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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
NASA NTRS2018

Perserving Samples and Their Scientific Integrity - Insights into MSR from the Astromaterials Acquisition and Curation Office at NASA Johnson Space Center

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (JSC), in Houston, TX (henceforth Curation Office) manages the curation of all past, present, and future extraterrestrial samples returned by NASA missions and shared collections from international partners, preserving their integrity for future scientific study while providing the samples to the international community in a fair and unbiased way. The Curation Office also curates flight and non-flight reference materials and other materials from spacecraft assembly of sample return missions that would have the potential to cross-contaminate a present or future NASA astromaterials collection. These materials are primarily collected during the assembly, test, and launch operations (ATLO) phase and after flight during the recovery and curation phase. In addition, the Curation Office curates non-flight, flight-like, and flown witness plates for sample return missions. These reference materials and witness plates provide the scientific community with the fundamental ability to reconstruct the contamination/alteration history of the sample collection through the course of the mission, with the overall goal of strengthening the scientific conclusions drawn from the study of returned materials.

Harrington, A. D.↗
NASA NTRS2020

Acoustic space occupancy: Combining ecoacoustics and lidar to model biodiversity variation and detection bias across heterogeneous landscapes

There is global interest in quantifying changing biodiversity in human-modified landscapes. Ecoacoustics may offer a promising pathway for supporting multi-taxa monitoring, but its scalability has been hampered by the sonic complexity of biodiverse ecosystems and the imperfect detectability of animal-generated sounds. The acoustic signature of a habitat, or soundscape, contains information about multiple taxa and may circumvent species identification, but robust statistical technology for characterizing community-level attributes is lacking. Here, we present the Acoustic Space Occupancy Model, a flexible hierarchical framework designed to account for detection artifacts from acoustic surveys in order to model biologically relevant variation in acoustic space use among community assemblages. We illustrate its utility in a biologically and structurally diverse Amazon frontier forest landscape, a valuable test case for modeling biodiversity variation and acoustic attenuation from vegetation density. We use complementary airborne lidar data to capture aspects of 3D forest structure hypothesized to influence community composition and acoustic signal detection. Our novel analytic framework permitted us to model both the assembly and detectability of soundscapes using lidar-derived estimates of forest structure. Our empirical predictions were consistent with physical models of frequency-dependent attenuation, and we estimated that the probability of observing animal activity in the frequency channel most vulnerable to acoustic attenuation varied by over 60%, depending on vegetation density. There were also large differences in the biotic use of acoustic space predicted for intact and degraded forest habitats, with notable differences in the soundscape channels predominantly occupied by insects. This study advances the utility of ecoacoustics by providing a robust modeling framework for addressing detection bias from remote audio surveys while preserving the rich dimensionality of soundscape data, which may be critical for inferring biological patterns pertinent to multiple taxonomic groups in the tropics. Our methodology paves the way for greater integration of remotely sensed observations with high-throughput biodiversity data to help bring routine, multi-taxa monitoring to scale in dynamic and diverse landscapes.

Airborne lidar↗
DOE OSTI2025

General Biology 2 Sugar Beet Lab - SU2025 - Final

This module uses the Department of Energy Systems Biology Knowledgebase (KBase) platform to explore topics such as genome assembly, metagenomics, and phylogenomics. Here students will use sequences from DNA that they collected to compare the metagenomes of microbial communities from the rhizosphere of plants grown in fertilized vs. unfertilized soils. Using these data students will evaluate the impact of fertilizer on these communities and how these microbial communities influence soil health and plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes. Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla. We provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils

Acid sulfate soils release metal laden, acidic waters that affect the environment, buildings, and human health. In this study, 16S rRNA gene amplicons, metagenomes, and metatranscriptomes all demonstrated distinct microbial communities and activities in the unoxidized potential acid sulfate soil, the overlying transition zone, and uppermost oxidized actual acid sulfate soil. Assembled genomes and mRNA transcripts also suggested abundant oxidized acid sulfate soil populations that aligned within the Gammaproteobacteria and Terracidiphilus. In contrast, potentially acid tolerant or moderately acidophilic iron oxidizing Gallionella and sulfur metabolizing Sulfuricella dominated the transition zone during catalysis of metal sulfide oxidation to form acid sulfate soil. Finally, anaerobic oxidation of methane coupled to nitrate, sulfate, and ferric reduction were suggested to occur in the reduced parent sediments. In conclusion, despite comparable metal sulfide dissolution processes e.g., biomining, Gallionella and Sulfuricella dominated the community and activities during conversion of potential to actual acid sulfate soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Accurate and complete genomes from metagenomes

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Functional insights of novel Bathyarchaeia reveal metabolic versatility in their role in peatlands of the Peruvian Amazon

ABSTRACT The decomposition of soil organic carbon within tropical peatlands is influenced by the functional composition of the microbial community. In this study, building upon our previous work, we recovered a total of 28 metagenome-assembled genomes (MAGs) classified as Bathyarchaeia from the tropical peatlands of the Pastaza-Marañón Foreland Basin (PMFB) in the Amazon. Using phylogenomic analyses, we identified nine genus-level clades to have representatives from the PMFB, with four forming a putative novel family (“CandidatusPaludivitaceae”) endemic to peatlands. We focus on theCa. Paludivitaceae MAGs due to the novelty of this group and the limited understanding of their role within tropical peatlands. Functional analysis of these MAGs reveals that this putative family comprises facultative anaerobes, possessing the genetic potential for oxygen, sulfide, or nitrogen oxidation. This metabolic versatility can be coupled to the fermentation of acetoin, propanol, or proline. The other clades outsideCa. Paludivitaceae are putatively capable of acetogenesis andde novoamino acid biosynthesis and encode a high amount of Fe 3+ transporters. Crucially, theCa. Paludivitaceae are predicted to be carboxydotrophic, capable of utilizing CO for energy generation or biomass production. Through this metabolism, they could detoxify the environment from CO, a byproduct of methanogenesis, or produce methanogenic substrates like CO 2 and H 2 . Overall, our results show the complex metabolism and various lineages of Bathyarchaeia within tropical peatlands pointing to the need to further evaluate their role in these ecosystems. IMPORTANCE With the expansion of theCandidatusPaludivitaceae family by the assembly of 28 new metagenome assembled genomes, this study provides novel insights into their metabolic diversity and ecological significance in peatland ecosystems. From a comprehensive phylogenic and functional analysis, we have elucidated their putative unique facultative anaerobic capabilities and CO detoxification potential. This research highlights their crucial role in carbon cycling and greenhouse gas regulation. These findings are essential for resolving the microbial processes affecting peat soil stability, offering new perspectives on the ecological roles of previously underexplored and underrepresented archaeal populations.

Microbiology↗
NASA NTRS2010

LRN, ERN:, & BERN @ Wireless Integrating the Sciences (WITS) Theatre

In order to develop a call to action for a learning tool that would work to best teach Science Technology Engineering and Math (STEM), the NASA Goddard team will partner with the inventor of Bop It!, an interactive game of verbs and following instructions; and Global Imagination, the developers of Magic Planet. In this paper Decision-making Orbital Health! (DOH!) will be described as a game derived from the basic functions necessary for Bop lt!, a familiar game. that will ask the educational audience to respond to changing commands to Bop It!, Twist It!, and Squeeze It! The success of the new version of the game, will be that the Earth will be making these commands from Dynamic Planet, and the crowd assembled can play wirelessly. Wireless Integrating The Sciences (WITS) Theatre : A balanced approach will describe how the communities local to Goddard and perhaps San Francisco will develop curriculum that helps kids teach kids with an engaging game and a STEM message. The performing arts will be employed to make it entertaining and appropriate to the size of the gathering, and the students educational level.

Hilliard, L.↗
NASA NTRSDate not supplied

Biofilm Mitigation Testing Phase III

Biofilm is produced from bacterial or fungal organisms that can survive in extreme conditions. The microorganisms attach themselves to surfaces and produce an extracellular polymeric matrix that develops into a community structure and ecosystem. Biofilm has been known to cause blockage and clogging inside the Water Processor Assembly (WPA) and Water Recovery System (WRS) piping. The WPA and WRS on the International Space Station (ISS) is responsible for recycling humidity condensate and urine distillate to produce potable water for the astronauts to survive. The Environmental Control and Life Support System (ECLSS) department is developing a way to mitigate biofilm accumulation inside the wastewater tank.

Biofilm↗
DOE OSTI2024

Dynamic ecosystem assembly and escaping the “fire trap” in the tropics: insights from FATES_15.0.0

Abstract. Fire is a fundamental part of the Earth system, with impacts on vegetation structure, biomass, and community composition, the latter mediated in part via key fire-tolerance traits, such as bark thickness. Due to anthropogenic climate change and land use pressure, fire regimes are changing across the world, and fire risk has already increased across much of the tropics. Projecting the impacts of these changes at global scales requires that we capture the selective force of fire on vegetation distribution through vegetation functional traits and size structure. We have adapted the fire behavior and effects module, SPITFIRE (SPread and InTensity of FIRE), for use with the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a size-structured vegetation demographic model. We test how climate, fire regime, and fire-tolerance plant traits interact to determine the biogeography of tropical forests and grasslands. We assign different fire-tolerance strategies based on crown, leaf, and bark characteristics, which are key observed fire-tolerance traits across woody plants. For these simulations, three types of vegetation compete for resources: a fire-vulnerable tree with thin bark, a vulnerable deep crown, and fire-intolerant foliage; a fire-tolerant tree with thick bark, a thin crown, and fire-tolerant foliage; and a fire-promoting C4 grass. We explore the model sensitivity to a critical parameter governing fuel moisture and show that drier fuels promote increased burning, an expansion of area for grass and fire-tolerant trees, and a reduction of area for fire-vulnerable trees. This conversion to lower biomass or grass areas with increased fuel drying results in increased fire-burned area and its effects, which could feed back to local climate variables. Simulated size-based fire mortality for trees less than 20 cm in diameter and those with fire-vulnerable traits is higher than that for larger and/or fire-tolerant trees, in agreement with observations. Fire-disturbed forests demonstrate reasonable productivity and capture observed patterns of aboveground biomass in areas dominated by natural vegetation for the recent historical period but have a large bias in less disturbed areas. Though the model predicts a greater extent of burned fraction than observed in areas with grass dominance, the resulting biogeography of fire-tolerant, thick-bark trees and fire-vulnerable, thin-bark trees corresponds to observations across the tropics. In areas with more than 2500 mm of precipitation, simulated fire frequency and burned area are low, with fire intensities below 150 kW m−1, consistent with observed understory fire behavior across the Amazon. Areas drier than this demonstrate fire intensities consistent with those measured in savannas and grasslands, with high values up to 4000 kW m−1. The results support a positive grass–fire feedback across the region and suggest that forests which have existed without frequent burning may be vulnerable at higher fire intensities, which is of greater concern under intensifying climate and land use pressures. The ability of FATES to capture the connection between fire disturbance and plant fire-tolerance strategies in determining biogeography provides a useful tool for assessing the vulnerability and resilience of these critical carbon storage areas under changing conditions across the tropics.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2012

An Efficient and Versatile Means for Assembling and Manufacturing Systems in Space

Within NASA Space Science, Exploration and the Office of Chief Technologist, there are Grand Challenges and advanced future exploration, science and commercial mission applications that could benefit significantly from large-span and large-area structural systems. Of particular and persistent interest to the Space Science community is the desire for large (in the 10- 50 meter range for main aperture diameter) space telescopes that would revolutionize space astronomy. Achieving these systems will likely require on-orbit assembly, but previous approaches for assembling large-scale telescope truss structures and systems in space have been perceived as very costly because they require high precision and custom components. These components rely on a large number of mechanical connections and supporting infrastructure that are unique to each application. In this paper, a new assembly paradigm that mitigates these concerns is proposed and described. A new assembly approach, developed to implement the paradigm, is developed incorporating: Intelligent Precision Jigging Robots, Electron-Beam welding, robotic handling/manipulation, operations assembly sequence and path planning, and low precision weldable structural elements. Key advantages of the new assembly paradigm, as well as concept descriptions and ongoing research and technology development efforts for each of the major elements are summarized.

Dorsey, John T.↗
DOE OSTI2021

The AGORA High-resolution Galaxy Simulations Comparison Project. III. Cosmological Zoom-in Simulation of a Milky Way–mass Halo

In this work, we present a suite of high-resolution cosmological zoom-in simulations to z = 4 of a 10 12 M⊙ halo at z = 0, obtained using seven contemporary astrophysical simulation codes (Art-I, Enzo, Ramses, Changa, Gadget-3, Gear, and Gizmo) widely used in the numerical galaxy formation community. The physics prescriptions for gas cooling and heating and star formation are the same as the ones used in our previous Assembling Galaxies of Resolved Anatomy (AGORA) disk comparison but now account for the effects of cosmological processes such as the expansion of the universe, intergalactic gas inflow, and the cosmic ultraviolet background radiation emitted by massive stars and quasars. In this work, we introduce the most careful comparison yet of galaxy formation simulations run by different code groups, together with a series of four calibration steps each of which is designed to reduce the number of tunable simulation parameters adopted in the final run. In the first two steps, we methodically calibrate the gas physics, such as cooling and heating, in simulations without star formation. In the third step, we seek agreement on the total stellar mass produced with the common star formation prescription used in the AGORA disk comparison, in stellar-feedback-free simulations. In the last calibration step, we activate stellar feedback, where each code group is asked to set the feedback prescription to as close to the most widely used one in its code community as possible, while aiming for convergence in the stellar mass at z = 4 to the values predicted by semiempirical models. After all the participating code groups successfully complete the calibration steps, we achieve a suite of cosmological simulations with similar mass assembly histories down to z = 4. With numerical accuracy that resolves the internal structure of a target halo (≲100 physical pc at z = 4), we find that the codes overall agree well with one another, e.g., in gas and stellar properties, but also show differences, e.g., in circumgalactic medium (CGM) properties. We argue that, if adequately tested in accordance with our proposed calibration steps and common parameters, high-resolution cosmological zoom-in simulations can have robust and reproducible results. New code groups are invited to join and enrich this comparison by generating equivalent models or to test the code's compatibility on their own, by adopting the common initial conditions, the common easy-to-implement physics package, and the proposed calibration steps. Further analyses of the zoom-in simulations presented here will be presented in forthcoming reports from the AGORA Collaboration, including studies of the CGM, simulations by additional codes, and results at lower redshift.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRSDate not supplied

Operational Workflow in a Sample Receiving Facility: Input from the MSR Operation Definition Team

The return of scientifically selected samples from Mars would provide a rare opportunity for investigation with the full range of the latest technology available. To take full advantage of this opportunity, it is important to plan ahead to ensure the pristine nature of the samples upon arrival within the Earth environment until scientific investigations can begin. The NASA/ESA science community-driven MSR Science Planning Group – Phase 2 (MSPG2) delivered recommendations and guidance regarding curation (1) and science (2,3) activities to be performed on the samples under containment. High-level requirements for the infrastructure were also developed by MSPG2 (4). In order to prepare infrastructure-targeted input for the ESA and NASA facility studies planned in the 2022-2023 timeframe, the MSR agency-led Operational Scenarios Definition Team (MOSDT) was assembled to conceptualize the sample operations that will inform future architecture teams. Emphasis was placed on the responsibility of MOSDT to use community-defined requirements and to represent the view of the international scientific community. The main deliverable of MOSDT was an operational workflow for a Sample Receiving Facility (SRF). Two other deliverables were produced: a report to narrate the workflow, and a list of instruments (see Hutzler et al., this conference). Activities described in the main sequence of the workflow range from engineering operations to curation to science, with the latter term being used here as the science to be done within a SRF. Side sequences (e.g. engineering inspection of hardware, head gas extraction) were also identified, and detailed when they would have a significant impact on the infrastructure of a SRF. It was necessary for the MOSDT to rely on assumptions for some steps and activities, and though these were kept to a minimum (and are described in both the report supporting the workflow and in the full presentation), in general, the assumptions and overall work were very conservative, as the impact of underestimating the scope of the SRF infrastructure was considered more detrimental than overestimating it. It is expected that future work will be able to confirm or inform these assumptions. The community was consulted during the course of the MOSDT work. This abstract’s aim is two-fold: on one hand, inform the scientific community and overall MSR stakeholders, to make the infrastructure studies and trade-off more understandable; on the other hand, to solicit feedback from a larger community audience for the next iterations planning for SRF design and activities.

Mars Sample Return↗
DOE OSTI2022

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum

Abstract Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35–43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The NIH Somatic Cell Genome Editing program

The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium’s plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled—along with validated datasets—into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit—and the knowledge generated by its applications—as a means to accelerate the clinical development of new therapies for a wide range of conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs

Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

59 BASIC BIOLOGICAL SCIENCES↗