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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2020

Bulk density, grain size, carbon, and nitrogen content of floodplain fine sediment along the East River, Colorado collected from 2014 to 2017

The dataset is comprised of grain size, bulk density, carbon and nitrogen content of soils sampled on the floodplain of the East River 4 to 11 km downstream of Gothic, CO near Crested Butte. This dataset was collected to characterize the sedimentological properties and carbon inventory of the East River floodplain. The data help quantify the flux and storage of sediment and carbon between the East River and the alluvial floodplain bounding the river. The samples were collected between 2014 and 2017. The soil samples come from a total of 156 locations and were sampled in the upper 40 to 60 cm of the floodplain and in abandoned channel segments or oxbows. Not all samples were analyzed for all properties, but 26 samples were analyzed for bulk density, full particle size distribution, carbon, and nitrogen content. An additional 48 samples were analyzed for particle size fraction greater than and less than 2 mm and total organic content determined by loss on ignition. The dataset is comprised of a total of six separate data files based on the sample type and analysis and another file lists the sample identifications and locations of samples with a complete suite of analyses.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Aligned FTICR-MS, Respiration, and Biochemical Transformation Data from Columbia River Sediment Incubations Associated with: “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism”

Columbia River hyporheic zone sediments from the Hanford Site 300 Area in eastern Washington were incubated in a full factorial design with different organic matter (OM) amendments. The aim of the experiment was to test the influence of OM thermodynamics on aerobic respiration across different organic carbon pools and concentrations. This dataset is comprised of (1) a csv with high resolution characterization of dissolved organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory), (2) a csv with sample IDs, replicates, amendments, dissolved oxygen (DO) measurements, and sampling time points, (3) a csv with sample IDs, replicates, respiration rates, FTICR summary metrics, and relative abundance of chemical classes; and (4) a csv with the number of chemical transformations in each sample replicate (microcosm). The data are associated with the publication “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism” published in ES&T Letters (Garayburu-Caruso et al., 2020). Please use the data package’s DOI to cite the data package. We ask that you acknowledge the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Subsurface Biogeochemical Research (SBR) program when using the data. All data are free to be used for any purpose, such as for manuscripts, presentations, and grant proposals. There is no obligation to include data package authors as co-authors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Sulfur x-ray absorption spectroscopy data from bedrock shale, soil, and floodplain sediment from the East River, Colorado watershed

This dataset includes sulfur x-ray absorption near edge spectroscopy (XANES) data collected on solid samples as a part of the Watershed Function Scientific Focus Area (SFA) located in the Upper Colorado River Basin. The data were collected in order to investigate the speciation of sulfur and degree of shale weathering in solid samples across the watershed and their impact on riverine export of sulfate. Solid samples, including shale, hillslope soil, and floodplain sediment samples collected in 2016-2018, were analyzed by bulk XANES. Density fractions of hillslope soil, including a light fraction representing particulate organic matter and a heavy fraction representing minerals are also analyzed by bulk XANES. Micro-focused XANES on a weathered shale sample (PLM6, 2.7 m) was also performed. Sample locations are included in the 'sample meta data.csv' file, and XANES data for each sample type are included in csv files.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

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

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

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

WHONDRS 2016 Sediment Organic Matter Characterization Data from Streams across HJ Andrews Experimental Forest, Oregon

This dataset supports a broader synoptic effort to map morphological, hydrological, chemical, and biological conditions across a fifth-order mountain stream network. Samples were generated through a collaborative synoptic sampling effort in 2016. The dataset provides sediment Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) from 60 sites across the HJ Andrews Experimental Forest, Oregon (https://andrewsforest.oregonstate.edu). Related data were collected as part of the event and were published separately in collaboration with other team members. The data are available at http://www.hydroshare.org/resource/ea6c0832885a46c3939e7bb22e48e754 and are described within https://doi.org/10.5194/essd-11-1567-2019 (Ward et al., 2019). The hydroshare data package contains processed FTICR-MS data from the samples included in this data package. The data were processed via Formultitude (previously called Formularity; https://github.com/PNNL-Comp-Mass-Spec/Formultitude). However, we have re-processed the data using Core-MS and included it in this data package. Additional related data collected in 2025 from a similar effort can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3023310 and http://www.hydroshare.org/resource/b274c4a234bf4b12b7cb8a54a696c629. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) a folder of sample data; (2) data dictionary; (3) file-level metadata; (4); (5) coordinates; and (6) readme. The sample data subfolder contains 12 Tesla (12T) FTICR-MS data. This folder contains the processed data and three subfolders, one containing the .xml files, one containing the CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .Rmd, .py, .cal, or .json.

Biogeochemistry↗
DOE OSTI2020

Data Report: X-Ray Diffraction of Sediments from Green Canyon Block 955, Gulf of Mexico

We performed 18 X-ray diffraction (XRD) measurements on sediment samples acquired at Holes H002 (6 samples) and H005 (12 samples) during the UT-GOM2-1 Expedition in Green Canyon Block 955, in the northern Gulf of Mexico. Results indicate a predominance of quartz, with significant proportions of alkali feldspar and carbonate, and minor amounts of amphibole, micas, and clays.

03 NATURAL GAS↗
DOE OSTI2020

Data Report: High-Resolution Microscopy Images of Sediments from Green Canyon Block 955, Gulf of Mexico

We took Leica microscopy images of sediment samples acquired at Holes H002 (4 samples) and H005 (1 sample) during the UT-GOM2-1 Expedition in Green Canyon Block 955, in the northern Gulf of Mexico. A total of 37 images were acquired. The images document a prevalence of spherical conchoidal minerals, cleavage planes typical of feldspar or mica, and black fragmented minerals which stand out from the surrounding matrix. Drilling mud intrusion is thought to contribute to a grey metallic matrix observed across multiple samples.

03 NATURAL GAS↗
DOE OSTI2021

Combined Technologies for In Situ Remediation of Tc-99 and U in Subsurface Sediments

In this study, combinations of chemical remedies were tested in bench-scale batch experiments to evaluate a two-step reduction-sequestration approach to effectively stabilize high concentrations of inorganic contaminant mixtures. Bench tests simulated contaminant and geochemical conditions of a perched aquifer located within the Central Plateau at the Hanford Site, located in southeastern Washington State (USA). Pairwise combinations of a reductant [e.g., zero valent iron, sulfur modified iron (SMI), or calcium polysulfide] and a sequestering agent [e.g., calcite, apatite, or dilute alkaline solution (e.g., NaOH)] were evaluated for immobilization and stabilization of technetium (Tc) (50,000 pCi/L), uranium (U) (150 mg/L), and nitrate (NO 3 ) (200 mg/L) in high ionic strength groundwater. The results of these batch studies demonstrated that reduction by SMI and sequestration in apatite or calcite are the most effective combination for these contaminant mixtures and conditions. Aqueous concentrations of Tc and U decreased by 95.6% ± 2.5% and 101.1% ± 5.2%, respectively, with SMI-apatite and 98.3% ± 0.0% and 101.2% ± 5.2%, respectively, with SMI-calcite. Sequential extractions showed that sequestered contaminants had limited capacity for re-oxidation; in fact, less than 10% of immobilized Tc and U was recovered by selective extraction of mineral phases most susceptible to oxidation. In addition, X-ray absorption near edge structure analysis of the sediment samples treated with SMI-calcite showed the presence of only U(IV), while both U(IV) and U(VI) were present in the SMI apatite combination [ratio of 0.43 U(IV):0.59 U(VI)].This study describes preliminary results that a two-step approach for stabilizing contaminant mixtures of long-lived radionuclides can be effective at reducing contaminant fluxes to groundwater from vadose and perched water zones.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Effects of Surface Water Fluctuations and Sediment Movement on Hyporheic Zone Biogeochemistry and Microbial Communities

The hyporheic zone (HZ) is the region beneath and adjacent to streams, rivers, and riverine estuaries where the bidirectional exchange of groundwater (GW) and surface water (SW) occurs. The HZ is an integral component of watersheds, a biologically-active zone providing critical control of SW quality and aquatic life. Much prior work has investigated microbially-mediated biogeochemical reactions in the HZ, mainly from a steady-state perspective. Yet key unique aspects of the HZ include 1) proximity to SW fluctuations (e.g., storms, dam operations) which cyclically drive DOC and DO into the bed and banks creating biogeochemical “hot moments,” and 2) continually shifting surface sediment. Both of these controls should substantially influence microbial communities, yet remain poorly understood, and a mechanistic predictive framework does not exist.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Identifying Hot Spots and Hot Moments of Metabolic Activity in Salt Marsh Sediments through BONCAT-FISH Microscale Mapping (Final Technical Report)

Understanding the biogeography and timing of microbial metabolic activity is a key priority for microbial ecologists. With such knowledge, the cumulative biogeochemical contributions of microbial communities become more predictable, and our ability to both understand the effects of environmental change on microbial activity and build synthetic communities with desired functions will increase substantially. In this project, we advanced this broad, ambitious goal in two substantial ways: we developed a multiplexed Fluorescence In Situ Hybridization (FISH) approach that links microbial identity with metabolic function, and we established a novel Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT) technique that can resolve the timing of anabolic activity, providing new resolution of when microbial constituents are growing. We deployed both of these techniques in multiple environmental settings to demonstrate their versatility. At the Little Sippewissett Salt Marsh, we combined a novel dual-BONCAT technique with fluorescence activated cell sorting to determine which population of cells was metabolically active during the day and which was active during the night. We found that Methylobacterium was active during daylight hours, potentially feeding on carbon-rich molecules released from plant roots. Sulfur-cycling microbes dominate the population active during the dark night-time hours. Overall, the work conducted under the auspices of this project developed two promising new techniques for identifying the “hot spots” and “hot moments” of microbial activity in complex communities with taxonomic and functional resolution. We focused largely on a salt marsh sediment context, but are confident that microbial ecologists seeking to understand the microbial role in biogeochemical cycles in a wide range of settings will find our newly developed techniques useful in future work.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Data From: Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO2 and N-2, Journal of Geophysical Research-Biogeosciences

This data package contains pumping data (.txt), parameter matrices, and R code (.R, .RData) to perform bootstrapping for parameter selection for the bioclogging model development. The pumping data were collected from the Russian River Riverbank Filtration site located in Sonoma County, California from 2010-2017 from three riverbank collection wells located alongside the study site. The pumping data is directly correlated with water table oscillations, so the code performs these correlations and simulates stochastic versions of water table oscillations. See Metadata Description.pdf for full details on dataset production. This dataset must be used with the R programming language. This dataset and R code is associated with the publication "Influence of Hydrological Perturbations and Riverbed Sediment Characteristics on Hyporheic Zone Respiration of CO2 and N-2"This research was supported by the Jane Lewis Fellowship from the University of California, Berkeley, the Sonoma County Water Agency (SCWA), the Roy G. Post Foundation Scholarship, the U.S. Department of Energy, Office of Science Graduate Student Research (SCGSR) Program, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award DE-AC02-05CH11231, and the UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Different methods of estimating riverbed sediment grain size diverge at the basin scale

Introduction: The distribution of sediment grain size in streams and rivers is often quantified by the median grain size (D50), a key metric for understanding and predicting hydrologic and biogeochemical function of streams and rivers. Manual D50 measurements are time-consuming and ignore larger grains, while approaches to model D50 based on catchment characteristics may over-generalize and miss site-scale heterogeneity. Machine learning-enabled object detection methods like You Only Look Once (YOLO) provides an alternative that enables estimation of D50 that is faster than manual measurements and more site-specific than predictions based on catchment characteristics. Methods: To understand the potential role of object detection methods for improving understanding of D50, we compared D50 estimates made manually, predicted from catchment characteristics, and using a YOLO-enabled approach across the Yakima River Basin. Results: We found distinct differences between methods for D50 averages and variability, and relationships between D50 estimates and basin characteristics. Discussion: We discuss the advantages and limitations of object detection methods versus current methods, and explore potential future directions to combine D50 methods to better estimate spatiotemporal variation of D50, and improve incorporation into basin-scale models.

grain size distribution↗
DOE OSTI2021

Cooling Delays from Iron Sedimentation and Iron Inner Cores in White Dwarfs

Do white dwarfs have inner cores made of iron? Neutron-rich nuclei like 56 Fe experience a net gravitational force and sediment toward the core. Using new phase diagrams and molecular dynamics simulations, we show that 56 Fe should separate into mesoscopic Fe-rich crystallites due to its large charge relative to the background. At solar abundances, these crystallites rapidly precipitate and form an inner core of order 100 km and 10 -3 M ⊙ that may be detectable with asteroseismology. Associated cooling delays could be up to a Gyr for low-mass white dwarfs but are only ~0.1 Gyr for massive white dwarfs, so while this mechanism may contribute to the Q-branch the heating is insufficient to fully explain it.

79 ASTRONOMY AND ASTROPHYSICS↗