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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Comparative Analysis of Corrinoid Profiles across Host-Associated and Environmental Samples

Vitamin B 12 (the cyanated form of cobalamin cofactors) is best known for its essential role in human health. In addition to its function in human metabolism, cobalamin also plays important roles in microbial metabolism and can impact microbial community function. Cobalamin is a member of the structurally diverse family of cofactors known as cobamides that are produced exclusively by certain prokaryotes. Cobamides are considered shared nutrients in microbial communities because the majority of bacteria that possess cobamide-dependent enzymes cannot synthesize cobamides de novo. Furthermore, different microbes have evolved metabolic specificity for particular cobamides, and therefore, the availability of cobamides in the environment is important for cobamide-dependent microbes. Determining the cobamides present in an environment of interest is essential for understanding microbial metabolic interactions. By examining the abundances of different cobamides in diverse environments, including 10 obtained in this study, we find that, contrary to its preeminence in human metabolism, cobalamin is relatively rare in many microbial habitats. Comparison of cobamide profiles of mammalian gastrointestinal samples and wood-feeding insects reveals that host-associated cobamide abundances vary and that fecal cobamide profiles differ from those of their host gastrointestinal tracts. Environmental cobamide profiles obtained from aquatic, soil, and contaminated groundwater samples reveal that the cobamide compositions of environmental samples are highly variable. As the only commercially available cobamide, cobalamin is routinely supplied during microbial culturing efforts. Furthermore, these findings suggest that cobamides specific to a given microbiome may yield greater insight into nutrient utilization and physiological processes that occur in these habitats.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Nonparametric Multiparticle Set Methods for Interpreting Environmental Samples

Collection and analysis of environmental samples is commonly used by a range of stakeholders in nuclear safeguards and security contexts. While the ubiquity of samples and their transport in the environment allow regular collection, developing and demonstrating methods for analyzing these samples is difficult. In this work, an environmental sample consists of a set of one or more individual particles. Recent advances in reactor simulation have allowed us to generate data that are more representative of real-world environmental samples, enabling statistically defensible method development and testing. The most notable of these advances is a drastic increase in the number of material depletion regions, which allows our simulations to capture the variation in isotopic composition seen at length scales consistent with environmental samples. Traditional approaches for handling multiparticle samples treat each particle in the sample individually, estimating the quantity of interest (e.g., core-average burnup) resulting from measurement and analysis of signatures (e.g., nuclide assays) from each individual particle. Individual estimates are then averaged to generate a single estimate of the quantity of interest over the entire sample. In this presentation, we introduce two novel approaches for interpreting environmental samples that comprise of multiple particles: (1) the Quantile-Quantile Comparator, which uses a multivariate generalization of quantile-quantile plots for comparing unknown statistical distributions, and (2) the Set Transformer, an attention-based neural network module designed to model interactions among elements (particles) in the input set (sample). Statistically representative sampling cannot be guaranteed as samples are passively collected and are beholden to what particles are available in the environment. These new analysis methods for set-input problems are expected to be more robust than traditional approaches to issues of sampling bias where particles are not uniformly distributed throughout regions of interest, as well as generally outperform traditional approaches by jointly considering all elements in the set. We will present results comparing the performance of traditional single particle approaches and the novel Quantile-Quantile Comparator and Set Transformer for interpretation of simulated environmental samples.

Phathanapirom, Birdy↗
DOE OSTI2023

Characterizing Reactor Operations from Realistic Simulated Environmental Samples: Combining High-Performance Computing and Data Analytics

Environmental sampling is a common technique employed by inspectors and facility operators in nuclear safeguards, proliferation detection, and process monitoring contexts. Interpreting measurements performed on samples or collections of samples and ensuring the information extracted is accurate and precise is difficult. To date, these analyses have relied on simulated data to enable systematic studies; however, these models are inherently limited by the fidelity of the models and the implicit spatial averaging of isotopic composition or other signatures of interest. To advance this capability, we have refined the spatial discretization and expanded the range of physics in the simulation codes we use to perform reactor simulations and depletion calculations. This allows us to generate data that are more representative of real environmental samples, especially for the length scale of the isotopic composition and associated variation. Accordingly, these new data allow a more realistic assessment of traditional and new data analytic analysis methods. Here we present motivation for developing reactor simulations using high-performance computing methods and resources, impacts of these new simulations on our assessment of data analysis and interpretation methods, and initial results of developing and systematically testing data analytic methods designed to overcome the challenges expected of real-world samples. We also quantify the performance of these analyses using defensible statistical methods.

Dayman, Ken J.↗
DOE OSTI2025

CABO-16S—a Combined Archaea, Bacteria, Organelle 16S rRNA database framework for amplicon analysis of prokaryotes and eukaryotes in environmental samples

Abstract Identification of both prokaryotic and eukaryotic microorganisms in environmental samples is currently challenged by the need for additional sequencing to obtain separate 16S and 18S ribosomal RNA (rRNA) amplicons or the constraints imposed by “universal” primers. Organellar 16S rRNA sequences are amplified and sequenced along with prokaryote 16S rRNA and provide an alternative method to identify eukaryotic microorganisms. CABO-16S combines bacterial and archaeal sequences from the SILVA database with 16S rRNA sequences of plastids and other organelles from the PR2 database to enable identification of all 16S rRNA sequences. Comparison of CABO-16S with SILVA 138.2 results in equivalent taxonomic classification of mock communities and increased classification of diverse environmental samples. In particular, identification of phototrophic eukaryotes in shallow seagrass environments, marine waters, and lake waters was increased. The CABO-16S framework allows users to add custom sequences for further classification of underrepresented clades and can be easily updated with future releases of reference databases. Addition of sequences obtained from Sanger sequencing of methane seep sediments and curated sequences of the polyphyletic SEEP-SRB1 clade resulted in differentiation of syntrophic and non-syntrophic SEEP-SRB1 in hydrothermal vent sediments. CABO-16S highlights the benefit of combining and amending existing training sets when studying microorganisms in diverse environments.

Eitel, Eryn M. (ORCID:0009000723919297)↗
DOE OSTI2026

Direct and rapid uranium isotopic analysis of environmental sample swipes via microextraction – LS-APGD/Orbitrap mass spectrometry

Accurate and precise isotopic analysis of actinides collected on environmental sample swipes from within nuclear facilities is an important safeguarding measure for detecting undeclared materials and activities. Traditional isotope ratio (IR) analysis of actinides using a bulk digestion approach can be laborious and time-consuming. Recently, direct analysis of environmental swipe samples using a microextraction approach has been explored as an alternative to conventional bulk digestion methods. The present study further evaluates this approach for accurate and precise isotopic analysis of uranium (U) in cotton swipe samples using the liquid sampling-atmospheric pressure glow discharge (LS-APGD)/Orbitrap-FTMS Booster detection system. The instrumental parameters were optimized, and quantitative capabilities were demonstrated through excellent linearity (R2 = 0.99) across a deposited mass range of 1 to 500 ng, with a limit of detection of 90 pg (in a 2 × 4 mm region) for total U; well below typical U concentrations (ng–mg range) in environmental sample swipes. The 235U/238U ratio showed excellent accuracy (−0.3% relative difference from the certificate value), with ∼20× improvement over previous microextraction-Orbitrap methods. Precision (∼1% relative standard deviation) was also greatly enhanced by ∼5×. This study also demonstrates that figures of merit achieved with neat U solution were not highly degraded when various external interfering elements/matrices were introduced. Finally, the developed method was successfully applied to analyze practical swipe samples representative of laboratory and outdoor environments. The presented figures of merit and applicability to practical samples further validate the capability of the platform for rapid analysis (<7 minutes) of environmental swipe samples.

Shrestha, Suraj [Clemson University, SC]↗
DOE OSTI2022

Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM): a method for detection of antimicrobial resistance in environmental samples

Effective monitoring of antibiotic resistance genes and their dissemination in environmental ecosystems has been hindered by the cost and efficiency of methods available for the task. We developed the Diversity of Antibiotic Resistance genes and Transfer Elements-Quantitative Monitoring (DARTE-QM), a method implementing TruSeq high-throughput sequencing to simultaneously sequence thousands of antibiotic resistant gene targets representing a full-spectrum of antibiotic resistance classes common to environmental systems. In this study, we demonstrated DARTE-QM by screening 662 antibiotic resistance genes within complex environmental samples originated from manure, soil, and livestock feces, in addition to a mock-community reference to assess sensitivity and specificity. DARTE-QM offers a new approach to studying antibiotic resistance in environmental microbiomes, showing advantages in efficiency and the ability to scale for many samples. This method provides a means of data acquisition that will alleviate some of the obstacles that many researchers in this area currently face.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Results of an In-Field Validation Exercise in Support of Wide-Area Environmental Sampling

The National Nuclear Security Administration’s (NNSA) Office of Nonproliferation and Arms Control (NA-24) is evaluating Wide-Area Environmental Sampling (WAES) as an additional safeguards verification tool for the International Atomic Energy Agency to detect undeclared nuclear activities. The NNSA is evaluating strategies for conducting a generic WAES campaign, the cost of a WAES campaign, and the effect of technological advancements that have occurred since the last major WAES review in 1999. Until now, the NNSA effort has focused on tabletop exercises (TTXs) in which high-performance computing allows for advanced modeling and simulation efforts to be applied to the WAES question. Although the modeling and simulations used in the TTXs are extremely valuable, field campaigns are still needed to validate the assumptions that underpin the models and the modeling process itself. During a 7 week period beginning in May 2023 and ending in June 2023, which included 4 weeks of active field collections, a multilaboratory team conducted its first in-field validation exercise. Prior to the in-field exercise, abbreviated TTXs were conducted to estimate the performance of all collection systems to be used during the field test. These TTXs guided the selection of materials to be released and the placement of the collection system. Based on these determinations, materials were procured to use in the field test, and an injection/release system was designed, built, and installed at the test facility. Background samples were collected during weeks one and four, and environmental collections against active releases were conducted during weeks two and three. The goals of this validation exercise included a demonstration of (1) the ability to provide controlled releases of particulates of surrogate materials, (2) the fielding and operation of collection systems (including deposition and active air collectors), and (3) the flexibility to revise equipment and campaign plans in the field. This paper presents the results and preliminary conclusions for this initial validation test. Based on these results, subsequent field campaigns are anticipated and will include the addition of other released materials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Comparison of the sensitivity of 236 U measurements in environmental samples by MC-ICP-MS and ATONA based high precision U TIMS measurements

The ATONA project is focused upon exploring the improvements in uranium isotope ratio measurements by thermal ionization mass spectrometry (TIMS) provided by a new, capacitor-based, amplifier technology. These “ATONA” Faraday amplifiers (Isotopx Ltd, UK) promise accurate, low-noise measurements of very small signals (< 1 femto-amp) in a traditional Faraday cup, which was only previously possible using an ion counter. This report outlines a series of experiments that were performed to assess the performance of the system in samples that test our rapid analysis procedures, and then compare the results against other mass spectrometry techniques currently available for environmental analyses. The following major goals were achieved: (1) illustrated the importance of 236 U measurements for the screening and analysis of environmental samples; (2) improved sensitivity for 236 U, and then identified 236 U in the 4350B standard at ultra-trace levels (3) Provided comparison of the 236 U sensitivity to multi-collector inductively coupled mass spectrometry techniques (4) Illustrated high TRL for the ATONA based measurement technique. This completes the reporting requirements for task 4 in the project LCP and highlights the utility of the system to make highly sensitive 236 U measurements in programmatically relevant sample matrices and at relevant uranium concentrations.

07 ISOTOPE AND RADIATION SOURCES↗
NASA NTRS2014

Characterization of Plastic Degrading Bacteria from Environmental Samples by Genetic and Biochemical Analysis

Plastic is the major waste-product during NASA space missions, recycling this waste-stream to produce other beneficial materials would decrease upmass. Bacterial called plastisomes have been demonstrated to metabolize non-biodegradable plastics such as polyethylene and polystyrene. Characterization and engineering of these bacteria, and their eventual incorporation as life support systems would enable space flight beyond lower earth orbit. We will utilize molecular techniques to identify and isolate the most productive plastisome. Environmental samples obtained from locations known to be rich in plastic will be cultured in a laboratory defined-media supplemented with plastic as the sole carbon source. Cultures will be monitored for growth over time. Ribosomal DNA will be amplified from cultures that exhibit growth using PCR. These amplified fragments will be sequenced to determine the identity of the consortia in the cultures. We will then perform bioinformatics analysis on the data to identify the plastisomes and generate phylogenetic trees. Morphological and physiological profile of the plastisomes will also be conducted by microscopy and biochemical tests. Our results would reveal a bacterial strain that can break down plastics efficiently. The implication for this project would not only benefit space exploration but also make a major impact towards sustainability development on Earth.

plastic conversion↗
DOE OSTI2025

Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan

Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.

A.Br.047 Vollum↗
DOE OSTI2024

High efficiency active environmental sampling of chemical traces

A method of sample collection includes collecting an analyte from a sampling surface using a rapidly curable liquid gel comprising one or more metal particles; co-aggregating the one or more metal particles from the rapidly curable liquid gel and the analyte from the sampling surface; and rapidly curing the rapidly curable liquid gel. The composition and sample preparation conditions may facilitate improved collection efficiency of analytes during environmental and forensic evidence sampling. In addition, the composition and sample preparation conditions may facilitate enhanced detection and identification of the analyte using e.g., Surface Enhanced Raman Spectrometry (SERS).

Junghans, Ann↗
DOE OSTI2023

nmrrr : A Reproducible Workflow for Binning and Visualizing NMR Spectra From Environmental Samples

Nuclear magnetic resonance (NMR) spectroscopy is a useful tool for detection and identification of molecular structural information, with increasing applications in environmental sciences. NMR instrument outputs are however heterogeneous and require extensive post-processing, creating barriers to their use and application by non-specialists. Here, we report on a new open-source R package, nmrrr, that processes and visualizes spectral data obtained from one-dimensional solution-state and solid-state NMR experiments; the package also performs relevant calculations commonly applied in natural organic matter communities, such as computing the relative abundance of various functional groups. We document the package's installation, dependencies, and functions; and provide a standard workflow for processing NMR data. This package is currently available on CRAN and GitHub, and community contributions are welcome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

FY26 MID-YEAR REPORT 238 Pu Measurement in Bulk Environmental Samples by Thermal Ionization Mass Spectrometry (TIMS)

Funding was received in December 2026 to optimize a nascent measurement capability for mass spectrometry of 238 Pu, as it would apply to relevant environmental collections in safeguards applications, i.e. NWAL swipes or other bulk collections such as soil, sediment, waters, or air filters. The measurement relies on differing ionization temperatures for U and Pu during thermal ionization and therefore leverages TIMS to partially separate and measure these elements. Collected counts of 238 Pu can be mathematically corrected for interfering counts of background 238 U, by addition of a U tracer (e.g. 235 U) to account for the 238 U present. The method has undergone initial characterization at LANL regarding detection limit, precision, and accuracy but requires further applicability-testing for possible use in safeguards.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1983

Biomass measurement of methane forming bacteria in environmental samples

Methane-forming bacteria contain unusual phytanylglycerol ether phospholipids which can be extracted from the bacteria in sediments and assayed quantitatively by high performance liquid chromatography (HPLC). In this procedure the lipids were extracted, the phospholipids recovered, hydrolyzed, purified by thin layer chromatography, derivatized and assayed by HPLC. Ether lipids were recovered quantitatively from Methanobacterium thermoautotrophicum and sediments at levels as low as 8 x 10(-14) moles. In freshwater and marine sediments the flux of methane to the atmosphere and the methane levels in the pore water reflects the recovery of the phytanyl glycerol ether lipid 'signature'. The proportion of the ether phospholipid to the total recoverable phospholipid was highest in anaerobic digester sewage sludge and deeper subsurface freshwater sediment horizons.

Methanobacterium/metabolism/physiology↗
NASA NTRS1974

Trace-element analysis of 1000 environmental samples per year using instrumental neutron activation analysis

The technology and methods developed at the Plum Brook Reactor to analyze 1000 samples per year and report data on as many as 56 elements are described. The manpower for the complete analysis of 20 to 24 samples per week required only 3 to 3.5 hours per sample. The solutions to problems encountered in sample preparation, irradiation, and counting are discussed. The automation of data reduction is described. Typical data on various sample matrices are presented.

Sheibley, D. W.↗
NASA NTRS1997

Gene-Based Detection of Microorganisms in Environmental Samples Using PCR

Contaminating microorganisms pose a serious potential risk to the crew's well being and water system integrity aboard the International Space Station (ISS). We are developing a gene-based microbial monitor that functions by replicating specific segments of DNA as much as 10(exp 12) x. Thus a single molecule of DNA can be replicated to detectable levels, and the kinetics of that molecule's accumulation can be used to determine the original concentration of specific microorganisms in a sample. Referred to as the polymerase chain reaction (PCR), this enzymatic amplification of specific segments of the DNA or RNA from contaminating microbes offers the promise of rapid, sensitive, quantitative detection and identification of bacteria, fungi, viruses, and parasites. We envision a small instrument capable of assaying an ISS water sample for 48 different microbes in a 24 hour period. We will report on both the developments in the chemistry necessary for the PCR assays to detect microbial contaminants in ISS water, and on progress towards the miniaturization and automation of the instrumentation.

Glass, John I.↗
NASA NTRS1960

Ionospheric Measurements Using Environmental Sampling Techniques

Two rockets were flown to peak altitudes of 220 km in September 1959 to test various methods planned for future measurements of ionization parameters in the ionosphere, exosphere, and interplanetary plasma. The experiments used techniques which sample the ambient environment in the immediate vicinity of the research vehicle. Direct methods were chosen since indirect propagation techniques do not provide the temperatures of charged particles, are insensitive to ion densities, and cannot measure local electron densities under all conditions. Very encouraging results have been obtained from a preliminary analysis of data provided by one of the two flights. A new rf probe technique was successfully used to determine the electron density profile. This was indicated by its agreement with the results of a companion cw propagation experiment, particularly when the probe data were corrected for the effects of the ion sheath which surrounds the vehicle. The characteristics of this sheath were determined directly in flight by an electric field meter which provided the sheath field, and by a Langmuir probe which measured the total potential across the sheath. The electron temperatures deduced from the Langmuir probe data are greater than the neutral gas temperatures previously measured for the same location and season, but these measurements possibly were taken under different atmospheric conditions. Ion densities were calculated from the ion trap data for several altitudes ranging from 130 to 210 km and were found to be within 20 percent of the measured electron densities.

Bourdeau, R. E.↗