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At least 37 records · Page 2

Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (June to October 2020)

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 June to October 2020 at two locations (OBJ1 and OBJ2) near the confluence of the Oh-Be-Joyful Creek and Slate River. The site is one of the field sites in focus for the SLAC National Accelerator Laboratory Groundwater Quality Science Focus Area (SFA) program. Sediment samples from a deep soil pit were collected from 30 cm depth below surface to just above the cobble layer (~190-250 cm depth) at discrete depths every 40 cm for microbial analyses. A total of 35 metagenomes were sequenced through the Joint Genome Institute (JGI) and can be found under Genomes Online Database (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 2848 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. 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.Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗

Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (September 2019)

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 September 2019 at one locations (OBJ1) near the confluence of the Oh-Be-Joyful Creek and Slate River. The site is one of the field sites in focus for the SLAC National Accelerator Laboratory Groundwater Quality Science Focus Area (SFA) program. Sediment samples from a deep soil pit were collected from 50 to 150 cm depth below surface at discrete depths every 20 cm for microbial analyses. A total of 6 metagenomes were sequenced through the Joint Genome Institute (JGI) and can be found under Genomes Online Database (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 2562 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. 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.Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗

Metagenome-assembled genomes from Slate River floodplain sediments near Crested Butte, CO, USA (June 2018)

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 June 2018 at two locations (OBJ1 and OBJ2) near the confluence of the Oh-Be-Joyful Creek and Slate River. The site is one of the field sites in focus for the SLAC National Accelerator Laboratory Groundwater Quality Science Focus Area (SFA) program. Sediment samples from a deep soil pit were collected from 50 to 150 cm depth below surface at discrete depths every 20 cm for microbial analyses. A total of 12 metagenomes were sequenced through the Joint Genome Institute (JGI) and can be found under Genomes Online Database (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 1233 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. 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.Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.

54 ENVIRONMENTAL SCIENCES↗

Synoptic NO3 in Slate River Watershed, Colorado (2022)

The synoptic nitrate (NO3) dataset in the Slate River Watershed, Colorado consists of NO3 data collected at 19 locations three times during the summer of 2022. Stream samples were collected in early summer (early July), mid summer (late August), and late summer (late September). The samples include mainstem, tributary, and point source input water samples. These data were collected to evaluate spatiotemporal variability in stream NO3 during the summer, and evaluate anthropogenic controls on stream NO3 dynamics. This data package contains: (1) a csv of all NO3 samples and (2) a csv of locations for each sampling site. The dataset additionally 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. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > FRESHWATE↗

Study to determine dielectric properties of sandstone, shale, coal, and slate

Triplicate dielectric constant and loss tangent measurements on samples of sandstone, shale, coal, and slate were performed. Each of the three necessary configurations of the coal material was sampled to obtain measurements, with each sample machined parallel to the coal layering orientation. The coal samples were machined perpendicular to the coal layering and measured. They were conditioned at 100% humidity and at room temperature and remeasured; then conditioned in an elevated environment, and remeasured for dielectric properties. The coal data appear to remain relatively constant over the microwave frequency region. At the Ghz frequencies, the relative dielectric constant of coal is slightly higher for the E-field parallel to the layers than for the perpendicular case.

Bassett, H. L.↗

Sulfur Isotropic Studies of Archean Slate and Graywacke from Northern Minnesota: Evidence for the Existence of Sulfate Reducing Bacteria

Sulfur isotopic studies of pyrite from metasediments in the 2.6 b.y. old Deer Lake greenstone sequence, Minnesota, were conducted in order to evaluate the possible importance of sulfate reducing bacteria in sulfide formation. Pyrite occurs as ovules up to 2 cm in diameter within graphitic slates, and as fine disseminations in metagraywacke units. SEM studies indicate the pyrite is framboidal in morphology. Delta notation values of pyrite from the Deer Lake sediments range from -2.3 to 11.1 0/00, with a peak at approximately +2 o/oo. Isotopic data is consistent with either high temperature inorganic reduction of circulating seawater sulfate, or low temperature bacterial reduction. However, the lack of sulfide bands or massive occurrences in the sediments, the restriction of pyrite mineralization to the sediments, and the absence of evidence for hot spring activity suggest that a diagenetic origin of pyrite is more feasible. Sulfide in such an environment would be produced principally by the action of sulfate reducing bacteria.

Ripley, E. M.↗

AIS Spectra for Stressed and Unstressed Plant Communities in the Carolina Slate Belt

Airborne imaging spectrometer (AIS) data were collected over a number of derelict heavy metal mine sites in the Carolina slate belt of North Carolina. A 32 channel (1156 to 1456 nm) data set was acquired in October, 1983 at the time of peak fall foliage display, and a 128 channel (1220 to 2420) data set was acquired near the end of the spring leaf flush in May, 1984. Spectral curves were extracted from the AIS data for differing ground cover types (e.g., pine forests, mixed deciduous forests, mine sites, and pastures). Variation in the width of an absorption feature located at approximately 1190 nm has been related to differences in forest type. Small differences in the location and shape of features in the near infrared plateau (1156 to 1300 nm) and the region 2000 to 2420 nm have yet to be evaluated. Because these variations were subtle, and because atmospheric effects were apparent in the data, high priority must be assigned to devising a means of removing atmospheric effects from AIS spectra.

Wickland, D. E.↗

Remote sensing of stressed vegetation in the Carolina slate belt

Remote sensing techniques have been used to detect stress in vegetation, but they have not been very successful for identifying which environmental factors cause the vegetation to appear stressed. Controlled comparisons of spectral characteristics of plant communities experiencing known combinations of stresses were designed to examine this problem. Landsat TM, NS-001 TMS, CIR, and AIS imagery was acquired for six stressed areas in the Carolina slate belt. Preliminary results indicated that the areas of stressed vegetation were identifiable, and that the stressed communities appeared to be undergoing early fall leaf senescence. The AIS data seemed to have the greatest potential for identifying differences among plant community spectra, but calibration will be necessary before these differences can be evaluated.

Wickland, D. E.↗

New Constraints on the Slate Islands Impact Structure, Ontario, Canada

The Slate Islands in northern Lake Superior represent the eroded remains of a complex impact crater, originally approximately 32 km in diameter. New field studies there reveal allogenic crater fill deposits along the eastern and northern portions of the islands indicating that this 500-800 Ma impact structure is not as heavily eroded as previously thought. Near the crater center, on the western side or Patterson Island, massive blocks of target rocks, enclosed within a matrix of fine-grained polymict breccia, record the extensive deformation associated with the central uplift. Shatter cones are a common structural feature on the islands and range from less than 3 cm to over 10 m in length. Although shatter cones are powerful tools for recognizing and analyzing eroded impact craters, their origin remains poorly constrained.

Sharpton, Virgil L.↗

Slate Islands, Lake Superior, Canada: A mid-size, Complex Impact Structure

The target rocks of the 30-32-km diameter Slate Islands impact structure in northern Lake Superior, Canada, are Archean supracrustal and igneous rocks and supracrustal Proterozoic rocks. Shatter cones, pseudotachylites, impact glasses, and microscopic shock metamorphic features were formed during the contact and compression phase of the impact process, followed, during excavation and central uplift, by polymict, clastic matrix breccias in the uplifted target, and by allogenic fall-back breccias (suevite and bunte breccia). Monomict, autoclastic breccias were mainly observed on Mortimer Island and the other outlying islands of the archipelago and were probably generated relatively late in the impact process (central uplift and/or crater modification). The frequency of low index planar shock metamorphic features in quartz was correlated with results from shock experiments to estimate shock pressures experienced by the target rocks. The resulting shock attenuation plan across the archipelago is irregular, probably because the shock wave did not expand from a point or spherical source, and because of the destruction of an originally more regular shock attenuation plan during the central uplift and crater modification stages of the impact process. No impact melt rock bodies have been positively identified on the islands. An impact melt may be present in the annular trough around the islands, though and-based on a weighted mixture of target rocks-may have an intermediate-mafic composition. No such impact melt was found on the archipelago. An Ar-40-Ar-39 release spectrum of a pseudotachylite provides an age of about 436 Ma for the impact structure, substantiating age constraints based on various stratigraphic considerations.

Dressler, B. O.↗

Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that contains the system and other systems evolves with the CAS as well. The effects of the emerging adaptation and co-evolution are difficult to capture with only combined mathematical and computational experimentation. Therefore, an ab initio flight simulation environment must accommodate individual vehicles, groups of self-organizing vehicles, and large-scale infrastructure behavior. Inspired by Massively Multiplayer Online Role Playing Games (MMORPG) and Serious Gaming, the proposed ab initio simulation environment is similar to online gaming environments in which player participants interact with each other, affect their environment, and expect the simulation to persist and change regardless of any individual player's active participation.

Allen, B. Danette↗

Lithological controls on soil geochemistry and clay mineralogy across Spodosols in the coastal temperate rainforest of southeast Alaska

The interaction of similar soil forming factors with different parent materials determines soil chemical weathering, influencing soil processes and properties. In the coastal temperate rainforests of southeast Alaska, Spodosols is the dominant soil order in well-drained parent materials regardless of the lithology. Yet, the role of lithology on chemical weathering, base cation depletion, and mineral transformation during pedogenesis remains elusive. Here, we established a lithosequence comprised of soils derived from tonalite, phyllite, slate, and metavolcanic rocks to test the hypothesis that despite the soils in southeast Alaska presenting similar taxonomy and morphology, the influence of lithology in chemical weathering intensity and mineralogy can be detected. We evaluated physicochemical properties, clay mineralogy, Fe-Al oxides, chemical weathering, and elemental mass balance on eleven Spodosols sampled along the lithosequence. We also propose a new weathering index, the Weathering Index for Spodosols (WISP), suitable to evaluate the weathering degree of soils with Al mobility and base-rich parent materials. This index fills a gap in traditional weathering indices that uses Al as an immobile element and/or does not evaluate the leaching of main base cations. We found the pedons across the lithosequence expressed similar physicochemical properties, with predominantly thick profiles, presenting andic properties, relatively thick spodic horizons, and thin E horizons. Podzolization imposed similar mineral transformation trends, mainly dissolution of chlorite, mica alteration to interstratified mica-vermiculite, and formation of smectite in E horizons. Kaolinite was detected in the soils from all lithologies, but only in trace amounts in phyllite soils. Fe oxides depth distribution was similar but with a higher concentration in the slate (44.5 ± 4.2 g/kg), followed by metavolcanic (31.6 ± 4.0 g/kg), phyllite (27.9 ± 3.8 g/kg), and tonalite soils (19.9 ± 5.7 g/kg) and predominantly as organometallic complexes (extracted by Na-pyrophosphate). The stronger weathering of chlorite and mica in the E horizons was reflected in larger losses of Mg and K, while Ca and Na were more depleted in the spodic horizons, suggesting plagioclase weathering. Slate soils were the most depleted in base cations, followed by phyllite, tonalite, and metavolcanic soils. The more depleted status of slate soils was supported by the higher WISP values (WISP = 62), followed by phyllite (WISP = 55), tonalite (WISP = 53), and metavolcanic soils (WISP = 45). Our results demonstrated that lithology controlled elemental depletion intensities, Fe oxide concentrations, and partially the clay fraction mineralogy in addition to podzolization acting as a dominant pedogenic process across all sites. These findings advance our understanding of the role of lithology on soil mineralogy/geochemistry that impacts critical soil functions, such as the soil carbon cycle, elemental fluxes, organo-mineral interactions, and solid-solution reactions.

54 ENVIRONMENTAL SCIENCES↗

Tonopah Test Range Air Monitoring: CY2020 Meteorological, Radiological, and Wind Transported Particulate Observations

In 1963, the U.S. Department of Energy (DOE) (formerly the Atomic Energy Commission [AEC]), implemented Operation Roller Coaster on the Tonopah Test Range (TTR) and an adjacent area of the Nevada Test and Training Range (NTTR) (formerly the Nellis Air Force Range). This operation resulted in radionuclide-contaminated soils at the Double Tracks site and Clean Slate I, II, and III sites. This report documents observations made during ongoing monitoring of radiological, meteorological, and dust conditions at stations installed adjacent to the Clean Slate sites and at the TTR Sandia National Laboratories (SNL) Range Operations Center (ROC). The monitoring effort supports the DOE Office of Legacy Management in its stewardship of the Clean Slate sites as part of their mission to protect human health and the environment at sites of former nuclear device development and testing. Specific monitoring objectives include determining if wind blowing across the Clean Slate sites is transporting particles of radionuclide-contaminated soil beyond the physical and administrative boundaries of the sites, and providing information for planning long-term stewardship of the sites.

54 ENVIRONMENTAL SCIENCES↗

A graphics processing unit accelerated sparse direct solver and preconditioner with block low rank compression

We present the GPU implementation efforts and challenges of the sparse solver package STRUMPACK. The code is made publicly available on github with a permissive BSD license. STRUMPACK implements an approximate multifrontal solver, a sparse LU factorization which makes use of compression methods to accelerate time to solution and reduce memory usage. Multiple compression schemes based on rank-structured and hierarchical matrix approximations are supported, including hierarchically semi-separable, hierarchically off-diagonal butterfly, and block low rank. Here, in this paper, we present the GPU implementation of the block low rank (BLR) compression method within a multifrontal solver. Our GPU implementation relies on highly optimized vendor libraries such as cuBLAS and cuSOLVER for NVIDIA GPUs, rocBLAS and rocSOLVER for AMD GPUs and the Intel oneAPI Math Kernel Library (oneMKL) for Intel GPUs. Additionally, we rely on external open source libraries such as SLATE (Software for Linear Algebra Targeting Exascale), MAGMA (Matrix Algebra on GPU and Multi-core Architectures), and KBLAS (KAUST BLAS). SLATE is used as a GPU-capable ScaLAPACK replacement. From MAGMA we use variable sized batched dense linear algebra operations such as GEMM, TRSM and LU with partial pivoting. KBLAS provides efficient (batched) low rank matrix compression for NVIDIA GPUs using an adaptive randomized sampling scheme. The resulting sparse solver and preconditioner runs on NVIDIA, AMD and Intel GPUs. Interfaces are available from PETSc, Trilinos and MFEM, or the solver can be used directly in user code. We report results for a range of benchmark applications, using the Perlmutter system from NERSC, Frontier from ORNL, and Aurora from ALCF. For a high frequency wave equation on a regular mesh, using 32 Perlmutter compute nodes, the factorization phase of the exact GPU solver is about 6.5× faster compared to the CPU-only solver. The BLR-enabled GPU solver is about 13.8× faster than the CPU exact solver. For a collection of SuiteSparse matrices, the STRUMPACK exact factorization on a single GPU is on average 1.9× faster than NVIDIA’s cuDSS solver.

97 MATHEMATICS AND COMPUTING↗