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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Automated single-ion peak fitting as an efficient approach for analyzing complex chromatographic data

Chromatography provides important detail on the composition of environmental samples and their chemical processing. However, the complexity of these samples and their tendency to contain many structurally and chemically similar compounds frequently results in convoluted or poorly resolved data. Data reduction from raw chromatograms of complex environmental data into integrated peak areas consequently often requires substantial operator interaction. This difficulty has led to a bottleneck in analysis that increases analysis time, decreases data quality, and will worsen as advances in field-based instrumentation multiply the quantity and informational density of data produced. In this work, we develop and validate an automated approach to fitting chromatographic data within a target retention time window with a combination of multiple idealized peaks (Gaussian peaks either with or without an exponential decay component). Herein we compare this single-ion peak fitting approach to drawn baseline integration methods of more than 70,000 peaks collected by field-based chromatographs spanning across a wide range of volatilities and functionalities. Accuracy of peak fitting under real-world conditions is found to be within 10%. The quantitative parameters describing the fit (e.g. coefficients, fit residuals, etc.) are found to provide valuable information to increase the efficiency of quality control and provide constraints to accurately integrate peaks that are significantly convoluted with neighboring peaks. Implementation of the peak fitting method is shown to yield accurate integration of peaks otherwise too poorly resolved to separate into individual compounds and improved quantitative metrics to determine the fidelity of the data reduction process, while substantially decreasing the time spent by operators on data reduction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Safeguards Verification Measurements using Laser Ablation, Absorbance Ratio Spectrometry in Gaseous Centrifuge Enrichment Plants

Laser Ablation Absorbance Ratio Spectrometry (LAARS) is a new verification measurement technology under development at the US Department of Energy’s (DOE) Pacific Northwest National Laboratory (PNNL). LAARS uses three lasers to ablate and then measure the relative isotopic abundance of uranium compounds. An ablation laser is tightly focused on uranium-bearing solids producing a small plume containing uranium atoms. Two collinear wavelength-tuned spectrometry lasers transit through the plume and the absorbance of U-235 and U-238 isotopes are measured to determine U-235 enrichment. The measurement has high relative precision and detection limits approaching the femtogram range for uranium. It is independent of chemical form and degree of dilution with nuisance dust and other materials. High speed sample scanning and pinpoint characterization allow measurements on millions of particles/hour to detect and analyze the enrichment of trace uranium in samples. The spectrometer is assembled using commercially available components at comparatively low cost, and features a compact and low power design. Future designs can be engineered for reliable, autonomous deployment within an industrial plant environment. Two specific applications of the spectrometer are under development: 1) automated unattended aerosol sampling and analysis and 2) on-site small sample destructive assay measurement. The two applications propose game-changing technological advances in gaseous centrifuge enrichment plant (GCEP) safeguards verification. The aerosol measurement instrument, LAARS-environmental sampling (ES), collects aerosol particles from the plant environment in a purpose-built rotating drum impactor and then uses LAARS-ES to quickly scan the surface of the impactor to measure the enrichments of the captured particles. The current approach to plant misuse detection involves swipe sampling and offsite analysis. Though this approach is very robust it generally requires several months to obtain results from a given sample collection. The destructive assay instrument, LAARS-destructive assay (DA), uses a simple purpose-built fixture with a sampling planchet to collect adsorbed UF6 gas from a cylinder valve or from a process line tap or pigtail. A portable LAARS-DA instrument scans the microgram quantity of uranium collected on the planchet and the assay of the uranium is measured to ~0.15% relative precision. Currently, destructive assay samples for bias defect measurements are collected in small sample cylinders for offsite mass spectrometry measurement.

Enrichment Monitoring↗
DOE OSTI2014

Toward a Fieldable Atomic Mass Spectrometer for Safeguards Applications: Sample Preparation and Ionization

The International Atomic Energy Agency’s (IAEA’s) long-term research and development plan calls for the development of new methods to detect misuse at nuclear fuel cycle facilities such as reprocessing and enrichment plants. At enrichment plants, for example, the IAEA’s contemporary safeguards approaches are based on a combination of routine and random inspections that include collection of UF6 samples from in-process material and selected cylinders for subsequent analyses. These analyses include destructive analysis (DA) in a laboratory (typically by mass spectrometry [MS]) for isotopic characterization, and environmental sampling (ES) for subsequent laboratory elemental and isotopic analysis (also both typically by MS). One area of new method development includes moving this kind of isotope ratio analytical capability for DA and ES activities into the field. Some of the reasons for these developments include timeliness of results, avoidance of hazardous material shipments, and guidance for additional sample collecting. However, this capability does not already exist for several reasons, such as that most lab-based chemical and instrumental methods rely on laboratory infrastructure (highly trained staff, power, space, hazardous material handling, etc.) and require significant amounts of consumables (power, compressed gases, etc.). In addition, there are no currently available, fieldable instruments for atomic or isotope ratio analysis. To address these issues, Pacific Northwest National Laboratory (PNNL) and collaborator, Clemson University, are studying key areas that limit the fieldability of isotope ratio mass spectrometry for atomic ions: sample preparation and ionization, and reducing the physical size of a fieldable mass spectrometer. PNNL is seeking simple and robust techniques that could be effectively used by inspectors who may have no expertise in analytical MS. In this report, we present and describe the preliminary findings for three candidate techniques: matrix-assisted laser desorption/ionization (MALDI) MS, liquid sampling-atmospheric pressure glow discharge (LS-APGD), and laser ablation/ionization (LAI) MS at atmospheric pressure. Potential performance metrics for these techniques will be presented, including detectability, response, isotope ratio accuracy and precision, and ease of use.

Barinaga, Charles J.↗
DOE OSTI2013

Analysis of 85Kr: a comparison at the 10-14 level using micro-liter samples

The isotopic abundance of 85Kr in the atmosphere, currently at the level of 10211, has increased by orders of magnitude since the dawn of nuclear age. With a half-life of 10.76 years, 85Kr is of great interest as tracers for environmental samples such as air, groundwater and ice. Atom Trap Trace Analysis (ATTA) is an emerging method for the analysis of rare krypton isotopes at isotopic abundance levels as low as 10214 using krypton gas samples of a few micro-liters. Both the reliability and reproducibility of the method are examined in the present study by an inter-comparison among different instruments. The 85Kr/Kr ratios of 12 samples, in the range of 10213 to 10210, are measured independently in three laboratories: a low-level counting laboratory in Bern, Switzerland, and two ATTA laboratories, one in Hefei, China, and the other in Argonne, USA. The results are in agreement at the precision level of 5%.

MASS SPECTROMETRY↗
DOE OSTI2024

Unraveling iron oxides as abiotic catalysts of organic phosphorus recycling in soil and sediment matrices

In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus. Dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this reaction. Evidence of this abiotic catalysis has relied on monitoring products in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Reactions of various organic phosphorus compounds with the different minerals identified in the environmental samples reveal up to twenty-fold greater catalytic reactivities with iron oxides than with silicate and aluminosilicate minerals. Importantly, accounting for inorganic phosphate both in solution and mineral-bound, the dephosphorylation rates of iron oxides were within reported enzymatic rates in soils. Our findings thus imply a missing abiotic axiom for organic phosphorus mineralization in phosphorus cycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Reduction of Non-CO2 Gas Emissions Through The In Situ Bioconversion of Methane

The primary objectives of this research were to seek previously unidentified anaerobic methanotrophs and other microorganisms to be collected from methane seeps associated with coal outcrops. Subsurface application of these microbes into anaerobic environments has the potential to reduce methane seepage along coal outcrop belts and in coal mines, thereby preventing hazardous explosions. Depending upon the types and characteristics of the methanotrophs identified, it may be possible to apply the microbes to other sources of methane emissions, which include landfills, rice cultivation, and industrial sources where methane can accumulate under buildings. Finally, the microbes collected and identified during this research also had the potential for useful applications in the chemical industry, as well as in a variety of microbial processes. Sample collection focused on the South Fork of Texas Creek located approximately 15 miles east of Durango, Colorado. The creek is located near the subsurface contact between the coal-bearing Fruitland Formation and the underlying Pictured Cliffs Sandstone. The methane seeps occur within the creek and in areas adjacent to the creek where faulting may allow fluids and gases to migrate to the surface. These seeps appear to have been there prior to coalbed methane development as extensive microbial soils have developed. Our investigations screened more than 500 enrichments but were unable to convince us that anaerobic methane oxidation (AMO) was occurring and that anaerobic methanotrophs may not have been present in the samples collected. In all cases, visual and microscopic observations noted that the early stage enrichments contained viable microbial cells. However, as the levels of the readily substrates that were present in the environmental samples were progressively lowered through serial transfers, the numbers of cells in the enrichments sharply dropped and were eliminated. While the results were disappointing we acknowledge that anaerobic methane oxidizing (AOM) microorganisms are predominantly found in marine habitats and grow poorly under most laboratory conditions. One path for future research would be to use a small rotary rig to collect samples from deeper soil horizons, possibly adjacent to the coal-bearing horizons that may be more anaerobic.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2011

LLNL Genomic Assessment: TMT Task 1.4 Final Report on Sequencing Knowledge Gaps

TMT has made great progress in filling many major gaps in bacterial genome diversity. However, relatively little progress has been made in filling the much bigger gaps in viral genome diversity. At the present time no TMT performer has a demonstrated ability to perform large scale production viral sequencing, something that is necessary if TMT is to make any progress in viral countermeasures. TMT has a current over-capacity for bacterial sequencing that needs to be ramped down to ensure that there are TMT-relevant reasons to sequence further bacterial isolates of several species (see below for details.) It is a critical need for TMT to establish a credible plan to be able to sequence hundreds of viral samples per year, including many deep quasi-species analyses. This plan ought to include establishing and/or maintaining relationships with scientists currently holding valuable strains or who would be predicted to be on the forefront of emerging outbreaks worldwide and able to obtain critical samples and/or sequence data. TMT should add and test the ability to do bacterial metagenomic sequencing (e.g., not just a single isolated plaque but the entire population variation of complex clinical and environmental samples.)

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1977

Surveying the earth's environment from space - Spectral, areal, temporal coverage trends

Attention is given to various areas of satellite applications to monitoring the earth's environment. These trends primarily concern spectral, areal, and temporal coverage. Various environmental monitors are discussed in terms of derived economic benefits. Several types of remote sensors for earth applications are described, noting spectral channels, resolution cell size, swath width, and data rate. A sample environmental monitoring system is presented which includes five geostationary satellites, and three or four low earth orbit spacecraft

Nagler, R. G.↗
DOE OSTI2017

Application of Synchrotron Radiation-based Methods for Environmental Biogeochemistry: Introduction to the Special Section

To understand the biogeochemistry of nutrients and contaminants in environmental media, their speciation and behavior under different conditions and at multiple scales must be determined. Synchrotron radiation-based X-ray techniques allow scientists to elucidate the underlying mechanisms responsible for nutrient and contaminant mobility, bioavailability, and behavior. The continuous improvement of synchrotron light sources and X-ray beamlines around the world has led to a profound transformation in the field of environmental biogeochemistry and, subsequently, to significant scientific breakthroughs. Following this introductory paper, this special collection includes 10 papers that either present targeted reviews of recent advancements in spectroscopic methods that are applicable to environmental biogeochemistry or describe original research studies conducted on complex environmental samples that have been significantly enhanced by incorporating synchrotron radiation-based X-ray technique(s). We believe that the current focus on improving the speciation of ultra-dilute elements in environmental media through the ongoing optimization of synchrotron technologies (e.g., brighter light sources, improved monochromators, more efficient detectors) will help to significantly push back the frontiers of environmental biogeochemistry research. As many of the relevant techniques produce extremely large datasets, we also identify ongoing improvements in data processing and analysis (e.g., software improvements and harmonization of analytical methods) as a significant requirement for environmental biogeochemists to maximize the information that can be gained using these powerful tools.

58 GEOSCIENCES↗
DOE OSTI2022

Machine learning approaches to streamline and enhance the analysis of multiscale imaging data for bioaerosol and soil particles

Bioaerosol and soil particles are ubiquitous in the environment. They are multicomponent and complex in nature displaying mixed inorganic and organic components. The way components are mixed in a bioaerosol sample is referred to as its mixing state. Soil particles are also a mixture of inorganic (mineral) and organic (soil organic matter) components. Bioaerosol particles contribute to a major fraction of coarse mode atmospheric particles, especially in the tropical areas, contributing up to 80 % of the particle mass concentration. The mixing state of particles is crucial to evaluate because it impacts several important environmental processes such as warm and cold cloud formation and radiation budget. Mixing states in aerosols are accompanied by chemical reactions across solid-liquid-gas interfaces. In this study, we utilized elemental compositions and microcopy images of thousands of atmospheric particles acquired by computer-controlled scanning electron microscope equipped with an energy-dispersive x-ray spectrometer to compute the mixing state of atmospheric particles. A 2D convolutional neural network (CNN), also known as convnet, was used to model the relationship between low resolution imaging data and higher resolution spectroscopy data, with the former as training input and the latter as target output. Two types of CNNs were implemented and tested; a basic CNN and an Inception-v3 network. For binary classification, the basic CNN achieved an accuracy of 84.29 % across all atom types, and the Inception-v3-like network achieved an accuracy 85.51 %. This study demonstrates the applicability of deep learning to handle large amounts of imaging/chemical spectroscopy data efficiently and evaluate particle mixing state from a range of environmental samples.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Comparative Metagenomics of Toxic Freshwater Cyanobacteria Bloom Communities on Two Continents

Toxic cyanobacterial blooms have persisted in freshwater systems around the world for centuries and appear to be globally increasing in frequency and severity. Toxins produced by bloom-associated cyanobacteria can have drastic impacts on the ecosystem and surrounding communities, and bloom biomass can disrupt aquatic food webs and act as a driver for hypoxia. Little is currently known regarding the genomic content of the Microcystis strains that form blooms or the companion heterotrophic community associated with bloom events. To address these issues, we examined the bloomassociated microbial communities in single samples from Lake Erie (North America), Lake Tai (Taihu, China), and Grand Lakes St. Marys (OH, USA) using comparative metagenomics. Together the Cyanobacteria and Proteobacteria comprised .90% of each bloom bacterial community sample, although the dominant phylum varied between systems. Relative to the existing Microcystis aeruginosa NIES 843 genome, sequences from Lake Erie and Taihu revealed a number of metagenomic islands that were absent in the environmental samples. Moreover, despite variation in the phylogenetic assignments of bloomassociated organisms, the functional potential of bloom members remained relatively constant between systems. This pattern was particularly noticeable in the genomic contribution of nitrogen assimilation genes. In Taihu, the genetic elements associated with the assimilation and metabolism of nitrogen were predominantly associated with Proteobacteria, while these functions in the North American lakes were primarily contributed to by the Cyanobacteria. Our observations build on an emerging body of metagenomic surveys describing the functional potential of microbial communities as more highly conserved than that of their phylogenetic makeup within natural systems.

09 BIOMASS FUELS↗
DOE OSTI2014

Nature of Nano-Sized Plutonium Particles in Soils at the Hanford Site

The occurrence of plutonium dioxide (PuO2) either from direct deposition or from the precipitation of plutonium-bearing solutions in contaminated soils and sediments has been well described, particularly for the Hanford site in Washington State. However, past research has suggested that plutonium may exist in environmental samples at the Hanford site in chemical forms in addition to large size PuO2 particles and that these previously unidentified nano-sized particles maybe more reactive and thus more likely to influence the environmental mobility of Pu. Here we present evidence for the formation of nano-sized plutonium iron phosphate hydroxide structurally related to the rhabdophane group nanoparticles in 216-Z9 crib sediments from Hanford using transmission electron microscopy (TEM). The distribution and nature of these nanoparticles varied depending on the adjacent phases present. Fine electron probes were used to obtain electron diffraction and electron energy-loss spectra from specific phase regions of the 216-Z9 cribs specimens from fine-grained plutonium oxide and phosphate phases. Energy-loss spectra were used to evaluate the plutonium N4,5 (4d → 5f ) and iron L2,3 absorption edges. The iron plutonium phosphate formation may depend on the local micro-environment in the sediments, availability of phosphate, and hence the distribution of these minerals may control long-term migration of Pu in the soil. This study also points to the utility of using electron beam methods for determining the identity of actinide phases and their association with other sediment phases.

Cribs, Soil Contamination↗
DOE OSTI2019

Supplemental Environmental Project, Supplemental Sampling and Monitoring Work Plan Regarding Settlement Agreement and Stipulated Final Order HWB-14-20, Addendum 3: Certification Package: Sampling and Monitoring

In accordance with the Supplemental Environmental Project (SEP), Settlement Agreement and Stipulated Final Order HWB-14-20 (signed January 22, 2016), Addendum 3: Supplemental Sampling and Monitoring Work Plan (sent December 12, 2016), this correspondence certifies that the Sampling and Monitoring subproject has been completed. When all Supplemental Sampling and Monitoring SEP subprojects are completed, Department of Energy (DOE) and TRIAD, LLC shall submit a signed and sworn Certification of Completion in accordance with the approved SEP Addendum 3.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Hybridization capture sequencing for Vibrio spp. and associated virulence factors

ABSTRACT Proliferation ofVibriospp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundanceVibriospp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69Vibriospp. and 162Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition,Vibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenicVibriospp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specificVibriospp., yielded significantly greater metagenomic insight, notably a variety of otherVibriospp., including detection ofVibrio cholerae,Vibrio fluvialis, andVibrio aestuarianus, in addition toVibrio parahaemolyticusandVibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios. IMPORTANCE The increasing prevalence of pathogenicVibriospp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundanceVibriospp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing ofVibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples. Results suggest pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.

Microbiology↗
DOE OSTI2012

Safeguards Verification Measurements using Laser Ablation, Absorbance Ratio Spectrometry in Gaseous Centrifuge Enrichment Plants

Laser Ablation Absorbance Ratio Spectrometry (LAARS) is a new verification measurement technology under development at the US Department of Energy (DOE) Pacific Northwest National Laboratory (PNNL). LAARS uses three lasers to ablate and then measure the relative isotopic abundance of uranium compounds. An ablation laser is tightly focused on uranium-bearing solids, producing a small atomic uranium vapor plume. Two collinear wavelength-tuned spectrometry lasers transit through the plume and the absorbance of U-235 and U-238 isotopes are measured to determine U-235 enrichment. The measurement is independent of chemical form and degree of dilution with nuisance dust and other materials. LAARS has high relative precision and detection limits approaching the femtogram range for U-235. The sample is scanned and assayed point-by-point at rates reaching 1 million measurements/hour, enabling LAARS to detect and analyze uranium in trace samples. The spectrometer is assembled using primarily commercially available components and features a compact design and automated analysis.Two specific gaseous centrifuge enrichment plant (GCEP) applications of the spectrometer are currently under development: 1) LAARS-Environmental Sampling (ES), which collects and analyzes aerosol particles for GCEP misuse detection and 2) LAARS-Destructive Assay (DA), which enables onsite enrichment DA sample collection and analysis for protracted diversion detection. The two applications propose game-changing technological advances in GCEP safeguards verification.

Uranium Enrichment Laser Safeguards↗
DOE OSTI2026

Cation Data for the East River Watershed, Colorado (2014-2025)

This data package contains mean values for cation concentration for water samples taken from the East River Watershed in Colorado. Inductively coupled plasma mass spectrometry (ICP-MS) has been used to measure the concentrations of elements of interest simultaneously for the East River Watershed, Colorado groundwater and surface water samples to inform insights on the biogeochemistry processes within the watershed. The East River is part of the Watershed Function Scientific Focus Area (WFSFA) located in the Upper Colorado River Basin, United States. For samples collected prior to 06-16-2021, the instrumentation, Elan DRC II, PerkinElmer SCIEX, automatically switches among the three models necessary to analyze all 37 elements. These 37 elements include: (1) Lithium (Li), Beryllium (Be), Boron (B), Sodium (Na), Magnesium (Mg), Aluminium (Al), Silicon (Si), Phosphorus (P), Titanium (Ti), Cobalt (Co), Nickel (Ni), Copper (Cu), Zinc (Zn), Germanium (Ge), Arsenic (As), Rubidium (Rb), Strontium (Sr), Zirconium (Zr), Molybdenum (Mo), Silver (Ag), Cadmium (Cd), Tin (Sn), Antimony (Sb), Caesium (Cs), Barium (Ba), Europium (Eu), Lead (Pb), Thorium (Th), Uranium (U) using standard model, argon Ar as reaction gas, (2) Potassium (K), Calcium (Ca), Vanadium (V), Chromium (Cr), Manganese (Mn), Iron (Fe) using dynamic reaction cell (DRC) model, ammonia NH3 as reaction gas, and (3) Phosphorus (P) and Selenium (Se) using DRC model, oxygen O2 as reaction gas. Note for the samples with higher concentrations of chloride (Cl-), asenic (As) concentrations were analysed with DRC model (oxygen O2 as reaction gas) to avoid the interference of chloride. For samples collected on and after 06-16-2021, an advanced Agilent 8900 triple quadrupole inductively coupled plasma mass spectrometry system (Agilent 8900 QQQ ICP-MS, Agilent Technologies) has been used to measure the concentrations of interested 36 elements simultaneously for environmental samples, including (1) Lithium (Li), Beryllium (Be) and Boron (B) using standard no gas mode, (2) Sodium (Na), Magnesium (Mg), Aluminium (Al) Phosphorus (P), Potassium (K), Chromium (Cr), Manganese (Mn), Iron (Fe), Cobalt (Co), Nickel (Ni), Copper (Cu), Zinc (Zn), Germanium (Ge), Arsenic (As), Rubidium (Rb), Strontium (Sr), Zirconium (Zr), Molybdenum (Mo), Silver (Ag), Cadmium (Cd), Tin (Sn), Antimony (Sb), Cesium (Cs), Barium (Ba), Europium (Eu), Lead (Pb), Thorium (Th) and Uranium (U) using standard helium (He) collision mode, (3) Titanium (Ti) and Vanadium (V) using high Energy (HEHe) helium (He) collision mode, and (4) Silicon (Si), Calcium (Ca) and Selenium (Se) using standard H2 reaction mode. All samples were prepared/diluted with 2% (v/v) ultrapure nitric acid in Milli-Q water (18.2 mega ohm-cm), and analyzed under a rigorous quality assurance and quality control (QA/QC) process. This data package contains (1) a zip file (cation_data_2014_2025.zip) containing a total of 5,849 files: 5.848 data files of cation data from across the Lawrence Berkeley National Laboratory (LBNL) Watershed Function Scientific Focus Area (SFA) which is reported in .csv files per location and a locations.csv (1 file) with latitude and longitude for each location; (2) a file-level metadata (v6_20260901_flmd.csv) file that lists each file contained in the dataset with associated metadata; (3) a data dictionary (v6_20260901_dd.csv) file that contains terms/column_headers used throughout the files along with a definition, units, and data type; (4) PDF and docx files for the detemination of Method Detection Limits (MDLs) for ICP-MS PerkinElmer DRC II instrumentation (Detemination_of_Method_Detection_Limits__MDLs__for_ICP_MS__PerkinElmer_Elan_DRC_II__LBL_Bldg74_Lab214D) for samples before November 2021; (5) PDF and docx files for the determination of MDLs for ICP-MS Agilent 8900 QQQ instrumentation (ICP_MS_Analysis_detection_limits_and_QA_QC_WenmingDong_updated_2026-08-06) for samples November 2021 and onward. Missing values within the anion data files are noted as either "-9999" or "0.0" for not detectable (N.D.) data. There are a total of 113 locations containing cation data. Update on 2021-04-11: Added Detemination of Method Detection Limits (MDLs) for ICP-MS document, which can be accessed as a PDF or with Microsoft Word. Update on 2022-06-10: versioned updates to this dataset was made along with these changes: (1) updated cation data for all locations up to 2021-12-31, (2) removal of units from column headers in datafiles, (3) added row underneath headers to contain units of variables, (4) removed suffix and prefix on two variables (“aqberylliumion_asberyllium” and “aqlithiumion_aslithium”), (5) added -9999 for empty numerical cells, and (6) the addition of the file-level metadata (flmd.csv) and data dictionary (dd.csv) were added to comply with the File-Level Metadata Reporting Format. Update on 2022-09-09: Updates were made to reporting format specific files (file-level metadata and data dictionary) to correct swapped file names, add additional details on metadata descriptions on both files, add a header_row column to enable parsing, and add version number and date to file names (v2_20220909_flmd.csv and v2_20220909_dd.csv). Update on 2023-08-08: Updates were made to both the data files and reporting format specific files. New available anion data was added, up until 2023-01-05. The file level metadata and data dictionary files were updated to reflect the additional data added. Update on 2024-03-11: Updates were made to both the data files and reporting format specific files. New available anion data was added, up until 2023-10-16. Further, revisions to the data files were made to remove incorrect data points (from 1970 and 2001). The reporting format specific files were updated to reflect the additional data added. Updated versions of the PDF and docx files for determination of MDLs for ICP-MS data were added to this dataset for samples starting in November 2021. Update on 2025-05-15: Updates were made to both the data files and reporting format specific files. New available cation data was added, up until the end of WY2024 (September 30, 2024). International Generic Sample Numbers (IGSNs), when registered, were added to the data files. The reporting format specific files were updated to reflect the additional data added. Update on 2026-09-01: Updates were made to both the data files and reporting format specific files. New available cation data was added, up until the end of WY2025 (September 30, 2025). Updated versions, as of 2026-08-06, of the PDF and docx files for determination of MDLs for ICP-MS data were added to this dataset for samples starting in November 2021.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

PanFP: Pangenome-based functional profiles for microbial communities

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. As a result, we present a computational method called pangenome based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU s taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome s functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8 0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed reference OTU picking strategies against specific reference sequence databases. In conclusion, we developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub.

16S rRNA survey↗
DOE OSTI2024

Data sets for Unraveling Iron Oxides as Abiotic Catalysts of Organic Phosphorus Recycling in Soil and Sediment Matrices

In biogeochemical phosphorus cycling, iron oxide minerals are acknowledged as strong adsorbents of inorganic and organic phosphorus species. The dephosphorylation of organic phosphorus is attributed only to biological processes, but iron oxides could also catalyze this hydrolytic cleavage. Limited evidence of this abiotic catalysis has relied on monitoring inorganic phosphate in solution, thereby ignoring iron oxides as both catalysts and adsorbents. Here we apply high-resolution mass spectrometry and X-ray absorption spectroscopy to characterize dissolved and particulate phosphorus species, respectively. In soil and sediment samples reacted with ribonucleotides, we uncover the abiotic production of particulate inorganic phosphate associated specifically with iron oxides. Experiments with various organic phosphorus compounds revealed up to 12-fold greater catalytic and adsorption reactivities with iron oxides than with the silicate and aluminosilicate minerals identified in the environmental samples. Remarkably, we obtained dephosphorylation rates by the iron oxides that are within reported enzymatic rates in soils. However, phosphorus cycle models do not yet include a quantitative account of the abiotic evolution of inorganic phosphate from organic phosphorus trapped on iron oxides in environmental matrices. Our findings imply a missing abiotic axiom for organic phosphorus mineralization in the phosphorus cycle.

54 ENVIRONMENTAL SCIENCES↗