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All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

Global Energetics of Solar Flares: Nonthermal Energies - Part III

This study entails the third part of a global flare energetics project, in which Ramaty High-Energy Solar Spectroscopic Imager (RHESSI) data of 191 M and X-class flare events from the first 3.5 years of the Solar Dynamics Observatory mission are analyzed. We fit a thermal and a nonthermal component to RHESSI spectra, yielding the temperature of the differential emission measure (DEM) tail, the nonthermal power-law slope and flux, and the thermal nonthermal cross-over energy eco. From these parameters, we calculate the total nonthermal energy E(sub nt) in electrons with two different methods: (1) using the observed cross-over energy e(sub co) as low-energy cutoff, and (2) using the low-energy cut off e(sub wt) predicted by the warm thick-target bremsstrahlung model of Kontar et al. Based on a mean temperature of T(sub e) = 8.6 MK in active regions, we find low-energy cutoff energies of e(sub wt) = 6.2 +/-1.6 keV for the warm-target model, which is significantly lower than the cross-over energies e(sub co) = 21 +/- 6 keV. Comparing with the statistics of magnetically dissipated energies E(sub mag) and thermal energies E(sub th) from the two previous studies, we find the following mean (logarithmic) energy ratios with the warm-target model: E(sub nt) = 0.41E(sub mag), E(sub th) = 0.08 E(sub mag), and E(sub th) = 0.15 E(sub nt). The total dissipated magnetic energy exceeds the thermal energy in 95% and the nonthermal energy in 71% of the flare events, which confirms that magnetic reconnection processes are sufficient to explain flare energies. The nonthermal energy exceeds the thermal energy in 85% of the events, which largely confirms the warm thick-target model.

Aschwanden, Markus J.↗
NASA NTRS2020

Optical Follow-Up of the Neutron Star-Black Hole Mergers S200105ae and S200115j

LIGO and Virgo’s third observing run revealed the first neutron star–black hole (NSBH) merger candidates in gravitational waves. These events are predicted to synthesize r-process elements creating optical/near-infrared ‘kilonova’ emission. The joint gravitational wave and electromagnetic detection of an NSBH merger could be used to constrain the equation of state of dense nuclear matter, and independently measure the local expansion rate of the Universe. Here, we present the optical follow-up and analysis of two of the only three high-significance NSBH merger candidates detected to date, S200105ae and S200115j, with the Zwicky Transient Facility. The Zwicky Transient Facility observed ~48% of S200105ae and ~22% of S200115j’s localization probabilities, with observations sensitive to kilonovae brighter than −17.5 mag fading at 0.5 mag d−1 in the g- and r-bands; extensive searches and systematic follow-up of candidates did not yield a viable counterpart. We present state-of-the-art kilonova models tailored to NSBH systems that place constraints on the ejecta properties of these NSBH mergers. We show that with observed depths of apparent magnitude ~22 mag, attainable in metre-class, wide-field-of-view survey instruments, strong constraints on ejecta mass are possible, with the potential to rule out low mass ratios, high black hole spins and large neutron star radii.

Shreya Anand↗
NASA NTRS2021

The Enigmatic Brown Dwarf WISEA J153429.75-104303.3 (a.k.a. "The Accident")

Continued follow-up of WISEA J153429.75−104303.3, announced in Meisner et al., has proven it to have an unusual set of properties. New imaging data from Keck/MOSFIRE and HST/WFC3 shows that this object is one of the few faint proper motion sources known withJ−ch2>8 mag, indicating a very cold temperature consistent with the latest known Y dwarfs. Despite this, it has W1−W2 and ch1−ch2 colors∼1.6 mag bluer than a typical Y dwarf. A new trigonometric parallax measurement from a combination of WISE, Spitzer, and HST astrometry confirms a nearby distance of-+16.31.21.4pc and a large transverse velocity of 207.4±15.9 km s−1. The absoluteJ,W2, and ch2 magnitudes are in line with the coldest known Y dwarfs, despite the highly discrepant W1−W2 andch1−ch2 colors. We explore possible reasons for the unique traits of this object and conclude that it is most likely an old, metal-poor brown dwarf and possibly the first Y subdwarf. Given that the object has an HST F110Wmagnitude of 24.7 mag, broadband spectroscopy and photometry from JWST are the best options for testing this hypothesis

J Davy Kirkpatrick↗
DOE OSTI2025

Metagenome-assembled genomes measured at 3 depths during snowmelt period in East River, CO (March, May, and June, September 2017)

Snowmelt is a critical biogeochemical period that accounts for large nitrogen (N) export events from high-elevation watersheds. Soil microbial populations bloom and immobilize N during snowmelt, yet the population size crashes in spring, which releases a pulse of soil N. We sought to discover the N sources fueling this microbial bloom and determine the fate of N following microbial die-off. Here, focusing on the snowmelt period within a headwater catchment of the Upper Colorado River Basin (East River, CO), we deployed strain-resolved metagenomics to identify the metabolic pathways and processes that mobilize soil N during and after snowmelt. Soil metagenome samples were taken from 6 snowpits from 3 depths (0-5cm, 5-15cm, >15cm) at 4 time points during snowmelt period (March 2017, May 2017, and June 2017, September 2017) generating 48 metagenomes. We reconstructed 474 metagenome-assembled genomes (MAGs) across all metagenomes.All 48 metagenomes were sequenced at JGI and raw data can be found under JGI (Joint Genome Institute) GOLD Study Gs0135149. Metagenome assemblies from IMG under the same study were used for genome binning. This dataset (1) a zip file of 474 MAGs (as fasta files, Gs0135149_bins_tar.gz), (2) sample metadata file with sample IGSNs (International Generic Sample Numbers) (samples.csv), (3) bounding box coordinates for the sampled locations (Gs0135149.kml), (4) metagenome metadata file listing IMG/M (Integrated Microbial Genomes/Metagenomes) metagenome accessions linking samples to metagenomes (metagenomes.csv), (5) location metadata file (locations.csv), (6) file-level metadata file (flmd.csv) and (7) data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled genomes from topsoils along a hillslope water gradient across early snowmelt to late summer in East River, CO

Drought is changing the American Mountain West at unprecedented rates with unknown consequences to soil microbiome composition and function. As a part of LBNL Watershed Science Focus Area (SFA), we investigated shifts in microbial community and transcriptional activity on a subalpine conifer-meadow transition zone throughout the summer of 2023 as soil dried down. This work took place in Crested Butte, CO on Snodgrass mountain, using a proxy for drought conditions.Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal community at 0-10cm from three sites along a hillslope water gradient across five timepoints from early snowmelt to late summer. 42 metagenomes were sequenced at Joint Genome Institute (JGI) and can be found under the JGI GOLD (Genomes Online Database) sequencing project Gs0166660. Metagenomes were assembled through an inhouse pipeline (see methods), binned using four autobinners (concoct, maxbin2, metabat2, and vamb) and consolidated using dastool. The consolidated bins from all metagenomes were pooled, filtered by completeness (>70%) and contamination (<10%), and dereplicated at 95% ANI using drep. This dataset (1) a zip file of 157 MAGs (as fasta files, Gs0166660_bins_tar.gz), (2) sample metadata file with sample IGSNs (International Generic Sample Numbers) (samples.csv), (3) bounding box coordinates for the sampled locations (Gs0166660.kml), (4) metagenome assembly and coassembly metadata file listing IMG/M (Integrated Microbial Genomes/Metagenomes) metagenome accessions linking samples to metagenomes (EastRiver_Drought_ESSDive_Metadata.csv), (5) location metadata file (locations.csv), (6) file-level metadata file (flmd.csv) and (7) data dictionary (dd.csv) file.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled genomes from topsoils collected during NEON campaign in East River, CO (06/14/2018-06/28/2018)

The Watershed Function Science Focus Area (WF SFA) at Lawrence Berkeley National Lab is working to build a mechanistic understanding of the distribution and dynamics of biogeochemical processes in mountainous watersheds and their response to perturbation. In June 2018, the NEON (National Ecological Observatory Network) Airborne Observatory Platform (AOP) performed a taskable airborne imaging campaign to collect visible to shortwave infrared (VSWIR) imaging spectroscopy and LiDAR data across 330 km2 in the Upper East River at Crested Butte, CO. We conducted a parallel ground sampling campaign to sample vegetation traits, as well as soil physical, chemical, and microbiological characteristics. We collected these samples from 438 sites across 12 locations spanning much of the elevation, topographic, and geologic variability across the study area. A subset of 250 samples were used for soil metagenomics which is presented here. In addition, at each site, vegetation samples were collected to measure species-specific leaf water content and leaf mass area, foliar elemental composition and foliar CN stable isotope ratios. Soil samples were collected to measure soil physical properties which include bulk density and soil texture analysis. A suite of soil chemical properties was measured from the samples collected at each site, including pH, organic matter, concentrations exchangeable cations, total elemental composition, and the concentrations of extractable N pools (e.g. total free amino acids, ammonium, nitrate, dissolved organic N, and total dissolved N). Additionally, we have measured soil microbial biomass CN stoichiometry. Here, we present 1982 metagenome-assembled genomes (MAGs) for the bacterial and archaeal community from topsoil collected from during NEON 2018 campaign. All metagenomes were sequenced at JGI (Joint Genome Institute) (GOLD Study ID: Gs0149986). Metagenomes were assembled using JGI Metagenome Workflow (10.1128/mSystems.00804-20). The dataset includes (1) zip files for 1982 MAG fasta files (neon_genomes1-5.tar.gz, split into 5 tarballs to keep tarballs under 0.5 GB), (2) neon_Gs0149986_samples_soilproperties_metagenomes.csv: the sample information together with the accession numbers for the underlying metagenomes and the associated soil physical and chemical measurements in NMDC (National Microbiome Data Collaborative) compliant format, (3) neon_Gs0149986.kml: location bounding box file for the sampled locations, (4) samples.csv: sample metadata file used to register Internationall Generic Sample Numbers (IGSNs), (5) flmd.csv: file level metadata file, and (6) dd.csv: data dictionary file. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2025

Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge

Abstract Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.

Science & Technology - Other Topics↗
DOE OSTI2024

SN 2021adxl: A luminous nearby interacting supernova in an extremely low-metallicity environment

SN 2021adxl is a slowly evolving, luminous, Type IIn supernova with asymmetric emission line profiles, similar to the well-studied SN 2010jl. We present extensive optical, near-ultraviolet, and near-infrared photometry and spectroscopy covering ∼1.5 years post discovery. SN 2021adxl occurred in an unusual environment, atop a vigorously star-forming region that is offset from its host galaxy core. The appearance of Ly α and O II , as well as the compact core, would classify the host of SN 2021adxl as a “Blueberry” galaxy, analogous to higher redshift, low-metallicity, star-forming dwarf “Green Pea” galaxies. Using several abundance indicators, we find a metallicity of the explosion environment of only ∼0.1 Z ⊙ , the lowest reported metallicity for a Type IIn SN environment. SN 2021adxl reaches a peak magnitude of M r ≈ −20.2 mag and since discovery, SN 2021adxl has faded by only ∼4 magnitudes in the r band with a cumulative radiated energy of ∼1.5 × 10 50 erg over 18 months. SN 2021adxl shows strong signs of interaction with a complex circumstellar medium, seen by the detection of X-rays, revealed by the detection of coronal emission lines, and through multi-component hydrogen and helium profiles. In order to further understand this interaction, we model the H α profile using a Monte Carlo electron scattering code. The blueshifted high-velocity component is consistent with emission from a radially thin spherical shell resulting in the broad emission components due to electron scattering. Using the velocity evolution of this emitting shell, we find that the SN ejecta collide with circumstellar material of at least ∼5 M ⊙ assuming a steady-state mass-loss rate of ∼4 − 6 × 10 −3 M ⊙ yr −1 for the first ∼200 days of evolution. SN 2021adxl was last observed to be slowly declining at ∼0.01 mag d −1 , and if this trend continues, SN 2021adxl will remain observable after its current solar conjunction. Continuing the observations of SN 2021adxl may reveal signatures of dust formation or an infrared excess, similar to that seen for SN 2010jl.

Brennan, S. J. (ORCID:0000000313256235)↗
DOE OSTI2024

Hawai‘i Supernova Flows: a peculiar velocity survey using over a Thousand Supernovae in the near-infrared

ABSTRACT We introduce the Hawai‘i Supernova Flows project and present summary statistics of the first 1217 astronomical transients observed, 668 of which are spectroscopically classified Type Ia Supernovae (SNe Ia). Our project is designed to obtain systematics-limited distances to SNe Ia while consuming minimal dedicated observational resources. To date, we have performed almost 5000 near-infrared (NIR) observations of astronomical transients and have obtained spectra for over 200 host galaxies lacking published spectroscopic redshifts. In this survey paper, we describe the methodology used to select targets, collect/reduce data, calculate distances, and perform quality cuts. We compare our methods to those used in similar studies, finding general agreement or mild improvement. Our summary statistics include various parametrizations of dispersion in the Hubble diagrams produced using fits to several commonly used SN Ia models. We find the lowest dispersions using the SNooPy package’s EBV_model2, with a root mean square deviation of 0.165 mag and a normalized median absolute deviation of 0.123 mag. The full utility of the Hawai‘i Supernova Flows data set far exceeds the analyses presented in this paper. Our photometry will provide a valuable test bed for models of SN Ia incorporating NIR data. Differential cosmological studies comparing optical samples and combined optical and NIR samples will have increased leverage for constraining chromatic effects like dust extinction. We invite the community to explore our data by making the light curves, fits, and host galaxy redshifts publicly accessible.

Do, Aaron (ORCID:0000000334297845)↗
DOE OSTI2025

Taking control of compressible modes: bulk viscosity and the turbulent dynamo

Many polyatomic astrophysical plasmas are compressible and out of chemical and thermal equilibrium, introducing a bulk viscosity into the plasma via the internal degrees of freedom of the molecular composition, directly impacting the decay of compressible modes, $\mathrm{{\boldsymbol {\mathit {v}}}}_{\parallel }(\boldsymbol {k})$. This is especially important for small-scale, turbulent dynamo processes in the interstellar medium (ISM), which are known to be sensitive to the effects of compression. To control the viscous properties of $\mathrm{{\boldsymbol {\mathit {v}}}}_{\parallel }(\boldsymbol {k})$, we perform trans-sonic, visco-resistive dynamo simulations with additional bulk viscosity $\nu _{\text{bulk}}$, deriving a new $\nu _{\text{bulk}}$ Reynolds number $\text{Re}_{\text{bulk}}$, and viscous Prandtl number $\text{P}\nu \equiv \text{Re}_{\text{bulk}}/ \text{Re}_{\text{shear}}$, where $\text{Re}_{\text{shear}}$ is the shear viscosity Reynolds number. We derive a framework for decomposing $E_{\rm mag}$ growth rates into incompressible and compressible terms via orthogonal tensor decompositions of $\boldsymbol {\nabla }\otimes \mathrm{{\boldsymbol {\mathit {v}}}}$, where $\mathrm{{\boldsymbol {\mathit {v}}}}$ is the fluid velocity. We find that $\mathrm{{\boldsymbol {\mathit {v}}}}_{\parallel }(\boldsymbol {k})$ play a dual role, growing and decaying $E_{\rm mag}$, and that field-line stretching is the main driver of growth, even in compressible dynamos. In the absence of $\nu _{\text{bulk}}$ ($\text{P}\nu \rightarrow \infty$), $\mathrm{{\boldsymbol {\mathit {v}}}}_{\parallel }(\boldsymbol {k})$ pile up on small-scales, creating a spectral bottleneck, which disappears for $\text{P}\nu \approx 1$. As $\text{P}\nu$ decreases, $\mathrm{{\boldsymbol {\mathit {v}}}}_{\parallel }(\boldsymbol {k})$ are dissipated at increasingly larger scales, in turn suppressing incompressible modes through a coupling between high-k modes. We emphasize the importance of further understanding the role of $\nu _{\text{bulk}}$ in compressible astrophysical plasmas, which we estimate could be as strong as the shear viscosity in the cold ISM, and highlight that compressible direct numerical simulations without bulk viscosity have unresolved compressible mode dissipation scales.

MHD↗
DOE OSTI2024

Final results of the search for new Milky Way satellites in the Hyper Suprime-Cam Subaru Strategic Program survey: Discovery of two more candidates

Abstract We present the final results of our search for new Milky Way (MW) satellites using the data from the Hyper Suprime-Cam (HSC) Subaru Strategic Program (SSP) survey over ∼1140 deg2. In addition to three candidates that we have already reported, we have identified two new MW satellite candidates in the constellations of Sextans, at a heliocentric distance of D⊙ ≃ 126 kpc, and Virgo, at D⊙ ≃ 151 kpc, named Sextans II and Virgo III, respectively. Their luminosities (Sext II: MV ≃ −3.9 mag; Vir III: MV ≃ −2.7 mag) and half-light radii (Sext II: rh ≃ 154 pc; Vir III: rh ≃ 44 pc) place them in the region of size–luminosity space of ultra-faint dwarf galaxies (UFDs). Including four previously known satellites, there are a total of nine satellites in the HSC-SSP footprint. This discovery rate of UFDs is much higher than that predicted from the recent models for the expected population of MW satellites in the framework of cold dark matter models, thereby suggesting that we encounter a too many satellites problem. Possible solutions to settle this tension are also discussed.

Homma, Daisuke↗
DOE OSTI2025

A metagenomic perspective on the microbial prokaryotic genome census

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Characterization of Soil and Rock Magnetic Properties along Multiple Hillslope Transects at Teller Road Site, Seward Peninsula, Alaska, 2018 and 2023

The magnetometer data was collected in multiple directions across the watershed hillslope at the NGEE Arctic Teller Road site at mile marker 27 (TL_MM27) on the Seward Peninsula, Alaska over multiple years in March 2018 and April 2023. The magnetic data were collected using a Geometrics Inc. G-858 gradiometer and G-857 base station in 2018 and the G-864 gradiometer and G857 base station in 2023. The data was collected (in all instances) by towing the gradiometer behind a snow machine around the watershed with the two sensors in a vertical profile with constant spacing during the continuous survey in that specific year. Magnetic total field measurements were collected by gradiometer and base station, and the data processing was performed in Geometrics MagMap2000 software. The processing steps were limited to removal of data spikes (despiking), reading dropouts, and correction/removal of bad GPS points. All offsets between sensors and GPS are stated within the data files and metadata, alongwith the processed and raw data. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).In this data submission there are two sets of raw magnetic data (.bin and .stn for 2018 and base for 2023; raw rover mag for 2023 is in .csv) inside two .zip files that identify the year the mag data was collected. The data are proprietary format to Geometrics and can be opened and processed with MagMap2000 which can be downloaded for free at Geometrics website. There are also two processed data files *.csv for each year and two metadata files *.csv.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Hyporheic zone, river, and groundwater metagenome resolved genomes and rpS3 genes in East River Watershed, Colorado USA Summer 2020, 2021

Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from water filter collected across 8 locations along the East River Watershed, CO, and 1 nearby groundwater well. The purpose was to look for connectivity and similarities across the network and to see the impact of the groundwater. As a part of Lawrence Berkeley National Laboratory (LBNL) Watershed Science Focus Area (SFA), we assessed community composition and strain similarities between the sites and we also compared it to previous metagenomic studies within the watershed looking at floodplain (Matheus Carnevali et al. 2021) and hillslope (Lavy et al. 2019) microbiomes. Here we present metagenome assembled genomes (MAGs) for the bacterial and archaeal communities from filters across 8 locations during August 2020 and July 2021. This resulted in 32 samples. The groundwater sample was sequenced at UC Berkley's QB3. The other 31 samples were sequenced at University of Maryland. Metagenomes were assembled using four autobinners and the best bins were selected using dasTool. The genomes were dereplicated at 95% with dRep and the subset of winning genomes were manually curated based on visual inspection of taxonomic profile, GC content, coverage, and a set of 51 bacterial single copy genes (BSCG), and 38 archaeal signal copy genes (ASCG). The dataset includes a zip file of 311 genomes (HZ_River_SW_MAGS_Dereplicated_95.zip). The dataset additionally includes a zipped file of ribosomal protein small subunit 3 (rpS3) proteins from the hyporheic zone and river data (rpS3_Proteins_HZ_River.zip), a metadata file used to register associated samples with IGSNs (International Generic Sample Numbers) (samples.csv), a location metadata file (locations.csv). This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

DNA↗
DOE OSTI2024

KBase Narrative - van den Bergh et al

We report 14 metagenome-assembled genomes (MAGs) recovered from agricultural soils, composts, and enrichment cultures enriched therefrom, originating from the Netherlands, Belgium and Switzerland. Recovered MAGs constitute methane-cycling related organisms sequenced from isolated cultures or environmental DNA, elucidating their metabolic potential in important ecological processes like the oxidation or production of atmospheric trace gases as methane, hydrogen, and carbon monoxide.

Rocha, Gabriel Silvestre↗
DOE OSTI2025

TUTORIAL: A new custom metabolic model for iron-oxidizing bacteria

In this tutorial narrative, we introduce a novel template developed to enable the creation of stoichiometric genome-scale metabolic models for iron-oxidizing bacteria. We demonstrate the development of this template by applying it to Sideroxydans lithotrophicus ES-1, and validate our model using transcriptomic data (Published in Zhou et al., 2022 AEM). Below, we further show that our template facilitates the modeling of mixotrophic iron-oxidizing bacteria and metagenome-assembled genomes (MAGs), by applying our template to the MAG of the mixotrophic iron oxidizer Leptothrix ochracea (Published in Tothero et al, 2024). This work represents the first instance of a generalized and adaptable template for modeling diverse iron-oxidizing microbial systems, expanding the accessibility and applicability of metabolic modeling in this field.

genome-scale model↗
DOE OSTI2024

Metagenome-assembled genomes provide insight into the metabolic potential during early production of Hydraulic Fracturing Test Site 2 in the Delaware Basin

Demand for natural gas continues to climb in the United States, having reached a record monthly high of 104.9 billion cubic feet per day (Bcf/d) in November 2023. Hydraulic fracturing, a technique used to extract natural gas and oil from deep underground reservoirs, involves injecting large volumes of fluid, proppant, and chemical additives into shale units. This is followed by a “shut-in” period, during which the fracture fluid remains pressurized in the well for several weeks. The microbial processes that occur within the reservoir during this shut-in period are not well understood; yet, these reactions may significantly impact the structural integrity and overall recovery of oil and gas from the well. To shed light on this critical phase, we conducted an analysis of both pre-shut-in material alongside production fluid collected throughout the initial production phase at the Hydraulic Fracturing Test Site 2 (HFTS 2) located in the prolific Wolfcamp formation within the Permian Delaware Basin of west Texas, USA. Specifically, we aimed to assess the microbial ecology and functional potential of the microbial community during this crucial time frame. Prior analysis of 16S rRNA sequencing data through the first 35 days of production revealed a strong selection for a Clostridia species corresponding to a significant decrease in microbial diversity. Here, we performed a metagenomic analysis of produced water sampled on Day 33 of production. This analysis yielded three high-quality metagenome-assembled genomes (MAGs), one of which was a Clostridia draft genome closely related to the recently classified Petromonas tenebris. This draft genome likely represents the dominant Clostridia species observed in our 16S rRNA profile. Annotation of the MAGs revealed the presence of genes involved in critical metabolic processes, including thiosulfate reduction, mixed acid fermentation, and biofilm formation. These findings suggest that this microbial community has the potential to contribute to well souring, biocorrosion, and biofouling within the reservoir. Our research provides unique insights into the early stages of production in one of the most prolific unconventional plays in the United States, with important implications for well management and energy recovery.

natural gas↗
DOE OSTI2025

DESI Mg II Absorbers: Extinction Characteristics and Quasar Redshift Accuracy

In this paper, we study how absorption-line systems affect the spectra and redshifts of quasi-stellar objects (QSOs), using catalogs of Mg II absorbers from the early data release and first data release of the Dark Energy Spectroscopic Instrument. We determine the reddening effect of an absorption system by fitting an unreddened template spectrum to a sample of 50,674 QSO spectra that contain Mg II absorbers. We find that reddening caused by intervening absorbers (v off > 3500 km s −1 ) has an average color excess of $\overline{E(B-V)}$ = 0.04 mag. We find that the E(B − V) tends to be greater for absorbers at low redshifts, or those having Mg II absorption lines with higher equivalent widths, but shows no clear trend with v off for intervening systems. However, the $\overline{E(B-V)}$ of associated absorbers, those at v off < 3500 km s −1 , shows a strong trend with v off , increasing rapidly with decreasing v off and peaking (∼0.15 mag) around v off = 0 km s −1 . We demonstrate that Mg II absorbers impact redshift estimation for QSOs by investigating the distributions of v off for associated absorbers. We find that at z > 1.5, these distributions broaden and bifurcate in a nonphysical manner. In an effort to mitigate this effect, we mask pixels associated with the Mg II absorption lines and recalculate the QSO redshifts. We find that we can recover voff populations in better agreement with those for z < 1.5 absorbers and in doing so typically shift background QSO redshifts by Δz ≈ ± 0.005.

79 ASTRONOMY AND ASTROPHYSICS↗