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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 1,207 records · Page 67
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons

Abstract Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Determination of X-ray detection limit and applications in perovskite X-ray detectors

X-ray detection limit and sensitivity are important figure of merits for perovskite X-ray detectors, but literatures lack a valid mathematic expression for determining the lower limit of detection for a perovskite X-ray detector. In this work, we present a thorough analysis and new method for X-ray detection limit determination based on a statistical model that correlates the dark current and the X-ray induced photocurrent with the detection limit. The detection limit can be calculated through the measurement of dark current and sensitivity with an easy-to-follow practice. Alternatively, the detection limit may also be obtained by the measurement of dark current and photocurrent when repeatedly lowering the X-ray dose rate. While the material quality is critical, we show that the device architecture and working mode also have a significant influence on the sensitivity and the detection limit. Our work establishes a fair comparison metrics for material and detector development.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations and developmental dynamics. Integrative analysis of the interactome with previous epigenome and transcriptome datasets from the same tissues revealed a strong correlation between the chromatin contacts and chromatin state at distal enhancers, as well as gene expression patterns at predicted target genes. We predicted target genes of 15,098 candidate enhancers and used them to annotate target genes of homologous candidate enhancers in the human genome that harbor risk variants of human diseases. We present evidence that schizophrenia and other adult disease risk variants are frequently found in fetal enhancers, providing support for the hypothesis of fetal origins of adult diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Effects of Al concentration on the structure and conductivity of lithium lanthanum zirconium oxide

Cubic Li 7-3x Al x La 3 Zr 2 O 12 (LLZO) is a promising, next-generation solid electrolyte due to its stability with Li-metal and high bulk conductivity (~1 mS cm -1 ). However, the source of the high conductivity is not completely understood. In this work, we address this key knowledge gap through the integration of elemental analysis, neutron diffraction sensitive to Li and O atoms, and impedance spectroscopy to understand the structure–property correlations for LLZO. We show the metal–oxygen framework structure remains constant with variation in Al substitution, resulting in a constant activation energy of ~0.35 eV and little effect on the bulk conductivity. Instead, Li concentration, Al blocking and trapping of mobile defects, and Li–Li nearest neighbor interactions largely control the Al substituted LLZO bulk conductivity, resulting in decreases from 0.73 to 0.22 mS cm -1 as the Al concentration increases from 0.17 to 0.32 mol. These results differ from those of Ta substituted LLZO, where the framework structure and Li–Li site distances play large roles in controlling the conductivity. The increased understanding of the controlling factors of conductivity allows for greater ability to tailor the design of and substitution into the LLZO structure for improved conductivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The influence of counterion structure identity on conductivity, dynamical correlations, and ion transport mechanisms in polymerized ionic liquids

We used equilibrium and non-equilibrium atomistic simulations to probe the influence of anion chemistry on the true conductivity, dynamical correlations, and ion transport mechanisms in polymeric ionic liquids. An inverse correlation was found between anion self-diffusivities, ionic mobilities, and the anion size for spherical anions. While some larger asymmetric anions had higher diffusivities than smaller spherical anions, their diffusivities and mobilities did not exhibit a direct correlation to the anion volumes. Here, the conductivity and anion dynamical correlations also followed the same trends as displayed by the diffusivity and mobility of anions. All the systems we examined displayed positively correlated motion among anions, suggesting a contribution that enhances the conductivity beyond the ideal Nernst–Einstein value. Analysis of ion transport mechanisms demonstrated very similar hopping characteristics among the spherical anions despite differences in their sizes.

36 MATERIALS SCIENCE↗
DOE OSTI2023

In-situ coating of silicon-rich films on tokamak plasma-facing components with real-time Si material injection

Abstract Experiments have been conducted in the DIII-D tokamak to explore the in-situ growth of silicon-rich layers as a potential technique for real-time replenishment of surface coatings on plasma-facing components (PFCs) during steady-state long-pulse reactor operation. Silicon (Si) pellets of 1 mm diameter were injected into low- and high-confinement (L-mode and H-mode) plasma discharges with densities ranging from 3.9– 7.5 × 10 19 m −3 and input powers ranging from 5.5 to 9 MW. The small Si pellets were delivered with the impurity granule injector at frequencies ranging from 4 to 16 Hz corresponding to mass flow rates of 5–19 mg s −1 (1– 4.2 × 10 20 Si s −1 ) at cumulative amounts of up to 34 mg of Si per five-second discharge. Graphite samples were exposed to the scrape-off layer and private flux region plasmas through the divertor material evaluation system to evaluate the Si deposition on the divertor targets. The Si II emission at the sample correlates with silicon injection and suggests net surface Si-deposition in measurable amounts. Post-mortem analysis showed Si-rich coatings containing silicon oxides, of which SiO 2 is the dominant component. No evidence of SiC was found, which is attributed to low divertor surface temperatures. The in-situ and ex-situ analysis found that Si-rich coatings of at least 0.4–1.2 nm thickness have been deposited at 0.4–0.7 nm s −1 . The technique is estimated to coat a surface area of at least 0.94 m 2 on the outer divertor. These results demonstrate the potential of using real-time material injection to form Si-enriched layers on divertor PFCs during reactor operation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Precise relative magnitude measurement improves fracture characterization during hydraulic fracturing

SUMMARY Microseismic monitoring is an important technique to obtain detailed knowledge of in-situ fracture size and orientation during stimulation to maximize fluid flow throughout the rock volume and optimize production. Furthermore, considering that the frequency of earthquake magnitudes empirically follows a power law (i.e. Gutenberg–Richter), the accuracy of microseismic event magnitude distributions is potentially crucial for seismic risk management. In this study, we analyse microseismicity observed during four hydraulic fracture treatments of the legacy Cotton Valley experiment in 1997 at the Carthage gas field of East Texas, where fractures were activated at the base of the sand-shale Upper Cotton Valley formation. We perform waveform cross-correlation to detect similar event clusters, measure relative amplitude from aligned waveform pairs with a principal component analysis, then measure precise relative magnitudes. The new magnitudes significantly reduce the deviations between magnitude differences and relative amplitudes of event pairs. This subsequently reduces the magnitude differences between clusters located at different depths. Reduction in magnitude differences between clusters suggests that some attenuation-related biases could be effectively mitigated with relative magnitude measurements. The maximum likelihood method is applied to understand the magnitude frequency distributions and quantify the seismogenic index of the clusters. Statistical analyses with new magnitudes suggest that fractures that are more favourably oriented for shear failure have lower b-value and higher seismogenic index, suggesting higher potential for relatively larger earthquakes, rather than fractures subparallel to maximum horizontal principal stress orientation.

58 GEOSCIENCES↗
DOE OSTI2020

Imaging systematics and clustering of DESI main targets

ABSTRACT We evaluate the impact of imaging systematics on the clustering of luminous red galaxies (LRG), emission-line galaxies (ELG), and quasars (QSO) targeted for the upcoming Dark Energy Spectroscopic Instrument (DESI) survey. Using Data Release 7 of the DECam Legacy Survey, we study the effects of astrophysical foregrounds, stellar contamination, differences between north galactic cap and south galactic cap measurements, and variations in imaging depth, stellar density, galactic extinction, seeing, airmass, sky brightness, and exposure time before presenting survey masks and weights to mitigate these effects. With our sanitized samples in hand, we conduct a preliminary analysis of the clustering amplitude and evolution of the DESI main targets. From measurements of the angular correlation functions, we determine power law fits $r_0 = 7.78 \pm 0.26\, h^{-1}$Mpc, γ = 1.98 ± 0.02 for LRGs and $r_0 = 5.45 \pm 0.1\, h^{-1}$Mpc, γ = 1.54 ± 0.01 for ELGs. Additionally, from the angular power spectra, we measure the linear biases and model the scale-dependent biases in the weakly non-linear regime. Both sets of clustering measurements show good agreement with survey requirements for LRGs and ELGs, attesting that these samples will enable DESI to achieve precise cosmological constraints. We also present clustering as a function of magnitude, use cross-correlations with external spectroscopy to infer dN/dz and measure clustering as a function of luminosity, and probe higher order clustering statistics through counts-in-cells moments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Using lower-redshift, non-CMB, data to constrain the Hubble constant and other cosmological parameters

Here we use updated Hubble parameter and baryon acoustic oscillation data, as well as other lower-redshift Type Ia supernova, Mg ii reverberation-measured quasar, quasar angular size, H ii starburst galaxy, and Amati-correlated gamma-ray burst data, to jointly constrain cosmological parameters in six cosmological models. The joint analysis provides model-independent determinations of the Hubble constant, H 0 = 69.7 ± 1.2 km s -1 Mpc -1 , and the current non-relativistic matter density parameter, Ω m0 = 0.295 ± 0.017. These error bars are factors of 2.2 and 2.3 larger than the corresponding error bars in the flat ΛCDM model from Planck TT,TE,EE+lowE+lensing cosmic microwave background anisotropy data. Based on the deviance information criterion (DIC), the flat ΛCDM model is most favored but mild dark energy dynamics and a little spatial curvature are not ruled out.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Transitioning from Stage-III to Stage-IV: cosmology from galaxy×CMB lensing and shear×CMB lensing

ABSTRACT We examine the cosmological constraining power from two cross-correlation probes between galaxy and cosmic microwave background (CMB) surveys: the cross-correlation of lens galaxy density with CMB lensing convergence 〈δgκCMB〉, and source galaxy weak lensing shear with CMB lensing convergence 〈γκCMB〉. These two cross-correlation probes provide an independent cross-check of other large-scale structure constraints and are insensitive to galaxy-only or CMB-only systematic effects. In addition, when combined with other large-scale structure probes, the cross-correlations can break degeneracies in cosmological and nuisance parameters, improving both the precision and robustness of the analysis. In this work, we study how the constraining power of 〈δgκCMB〉 + 〈γκCMB〉 changes from Stage-III (ongoing) to Stage-IV (future) surveys. Given the flexibility in selecting the lens galaxy sample, we also explore systematically the impact on cosmological constraints when we vary the redshift range and magnitude limit of the lens galaxies using mock galaxy catalogs. We find that in our setup, the contribution to cosmological constraints from 〈δgκCMB〉 and 〈γκCMB〉 are comparable in the Stage-III data sets; but in Stage-IV surveys, the noise in 〈δgκCMB〉 becomes subdominant to cosmic variance, preventing 〈δgκCMB〉 to further improve the constraints. This implies that to maximize the cosmological constraints from future 〈δgκCMB〉 + 〈γκCMB〉 analyses, we should focus more on the requirements on 〈γκCMB〉 instead of 〈δgκCMB〉. Furthermore, the selection of the lens sample should be optimized in terms of our ability to characterize its redshift or galaxy bias instead of its number density.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Role of the likelihood for elastic scattering uncertainty quantification

In the last decade, uncertainty quantification (UQ) for optical model potentials (OMPs) has become a focal point for nuclear reaction theory, and several competing approaches for OMP UQ have recently been developed. Here, we clarify recent efforts to compare frequentist and Bayesian approaches in the context of OMP UQ [G. B. King et al., Phys. Rev. Lett. 122, 232502 (2019)]. We replicate a portion of that OMP UQ study but use independent statistical tools. Specifically, we compare two methods for OMP parameter inference from elastic scattering data: the Levenberg-Marquardt algorithm for χ 2 minimization on one hand and Markov chain Monte Carlo (MCMC) sampling on the other. Separately, we assess the common practice of using a renormalized likelihood (χ 2 /N), N being the number of data points, instead of the canonical weighted-least-squares likelihood (χ 2 ), as a way of accounting for unknown data correlations. Here, we show that for a generic linear model and for a five-parameter OMP analysis, frequentist and uniform-prior Bayesian approaches recover the same optimum and uncertainty estimates—not systematically larger uncertainties for the Bayesian approach, as was concluded in G. B. King et al., Phys. Rev. Lett. 122, 232502 (2019). Further, we show that if an additional, near-degenerate parameter is introduced into the same OMP analysis such that the parameter posterior becomes non-Gaussian, then covariance-based estimates of uncertainty become unreliable. Finally, we show that regardless of optimization approach, if χ 2 /N is used for the likelihood, the resulting parametric uncertainties increase by $\sqrt{N}$, and that this is responsible for the conclusions drawn in the revisited study. Based on our replication results, we find that a fortuitous cancellation of unreported errors and the renormalization factor can lead to improvement in empirical coverages, as was the case in the original comparative study. We emphasize that developing and applying a realistic likelihood function is an essential task in a UQ analysis, and that several recent UQ studies that employed a renormalized likelihood (i.e., including a 1/N factor) may have yielded unrealistically large uncertainties for elastic-scattering observables. If the parameter posterior deviates from multivariate-normal, a sampling-based approach like MCMC has a clear advantage over methods that assume the Laplace approximation holds. We note that empirical coverage can serve as an important internal check for the analyst whose model or data may have additional, unaccounted-for uncertainties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Revisiting metastable immiscibility in SiO 2 –Al 2 O 3 : Structure and phase separation of supercooled liquids and glasses

Understanding and controlling liquid–liquid phase separation in aluminosilicates is crucial for optimizing glass properties. However, the metastable nature of aluminosilicates’ phase separation has made it difficult to study experimentally, and uncertainty persists regarding the compositional and temperature extents of the miscibility gap. Here, we present new experimental evidence that suggests a consolute temperature between 1440 and 1590°C and endmember compositions of 7 and 62 mol.% Al 2 O 3 for the phase-separated glasses. Using containerless melt processing, deeply supercooled liquids over the 0–60 mol.% Al 2 O 3 range are probed with in situ small- and wide-angle X-ray scattering, which simultaneously reveals changes in nanoscale density heterogeneity and atomic structure. Correlations between phase separation and atomic coordination environments are compared for liquids and glasses. Pair distribution function analysis shows mean O–(Si + Al) coordination increases with Al 2 O 3 content and decreases with temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Benchmarking large language models for materials synthesis: The case of atomic layer deposition

In this work, we introduce an open-ended question benchmark, ALDbench, to evaluate the performance of large language models (LLMs) in materials synthesis, and, in particular, in the field of atomic layer deposition, a thin film growth technique used in energy applications and microelectronics. Our benchmark comprises questions with a level of difficulty ranging from the graduate level to domain expert current with the state of the art in the field. Human experts reviewed the questions along the criteria of difficulty and specificity, and the model responses along four different criteria: overall quality, specificity, relevance, and accuracy. We ran this benchmark on an instance of OpenAI’s GPT-4o. The responses from the model received a composite quality score of 3.7 on a 1–5 scale, consistent with a passing grade. However, 36% of the questions received at least one below average score. An in-depth analysis of the responses identified at least five instances of suspected hallucination. Finally, we observed statistically significant correlations between the difficulty of the question and the quality of the response, the difficulty of the question and the relevance of the response, the specificity of the question, and the accuracy of the response as graded by the human experts. Furthermore, this emphasizes the need to evaluate LLMs across multiple criteria beyond difficulty or accuracy.

Artificial intelligence↗
DOE OSTI2023

A “Master Curve” Describing Reaction Inhomogeneity and Plating Onset during Fast-Charging of Graphite Electrodes

Lithium plating in porous graphite electrodes is a major limitation for fast charging. Theoretical evidence suggests plating during fast charging is largely due to inhomogeneous intercalation through the electrode thickness (caused by ionic/mass transfer limitations and inherent thermodynamic properties of the graphite material). Numerical and analytical predictions of plating onset during fast charging have been proposed but not compared directly with experiments. This work validates these model predictions against plating onset measurements via the “dOCV” method in graphite half-cells, for various electrode thicknesses and C-rates. Remarkably, it is shown that experimental and theoretical trends in plating onset (vs C-rate and electrode thickness) collapse to a single “master curve” using a nondimensional “reaction inhomogeneity” parameter. This observation supports the hypothesized reaction inhomogeneity mechanism for accelerating plating onset and provides practical guidance for electrode design. Furthermore, this work develops theory to quantify reaction inhomogeneity in situ directly from voltage V vs capacity Q data, using dQ / dV analysis. Here again, experiments and numerical predictions show good agreement, where peaks that correspond to LiC 6 correlate with plating onset. This work provides experimental validation of theoretical tools that can predict plating onset, aid electrode design, and give insight for plating onset mechanisms during fast charging.

25 ENERGY STORAGE↗
DOE OSTI2020

Screening IMS Seismic Detections using Dynamic Correlation Processor: Progress report for 2020

LLNL completed the FY20 workplan entailing application of the Dynamic Correlation Processor (DCP) to International Monitoring System (IMS) primary seismic data in 2019 and 2020. The effective analysis period was curtailed to January 1 through November 12, 2019 due to a data compression change that rendered later data unusable. Fixing the data compression error is a priority for our data source, and we plan to extend the period of data analysis when the fix is implemented. We found that the percentage overlap between detections generated by the International Data Centre (IDC) DFX software and detections generated by DCP varied widely by station. Overlap is 30-40% at some stations, suggesting that a large percentage of DFX detections could be screened (removed) from the detection-event association algorithm. However, detection overlap was much lower, a few percent, at many stations and the percentage overlap was low at stations known to have many mines and other local sources of seismicity. Unexpectedly low detection overlap at many stations prompted us to examine results for the ARCES station in detail. There is considerable mine activity near ARCES, but our initial FY20 analysis found only ~2% DCP/DFX detection overlap. Differences in the pre-processing (e.g. beam recipes) used by DCP and DFX appear to be the cause of low detection overlap at ARCES. DCP uses wideband filters to improve detector robustness and the IDC uses narrow-band pre-filtering to improve sensitivity. After reprocessing ARCES using the IDC beam recipe, DCP/DFX overlap increased to ~74%. This result shows that we must reprocess the IMS network using the IDC station-specific beam recipes if we are to effectively screen DFX detections and improve automatic event building performance at the IDC.

58 GEOSCIENCES↗
DOE OSTI2021

Controlled Pyroshock Test Transients Can Be Used To Better Match Operational Shock Transients and Reduce Artificial Pyroshock Test Failures [Slides]

Shock analysis is typically done via SRS (shock response spectrum). Oftentimes shock analysis is not performed because most loads specifications only supply SRS requirements with no representative shock transients that can be used for analysis. SRS analysis is too conservative. There is no structural dynamics involved as all modes are assumed to have peak responses simultaneously and in-phase with each other. It is possible that all other loads and combination of loads show the design to be good, whereas SRS analysis (1000 g’s are involved) results may require redesign. Multiple shock transients can satisfy a SRS, yet most loads documents don’t provide a representative shock transient that could be used for shock analysis. Shock testing is less common than harmonic and random vibration testing. Engineers typically go into shock tests with very little knowledge of what to expect. A pass/fail type of approach with very little engineering done to prepare for the test or to control the type of shock transient is used. Most engineers will not model the shock test fixture due to lack of knowledge about the details of the test setup. Shock analysis and testing is often an open loop type situation with no test setup modeling, no test correlation, and no control over the test shock transient. In this work, if we can create applied test force transient that comes close to matching calculated force transient then a more reasonable acceleration transient will be created at the test reference accelerometer that better matches operational shocks.

42 ENGINEERING↗
DOE OSTI2022

Transitioning from Stage-III to Stage-IV: Cosmology from galaxy×CMB lensing and shear×CMB lensing (Final Report for Grant SC0021429 "Cosomology with Galaxy and CMB Surveys: Mitigating Systematic Effects Through Combining Datasets")

We examine the cosmological constraining power from two cross-correlation probes between galaxy and cosmic microwave background (CMB) surveys: the cross-correlation of lens galaxy density with CMB lensing convergence $\langle δ_g$$^κ\text{CMB}\rangle$, and source galaxy weak lensing shear with CMB lensing convergence $\langle^{γκ}$$_{\text{CMB}}\rangle$. These two cross-correlation probes provide an independent cross-check of other large-scale structure constraints and are insensitive to galaxy-only or CMB-only systematic effects. In addition, when combined with other large-scale structure probes, the cross-correlations can break degeneracies in cosmological and nuisance parameters, improving both the precision and robustness of the analysis. In this work, we study how the constraining power of $\langle δ_g$$^κ\text{CMB}\rangle + \langle^{γκ}$$_{\text{CMB}}\rangle$ changes from Stage-III (ongoing) to Stage-IV (future) surveys. Given the flexibility in selecting the lens galaxy sample, we also explore systematically the impact on cosmological constraints when we vary the redshift range and magnitude limit of the lens galaxies using mock galaxy catalogs. We find that in our setup, the contribution to cosmological constraints from $\langle δ_g$$^κ\text{CMB}\rangle$ and $\langle^{γκ}$$_{\text{CMB}}\rangle$ are comparable in the Stage-III data sets; but in Stage-IV surveys, the noise in$\langle δ_g$$^κ\text{CMB}\rangle$ becomes subdominant to cosmic variance, preventing $\langle δ_g$$^κ\text{CMB}\rangle$ to further improve the constraints. This implies that to maximize the cosmological constraints from future $\langle δ_g$$^κ\text{CMB}\rangle$ + $\langle^{γκ}$$_{\text{CMB}}\rangle$ analyses, we should focus more on the requirements on$^{γκ}$$_{\text{CMB}}\rangle$ instead of$\langle δ_g$$^κ\text{CMB}\rangle$. Furthermore, the selection of the lens sample should be optimized in terms of our ability to characterize its redshift or galaxy bias instead of its number density.

79 ASTRONOMY AND ASTROPHYSICS↗
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↗