244 Pu material, to be ~7 fg. Additionally, a mixed uranium (U) and Pu deposition was made to determine the method's ability to simultaneously extract U and Pu and determine the isotopic composition of both analytes.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Synchrotron X-rays reveal the modes of Fe binding and trace metal storage in the brown algae Laminaria digitata and Ectocarpus siliculosus

Abstract Iron is accumulated symplastically in kelp in a non-ferritin core that seems to be a general feature of brown algae. Microprobe studies show that Fe binding depends on tissue type. The sea is generally an iron-poor environment and brown algae were recognized in recent years for having a unique, ferritin-free iron storage system. Kelp (Laminaria digitata) and the filamentous brown alga Ectocarpus siliculosus were investigated using X-ray microprobe imaging and nanoprobe X-ray fluorescence tomography to explore the localization of iron, arsenic, strontium, and zinc, and micro-X-ray absorption near-edge structure (μXANES) to study Fe binding. Fe distribution in frozen hydrated environmental samples of both algae shows higher accumulation in the cortex with symplastic subcellular localization. This should be seen in the context of recent ultrastructural insight by cryofixation–freeze substitution that found a new type of cisternae that may have a storage function but differs from the apoplastic Fe accumulation found by conventional chemical fixation. Zn distribution co-localizes with Fe in E. siliculosus, whereas it is chiefly located in the L. digitata medulla, which is similar to As and Sr. Both As and Sr are mostly found at the cell wall of both algae. XANES spectra indicate that Fe in L. digitata is stored in a mineral non-ferritin core, due to the lack of ferritin-encoding genes. We show that the L. digitata cortex contains mostly a ferritin-like mineral, while the meristoderm may include an additional component.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Improved precision in As speciation analysis with HERFD-XANES at the As K -edge: the case of As speciation in mine waste

High-energy-resolution fluorescence-detected (HERFD) X-ray absorption near-edge spectroscopy (XANES) is a spectroscopic method that allows for increased spectral feature resolution, and greater selectivity to decrease complex matrix effects compared with conventional XANES. XANES is an ideal tool for speciation of elements in solid-phase environmental samples. Accurate speciation of As in mine waste materials is important for understanding the mobility and toxicity of As in near-surface environments. In this study, linear combination fitting (LCF) was performed on synthetic spectra generated from mixtures of eight measured reference compounds for both HERFD-XANES and transmission-detected XANES to evaluate the improvement in quantitative speciation with HERFD-XANES spectra. The reference compounds arsenolite (As 2 O 3 ), orpiment (As 2 S 3 ), getchellite (AsSbS 3 ), arsenopyrite (FeAsS), kaňkite (FeAsO 4 ·3.5H 2 O), scorodite (FeAsO 4 ·2H 2 O), sodium arsenate (Na 3 AsO 4 ), and realgar (As 4 S 4 ) were selected for their importance in mine waste systems. Statistical methods of principal component analysis and target transformation were employed to determine whether HERFD improves identification of the components in a dataset of mixtures of reference compounds. LCF was performed on HERFD- and total fluorescence yield (TFY)-XANES spectra collected from mine waste samples. Arsenopyrite, arsenolite, orpiment, and sodium arsenate were more accurately identified in the synthetic HERFD-XANES spectra compared with the transmission-XANES spectra. In mine waste samples containing arsenopyrite and either scorodite or kaňkite, LCF with HERFD-XANES measurements resulted in fits with smaller R -factors than concurrently collected TFY measurements. The improved accuracy of HERFD-XANES analysis may provide enhanced delineation of As phases controlling biogeochemical reactions in mine wastes, contaminated soils, and remediation systems.

58 GEOSCIENCES↗
DOE OSTI2020

Whole-Genome Sequence of Brevibacillus borstelensis SDM, Isolated from a Sorghum-Adapted Microbial Community

The isolation of novel microbes from environmental samples continues to be a key strategy for the discovery of new metabolic capacities for the degradation and transformation of lignocellulose. We report the draft genome sequence of a new strain of Brevibacillus borstelensis isolated from a sorghum-adapted microbial community derived from a compost sample.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18

Bacteriophages are useful nonantibiotic therapeutics for bacterial infections as well as threats to industries utilizing bacterial agents. This study identified Phaeobacter virus MD18 , a phage antagonist of Phaeobacter inhibens , a bacterium with promising use as a probiotic for aquatic farming industries. Genomic analysis suggested that Phaeobacter phage MD18 has evolved to enhance its replication in P. inhibens by adopting favorable tRNA genes as well as through genomic sequence adaptation to resemble host codon usage. Lastly, a high-throughput analysis of P. inhibens transposon insertion mutants identified genes that modulate host susceptibility to phage MD18 and implicated the type IV pilus as the likely receptor recognized for adsorption. This study marks the first characterization of the relationship between P. inhibens and an environmentally sampled phage, which informs our understanding of natural threats to the bacterium and may promote the development of novel phage technologies for genetic manipulation of this host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

ABSTRACT Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics. IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Accelerating large scale de novo metagenome assembly using GPUs

Metagenomic workflows involve studying uncultured microorganisms directly from the environment. These environmental samples when processed by modern sequencing machines yield large and complex datasets that exceed the capabilities of metagenomic software. The increasing sizes and complexities of datasets make a strong case for exascale-capable metagenome assemblers. However, the underlying algorithmic motifs are not well suited for GPUs. This poses a challenge since the majority of next-generation supercomputers will rely primarily on GPUs for computation. In this paper we present the first of its kind GPU-Accelerated implementation of the local assembly approach that is an integral part of a widely used large-scale metagenome assembler, MetaHipMer. Local assembly uses algorithms that induce random memory accesses and non-deterministic workloads, which make GPU offloading a challenging task. Our GPU implementation outperforms the CPU version by about 7x and boosts the performance of MetaHipMer by 42% when running on 64 Summit nodes.

Awan, Muaaz Gul↗
DOE OSTI2025

genomeocean: a pretrained microbial genome foundational model (genomeoceanLLM) v1.0

We present Genomeocean, a foundational genome language model that represents the microbial genome sequences from complex environmental samples. By training on a large, diverse metagenomic dataset, Genomeocean learns species-specific sequence composition and can generate long, realistic open reading frames (ORFs). Our model employs a Byte-pair-encoding (BPE) tokenization strategy, allowing it to efficiently process large genomic datasets and generate long sequences up to 50kb. We demonstrate that fine-tuning Genomeocean can generate novel gene clusters encoding biosynthetic pathways, showcasing its ability to model both fundamental and complex biological processes. Our work establishes Genomeocean as a powerful tool for understanding microbial genome biology and paves the way for its application in a range of fields, from synthetic biology to microbiome research.

Wang, Zhong [Lawrence Berkeley National Laboratory↗
DOE OSTI2024

Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments

Background: The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood. Results: We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34 TS , both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11 T and Phoenicimicrobium oleiphilum HX-OS.bin.34 TS ferment sugars and n-alkanes, respectively, producing H 2 , CO 2 , and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments. Conclusion: Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Formation of Aerosol Nanoparticles by Gas-Phase Hydrolysis Reaction of Uranium Hexafluoride

The aerosol physics of uranyl particle formation has been addressed in this research using advanced aerosol instrumentation and an aerosol dynamics model. Based on the research works, we conclude that the formation and growth of aerosol particles by gas-phase UF6 hydrolysis strongly depends on the availability of water molecules in our reactor conditions. The total number concentration of the UO 2 F 2 particulate material that could be produced in the hydrolysis reaction is also regulated primarily by the availability of water molecule concentration. The higher the water molecule concentration, the higher the number and the larger the size of UO 2 F 2 aerosol particles that could be produced in a reactor custom-built at ORNL. Although the aerosol reactor was enabling the study of particle formation kinetics, the instrumentation was still insufficient in characterizing the chemical composition of the produced particles as well as the time-dependent evolution of the particulate species. The temporal evolution could impact the eventual fate of the particles upon release to the environment (i.e., the physio-chemical transformation, transport, and removal). On uranyl particle formation kinetics, we found that the growth rates of aerosol particles appeared to approach a single number in the range of 0.05 ± 0.03 - 0.08 ± 0.04 nm/s, statistically, as the ω value becomes smaller than 1. The size of primary particles from the UF6 hydrolysis at water-deprived condition was estimated to be 3.6 ± 0.4 nm; the higher the availability of water molecules, the larger the primary particles. The ability to precisely control the availability of water molecules in the reaction could lead to the production of nearly monodispersed aerosol particles. In other words, the result suggests that one can precisely manipulate the size of UO 2 F 2 aerosol particles by controlling the water vapor availability and interaction of water molecules with U F6 in the reaction. This finding has significant implications in the engineering manufacturing of fuel powder materials and possibly to future development and deployment of an environmental sampling apparatus.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Engineering Methanogenic Microbiomes to Redirect Flux to Biomass

In this study, we present a method for acquiring and characterizing novel microbial consortia that regulates methanogens and methanotrophs through selective cultivation and metagenomic analysis of indigenous microorganisms in the environment. In addition, we present the work performed as part of this project to model the pathways that act as limiting factors in microbial methane metabolism based on a carbon cycle model. In this report, we describe the methods for selective cultivation of methane-metabolism-related microorganisms from environmental samples, the method for monitoring their methane consumption performance, and the method and results for verifying their functions using quantitative PCR and metagenomics techniques. The microbial consortia containing methanotrophs were obtained through selective cultivation and molecular biological verification, and their methane consumption performance was evaluated. In addition, the potential of the existence of bacteriophages interacting with methane metabolism-related microorganisms was identified through metagenomic sequencing.

09 BIOMASS FUELS↗
DOE OSTI2025

Automated Airborne Pathogen Monitoring for Agriculture (CRADA Final Report)

As part of the Cyclotron Road program, Root Applied Sciences investigated the use of DNA-based assays under field conditions to detect airborne plant pathogens in environmental samples. Robust DNA-based assays are critical for automated monitoring of plant pathogen concentrations in the air using Root’s air samplers. A fully automated air sampler coupled with DNA-based assays capable of operating under field conditions will accelerate the delivery of disease risk alerts based on airborne inoculum loads. Timely and accurate alerts of pathogen loads in the air can help growers manage airborne diseases more precisely, avoiding fungicide applications when there is no threat, and focusing cultural practices in the right areas. This project built upon other work done by Root to study the in-field performance of a liquid DNA-based assay for detection of grape powdery mildew. Growers working with Root’s airborne powdery mildew monitoring system have reported 20-80% reductions in pesticides.

60 APPLIED LIFE SCIENCES↗