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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Data for "Which plant traits increase soil carbon sequestration? Empirical evidence from a long-term poplar genetic diversity trial"

This archive contains all data and code used by the following publication: Field, J. L., Sloan, B. P., Craig, M. E., Calloway, P., Ottinger, S. L., Mead, T., Abramoff, R. Z., Venegas, M. P., Chhetri, H. B., Haiby, K., Kalluri, U. C., Muchero, W., Schadt, C. W., & Mayes, M. A. (2025). Which plant traits increase soil carbon sequestration? Empirical evidence from a long-term poplar genetic diversity trial (p. 2025.02.17.638464). bioRxiv. https://doi.org/10.1101/2025.02.17.638464 Our analysis combined several soil and root data sets collected by Oak Ridge National Laboratory (ORNL) researchers/collaborators from the Clatskanie Poplar Common Garden in Clatskanie, OR by from 2009-2024. The raw data data files are located */02-data/01-raw/* which we harmonized using the codes in */01-codes/01-harmonize-clatskanie-data-pub.qmd*. The final processed data set used in the paper is found at */02-data/02-processed/clatskanie-c-fit-data.csv* and its columns are described in the table below.

Sloan, Brandon [ORNL] (ORCID:0000000316304271)↗
DOE OSTI2020

Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host–pathogen conflict

DNA viruses in the family Poxviridae encode poxin enzymes that degrade the immune second messenger 2'3'-cGAMP to inhibit cGAS-STING immunity in mammalian cells. The closest homologs of poxin exist in the genomes of insect viruses suggesting a key mechanism of cGAS-STING evasion may have evolved outside of mammalian biology. Here we use a biochemical and structural approach to discover a broad family of 369 poxins encoded in diverse viral and animal genomes and define a prominent role for 2'3'-cGAMP cleavage in metazoan host-pathogen conflict. Structures of insect poxins reveal unexpected homology to flavivirus proteases and enable identification of functional self-cleaving poxins in RNA-virus polyproteins. Our data suggest widespread 2'3'-cGAMP signaling in insect antiviral immunity and explain how a family of cGAS-STING evasion enzymes evolved from viral proteases through gain of secondary nuclease activity. Poxin acquisition by poxviruses demonstrates the importance of environmental connections in shaping evolution of mammalian pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Functional and genomic diversity of the sorghum phyllosphere microbiome

A collection of 47 bacteria isolated from the mucilage of aerial roots of energy sorghum is available at the Great Lakes Bioenergy Research Center, Michigan State University, Michigan, USA. We enriched bacteria with putative plant-beneficial phenotypes and included information on phenotypic diversity, taxonomy, and whole genome sequences.

agroecosystems↗
DOE OSTI2020

Polarization diversity optical interface assembly

Examples herein relate to polarization diversity optical interface assemblies including a single mode optical fiber and first and second grating couplers disposed on a substrate. The first and second grating couplers are coupled to first and second waveguides, respectively. The assemblies further includes an optical connector to couple light between the single mode optical fiber and each of the first and second grating couplers. The optical connector includes a ferrule and a walk-off crystal. The ferrule is coupled to a portion of the single mode optical fiber. The walk-off crystal is configured to spatially separate the light into first and second orthogonal polarization modes prior to passing through the respective first and second grating couplers and/or combine the first and second polarization modes of the light prior to passing through the single mode optical fiber.

42 ENGINEERING↗
DOE OSTI2022

Studying Performance Portability of LAMMPS across Diverse GPU-based Platforms

The molecular dynamics simulation software, LAMMPS, utilizes the Kokkos acceleration library to port computation to a diverse set of architectures including those based on GPU accelerators. In addition to Kokkos, LAMMPS contains a vast code base that leverages the CUDA application programming interface using library functions such as cuFFT, CUDA’s fast-fourier transform (FFT) library, and, more recently, also support for AMD’s Heterogeneous Interface for Portability (HIP) that is rapidly growing. While preparing LAMMPS tests for the AMD GPU-based test system precursors to Frontier, we investigated several strategies for accelerating LAMMPS on AMD GPUs, using the AMD Instinct MI100 and MI250X. In this work, we integrated the HIP FFT library, hipFFT, into the particle-particle particle-mesh (PPPM) long-range solver, which allowed the porting of PPPM calculations to the GPUs. Kokkos behavior on the MI100 and MI250X was also investigated through the package kokkos command of LAMMPS, targeting com- munication, memory usage, and particle grid decomposition. The Tersoff, Reax, Lennard-Jones (LJ), EAM, Granular, and PPPM potentials were investigated in this effort, and results from these experiments are provided. The selected potentials were run on Spock (AMD Instinct MI100), Crusher (AMD Instinct MI250X), AFW HPC11 (NVIDIA A100) and Summit (NVIDIA V100), for comparison. Operational roofline models were constructed and analyzed for the Tersoff, Reax, and Lennard-Jones potentials on Crusher and Summit.

Hagerty, Nick↗
DOE OSTI2023

Land-use history, fire regime, and large-mammal herbivory affect deer-preferred plant diversity in longleaf pine woodlands

Since ecological systems often experience multiple disturbances, understanding changes in important ecological interactions, such as plant-herbivore interactions, may require studies capable of disentangling the unique and interactive effects of multiple forms of disturbance. For example, understanding how mammalian herbivores affect plant communities may require understanding how widespread past disturbances, such as agricultural land use, interact with contemporary disturbances, such as prescribed fire. Here, we tested if past agricultural land use and contemporary fire regime modified the effects of mammalian herbivory on focal plant communities by measuring the richness of plant species preferred by deer at 26 longleaf pine woodlands containing paired open and large-mammal exclusion plots. Land-use history significantly affected the community composition of deer-preferred species, and focal species were 8.19 times more likely to be present in post-agricultural sites than non-agricultural sites. Large-mammal herbivory only affected plant species richness in woodlands with low fire frequencies wherein focal species were on average 2.23 times more likely to be present in exclusion plots than open plots. These results suggest that past and present disturbances can mediate contemporary plant-animal interactions and may explain spatial patterns in the intensity of large-mammal herbivory. Our findings also suggest that common management practices, such as use of prescribed burns, may indirectly promote plant species richness by reducing deer herbivory.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Bacterial and fungal growth on fungal necromass and its diverse components: Shared profiles and divergent constraints revealed by high‐throughput phenotyping

1. While fungal necromass is increasingly recognized as a major source of persistent carbon (C) in soils, the relative functional roles of bacteria and fungi in decomposing necromass are not fully resolved, and the processes that select for necromass decomposer communities from the broader soil microbial community are an emerging area of interest. 2. In this study, we characterized the growth of 52 bacterial and 83 fungal strains isolated from necromass and soil on 22 C substrates, including different necromass phenotypes, fungal cell wall polymers, dimers and monomers. 3. We found that the isolation habitat of the strains used in this experiment (necromass vs. soil) had no effect on the substrates they were able to use. Isolates from both microbial domains were able to grow on different labile carbon substrates, polymers and necromass phenotypes. However, fungal growth was most limited by necromass melanin content, while bacterial growth was more limited by the abundance of cell wall polysaccharides. Additionally, overall differences in substrate use between bacteria and fungi were most pronounced on polymer substrates. 4. Collectively, our results suggest that there is substantial functional overlap in necromass substrate use across microbial domains, but some notable differences in bacterial and fungal utilization of cell wall polymers, which can function as a direct energy source or a means of accessing other compounds within necromass. Future studies assessing bacteria and fungi decomposing necromass together rather than in isolation will help to uncover potential physical and chemical interactions within and between these two domains during the decay of this important source of persistent soil C.

dead fungal biomass↗
DOE OSTI2021

Explore the Potential to Formulate Feedstock Blends from Diverse Biomass inputs for Improved Processing Performance at Lower Costs

This work aims to understand the pelleting characteristics of 2-inch top-pine residue blended with switchgrass at high moisture content. The process variables tested are blend moisture content, length-to-diameter (L/D) ratio in the pellet die, and the blend ratio. A flat-die pellet mill was also used in this study. The pine and switchgrass blend ratios that were tested include (1) 25% 2-inch top pine residue with 75% switchgrass; (2) 50% 2-inch top pine residue with 50% switchgrass; and (3) 75% 2-inch top pine residue with 25% switchgrass. The pelleting process conditions tested included the L/D ratio in the pellet die (i.e., 1.5 to 2.6) and the blend moisture content (20 to 30%, w.b.). Analysis of experimental data indicated that blending 25% switchgrass with 75% 2-inch top pine residue and 50% switchgrass with 50% 2-inch top pine residue resulted in pellets with a bulk density of >550 kg/m3 and durability of >95. Optimization of the response surface models developed for process conditions in terms of product properties indicated that a higher L/D ratio of 2.6 and a lower blend-moisture content of 20% (w.b.) maximized bulk density and durability. Higher pine in the blends improved the pellet durability and reduced energy consumption. Tests were also conducted on blends of pine and switchgrass using a pilot scale pellet mill by varying the blend moisture content and compression ratio of the pellet die. Pelleting tests on pure pine and switchgrass and their blends in a pilot scale ring die pellet mill with a throughput of 1 ton/h has indicated pellets with durability >500 kg/m3 and durability in the range of >90 and >95 %. The demonstration of high moisture pelleting of blends of 2- and 6-inch top pine residues and switchgrass blends indicated that good quality pellets with durability >90 % and bulk density of >500 kg/m3 can be produced.

09 BIOMASS FUELS↗
DOE OSTI2021

An Evaluation of the Impact of Glycolate and Glycolate Mitigation on the Defense Waste Processing Facility Recycle Diversion Project Flowsheet

The Savannah River Site (SRS) Defense Waste Processing Facility (DWPF) processes radioactive High Level Waste (HLW) sludge solids from the Concentration, Storage, and Transfer Facilities (CSTF); which includes the SRS Tank Farm and Evaporator facilities, and a concentrated Cs-137 laden stream and a Monosodium Titanate (MST) and sludge solids stream from the SRS Salt Waste Processing Facility (SWPF). The waste is chemically adjusted with acids and reductant (currently with 50 wt.% nitric acid and ~90 wt.% formic acid, but eventually formic acid will be substituted with ~70 wt.% glycolic acid), and frit is added so that a durable, borosilicate glass waste form can be produced when the material is vitrified in the melter. As a result of the evaporation of water during both the melter feed preparation and the melter feed vitrification steps in DWPF, a recycle waste stream is generated, neutralized, and sent back to the CSTF. The recycle waste is a dilute aqueous stream originating from the collection of condensate liquids containing some minor sludge, MST, and frit solids and other waste components resulting from melter feed entrainment during foamover events and transfer of volatile species into the condensate. The recycle stream volume is significant and is expected to approach 3 million gallons per year once SWPF reaches full operation, requiring the use of multiple large CSTF tanks for storage. The recycle waste is currently collected in the SRS Tank Farm and periodically evaporated in the 242-16H (2H) Evaporator to conserve storage space.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Mitochondrial genome diversity across the subphylum Saccharomycotina

Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular diversity and evolution of far-red light-acclimated photosystem I

The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.

ancestral sequence reconstruction↗
DOE OSTI2021

WEST Diversity Panel GBS information (Ferguson et al., 2020)

Genotyping by sequencing information (5,512,653 SNPs on 850 individuals [842 unique]) used in the manuscript "Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions" (Ferguson et al., 2020) DOI:10.1101/2020.11.02.365213.

09 BIOMASS FUELS↗
DOE OSTI2023

Characterization, Structure, and Reactivity of Hydroxyl Groups on Metal‐Oxide Cluster Nodes of Metal–Organic Frameworks: Structural Diversity and Keys to Reactivity and Catalysis

Among the most stable metal–organic frameworks (MOFs) are those incorporating nodes that are metal oxide clusters with frames such as Zr 6 O 8 . This review is a summary of the structure, bonding, and reactivity of MOF node hydroxyl groups, emphasizing those bonded to nodes containing aluminum and zirconium ions. Hydroxyl groups are often present on these nodes, sometimes balancing the charges of the metal ions. They arise during MOF syntheses in aqueous media or in post-synthesis treatments. They are identified with infrared and 1 H nuclear magnetic resonance spectroscopies and characterized by their reactivities with polar compounds such as alcohols. Terminal OH, paired µ 2 -OH, and aqua groups on nodes are catalytic sites in numerous reactions. Relatively unreactive hydroxyl groups (such as isolated µ 2 -OH groups) may replace reactive groups and inhibit catalysis; some node hydroxyl groups (e.g., µ 3 -OH) are mere spectators in catalysis. There are similarities between MOF node hydroxyl groups and those on the surfaces of bulk metal oxides, zeolites, and enzymes, but the comparisons are mostly inexact, and much remains to be understood about MOF node hydroxyl group chemistry. It is posited that understanding and controlling this chemistry will lead to tailored MOFs and improved adsorbents and catalysts.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Resolving Diverse Oxygen Transport Pathways Across Sr‐Doped Lanthanum Ferrite and Metal‐Perovskite Heterostructures

Abstract Perovskite structured transition metal oxides are important technological materials for catalysis and solid oxide fuel cell applications. Their functionality often depends on oxygen diffusivity and mobility through complex oxide heterostructures, which can be significantly impacted by structural and chemical modifications, such as doping. Further, when utilized within electrochemical cells, interfacial reactions with other components (e.g., Ni‐ and Cr‐based alloy electrodes and interconnects) can influence the perovskite's reactivity and ion transport, leading to complex dependencies that are difficult to control in real‐world environments. Here, this work uses isotopic tracers and atom probe tomography to directly visualize oxygen diffusion and transport pathways across perovskite and metal‐perovskite heterostructures, that is, (Ni‐Cr coated) Sr‐doped lanthanum ferrite (La 0.5 Sr 0.5 FeO 3 ; LSFO). Annealing in 18 O 2(g) results in elemental and isotopic redistributions through oxygen exchange (OE) in the LSFO while Ni‐Cr undergoes oxidation via multiple mechanisms and transport pathways. Complementary density functional theory calculations at experimental conditions provide rationale for OE reaction mechanisms and reveal a complex interplay of different thermodynamic and kinetic drivers. These results shed light on the fundamental coupling of defects and oxygen transport in an important class of catalytic materials.

36 MATERIALS SCIENCE↗