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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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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Evolutionary history constrains microbial traits across environmental variation

Organisms influence ecosystems, from element cycling to disturbance regimes, to trophic interactions, to energy partitioning. Microorganisms are part of this influence, and understanding their ecology in nature requires studying traits of these organisms quantitatively in their natural habitats, a challenging task, but one which new approaches now make possible. Here, we show that growth rate and carbon assimilation rate of soil microorganisms are more influenced by evolutionary history than by climate, even across a broad climatic gradient spanning major temperate life zones, from mixed conifer forest to high desert grassland. Most of the explained variation (~50% to ~90%) in growth rate and carbon assimilation rate was attributable to difference among taxonomic groups indicating a strong influence of evolutionary history, and taxonomic groupings were more predictive for organisms responding to resource addition. With added carbon and nitrogen substrates, differences among taxonomic groups explained ~8 times more variance in growth rate than did the differences in ecosystem type. Taxon-specific growth and carbon assimilation rates were highly intercorrelated across the four ecosystems, constrained by the taxonomic identity of the organisms, such that plasticity driven by environment was limited across ecosystems varying in temperature, precipitation, and dominant vegetation. Taken together our results suggest that, similar to multicellular life, the traits of prokaryotes in their natural habitats are constrained by evolutionary history to a greater degree than environmental variation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Life and death in the soil microbiome: how ecological processes influence biogeochemistry

We report soil microorganisms shape global element cycles in life and death. Living soil microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter — Earth’s largest terrestrial carbon pool and the primary source of plant nutrients. Their metabolic functions are influenced by ecological interactions with other soil microbial populations, soil fauna and plants, and the surrounding soil environment. Remnants of dead microbial cells serve as fuel for these biogeochemical engines because their chemical constituents persist as soil organic matter. This non-living microbial biomass accretes over time in soil, forming one of the largest pools of organic matter on the planet. In this Review, we discuss how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. With recent omics advances, many of the traits that frame microbial population dynamics and their ecophysiological adaptations can be deciphered directly from assembled genomes or patterns of gene or protein expression. Thus, it is now possible to leverage a trait-based understanding of microbial life and death within improved biogeochemical models and to better predict ecosystem functioning under new climate regimes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A functional microbiome catalogue crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mangrove peat and algae leachates elicit rapid and contrasting molecular and microbial responses in coastal waters

Abstract As sea level rises, previously sequestered blue carbon can be exported offshore as particulate or dissolved organic matter where it may be re-mineralized or sequestered. The priming effect, or interactive effects of organic matter turnover with a mixed substrate, is well described in soils, but still debated in aquatic systems. Priming may contribute to enhanced blue carbon re-mineralization in coastal environments. Here we examined mangrove-derived dissolved organic matter turnover in a lab incubation, with leachates from mangrove peat, 13 C-labeled algae, and peat+algae (primed). Particulate and dissolved organic matter were assessed; microbial metatranscriptomes were evaluated; and dissolved organic matter was characterized with high resolution mass spectrometry. Stable isotopes indicated rapid allocation of algal-derived dissolved organic matter into particulate organic matter. The algal treatment had the greatest increase in carbon dioxide, but primed and peat treatments had the greatest loss of dissolved organic carbon, greater RNA concentrations, and similar changes in total carbon dioxide. This suggests that, while total carbon dioxide did not increase under priming conditions, the addition of a peat substrate may promote microbial biomass production relative to carbon dioxide production. This work highlights that more targeted studies investigating the specific mechanisms of priming are necessary to address the molecular and microbial transformations associated with priming in aquatic systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Advected carbon younger than the sediment fuels microbial metabolism in a pumped deep aquifer

Ever deeper wells are drilled worldwide to pump potable groundwater. Recent studies argue that overpumping compresses clays and releases reactive dissolved organic carbon (DOC), which in turn drives a series of microbial reactions that affect groundwater potability including arsenic concentrations. Here, we use a novel method to measure the radiocarbon ages of microbial RNA to determine the source of reactive or metabolizable DOC and argue against the compression of clays as the sole source of carbon. We show that microbial RNA (5,230; 5,550; 6,250 yr; n = 3 wells), DOC (280-10,800 yr; n = 13), and methane (modern to 6,240 yr; n = 3), from an overpumped deep aquifer in Bangladesh are much younger than the overlying clay layers deposited during the Pleistocene over 12,000 years ago. Mass-balance indicates that at least half of the carbon incorporated into RNA has to come from reactive DOC or methane that is advected downward via vertical recharge. This metabolism of advected organic carbon could have implications for the quality of water pumped from deep aquifers.

Biological and medical sciences↗
DOE OSTI2024

Formation and transformation of iron oxy-hydroxide precursor clusters to ferrihydrite

Iron (Fe) oxy-hydroxide minerals such as ferrihydrite (Fh) are ubiquitous in Earth-surface environments and important in biogeochemical element cycling. Recent research has suggested that their formation is preceded by the precipitation of ultrasmall (~1 nm) Keggin-like Fe oxy-hydroxide clusters. However, relatively little is understood about the structure of the precursor clusters and the impacts of pH and time on their growth and transformation to more stable phases. Here, we used a new method that involves mixed flow reactors (MFR) to synthesize these Fe oxy-hydroxide precursor clusters at pH 1.0, 1.5, 2.5, and 4.5. In situ and ex situ synchrotron scattering measurements and laboratory small-angle X-ray scattering (SAXS) were used to study the structure and size of Fe oxy-hydroxide clusters and their transformation products, respectively. Results show that with increasing pH, the particle size and structural order of samples increase, forming solids that resemble 2-line Fh at pH 4.5. The experimental data were compared with X-ray pair distribution functions (PDF) calculated for a range of Fe(III) oxyhydroxide clusters, including Fe 13 Keggin isomers computed previously using density functional theory (DFT), which yielded at best only partial agreement at short range (<5 Å). Aging of the clusters synthesized at pH 1.5 and 2.5 results in growth and transformation via Ostwald ripening to mixtures of goethite (Gt) and lepidocrocite (Lp). This process was inhibited by immediately reacting the early-formed clusters with phosphate (PO 4 3– ), suggesting that oxyanion surface complexes can stabilize the initial clusters by preventing growth and crystallization to more stable phases.

58 GEOSCIENCES↗
DOE OSTI2025

Freeze-induced crystallization: An overlooked pathway for mineral genesis in natural waters

Natural ice plays salient roles in making the Earth habitable and sustainable. Previously overlooked, its role in chemical processes is now of emerging interest, particularly due to the freeze concentration effect, which can substantially promote chemical reactions during ice formation. We demonstrate here that ice formation can serve as a dynamic and unique pathway for mineral genesis. Freezing solutions containing dissolved manganese and carbonates produced rhodochrosite (Mn II CO 3 ) even under slightly undersaturated conditions. At room temperature, by contrast, this occurred when the solution saturation level was increased by ca. 30,000 times. The cryogenic rhodochrosite formed spherical aggregates of nano-polycrystallites, distinctly different from the cubic monocrystalline particles observed at room temperature. The distinct feature likely resulted from the combined effects of the intensified supersaturation induced by the freeze concentration effect and the low temperatures within liquid-like layers, conditions that make liquid-like layers an exceptional environment for mineral genesis, unlike typical natural water systems. The cryogenic rhodochrosite formation was successfully demonstrated using in situ, real-time X-ray absorption spectroscopy (XAS), enabling direct observation of freeze-induced solid formation. In conclusion, our findings reveal that freeze-induced crystallization may be an active mineralization pathway, potentially influencing elemental cycles within the cryosphere and contributing to minerals with distinguishing properties and reactivities in the environment.

Earth, Atmospheric, and Planetary Sciences↗
DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes

Abstract Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500 μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with 13C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100 μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500 μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Direct observation of anisotropic growth of water films on minerals driven by defects and surface tension

Knowledge of the occurrences of water films on minerals is critical for global biogeochemical and atmospheric processes, including element cycling and ice nucleation. The underlying mechanisms controlling water film growth are, however, misunderstood. Using infrared nanospectroscopy, amplitude-modulated atomic force microscopy, and molecular simulations, we show how water films grow from water vapor on hydrophilic mineral nanoparticles. We imaged films with up to four water layers that grow anisotropically over a single face. Growth usually begins from the near edges of a face where defects preferentially capture water vapor. Thicker films produced by condensation cooling completely engulf nanoparticles and form thicker menisci over defects. The high surface tension of water smooths film surfaces and produces films of inhomogeneous thickness. Nanoscale topography and film surface energy thereby control anisotropic distributions and thicknesses of water films on hydrophilic mineral nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

ABSTRACT Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

Lui, Lauren M.↗
DOE OSTI2024

Ultrahigh-resolution mass spectrometry data associated with the manuscript “A functional microbiome catalog crowdsourced from North American rivers"

This data package is associated with the publication “A functional microbiome catalog crowdsourced from North American rivers” submitted to Nature (Borton et al., 2024); (https://www.biorxiv.org/content/10.1101/2023.07.22.550117v1). Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires understanding the spatial drivers of river microbiomes. However, the unifying microbial determinants governing river biogeochemistry are hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we employed a community science effort to accelerate the sampling of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb is a publicly available resource that paves the way for watershed predictive modeling and microbiome-based management practices. This resource profiled the identity, distribution, function, and expression of thousands of microbial genomes across rivers covering 90% of United States watersheds. We identified the most cosmopolitan microbiome members, while also revealing local drivers of strain endemism across ecological dimensions. We provide the first evidence that microbial functional trait expression followed the tenets of the River Continuum Concept, suggesting the structure and function of river microbiomes is predictable. The Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) data were one of many different data types used in establishing the ecological dimensions along which different microbes were detected .This data package only contains the processed FTICR-MS data associated with this manuscript; all other data is accessible via Zenodo (https://zenodo.org/records/8173287), GitHub (https://github.com/jmikayla1991/Genome-Resolved-Open-Watersheds-database-GROWdb), KBase (https://doi.org/10.25982/109073.30/1895615), and NCBI via Bioproject PRJNA946291.This dataset consists of (1) a file-level metadata (flmd) file; (2) a data dictionary (dd) file; (3) a readme; (4) three Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) processed data files (a ‘data’ file containing peak-by-sample observations, a ‘mol’ file containing peak metadata, and a transformation profile containing transformation-by-sample observations). All files are .csv or .pdf.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Perspectives on biorefineries in microbial production of fuels and chemicals

Microbes drive our complex biosphere by regulating the global ecosystem through cycling elements and energy. Humankind has barely begun leveraging this biotransformation capacity to impact global economies and ecologies. Advances in genetic engineering, molecular analysis, metabolic flux modeling, microbial consortia/biome mapping and engineering, cell-free bioproduction, artificial intelligence/machine learning and the ever expanding -omics frontiers have set the stage for paradigm changes to how humankind produces, uses, transforms, and recycles carbon and energy through microbes. Harnessing this enormous potential could drive a global bioeconomy and manage carbon at a planetary level but requires understanding and application at a grand scale across a broad range of science and engineering disciplines. The penultimate manifestation of these advances is the “bio-refinery”, which is often referenced, but is a long way from being fully developed as a global carbon management platform. Broadening the feed stocks, processing operations, and product portfolio to a sequential cascade optimizing the conversion as a whole instead of limited outputs could greatly advance deployment and stability of a bioeconomy.

09 BIOMASS FUELS↗
DOE OSTI2021

A Method to Preserve Wetland Roots and Rhizospheres for Elemental Imaging

Roots extensively interact with their soil environment but visualizing such interactions between roots and the surrounding rhizosphere is challenging. The rhizosphere chemistry of wetland plants is particularly challenging to capture because of steep oxygen gradients from the roots to the bulk soil. Here a protocol is described that effectively preserves root structure and rhizosphere chemistry of wetland plants through slam-freezing and freeze drying. Slam-freezing, where the sample is frozen between copper blocks pre-cooled with liquid nitrogen, minimizes root damage and sample distortion that can occur with flash-freezing while still minimizing chemical speciation changes. While sample distortion is still possible, the ability to obtain multiple samples quickly and with minimal cost increases the potential to obtain satisfactory samples and optimizes imaging time. The data show that this method is successful in preserving reduced arsenic species in rice roots and rhizospheres associated with iron plaques. This method can be adopted for studies of plant-soil relationships in a wide variety of wetland environments that span concentration ranges from trace-element cycling to phytoremediation applications.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

Air cargo: An Integrated Systems View. 1978 Summer Faculty Fellowship Program in Engineering Systems Design

The national air cargo system is analyzed and how it should be in 1990 is prescribed in order to operate successfully through 2015; that is through one equipment cycle. Elements of the system which are largely under control of the airlines and the aircraft manufacturers are discussed. The discussion deals with aircraft, networks, facilities, and procedures. The regulations which govern the movement of air freight are considered. The larger public policy interests which must be served by the kind of system proposed, the air cargo integrated system (ACIS), are addressed. The possible social, economical, political, and environment impacts of the system are considered. Recommendations are also given.

Keaton, A.↗
NASA NTRS1982

Controlled ecological life support system - biological problems

The general processes and controls associated with two distinct experimental paradigms are examined. Specific areas for research related to biotic production (food production) and biotic decomposition (waste management) are explored. The workshop discussions were directed toward Elemental cycles and the biological factors that affect the transformations of nutrients into food, of food material into waste, and of waste into nutrients were discussed. To focus on biological issues, the discussion assumed that (1) food production would be by biological means (thus excluding chemical synthesis), (2) energy would not be a limiting factor, and (3) engineering capacity for composition and leak rate would be adequate.

Moore, B., III↗
NASA NTRS1985

Remote sensing of wetland biomass and productivity for global biosystem research

The study of ecosystem function and the contributions of particular ecosystems to global elemental cycling will require data collection from orbital platforms. Presently used ground sampling techniques are not adequate for large area vegetation assessments. The research was directed toward an understanding of the relationship between spectral radiance and plant canopy biomass. Changes in the architecture of the canopy alters the observed spectral radiance patterns. The green components of a plant canopy interacts most strongly with incident radiation and usually reflect edaphic conditions as they relate to plant vigor. Plant biomass serves as an excellent integrator of the environmental factors encountered by the plant and can be used as an indicator for predicting soil redox, nutrient status, microbial activity, etc. The use was examined of TM spectral data to discriminate biomass classes and, in turn, to relate the biomass classes to the chemical status of the soil. Several preliminary studies have indicated that solar angle can be used to improve biomass predictions. This important observation also suggests that latitudinal extrapolation of the biomass predicting models will be possible if selected characteristics of the incident radiation are known.

Hardisky, M. A.↗
NASA NTRS2001

The Bermuda Bio-Optics Program (BBOP)

The Bermuda Bio-Optics Project (BBOP) is a collaborative effort between the Institute for Computational Earth System Science (ICESS) at the University of California at Santa Barbara (UCSB) and the Bermuda Biological Station for Research (BBSR). This research program is designed to characterize light availability and utilization in the Sargasso Sea, and to provide an optical link by which biogeochemical observations may be used to evaluate bio-optical models for pigment concentration, primary production, and sinking particle fluxes from satellite-based ocean color sensors. The BBOP time-series was initiated in 1992, and is carried out in conjunction with the US JGOFS Bermuda Atlantic Time-series Study (BATS) at the Bermuda Biological Station for Research. The BATS program itself has been observing biogeochemical processes (primary productivity, particle flux at and elemental cycles) in the mesotrophic waters of the Sargasso Sea since 1988. Closely affiliated with BBOP and BATS is a separate NASA-funded study of the spatial variability of biogeochemical processes in the Sargasso Sea using high-resolution Advanced Very High Resolution Radiometer (AVHRR) and Sea-Viewing Wide Field-of-view Sensor (SeaWiFS) data collected at Bermuda. The collaboration between BATS and BBOP measurements has resulted in a unique data set that addresses not only the SIMBIOS goals but also the broader issues of important factors controlling the carbon cycle.

Siegel, David A.↗