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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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16 records

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NASA NTRS2013

Underway Sampling of Marine Inherent Optical Properties on the Tara Oceans Expedition as a Novel Resource for Ocean Color Satellite Data Product Validation

Developing and validating data records from operational ocean color satellite instruments requires substantial volumes of high quality in situ data. In the absence of broad, institutionally supported field programs, organizations such as the NASA Ocean Biology Processing Group seek opportunistic datasets for use in their operational satellite calibration and validation activities. The publicly available, global biogeochemical dataset collected as part of the two and a half year Tara Oceans expedition provides one such opportunity. We showed how the inline measurements of hyperspectral absorption and attenuation coefficients collected onboard the R/V Tara can be used to evaluate near-surface estimates of chlorophyll-a, spectral particulate backscattering coefficients, particulate organic carbon, and particle size classes derived from the NASA Moderate Resolution Imaging Spectroradiometer onboard Aqua (MODISA). The predominant strength of such flow-through measurements is their sampling rate-the 375 days of measurements resulted in 165 viable MODISA-to-in situ match-ups, compared to 13 from discrete water sampling. While the need to apply bio-optical models to estimate biogeochemical quantities of interest from spectroscopy remains a weakness, we demonstrated how discrete samples can be used in combination with flow-through measurements to create data records of sufficient quality to conduct first order evaluations of satellite-derived data products. Given an emerging agency desire to rapidly evaluate new satellite missions, our results have significant implications on how calibration and validation teams for these missions will be constructed.

remote sensing↗

DOE OSTI2023

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

ABSTRACT Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8–2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life. IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers’ efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

The Arctic Ocean as a dead end for floating plastics in the North Atlantic branch of the Thermohaline Circulation

The subtropical ocean gyres are recognized as great marine accumulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively sampled for floating plastic debris from the Tara Oceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Diel Transcriptional Oscillations of a Plastid Antiporter Reflect Increased Resilience of Thalassiosira pseudonana in Elevated CO 2

Acidification of the ocean due to high atmospheric CO 2 levels may increase the resilience of diatoms causing dramatic shifts in abiotic and biotic cycles with lasting implications on marine ecosystems. Here, we report a potential bioindicator of a shift in the resilience of a coastal and centric model diatom Thalassiosira pseudonana under elevated CO 2 . Specifically, we have discovered, through EGFP-tagging, a plastid membrane localized putative Na + (K + )/H + antiporter that is significantly upregulated at >800 ppm CO 2 , with a potentially important role in maintaining pH homeostasis. Notably, transcript abundance of this antiporter gene was relatively low and constant over the diel cycle under contemporary CO 2 conditions. In future acidified oceanic conditions, dramatic oscillation with >10-fold change between nighttime (high) and daytime (low) transcript abundances of the antiporter was associated with increased resilience of T. pseudonana. By analyzing metatranscriptomic data from the Tara Oceans project, we demonstrate that phylogenetically diverse diatoms express homologs of this antiporter across the globe. We propose that the differential between night- and daytime transcript levels of the antiporter could serve as a bioindicator of a shift in the resilience of diatoms in response to high CO 2 conditions in marine environments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean

Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on “who is doing what, where, and how?”, this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory—determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae

Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Viroid-like “obelisk” agents are widespread in the ocean and exceed the abundance of RNA viruses in the prokaryotic fraction

Abstract “Obelisks” are recently discovered ribonucleic acid (RNA) viroid-like elements present in diverse environments with no phylogenetic similarity to any known biological agent. obelisks were first identified in the human gut and in a commensal bacterium acting as a replicative host. They have a circular ∼1 kb RNA genome, rod-like secondary structures, and the encoding of a protein superfamily called “Oblins”. We performed a large-scale search of obelisks in the ocean using the Pebblescout program and the transcriptomic Sequence Archive Read databases, revealing the biogeography and abundance of these viroid-like RNA elements. We detected 55 obelisk genomes resulting in 35 marine clusters at the species level. These obelisks were detected in the prokaryotic fraction and to a lesser extent in the eukaryotic fraction, and distributed across all the oceans from surface to mesopelagic including the Arctic, and even in the coldest seawater of Earth beneath the Antarctic Ross Ice Shelf. The obelisk hallmark protein Oblin-1 confirmed by 3D models was found in various marine samples. Some of the detected marine obelisks harbor hammerhead self-cleaving ribozymes in both polarities. In the prokaryotic, but not the eukaryotic, fraction of the Tara Ocean dataset, relative abundance of obelisks calculated by transcriptomic fragment recruitment indicated that they are abundant in marine samples, reaching or even exceeding the relative abundance of the previously discovered uncultured RNA viruses. In conclusion, obelisks are abundant and widespread viroid-like elements that should be included in ocean biogeochemical models.

Environmental Sciences & Ecology↗

DOE OSTI2018

A most wanted list of conserved microbial protein families with no known domains

The number and proportion of genes with no known function are growing rapidly. To quantify this phenomenon and provide criteria for prioritizing genes for functional characterization, we developed a bioinformatics pipeline that identifies robustly defined protein families with no annotated domains, ranks these with respect to phylogenetic breadth, and identifies them in metagenomics data. We applied this approach to 271 965 protein families from the SFams database and discovered many with no functional annotation, including >118 000 families lacking any known protein domain. From these, we prioritized 6 668 conserved protein families with at least three sequences from organisms in at least two distinct classes. These Function Unknown Families (FUnkFams) are present in Tara Oceans Expedition and Human Microbiome Project metagenomes, with distributions associated with sampling environment. Our findings highlight the extent of functional novelty in sequence databases and establish an approach for creating a “most wanted” list of genes to prioritize for further characterization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Structural and Proteomic Studies of the Aureococcus anophagefferens Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing

Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual virus particles themselves are rare. We used shotgun proteomics to quantitatively identify 43 virus-encoded proteins packaged within purified Aureococcus anophagefferens Virus (AaV) particles, normalizing data to the per-virion level using a 9.5-Å-resolution molecular reconstruction of the 1900-Å (AaV) particle that we generated with cryogenic electron microscopy. This packaged proteome was used to determine similarities and differences between members of different giant virus families. We noted that proteins involved in sugar degradation and binding (e.g., carbohydrate lyases) were unique to AaV among characterized giant viruses. To determine the extent to which this virally encoded metabolic capability was ecologically relevant, we examined the TARA Oceans dataset and identified genes and transcripts of viral origin. Our analyses demonstrated that putative giant virus carbohydrate lyases represented up to 17% of the marine pool for this function. In total, our observations suggest that the AaV particle has potential prepackaged metabolic capabilities and that these may be found in other giant viruses that are widespread and abundant in global oceans.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Biases in genome reconstruction from metagenomic data

Background Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs. Methods We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software—nucleotide composition and sequence repetitiveness—were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Tara Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages. Results Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.

54 ENVIRONMENTAL SCIENCES↗

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↗

DOE OSTI2026

As above, not so below: Ion fractionation in planetary analog ices

The geophysical evolution and astrobiological potential of ocean worlds are indelibly linked to the chemical compositions of their oceans and ice shells. In the absence of direct measurements, empirical estimates of subsurface ocean compositions have relied on the assumption that the ionic compositions of ice shell surfaces are representative of their underlying ocean compositions. Here, we present experimental results demonstrating that ion fractionation—the differential entrainment of ion species in forming ices—is likely a prevalent process on ocean worlds, suggesting that planetary ice shell compositions do not directly reflect their underlying ocean compositions. We measure in-ice depletions and amplifications of relative ion concentrations ranging between −40 and +77%, compared to the parent fluid composition. Although this may complicate the interpretation of spacecraft data, ion fractionation provides a mechanism for generating compositionally diverse ices that could help explain the geological complexity of planetary ice shells.

58 GEOSCIENCES↗

DOE OSTI2020

Clades of huge phages from across Earth’s ecosystems

Bacteriophages typically have small genomes and depend on their bacterial hosts for replication. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2021

Assessing Disaggregated SMAP Soil Moisture Products in the United States

A soil moisture (SM) disaggregation algorithm based on thermal inertia (TI) theory was implemented to downscale the Soil Moisture Active Passive (SMAP) Enhanced product(SPL2SMPE) from 9 km to 1 km over the continental United States. The algorithm applies land surface temperature and normalized difference vegetation index from Moderate Resolution Imaging Spectroradiometer (MODIS) at higher spatial resolution to estimate relative soil wetness within a coarse SMAP grid -this MODIS-derived relative wetness is then used to produce the downscaled SMAP SM. Results from the algorithm were evaluated in terms of their spatiotemporal coverage and accuracy using in situ measurements from SMAP Core Validation Sites (CVS), the US Department of Agriculture Soil Climate Analysis Network (USDA-SCAN), and the National Oceanic and Atmospheric Administration Climate Reference Network(NOAA-CRN). Results were also compared with the baselineSPL2SMPE and the SMAP/Sentinel-1 (SPL2SMAPS) 1kmproduct. Overall, the unbiased root mean square error (ubRMSE)of the disaggregated SM at the CVS using the TI approach is approximately 0.04 m3=m3, which is the SMAP mission requirement for the baseline products. The TI approach out performs the SMAP/Sentinel SL2SMAPS 1km product by approximately0.02 m3=m3. Over the agriculture/crop areas from SCAN and CRN sparse network stations, the TI approach exhibits better ubRMSE compared to SPL2SMPE andSPL2SMAPS byabout0.01 and 0.02 m3=m3, indicating its advantage in these areas. However, a drawback of this approach is that there are data gaps due to cloud cover as optical sensors cannot have a clear view of the land surface.

Soil moisture↗

NASA NTRS2019

Dynamic Characterization of the Crew Module Uprighting System for NASA’s Orion Crew Module

The Orion Crew Module Uprighting System is a set of five airbag that are responsible for the uprighting of the crew module in the case of an inverted splashdown. A series of tests during the Underway Recovery Test 7 (URT-7) were run in preparation for the Artemis I mission, where the dynamic characterization of the CMUS in an ocean wave environment was performed. A Datawell Waverider DWR-G4 wave buoy was deployed to the characterize the wave environment during these tests. The heave measurements from this buoy were projected to the Orion Crew Module Buoyancy Test Article location by two different methods: (1) directly time-shifting the data, and (2) performing a frequency-domain, phase-shifting operation. Results demonstrate that the phase-shifting operation led to better correlation with the true crew module response to wave excitation as compared with the purely time-shifted method. Additionally, a novel approach to localize an object in a bidirectional wave field based on its heave response is presented and validated with URT- 7 data. Given a wave measurement device at a known location, one can estimate the relative distance to another object based solely off its heave response. Results show that if signals have sufficiently good correlation, this method can be used to estimate the relative separation between two objects in the same wave field.

Vertaska, Ivan Bertaska↗

DOE OSTI2025

Learned magnetic map cues and two mechanisms of magnetoreception in turtles

Growing evidence indicates that migratory animals exploit the magnetic field of the Earth for navigation, both as a compass to determine direction and as a map to determine geographical position. It has long been proposed that, to navigate using a magnetic map, animals must learn the magnetic coordinates of the destination, yet the pivotal hypothesis that animals can learn magnetic signatures of geographical areas has, to our knowledge, yet to be tested. Here, in this work, we report that an iconic navigating species, the loggerhead turtle ( Caretta caretta ), can learn such information. When fed repeatedly in magnetic fields replicating those that exist in particular oceanic locations, juvenile turtles learned to distinguish magnetic fields in which they encountered food from magnetic fields that exist elsewhere, an ability that might underlie foraging site fidelity. Conditioned responses in this new magnetic map assay were unaffected by radiofrequency oscillating magnetic fields, a treatment expected to disrupt radical-pair-based chemical magnetoreception, suggesting that the magnetic map sense of the turtle does not rely on this mechanism. By contrast, orientation behaviour that required use of the magnetic compass was disrupted by radiofrequency oscillating magnetic fields. The findings provide evidence that two different mechanisms of magnetoreception underlie the magnetic map and magnetic compass in sea turtles.

animal behaviour↗