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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs)

Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirk) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

WA-TmG.2.0

Soil samples were collected in triplicate in the Fall of 2017 across three grassland locations having differences in historical annual precipitation. For each of the three field site soil collections, one deeply sequenced composite metagenome (> 1 terabase) was obtained and individually sequenced in replicate to provide three additional terabase metagenomes for replicate statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation. This data package provides new knowledge of viral types, abundances, diversity, and auxiliary metabolic genes (AMGs) in grassland soils for predicting viral response to changes in their environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

IA-TmG.2.0

Soil samples were collected in triplicate in the Fall of 2017 across three grassland locations having differences in historical annual precipitation. For each of the three field site soil collections, one deeply sequenced composite metagenome (> 1 terabase) was obtained and individually sequenced in replicate to provide three additional terabase metagenomes for replicate statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation. This data package provides new knowledge of viral types, abundances, diversity, and auxiliary metabolic genes (AMGs) in grassland soils for predicting viral response to changes in their environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Iso-VIG14.1.0

Soil samples were collected in triplicate in the Fall of 2017 across the three grassland locations having differences in historical annual precipitation (WA-TmG.1.0, KS-TmG.1.0, and IA-TmG.1.0). For each location, one deeply sequenced composite metagenome (> 1 terabase) were screened for viruses,In addition, each of the three field soil samples were individually sequenced to provide three replicate metagenomes (WA-TmG.2.0, KS-TmG.2.0, and IA-TmG.2.0) for statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

KS-TmG.2.0

Soil samples were collected in triplicate in the Fall of 2017 across three grassland locations having differences in historical annual precipitation. For each of the three field site soil collections, one deeply sequenced composite metagenome (> 1 terabase) was obtained and individually sequenced in replicate to provide three additional terabase metagenomes for replicate statistical comparison in addition to screening for viral soil contigs for assessing the impact of historical annual precipitation. This data package provides new knowledge of viral types, abundances, diversity, and auxiliary metabolic genes (AMGs) in grassland soils for predicting viral response to changes in their environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Using Methyl Bromide for Interspecies Cell–Cell Signaling and As a Reporter in a Model Soil Consortium

Synthetic microbial communities are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five member MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that Variovorax beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally-relevant hydration conditions. We find that methyl halide production can report on a MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. Finally, these tools will be useful for future studies that investigate how MSC respond to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

SFA-VirOmics

PNNL's Soil Microbiome Science Focus Area (SFA) is focused on understanding the basic biology underpinning how interactions among various soil microbial community members, across trophic levels, lead to the emergence of community functions. Moisture, in particular, drives microbial interactions and influences everything from cell function to substrate fate within soils. The group predicts this results in repeatable, predictable phenotypes. The sum of these phenotypes comprises the “soil metaphenome”. Understanding how the soil metaphenome shifts in response to moisture will provide a basis for modeling and predicting these shifts in reaction network responses. Visit the PNNL Soil Microbiome Science Focus Area Program homepage for more information. PNNL’s Soil Microbiome SFA Virome Dataset Annotation page is an extension to the PNNL Soil Microbiome SFA repository on DataHub allows for exploring and downloading integrated experimental omics dataset annotations, associated experimental metadata, pre- and post-processed viral data files, and other associated materials directly related to experimental viral project data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Heterotrophic respiration by soil microbes in a changing climate

Soil microbes strongly influence the soil organic carbon (SOC) pool, which globally stores ~2,000 PgC. Specifically, the balance between microbial heterotrophic respiration (R H ), which degrades SOC, and plant–microbe interactions that stabilize SOC determines whether terrestrial ecosystems are a net source or sink of CO 2 to the atmosphere. Here, in this Review, we evaluate how climate change alters these competing processes. R H is approximately half of total soil respiration, at ~50 PgC yr −1 , with 70% occurring in topsoils. Warming accelerates microbial metabolism, with a 10 °C temperature increase estimated to raise R H by ~50%, an effect that is particularly strong in Arctic soils. Warming also reduces soil moisture, further modulating R H , which responds nonlinearly to soil moisture, being limited by saturation and desiccation and meeting a maximum at intermediate levels. Consequently, R H is highly sensitive to future precipitation changes and drought. However, soil management strategies could enhance SOC stocks and persistence under climate change. Bacterial and fungal inoculants can promote SOC production and stabilization, while deep-rooting plants increase SOC inputs to deeper layers that experience lower R H . Agricultural practices and biochar amendments can also enhance SOC and reduce R H . Expanding field trials across regions, climates and soil types would improve empirical understanding of these responses and support better representation of R H in predictive models, enabling more accurate assessments of climate impacts on SOC storage.

Jansson, Janet K. [Pacific Northwest National Labo↗
DOE OSTI2021

DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes

Viromics is becoming an increasingly popular method for characterizing soil viral communities. DNase treatment of the viral size fraction prior to DNA extraction is meant to reduce contaminating free DNA and is a common step within viromics protocols to ensure that sequences are of viral origin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Corrinoids as model nutrients to probe microbial interactions in a soil ecosystem

Earth’s soils are habitats for microbial communities that drive biogeochemical cycling, plant growth, and carbon storage and persistence. The thousands of microbial species living in soil form an intricate web of interactions involving the exchange of molecules produced by different microbes. Understanding in detail how these molecular exchanges occur and how they shape microbial communities may lead to new methods to improve soil health, bioremediation efforts, and better understanding of biogeochemical processes. The overall goal of this research is to gain a deeper knowledge of the microbial interactions that drive soil community structure. However, the high functional and genomic diversity in soil microbiomes has posed a challenge for current microbiology methods to achieve this goal. This research leverages a model group of key metabolites related to cobalamin (vitamin B 12 ), known as corrinoids, to investigate microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

EMSL Community Science Campaign Meeting: Critical Minerals and Materials - Rhizo Critical Campaign Breakout Session Report Summary

The “Critical Minerals Biogeochemistry in the Rhizosphere – Ultramafic Soils (Rhizo Critical)” campaign breakout (BO) session was organized to identify major knowledge gaps and fundamental research needs in rhizosphere microbiology and geochemistry that, if addressed, could transform our ability to recover critical minerals from ultramafic soil systems. We sought to identify significant challenges that must be surmounted in the pursuit of deeper science knowledge. Our ultimate goal is to understand this landscape well enough to identify and prioritize opportunities for EMSL to make the greatest impact with Environmental Transformations and Interactions (ETI) science area research campaigns focused on the biogeochemical processes controlling the behavior of critical minerals and materials in the rhizosphere. The increasing demand for critical materials and minerals (CMM) in the U.S. has heightened interest in low-grade ores with much attention on ultramafic soils, which contain valuable metals such as nickel (Ni), chromium (Cr), manganese, cobalt (Co), and copper (Lee et al., 2025; DOE CMM Report, 2023) used in advanced battery, magnet, wiring and wind turbines, and stainless steel technologies. Metal hyperaccumulating plants grown in ultramafic soils can extract economically valuable concentrations of CMMs through the process of phytomining. This technology has evolved from phytoremediation, which involves using plants to cleanse contaminated environments by removing, detoxifying, or stabilizing pollutants like metals and organic compounds. Hyperaccumulator plants are capable of storing metals in their living tissues at concentrations hundreds to thousands of times higher than those found in 'normal' plants. For instance, while the average concentration of Ni in the dry matter of plants growing in typical soils is usually less than 5 µg g?¹, Ni hyperaccumulation is defined by concentrations exceeding 1,000 µg g?¹ (Corzo Remigio et al., 2020; Reeves et al., 2018). Phytomining research has primarily focused on Ni (Rylott and van der Ent, 2025), for which the U.S. has very limited conventional mines in operation. Most soils typically contain Ni concentrations ranging from 7 to 50 mg kg-1, whereas serpentine soils exhibit significantly higher levels, with Ni content often ranging between 700 and 8,000 mg kg-1 (Sobczyk et al., 2017). While more than 500 plant species in over 50 different families have been identified as Ni hyperaccumulators (Kidd et al., 2018), Ni phytomining (and phytominng in general) remains largely untested because most studies are short-term, small-scale, and conducted under simplified or artificially enriched conditions, so they fail to capture the low metal concentrations, environmental variability, and management constraints that would be needed for a field-scale demonstration. Few hyperaccumulator species have been validated as true “metal crops,” and their biomass production, stress tolerance, and rooting characteristics are usually too poor to yield economically meaningful metal outputs. Critically, the basic mechanisms of metal uptake, transport, and sequestration, especially as shaped by belowground processes such as root exudation, rhizosphere chemistry, and root–microbe interactions that control metal mobility and bioavailability (Montreemuk et al., 2023; Kidd et al., 2018; Durand et al., 2023; Alford et al., 2010), are still only partially understood, and downstream metal recovery from biomass is rarely optimized. Because these limitations stem from gaps in fundamental knowledge rather than from a failure of the concept itself (Rylott and van der Ent, 2025; van der Ent et al., 2015), there is a strong need for basic science that dissects plant metal homeostasis, rhizosphere and microbial processes, and their integration with soil chemistry and process engineering to design more robust, scalable phytomining systems.

Ahkami, Amirhossein↗
DOE OSTI2022

Effects of short-interval reburns in the boreal forest on soil bacterial communities compared to long-interval reburns

Abstract Increasing fire frequency in some biomes is leading to fires burning in close succession, triggering rapid vegetation change and altering soil properties. We studied the effects of short-interval (SI) reburns on soil bacterial communities of the boreal forest of northwestern Canada using paired sites (n = 44). Both sites in each pair had burned in a recent fire; one site had burned within the previous 20 years before the recent fire (SI reburn) and the other had not. Paired sites were closely matched in prefire ecosite characteristics, prefire tree species composition, and stand structure. We hypothesized that there would be a significant effect of short vs. long fire-free intervals on community composition and that richness would not be consistently different between paired sites. We found that Blastococcus sp. was consistently enriched in SI reburns, indicating its role as a strongly ‘pyrophilous’ bacterium. Caballeronia sordidicola was consistently depleted in SI reburns. The depletion of this endophytic diazotroph raises questions about whether this is contributing to—or merely reflects—poor conifer seedling recolonization post-fire at SI reburns. While SI reburns had no significant effect on richness, dissimilarity between short- and long-interval pairs was significantly correlated with difference in soil pH, and there were small significant changes in overall community composition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Bacterial Tradeoffs in Growth Rate and Extracellular Enzymes

Like larger organisms, bacteria possess traits, or phenotypic characteristics, that influence growth and impact ecosystem processes. Still, it remains unclear how these traits are organized across bacterial lineages. Using 49 bacterial strains isolated from leaf litter in Southern California, we tested the hypothesis that bacterial growth rates trade off against extracellular enzyme investment. We also tested for phylogenetic conservation of these traits under high and low resource conditions represented, respectively, by Luria broth (LB) and a monomer-dominated medium extracted from plant litter. In support of our hypotheses, we found a negative correlation between the maximum growth rate and the total activity of carbon-, nitrogen-, and phosphorus-degrading extracellular enzymes. However, this tradeoff was only observed under high resource conditions. We also found significant phylogenetic signal in maximum growth rate and extracellular enzyme investment under high and low resource conditions. Driven by our bacterial trait data, we proposed three potential life history strategies. Resource acquisition strategists invest heavily in extracellular enzyme production. Growth strategists invest in high growth rates. Bacteria in a third category showed lower potential for enzyme production and growth, so we tentatively classified them as maintenance strategists that may perform better under conditions we did not measure. These strategies were related to bacterial phylogeny, with most growth strategists belonging to the phylum Proteobacteria and most maintenance and resource acquisition strategists belonging to the phylum Actinobacteria. By accounting for extracellular enzyme investment, our proposed life history strategies complement existing frameworks, such as the copiotroph-oligotroph continuum and Grime’s competitorstress tolerator-ruderal triangle. Our results have biogeochemical implications because allocation to extracellular enzymes versus growth or stress tolerance can determine the fate and form of organic matter cycling through surface soil.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Study of an Unrefined Humate Solution as a Possible Attenuation-based Remedy for Uranium Contamination in Acidic Groundwater - 20351

The Savannah River Site (SRS), joined the environmental cleanup program in 1981 after the Cold War, and was designated as a hazardous waste management facility. About 1.8 billion gallons of acid wastes were disposed into the F/H Area Seepage Basin that included many radionuclides and dissolved metals, resulting in highly contaminated groundwater plumes with pH of 3 - 5.5. The acidity of the plumes contributes to the mobility of several constituents of concern (COC) such as H-3, U-238, I-129, and Sr-90 for the F-Area plume and H-3, Sr-90 and mercury for the H-Area plume. An active treatment (pump-and-treat and re-injection) system was constructed and put in place in 1997 to address the removal of metals and radionuclides from the contaminated groundwater. As remediation projects advanced, active treatments were transitioned to more passive or enhanced-passive approaches such as the subsurface barrier with base injection system, which has been controlling the mobility of contaminants. However, new and more efficient attenuation-based remedies are always sought. Several studies have proposed that humic substances can be used to remediate sites contaminated with heavy metals by creating a permeable reactive barrier. Humic substances (HS) are major components of soil organic matter. HS are polyfunctional organic macromolecules formed by the chemo-microbiological decomposition of biomass or dead organic matter. These substances are usually divided into three main fractions: humin (insoluble at all pH values), humic acid (soluble at pH greater than 3.5), and fulvic acid (soluble at all pH values). Humic substances are major components of the soil at SRS and, in addition, are also helpful in the removal process of uranium. This research focuses on uranium (VI), which is a key contaminant of concern in the F-Area groundwater plume. The interaction of uranium with sediment in the presence or absence of humic substances involves complex mechanisms that are not yet well understood. The interaction of U(VI) with humic substances can affect the adsorption of U on sediment, altering its mobility in the subsurface. The objective of this study is to study the mobility of uranium in the presence of humic acid and to determine if sediments amended by humic acid can enhance the sorption of heavy metals onto sediments. In this research, experiments were conducted using background (clean) F-Area aquifer sediments to understand and predict uranium mobility. A blended material, humate, containing both humic and fulvic acids and a chemically modified humate (KW15 modified humic or mod-HA) was studied as a possible amendment for uranium remediation in SRS groundwater. Batch experiments were conducted in triplicates using 20 ml of aqueous suspension in DI water containing SRS sediment and mod-HA and studied the effect of pH, kinetics of humate sorption onto SRS sediment and also studied the sorption of uranium onto mod-HA amended SRS sediment. Results indicate that mod-HA amended sediment increases uranium removal significantly. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Saccharomycopsis praedatoria sp. nov., a predacious yeast isolated from soil and rotten wood in an Amazonian rainforest biome

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589 T . The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

60 APPLIED LIFE SCIENCES↗