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NASA NTRS2018

CEOS Virtual Data Repositories for WGISS Data Assets

The Committee on Earth Observation Satellites (CEOS), established in 1984 to coordinate civil space-borne observations of the Earth, through its Working Group on Information Systems and Services (WGISS) has been working towards aligning data repositories held by each of the member international agencies. The CEOS agencies hold a vast amount of earth observation data across science domains. WGISS has been working to agree on community standards for data and information discovery and to increase the interoperability and alignment among the member data repositories.

Enloe, Yonsook↗

NASA NTRS2019

GeneLab: A Systems Biology Platform for Omics Analysis

NASA GeneLab is an open-access repository for omics datasets generated by biological experiments conducted in space or experiments relevant to spaceflight (e.g. simulated cosmic radiation, simulated microgravity, bed rest studies). The GeneLab Data Systems (GLDS) version 4.0 will be available on October 1st 2019, and will provide the latest in terms of professional state-of-the-art bioinformatics platform for the space biology and radiation community to upload their data into an omics data commons, to process their data with vetted standard workflows and to compare to existing analyses. Started in 2015 as a repository designed to archive omics data from space experiments, GeneLab has expanded its scope to all ionizing radiation omics experiments conducted on the ground and has put considerable effort in providing carefully characterized radiation metadata on all dataset. GeneLab is also providing processed data derived from the raw data covering a large spectrum of omics (genome, epigenome, transcriptome, epitranscriptome, proteome, metabolome) to help users explore important questions: 1) Which genes or proteins are expressed differently in space for various living organisms? 2) What specific DNA mutations or epigenetic changes happen in space or after exposure to ionizing radiation? and 3) How does genetics affect these responses? Processed data available on GeneLab are derived by standard data analysis workflows vetted by hundreds of scientists who volunteered to join one of the four GeneLab Analysis Working Groups (Animal AWG, Plant AWG, Microbe AWG, Multi-Omics AWG). In this presentation, we will discuss how to bridge the gap between irradiation studies performed on earth and biological experiments conducted in space since the early 1990's. We will discuss how radiation dosimetry was estimated for datasets derived from samples collected during the Space Shuttle era or on the International Space Station. Finally, we will address future strategies regarding dose monitoring in future missions into space, inter-agency efforts to unify data under one umbrella, and knowledge dissemination across the radiation research community and the space biology community.

open-science↗

NASA NTRS2019

NASA GeneLab Space Omics Database: Expanding from Space to Ionizing Radiation Data on the Ground

NASA GeneLab is an open-access repository for omics datasets generated by biological experiments conducted in space or ground experiments relevant to spaceflight (e.g. simulated cosmic radiation, simulated microgravity, bed rest studies). The GeneLab Data Systems (GLDS) version 4.0 will be available on October 1st 2019, and will provide a state-of-the-art bioinformatics platform for the space biology and radiation communities to upload their data into an omics data commons, to process their data with vetted standard workflows and to compare with existing analyses. Started in 2015 as a repository designed to archive omics data from space experiments, GeneLab has expanded its scope to all ionizing radiation omics experiments conducted on the ground and has put considerable effort in providing carefully characterized radiation metadata on all datasets. GeneLab is also providing processed data derived from the raw data covering a large spectrum of omics (genome, epigenome, transcriptome, epitranscriptome, proteome, metabolome) to help users explore important questions: 1) Which genes or proteins are expressed differently in space for various living organisms? 2) What specific DNA mutations or epigenetic changes happen in space or after exposure to ionizing radiation? and 3) How does genetics affect these responses? Processed data available on GeneLab are derived by standard data analysis workflows vetted by hundreds of scientists who volunteered to join one of the four GeneLab Analysis Working Groups (Animal AWG, Plant AWG, Microbe AWG, Multi-Omics AWG). In this presentation, we will discuss how to bridge the gap between irradiation studies performed on earth and biological experiments conducted in space since the early 1990's. We will discuss how radiation dosimetry was estimated for datasets derived from samples collected during the Space Shuttle era on the International Space Station and on other orbiting platforms. Finally, we will address future strategies regarding dose monitoring in future missions into space, inter-agency efforts to unify data under one umbrella, and knowledge dissemination across the radiation research community and the space biology community.

open-science↗

NASA NTRS2009

Expolanet community report

The Exoplanet Community Report surveys the rapidly emerging field of exoplanet science. This survey is intended to assess the state of the art and also support the Committee and panels of the 2010 astronomy and astrophysics decadal survey, organized by the National Research Council of the National Academy of Sciences. Each of the eight chapters in this volume summarizes the issues, scientific potential, state-of-the-art, and technology needed for the respective observational technique. Our tempered optimism in each area springs from our belief that exoplanet science is the most exciting new area in astrophysics, for scientists and the public alike.

Unwin, S. C.↗

NASA NTRS2006

The SIM PlanetQuest science program

SIM PlanetQuest (hereafter, just SIM) is a NASA mission to measure the angular positions of stars with unprecedented accuracy. We outline the main astrophysical science programs planned for SIM, and related opportunities for community participation. We focus especially on SIM’s ability to detect exoplanets as small as the Earth around nearby stars. The planned synergy between SIM and other planet-finding missions including Kepler and GAIA, and planetcharacterizing missions including the James Webb Space Telescope (JWST), Terrestrial Planet Finder – Coronagraph (TPF-C), and Terrestrial Planet Finder – Interferometer (TPF-I), is a key element in NASA’s Navigator Program to find Earth-like planets, determine their habitability, and search for signs of life in the universe. SIM's technology development is now complete and the project is proceeding towards a launch early next decade.

Marr, James C. IV↗

NASA NTRS2021

NASA's Surface Biology and Geology Concept Study: Status and Next Steps

The National Academies Decadal Survey for Earth Science recommended that NASA pursue global imaging spectroscopy and thermal infrared measurements in the coming decade [1]. Both measurements would offer repeat coverage on approximately five-day to biweekly cadence, with comprehensive coverage of the globe's coastal and terrestrial area. This would be an unprecedented volume of data with the potential to transform remote sensing practice. To address this recommendation, NASA has sponsored a concept study by NASA research centers and associated university partners (https://sbg.jpl.nasa.gov). This study is determining a family of architecture options - including launch vehicle, spacecraft, instrument, and suborbital components - that could address the Decadal Survey objectives. The architecture study is driven by science needs and builds on input of the research community. As of this writing, the study is entering a phase in which a large field of system possibilities is pared down to a representative handful for an ultimate decision by NASA.

Imaging Spectroscopy↗

DOE OSTI2022

Real-World Experiences Adopting Workflows at Exascale on the ExaAM Project

The purpose of this study is to discuss the experiential lessons associated with adopting scientific workflows in the Exascale Additive Manufacturing project (ExaAM) through the lens of Perceived Characteristic of Innovation (PCI). Besides the implementation, the factors we considered critical to the adoption of the workflow are provenance, sustainable automation, implementation challenges, and integration/compatibility challenges. Through conversations and interviews among the program managers, project leads, and software engineers, we have developed critical insight and strategies to overcome the obstacles and augment the successful adoption and long-term use of these workflows in ExaAM and beyond. We hope our work will pave the way for others in the research community to develop and use workflows in their respective science domains.

Malviya, Addi Thakur↗

DOE OSTI2020

Reducing host DNA contamination in 16S rRNA gene surveys of anthozoan microbiomes using PNA clamps

Efforts to study the microbial communities associated with corals can be limited by inefficiencies in the sequencing process due to high levels of host amplification by universal bacterial 16S rRNA gene primers. Here, we develop an inexpensive peptide nucleic acid (PNA) clamp that binds to a target sequence of host DNA during PCR and blocks amplification. We then test the ability of this PNA clamp to mitigate host contamination and increase overall microbial sequence coverage on samples from three coral species: the gorgonians Eunicea flexuosa and Gorgonia ventalina, and the scleractinian Porites panamensis. The 20-bp PNA clamp was designed using DNA from E. flexuosa. Adding the PNA clamp during PCR increased the percentage of microbial reads in E. flexuosa samples more than 11-fold. Microbial community diversity was similar without- and with-PNA clamps, as were the relative frequencies of the ten most abundant ASVs (amplicon sequence variants), indicating that the clamps successfully blocked host DNA amplification while simultaneously increasing microbial DNA amplification proportionally across the most abundant taxa. The reduction of E. flexuosa DNA correlated with an increase in the abundance of rarer taxa. The clamp also increased the average percentage of microbial reads in another gorgonian, G. ventalina, by 8.6-fold without altering the microbial community beta diversity, and in a distantly related scleractinian coral, P. panamensis, by nearly double. The reduction of host contamination correlated with the number of nucleotide mismatches between the host amplicon and the PNA clamp. The PNA clamp costs as little as $0.48 per sample, making it an efficient and cost-effective solution to increase microbial sequence coverage for high-throughput sequencing of coral microbial communities.

16S rRNA gene sequencing↗

DOE OSTI2021

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants ( Panicum virgatum ) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Description and Demonstration of the Coupled Community Earth System Model v2 – Community Ice Sheet Model v2 (CESM2‐CISM2)

Abstract Earth system/ice‐sheet coupling is an area of recent, major Earth System Model (ESM) development. This work occurs at the intersection of glaciology and climate science and is motivated by a need for robust projections of sea‐level rise. The Community Ice Sheet Model version 2 (CISM2) is the newest component model of the Community Earth System Model version 2 (CESM2). This study describes the coupling and novel capabilities of the model, including: (1) an advanced energy‐balance‐based surface mass balance calculation in the land component with downscaling via elevation classes; (2) a closed freshwater budget from ice sheet to the ocean from surface runoff, basal melting, and ice discharge; (3) dynamic land surface types; and (4) dynamic atmospheric topography. The Earth system/ice‐sheet coupling is demonstrated in a simulation with an evolving Greenland Ice Sheet (GrIS) under an idealized high CO 2 scenario. The model simulates a large expansion of ablation areas (where surface ablation exceeds snow accumulation) and a large increase in surface runoff. This results in an elevated freshwater flux to the ocean, as well as thinning of the ice sheet and area retreat. These GrIS changes result in reduced Greenland surface albedo, changes in the sign and magnitude of sensible and latent heat fluxes, and modified surface roughness and overall ice sheet topography. Representation of these couplings between climate and ice sheets is key for the simulation of ice and climate interactions.

Muntjewerf, Laura↗

DOE OSTI2020

Community-Driven Metadata Standards for Agricultural Microbiome Research

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Emergency Management of Tomorrow Research – Task 3B Research and Development Community Awareness: Eliciting Emergency Management Stakeholder Input

The Department of Homeland Security (DHS) Science and Technology Directorate (S&T) is partnering with Pacific Northwest National Laboratory (PNNL) to execute the Emergency Management (EM) of Tomorrow Research (EMOTR) program to identify current EM research, elicit capability needs from EM practitioners, and identify where technology, such as artificial intelligence (AI), may benefit the future of EM and emergency operations centers. This report details the methodology, analysis, and insights of interviews and focus groups conducted as part of the task to elicit stakeholder input.

99 GENERAL AND MISCELLANEOUS↗

NASA NTRS2022

U.S. Space-Based Earth Observations in 21 st -Century Science Diplomacy

Science diplomacy can take the form of cooperation or competition. As the global community faces new challenges, ranging from dangerous changes in Earth’s climate to increasingly coercive authoritarian regimes, civil space-based Earth observations offer the United States unique opportunities to employ science diplomacy in cooperation and competition. Investments in space-based Earth observations will be a great benefit as the United States orients itself to the diplomatic challenges of the 21st century.

Ian G. Brosnan↗

DOE OSTI2021

Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages

Cryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.). A total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The “Candidatus Jiangella antarctica” has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa. Our findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Models and Methods for Sparse (Hyper)Network Science in Business, Industry, and Government

The authors are hosting an AMS sponsored Mathematics Research Community (MRC) focusing on two themes that have garnered intense attention in network models of complex relational data: (1) how to faithfully model multi-way relations in hypergraphs, rather than only pairwise interactions in graphs; and (2) challenges posed by modelling networks with extreme sparsity. Here we introduce and explore these two themes and their challenges. In this work, we hope to generate interest from researchers in pure and applied mathematics and computer science.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

DoE as a “Digital Innovation” Sponsor of the WCRP OSC2023 (Final Report)

The WCRP Open Science Conference (https://wcrp-osc2023.org/) was a once-in-a-decade opportunity to jointly explore the transformative actions urgently needed to ensure a sustainable future. Held in Kigali, Rwanda on October 23 -27, 2023, it showcased advances in climate science, helped identify gaps and opportunities, and provided a forum for communities to jointly develop future activities. Scientists, practitioners, politicians, policy makers, intergovernmental agencies and NGOs showcased their work, learned from each other, and explored new ways to work together.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Report on New and Upgraded National User Facilities in Basic Energy Sciences

On December 1, 2023, the Director of the of the Office of Science (SC) charged all the Department of Energy Office of Science Federal Advisory Committees to respond to look toward the scientific horizon and identify what new or upgraded facilities will best serve the SC community needs in the next ten years (2024-2034). This report by the Basic Energy Sciences Advisory Committee (BESAC) assess facilities for the Basic Energy Sciences (BES) program.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2024

Report of the FESAC Facilities Construction Projects Subcommittee

On December 1, 2023, the Director of the of the Office of Science (SC) charged all the Department of Energy Office of Science Federal Advisory Committees to respond to look toward the scientific horizon and identify what new or upgraded facilities will best serve the SC community needs in the next ten years (2024-2034). This report by the Fusion Energy Sciences Advisory Committee (FESAC) assess facilities for the Fusion Energy Sciences (FES) program.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗