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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Mineral Protection and Resource Limitations Combine to Explain Profile-Scale Soil Carbon Persistence

The fate of soil carbon (C) is largely controlled by microbial oxidation of organic matter (OM), which is constrained by a variety of mechanisms. OM association with soil minerals provides pronounced protection against microbial decomposition. However, factors such as climate, occlusion, and resource limitations also contribute to OM preservation. Here, we explore the factors explaining C distribution and age within an upland rainforest soil in Hawai'i, a site with abundant preferential flow paths (PFPs) and high short-range order (SRO) mineral content. We characterized lateral and vertical changes in Δ 14 C, SRO mineral content, C-functional group chemistry, and microbial community composition to elucidate the contributions of multiple protection mechanisms to OM preservation. Consistent with our expectation, SRO mineral content and Δ 14 C were strongly correlated (R 2 = 0.95), indicating strong mineral protection of OM throughout the profile. Surprisingly, distance from PFP was also a significant predictor of Δ 14 C and improved model fit, particularly in the shallow horizons (R 2 = 0.97). Elevated C/N ratios, decreased microbial abundance, and greater SRO mineral content suggest nitrogen limitations and enhanced mineral protection constrain OM turnover with distance from PFPs in deep, subsurface mineral horizons. Steady microbial abundance, increasing putative anaerobe abundance, and changes in C-functional group chemistry indicate oxygen limitations constrain OM turnover in the matrix of shallow mineral horizons. Given that oxygen and nutrient limitations contribute to OM preservation in this high SRO system—an exemplar of mineral protection—resource limitations may play an even more important role in OM preservation in other well-structured soils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin

The subsurface is among Earth’s largest biomes, but the extent to which microbial communities vary across tectonic plate boundaries or interact with subduction-scale geological processes remains unknown. Here we compare bacterial community composition with deep-subsurface geochemistry from 21 hot springs across the Costa Rican convergent margin. We find that cation and anion compositions of the springs reflect the dip angle and position of the underlying tectonic structure and also correlate with the bacterial community. Co-occurring microbial cliques related to cultured chemolithoautotrophs that use the reverse tricarboxylic acid cycle (rTCA) as well as abundances of metagenomic rTCA genes correlate with concentrations of slab-volatilized carbon. This, combined with carbon isotope evidence, suggests that fixation of slab-derived CO2 into biomass may support a chemolithoautotrophy-based subsurface ecosystem. We calculate that this forearc subsurface biosphere could sequester 1.4 × 10 9 to 1.4 × 10 10 mol of carbon per year, which would decrease estimates of the total carbon delivered to the mantle by 2 to 22%. Furthermore, based on the observed correlations, we suggest that distribution and composition of the subsurface bacterial community are probably affected by deep tectonic processes across the Costa Rican convergent margin and that, by sequestering carbon volatilized during subduction, these chemolithoautotrophic communities could in turn impact the geosphere.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Harnessing photoenzymatic reactions for unnatural biosynthesis in microorganisms

Photobiocatalysis provides a powerful strategy for integrating light and biological catalysts to drive abiological transformations. However, its scalability is hindered by high enzyme loading, reliance on costly cofactors and instability under radical-generating conditions. Here we report the integration of light-driven enzymatic reactions into the cellular metabolism of Escherichia coli, bridging flavin-based photobiocatalysis with biosynthesis. Using synthetic biology strategies, we engineered microbial cells to continuously produce olefin substrates and ene-reductase while regenerating cofactors directly from glucose. By externally supplying radical precursors or introducing synthetic pathways for their in situ production, we enabled fermentation-based microbial photobiosynthesis, achieving high titres and demonstrating feasibility for scale-up in a bioreactor. This approach extends photobiocatalysis from in vitro applications to in vivo semi- and complete biosynthesis, revealing its full potential for integrating light-driven reactions into cellular metabolism.

Biocatalysis↗
DOE OSTI2026

Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.

Biological and medical sciences↗
DOE OSTI2025

Potential Risks Associated with Short-Term Hydrogen Storage in Methane Reservoirs

Hydrogen (H2) has been identified as a flexible energy carrier with zero emissions. It is possible to utilize H2 by storing Hyblend, or H2 blended with CH4, in existing natural gas infrastructure. However, the compatibility of adapting the current CH4 storage strategies to include H2 injection has not been fully demonstrated. It is essential that we understand the impact of H2 gas on the naturally occurring microbial community of subsurface storage reservoirs before deploying large-scale H2-CH4 storage. We designed a series of experiments that allowed us to identify potential challenges of HyBlend Storage in existing methane reservoirs (Figure 1). First, we characterized two field fluid samples from a methane reservoir located in Western United States. Next, we used these samples to complete a series of short-term reactor experiments at reservoir conditions for a natural gas (100% CH4) and HyBlend (80% CH4/20% H2) storage environment.

geomicrobiology↗
DOE OSTI2021

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

16S amplicon sequencing↗
DOE OSTI2022

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station

The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10 5 cfu/m 2 . Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluation of Degradation Mechanisms for Solid Secondary Waste Grout Waste Forms

The overall objective of this work is to provide defensibility for the long-term performance of grouted Hanford SSW streams when disposed in a near surface disposal facility, IDF, on the Hanford Site. Providing defensibly for the long-term performance of the grouted waste forms is consistent with the research and development activities identified in the Performance Assessment Maintenance Plan, (Westcott et al. 2019), that are necessary to address the assumptions made in the PA. Specifically, this work addresses two areas identified for further research and development activities in the plan: (1) “Evaluate ongoing research on transport characteristics of cementitious materials using accelerated tests to approximate the effects of aging/alteration/weathering”; and (2) “Evaluate ongoing research on microbial effects on transport processes in cementitious materials.” The assembled subject matter expert team evaluated a list of degradation mechanisms and supporting processes and provided rankings of areas where further research and development (R&D) are needed. From this assessment, high priority R&D areas include: (1) the effects of carbonation, Ca leaching, and SSW dimensional change in grout waste forms; (2) updated model representations of grouted waste forms; and (3) scaled testing demonstrations. Moderate priority items including a paper study on possible microbial influence, reoxidation rates, radionuclide/contaminant dissolution from SSW in the grout and freeze thaw behavior. Other processes evaluated were either deemed unlikely to occur, to have little impact on the SSW waste forms, or to occur at time frames beyond those considered (>10,000 years). The assessments and proposed R&D approaches are expected to support an update to the WRPS SSW roadmap.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Root and Microbial Soil CO 2 and CH 4 Fluxes Respond Differently to Seasonal and Episodic Environmental Changes in a Temperate Forest

Upland forest soils are typically major atmospheric carbon dioxide (CO 2 ) sources and methane (CH 4 ) sinks, but the contributions of root and microbial processes, as well as their separate temporal responses to environmental change, remain poorly understood. This 2-year study was conducted in a temperate, deciduous forest located on the Chesapeake Bay in Maryland, USA. We used temporal CO 2 and CH 4 flux measurements, exclusion-source partitioning, and an ecosystem-scale flooding experiment to understand how carbon (C) fluxes, and their root and microbial sources, respond to seasonal and episodic environmental change. Here, we show that the root-and-rhizosphere component of soil CO 2 and CH 4 flux is significant and that its dependence on soil temperature and volumetric water content (VWC) influences soil C dynamics at seasonal timescales. Experimental flooding shows that CO 2 and CH 4 flux responses to episodic moisture change were driven by suppression of soil heterotrophs, while root respiration did not respond to transient hydrologic disturbance. Methane uptake responded strongly to episodic inundation, reinforcing the important role of soil moisture in the short-term control of the forest soil CH 4 sink. However, despite the clear seasonality of CH 4 uptake, as well as its strong response to short-term experimental inundation, temperature and VWC were weak predictors of CH 4 uptake at a seasonal timescale. We suggest that CH 4 consumption in the long-term may be determined by vegetation, nutrients, microbial communities, or other factors correlated with seasonal changes. Our results indicate that root and microbial sources of both CO 2 and CH 4 flux respond differently in timing and magnitude to seasonal and episodic environmental change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host–microbiome metabolic interactions.

59 BASIC BIOLOGICAL SCIENCES↗
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

Metaoptics Enabled Multifunctional Imaging

Despite the fact that most microorganisms occupy two- and three-dimensional space in heterogeneous arrangements and in proximity to other microorganisms of different species, much of our current knowledge about their metabolic processes is derived from homogenizing, then analyzing, the chemical content of cultures containing a single microbial species. This project addressed this fundamental dichotomy by developing a set of optical imaging principles combining multiple new technologies. The imaging strategies developed in this project combine metaoptics structures with active in situ nanoscale control of the chemical environment and applied them to a microbial system, Myxococcus xanthus, with particular relevance to the DoE mission. The combination of metaoptical architectures and nanoscale control over the molecular environment enables: (a) precise control over the electromagnetic (EM) field at length scales smaller than the wavelength of light; (b) control of the interaction of the EM field with critical molecular systems in DOE relevant microbes; (c) control over the chemical environment – especially the presence and quantity of reactive oxygen species (ROS) that can affect redox homeostasis; and (d) the ability to ask new kinds of questions not accessible to ‘omics’ approaches or standard methods of biological imaging. These capabilities are applicable to detailed studies of metabolic pathways in microbes and to lignocellulosic biomass deconstruction. To accomplish these objectives, we pursued two over-arching technical goals: (1) the development of new metaoptics-enabled approaches to imaging and spectroscopic characterization; and (2) the development of tools to control the chemical environment of a microbial sample with nanometer-scale precision. Goal 1 was addressed through the design, fabrication, and characterization of new metasurfaces capable of super-resolution imaging through extreme confinement of the optical field. Goal 2 was addressed by controlling the redox potential on the nanoscale in microbial communities and characterizing their effect on intrinsic bacterial fluorophores which act as molecular sentinels and through characterization of soluble factors secreted by Myxococcus xanthus by confocal Raman imaging. The optical imaging/sensing approaches developed here make it possible to use these powerful new imaging and sensing modalities in metabolic studies by making it possible to visualize and track the spatial and temporal expression patterns of natural or engineered pathways in microorganisms.

09 BIOMASS FUELS↗
DOE OSTI2024

Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs

Abstract Hydraulic fracturing has unlocked vast amounts of hydrocarbons trapped within unconventional shale formations. This large-scale engineering approach inadvertently introduces microorganisms into the hydrocarbon reservoir, allowing them to inhabit a new physical space and thrive in the unique biogeochemical resources present in the environment. Advancing our fundamental understanding of microbial growth and physiology in this extreme subsurface environment is critical to improving biofouling control efficacy and maximizing opportunities for beneficial natural resource exploitation. Here, we used metaproteomics and exometabolomics to investigate the biochemical mechanisms underpinning the adaptation of model bacterium Halanaerobium congolense WG10 and mixed microbial consortia enriched from shale-produced fluids to hypersalinity and very low reservoir flow rates (metabolic stress). We also queried the metabolic foundation for biofilm formation in this system, a major impediment to subsurface energy exploration. For the first time, we report that H. congolense WG10 accumulates tyrosine for osmoprotection, an indication of the flexible robustness of stress tolerance that enables its long-term persistence in fractured shale environments. We also identified aromatic amino acid synthesis and cell wall maintenance as critical to biofilm formation. Finally, regulation of transmembrane transport is key to metabolic stress adaptation in shale bacteria under very low well flow rates. These results provide unique insights that enable better management of hydraulically fractured shale systems, for more efficient and sustainable energy extraction.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2022

SynMADE: synthetic microbiota across diverse ecosystems

The last two decades have witnessed rapid advances in engineering individual microbial strains to produce biochemicals and biomaterials. Furthermore, engineering microbial consortia has been relatively slow. Using systems and synthetic biology approaches, researchers have been developing tools for engineering complex microbiota. In this article, I discuss future directions and visions regarding developing microbiota as a biomanufacturing host. Specifically, I propose that we can develop the soil microbial community itself as a huge bioreactor. Ultimately, researchers will provide a generalizable system that enables us to understand microbial consortium’s interaction and metabolism at diverse temporal and spatial scales to address global problems, including the climate crisis, food inequality, waste issue, and sustainable bioproduction.

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 OSTI2025

Polyphenol rewiring of the microbiome reduces methane emissions

Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, ~40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens—either through direct toxic effects or by diverting their substrates and energy—to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72%–84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from Days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.

54 ENVIRONMENTAL SCIENCES↗