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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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26 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1978

The meaning of desert color in earth orbital photographs

The color of desert surfaces as seen in earth orbital photographs is indicative of soil composition. Apollo-Soyuz photographs of the Sturt and Simpson Deserts of Australia confirm that sand grains become redder as the distance from the source increases. Reddening is caused by a thin iron-oxide coating on individual sand grains and can be used, in some cases, to map relative-age zones. Photographs of the Western (Libyan) Desert of Egypt indicate three distinct and nearly parallel color zones that have been correlated in the field with: (1) arable soil composed of quartz, clay, and calcium carbonate particles; (2) relatively active sand with or without sparse vegetation; and (3) relatively inactive sand mixed with dark (desert-varnished) pebbles. The youngest sands are in the form of longitudinal dunes, which are migrating to the south-southeast along the prevailing wind direction. Some of the young dune fields are encroaching on the western boundary of the fertile Nile Valley.

El-Baz, F.↗
NASA NTRS1996

Cellular Precipitates Of Iron Oxide in Olivine in a Stratospheric Interplanetary Dust Particle

The petrology of a massive olivine-sulphide interplanetary dust particle shows melting of Fe,Ni-sulphide plus complete loss of sulphur and subsequent quenching to a mixture of iron-oxides and Fe,Ni-metal. Oxidation of the fayalite component in olivine produced maghemite discs and cellular intergrowths with olivine and rare andradite-rich garnet. Cellular reactions require no long-range solid-state diffusion and are kinetically favourable during pyrometamorphic oxidation. Local melting of the cellular intergrowths resulted in three dimensional symplectic textures. Dynamic pyrometamorphism of this asteroidal particle occurred at approx. 1100 C during atmospheric entry flash (5-15 s) heating.

Rietmeijer, Frans J. M.↗
NASA NTRS2004

Acquisition of a Gas Chromatograph/Mass Spectrometer System for Laboratory Study of Prebiotic Organic Geochemical Processes on the Early Earth, Mars, and Meteorites

This was a major equipment grant that provided funds ($72K) for purchase of a benchtop gas chromatograph-mass spectrometer (GC-MS) for use in experimental studies of prebiotic organic compounds. An Agilent model 689015973 GC-MS was purchased and installed in the PI's lab in August of 2003. The instrument is now being used for a variety of research projects. The primary use of the instrument is to analyze and quantify organic products of laboratory experiments conducted by the PI. One example is shown, which shows organic products (predominantly n-alkanes) formed during Fischer-Tropsch-type abiotic synthesis under hydrothermal conditions. The analytical capabilities of the GC- MS allowed identification of the numerous organic products of this as well as other laboratory experiments. A key use of the instrument in this research is that the mass spectrometer capabilities allow use of isotopically labeled reactants to trace the progress of reactions and evaluate background contaminants. collaborative projects with other scientists involved in exobiology & astrobiology research (e.g., Mitch Schulte, NASA Ames; Katrina Edwards, Woods Hole Oceanographic Institution). For instance, an analysis of membrane lipids of an lithoautotrophic iron-oxidizing bacteria being grown on basalt as a source of metabolic energy, a project where the instrument is being used to evaluate possible biomarker compounds from these organisms is shown. These iron oxidizers are thought to be similar to those living within the ocean crust, and are being investigated as possible analog organisms to those on the early Earth or crust of Mars. The instrument has also been used by an outside investigator (graduate student Brandon Canfeld, Arizona State University) for identification and isotopic characterization of experimental products of abiotic organic synthesis experiments he is conducting with Dr. John Holloway. analysis of quality control samples for other NASA-funded projects. For instance, an analysis of residual hydrocarbon contaminants on the internal surface of the shell of an atmospheric sounding rocket is shown. This analysis was used to help determine the source of the contaminating compounds. In the future, the instrument will continue to be used for quality control analysis in clean rooms and instrument construction facilities within the Laboratory for Atmospheric and Space Physics, where the GC-MS is housed.

McCollom, Thomas↗
NASA NTRS2013

Detecting Nanophase Weathering Products with CheMin: Reference Intensity Ratios of Allophane, Aluminosilicate Gel, and Ferrihydrite

X-ray diffraction (XRD) data collected of the Rocknest samples by the CheMin instrument on Mars Science Laboratory suggest the presence of poorly crystalline or amorphous materials [1], such as nanophase weathering products or volcanic and impact glasses. The identification of the type(s) of X-ray amorphous material at Rocknest is important because it can elucidate past aqueous weathering processes. The presence of volcanic and impact glasses would indicate that little chemical weathering has occurred because glass is highly susceptible to aqueous alteration. The presence of nanophase weathering products, such as allophane, nanophase iron-oxides, and/or palagonite, would indicate incipient chemical weathering. Furthermore, the types of weathering products present could help constrain pH conditions and identify which primary phases altered to form the weathering products. Quantitative analysis of phases from CheMin data is achieved through Reference Intensity Ratios (RIRs) and Rietveld refinement. The RIR of a mineral (or mineraloid) that relates the scattering power of that mineral (typically the most intense diffraction line) to the scattering power of a separate mineral standard such as corundum [2]. RIRs can be calculated from XRD patterns measured in the laboratory by mixing a mineral with a standard in known abundances and comparing diffraction line intensities of the mineral to the standard. X-ray amorphous phases (e.g., nanophase weathering products) have broad scattering signatures rather than sharp diffraction lines. Thus, RIRs of X-ray amorphous materials are calculated by comparing the area under one of these broad scattering signals with the area under a diffraction line in the standard. Here, we measured XRD patterns of nanophase weathering products (allophane, aluminosilicate gel, and ferrihydrite) mixed with a mineral standard (beryl) in the CheMinIV laboratory instrument and calculated their RIRs to help constrain the abundances of these phases in the Rocknest samples.

Rampe, E. B.↗
NASA NTRSDate not supplied

WEATHERING ON VENUS: CONSTRAINTS FROM MODEL AND EXPERIMENTAL RESULTS

The surface of Venus is in contact with a hot (~470° C), high pressure (92 bars), and caustic (CO2 with S) atmosphere, which should cause progressive alteration of the crust [1, 2]. Alteration should form rock coatings of iron-oxides and sulfates, since water is not stable on the surface to make clay minerals [1, 3]. These coatings could, in theory, be used as a way to age date different lava flows, since the amount of alteration should correlate with the age of the rock exposed to the atmosphere [4, 5]. However, the exact alteration mineralogy and rate are still not well constrained [5]. Further, how the alteration mineralogy affects orbital emissivity measurements of the Venus surface is similarly not well understood [6]. Here we review the recent geochemical modeling [1, 7] and experimental [8-15] studies to constrain the main alteration minerals, potential alteration rates, and open questions about the surface mineralogy of Venus.

J. Filiberto↗
DOE OSTI2020

Electron transfer calculations between edge sharing octahedra in hematite, goethite, and annite

A key reaction underlying the charge transport in iron containing oxides, clays, micas is the Fe$^{2+}$-Fe$^{3+}$ exchange reaction between edge-sharing iron octahedra. These reactions facilitate conduction in these minerals by the thermally-activated hopping of small polarons across the lattice. Depending on the mineral and local charge state the small polaron can either encase an electron or hole. The probability for conduction of small polarons depends strongly on the height and adiabicity of the reaction barrier, with larger and more diabatic barriers yielding slow conduction associated with either weak coupling or a large prerequisite rearrangement of the lattice during charge transport. To model these reactions, a first principle electron transfer (ET) method was developed to model the small polaron hopping between the edge-sharing octahedra sites in hematite ($e^{-}$ polaron), goethite ($e^{-}$ polaron), and annite ($h^{+}$ polaron) bulk structures. The ET method is based on electronic structure methods (i.e., plane-wave Density Functional Theory) capable of performing calculations with periodic cells and large size systems efficiently while at the same time being accurate enough to be used in the estimation of the electron-transfer coupling matrix element, $V_{AB}$, and the electron transfer transmission factor, $\kappa_{el}$. Additionally, the calculations confirmed the existence of small polarons in all three minerals, and the reactions were predicted to be strongly adiabatic. It was found that transfer of a hole in the octahedral layer of annite had an adiabatic barrier of $0.311$ eV, and the transfer of an extra electron in hematite and goethite had adiabatic barriers of $0.242$ eV and $0.232$ eV respectively. The electronic coupling parameters,$V_{AB}$, were found to be $0.188$ eV, $0.196$ eV, and $0.102$ eV respectively for hematite, goethite, and annite. While similar bonding topologies pertain, the underlying basis for the differences is the subtle differences in local structures.

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

Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon

ABSTRACT Leptothrix ochracea creates distinctive iron-mineralized mats that carpet streams and wetlands. Easily recognized by its iron-mineralized sheaths, L. ochracea was one of the first microorganisms described in the 1800s. Yet it has never been isolated and does not have a complete genome sequence available, so key questions about its physiology remain unresolved. It is debated whether iron oxidation can be used for energy or growth and if L. ochracea is an autotroph, heterotroph, or mixotroph. To address these issues, we sampled L. ochracea -rich mats from three of its typical environments (a stream, wetlands, and a drainage channel) and reconstructed nine high-quality genomes of L. ochracea from metagenomes. These genomes contain iron oxidase genes cyc2 and mtoA, showing that L. ochracea has the potential to conserve energy from iron oxidation. Sox genes confer potential to oxidize sulfur for energy. There are genes for both carbon fixation (RuBisCO) and utilization of sugars and organic acids (acetate, lactate, and formate). In silico stoichiometric metabolic models further demonstrated the potential for growth using sugars and organic acids. Metatranscriptomes showed a high expression of genes for iron oxidation; aerobic respiration; and utilization of lactate, acetate, and sugars, as well as RuBisCO, supporting mixotrophic growth in the environment. In summary, our results suggest that L. ochracea has substantial metabolic flexibility. It is adapted to iron-rich, organic carbon-containing wetland niches, where it can thrive as a mixotrophic iron oxidizer by utilizing both iron oxidation and organics for energy generation and both inorganic and organic carbon for cell and sheath production. IMPORTANCE Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea , which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.

59 BASIC BIOLOGICAL SCIENCES↗