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DOE OSTI2024

Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.

Microbiology↗

DOE OSTI2021

Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi

Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor’s microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with Pinus taeda (native host) and Populus trichocarpa (non-native host). Gene expression of interacting fungal and bacterial rhizosphere communities was compared among three plant-pairs: Populus growing with Populus , Populus with Pinus , and Pinus with Pinus . Our results demonstrate that heterospecific plant partners affect the assembly of root microbiomes, including the changes in the structure of host specific community. Comparative metatranscriptomics reveals that several species of ectomycorrhizal fungi (EMF) and saprotrophic fungi exhibit different patterns of functional and regulatory gene expression with these two plant hosts. Heterospecific plants affect the transcriptional expression pattern of EMF host-specialists (e.g., Pinus -associated Suillus spp.) on both plant species, mainly including the genes involved in the transportation of amino acids, carbohydrates, and inorganic ions. Alteration of root microbiome by neighboring plants may help regulate basic plant physiological processes via modulation of molecular functions in the root microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2013

Engineering Specification for Large-aperture UVO Space Telescopes Derived from Science Requirements

The Advance Mirror Technology Development (AMTD) project is a three year effort initiated in FY12 to mature by at least a half TRL step six critical technologies required to enable 4 to 8 meter UVOIR space telescope primary mirror assemblies for both general astrophysics and ultra-high contrast observations of exoplanets. AMTD uses a science-driven systems engineering approach. We mature technologies required to enable the highest priority science AND result in a high-performance low-cost low-risk system. To provide the science community with options, we are pursuing multiple technology paths. We have assembled an outstanding team from academia, industry, and government with extensive expertise in astrophysics and exoplanet characterization, and in the design/manufacture of monolithic and segmented space telescopes. A key accomplishment is deriving engineering specifications for advanced normal-incidence monolithic and segmented mirror systems needed to enable both general astrophysics and ultra-high contrast observations of exoplanets missions as a function of potential launch vehicles and their mass and volume constraints.

Stahl, H. Philip↗

NASA NTRS2013

Engineering Specification for Large-aperture UVO Space Telescopes Derived from Science Requirements

Stahl, H. Philip↗

NASA NTRS1985

Test results of an organic Rankine-cycle power module for a small community solar thermal power experiment

The organic Rankine-cycle (ORC) power conversion assembly was tested. Qualification testing of the electrical transport subsystem was also completed. Test objectives were to verify compatibility of all system elements with emphasis on control of the power conversion assembly, to evaluate the performance and efficiency of the components, and to validate operating procedures. After 34 hours of power generation under a wide range of conditions, the net module efficiency exceeded 18% after accounting for all parasitic losses.

Clark, T. B.↗

DOE OSTI2022

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies

High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Abstract Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA). Final report

The goal of the Stahl lab is to use a combination of isotopic, genomic, and activity-based analyses in the field, of selected field isolates, and defined synthetic communities to identify sources and sinks of different nitrogen species in the field, focusing on the FRC at the ORNL. The most general research objective is to characterize variants in the pathway for denitrification among field isolates and synthetic microbial assemblies as a foundation for predicting the biotic and abiotic controls of nitrogen and carbon transformations in the field. Specifically, we have focused on characterizing environmental controls of nitrous oxide emissions, an important greenhouse gas and ozone depleting molecule. Studies have mapped the flux of nitrous oxide and controlling genetic elements within the FRC subsurface, indicating the importance of different enzyme variants in nitrous oxide production and consumption in controlling surface emissions. We have developed methods to quantify and catalog the isotopic signatures imparted on nitrous oxide by different nitrous oxide reductase variants in isolated organisms and model synthetic communities. We have developed methods to quantify and catalog the nitrous oxide affinity of field relevant isolates and their biomass yield when respiring nitrous oxide on different carbon substrates. We continue to expand the collection of field-relevant microbial isolates within ENIGMA by focused enrichment and isolation from field material. These objectives have been facilitated by the development of new technologies, including: 1) the development of a multiplexed automated optical density measurement system for quantifying growth kinetics of microorganisms dependent on gaseous substrates in monoculture or gas exchange in synthetic communities and 2) the development of a microcalorimetric analysis format to quantify the impact of environmental stress on microbial maintenance energy. Since field relevant processes are mediated by assemblies of organisms interacting with each other and their local environment, we have also collaborated with other ENIGMA investigators on the assembly and characterization of synthetic communities. These studies have evaluated the role of organisms lacking a complete pathway for denitrification in the control of field processes, measuring process rates of assemblies of organisms that individually lack the full denitrification pathway but mediate the complete denitrification when growing together. These efforts have so far resulted in the publication of 18 peer reviewed papers ranging from ecological and physiological drivers of pathway optimization to field-scale process characterization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (> 20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the ‘Williams’ haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of ‘Fiskeby III,’ a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2018

Improved Pyrotechnic Shock Scaling Method Based on Shock Response Spectrum and Statistical Energy Analysis

It has been more than forty years since the pyrotechnic shock scaling method was introduced. The scaling method estimates the attenuation of the Shock Response Spectrum (SRS) based on the distance from the source, structural configurations, types of structural joints and interfaces, and intervening structure [1]. The method has been successfully used in the spacecraft community countless times and still is frequently used to develop pyrotechnic shock requirements at various levels of assembly of a spacecraft. However, since the method was derived empirically from a limited set of shock test data [2], the aerospace community has been looking for an alternative approach. In this paper, a computational scaling method based on Statistical Energy Analysis (SEA) is re-visited. SEA is traditionally used as a method for investigating the diffusion of acoustic and vibratory energies of a system at steady-state [3]. Previously, an approach using the SRS as an acceleration constraint condition to the SEA model was introduced to estimate the attenuation from a shock source [4,5]. In the current investigation, additional examples are provided to further validate the approach. In addition, responses in the time domain are produced by the Local Modal Phase Reconstruction (LMPR) approach which was recently introduced to the community [6].

Fernandez, Juan P.↗

NASA NTRS1972

Apollo 15 and 16 ground-commanded television assembly.

During the Apollo 15 and 16 missions, a special camera provided the scientific community and the home viewer with real-time coverage of the lunar exploration. The lunar blast-off of the Apollo 16 ascent module was tracked by the mission controller at NASA's Manned Space Center and watched 250,000 miles away on earth. The operation of this television camera and the remote control unit are described and block diagrams given. Ground-command capability from the Mission Control Center permitted versatility and optimization of the TV coverage, without diverting the astronauts from their primary role of lunar exploration.

Soltoff, B. M.↗

DOE OSTI2024

Exabiome: Advancing Microbial Science through Exascale Computing

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection, and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilize exascale resources to understand the functional diversity of billions of dark matter proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1994

Robotics technology developments in the United States space telerobotics program

In the same way that the launch of Yuri Gagarin in April 1961 announced the beginning of human space flight, last year's flight of the German ROTEX robot flight experiment is heralding the start of a new era of space robotics. After a gap of twelve years since the introduction of a new capability in space remote manipulation, ROTEX is the first of at least ten new robotic systems and experiments which will fly before the year 2000. As a result of redefining the development approach for space robotic systems, and capitalizing on opportunities associated with the assembly and maintenance of the space station, the space robotics community is preparing a whole new generation of operational robotic capabilities. Expanding on the capabilities of earlier manipulation systems such as the Viking and Surveyor soil scoops, the Russian Lunakhods, and the Shuttle Remote Manipulator System (RMS), these new space robots will augment astronaut on-orbit capabilities and extend virtual human presence to lunar and planetary surfaces.

Lavery, David↗

NASA NTRS2021

NASA Human Systems Integration Handbook

This handbook is intended to provide general guidance and information on Human Systems Integration (HSI) for the NASA community and the applicability of HSI to NASA programs and projects. The primary goals are to increase awareness and consistency across the Agency, advance the practice and implementation of HSI principles, and provide invaluable information and guidance to HSI practitioners in the performance of their duties. Specific aims of this handbook are to define HSI, illustrate the value of HSI in programmatic decisions, demonstrate how HSI fits into the NASA project life cycle process, describe how HSI applies across all three NASA Technical Authorities, provide guidance on HSI processes and products, and provide helpful information on HSI resources within the NASA community. Largely within the engineering community, a system is thought of as the integration or assemblance of hardware and software that together perform a function. HSI considers a system to be the integration of hardware, software, humans, data, and processes, where the human in HSI refers to all personnel involved with a given system, including system owners, users/customers, operators, maintainers, assemblers, support personnel, logistics suppliers, training personnel, test personnel, and others. This handbook should be used as a companion for implementing NPR 7123.1, Systems Engineering Processes and Requirements, the NASA Systems Engineering Handbook, NASA directives, and any Center-specific handbooks and directives developed for implementing programs and projects. As of 2021, both NPR 7123.1 and NPR 7120.5 require HSI to be implemented within NASA technical efforts.

Lisa O Rippy↗

NASA NTRS2013

Overview and Recent Accomplishments of the Advanced Mirror Technology Development (AMTD) for Large Aperture UVOIR Space Telescopes Project

Per Astro2010, a new, larger UVO telescope is needed to answer fundamental scientific questions, such as: is there life on Earth-like exoplanets; how galaxies assemble stellar populations; how baryonic matter interacts with intergalactic medium; and how solar systems form and evolve. And, present technology is not mature enough to affordably build and launch any potential UVO concept. Advanced Mirror Technology Development (AMTD) is a funded SAT project. Our objective is to mature to TRL-6 the critical technologies needed to produce 4-m or larger flight-qualified UVOIR mirrors by 2018 so that a viable mission can be considered by the 2020 Decadal Review. AMTD uses a science-driven systems engineering approach. We mature technologies required to enable the highest priority science AND result in a high-performance low-cost low-risk system. To provide the science community with options, we are pursuing multiple technology paths. We have assembled an outstanding team from academia, industry, and government with extensive expertise in astrophysics and exoplanet characterization, and in the design/manufacture of monolithic and segmented space telescopes. One of our key accomplishments is that we have derived engineering specifications for advanced normal-incidence monolithic and segmented mirror systems needed to enable both general astrophysics and ultra-high contrast observations of exoplanets missions as a function of potential launch vehicle and its inherent mass and volume constraints. We defined and initiated a program to mature 6 key technologies required to fabricate monolithic and segmented space mirrors.

Stahl, H. Philip↗

NASA NTRS2020

State of the Profession Considerations: NASA Langley Research Center Capabilities / Technologies for Autonomous In-Space Assembly and Modular Persistent Assets

Successfully implementing OSAM into next generation revolutionary observatories requires integrating expertise and technologies in modular space structures, assembly operations, autonomy, and modeling/simulation. LaRC OSAM technologies/capabilities have been presented to inform the Planetary Science and Astrobiology Decadal Survey community of the robust and mature existing capability to support an OSAM based architecture for their next observatory. LaRC Structures and Assembly capabilities enable; a modular telescope architecture, high-performance structural modules, and robotic assembly techniques. LaRC Autonomy capabilities ensure that the robotic assembly will be accomplished in a safe and robust manner and only require humans in a supervisory role. The LaRC toolbox of Modeling and Simulation capabilities that is calibrated using module-level ground testing, will ensure that the performance of the fully assembled observatory, a very large zero-g system that will never be assembled/tested in a gravity environment, meets all performance requirements when it enters into service. Integrating all three LaRC capabilities and including embedded metrology, will enable servicing, repair, instrument upgrades (and/or replacement) while ensuring a very long lifetime for the observatory and providing a return-on-investment that is substantially greater than the initial cost. Further confidence will be achieved as OSAM technologies are validated in a new LaRC OSAM laboratory that allows large-scale collaborative testing of modular hardware, simulation software and algorithms, and autonomous agents.

Large space structures↗

NASA NTRS2020

Twenty Years of Terra MODIS Spectral Performance using the Spectro-Radiometric Calibration Assembly

The Moderate Resolution Imaging Spectroradiometer (MODIS) instrument on-board the Terra spacecraft has provided valuable Earth data to the science community for the last 20 years. Equipped with several on-board calibrators (OBCs), MODIS has continued to operate nominally since its launch in December 1999. The Spectro-Radiometric Calibration Assembly (SRCA) is one such OBC that is able to provide on-orbit measurements of the MODIS reflective solar bands (RSBs) in radiometric, spatial and spectral modes. While the SRCA is operating in spectral mode, it is able to monitor the center wavelength (CW), bandwidth (BW) and in-band relative spectral response (RSR) of most RSBs. Prelaunch measurements of the CWs, BWs and RSRs of the RSBs were performed at the system level using the Spectral measurement Assembly (SpMA). Using both the prelaunch measurements and the measurements obtained on-orbit using the SRCA, the changes in the spectral response of the MODIS reflective bands can be monitored throughout the mission. This paper will provide a brief description of the spectral calibration approach and report on-orbit changes in these spectral performance parameters and their uncertainties over the last 20 years. It will also address changes to the SRCA operation on-orbit and their impact on measured spectral calibration results. Despite two decades in orbit, the spectral responses for most Terra MODIS reflective bands continue to remain within their design specifications.

MODIS↗