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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Particulate and dissolved metabolite distributions along a latitudinal transect of the western Atlantic Ocean

Abstract Metabolites, or the small organic molecules that are synthesized by cells during metabolism, comprise a complex and dynamic pool of carbon in the ocean. They are an essential currency in interactions at the population and community levels of biological organization. Characterizing metabolite distributions inside microbial cells and dissolved in seawater is essential to understanding the controls on their production and fate, as well as their roles in shaping marine microbial food webs. Here, we apply a targeted metabolomics method to quantify particulate and dissolved distributions of a suite of biologically relevant metabolites including vitamins, amino acids, nucleic acids, osmolytes, and intermediates in biosynthetic pathways along a latitudinal transect in the western Atlantic Ocean. We find that, in the upper 200 m of the water column, most particulate or intracellular metabolites positively covary with the most abundant microbial taxa. In contrast, dissolved metabolites exhibited greater variability with differences in distribution between ocean regions. Although fewer particulate metabolites were detected below 200 m, the particulate metabolites identified in the deep ocean may be linked to adaptive physiological strategies of deep‐sea microbes. Based on the identified metabolite distributions, we propose relationships between certain metabolites and microbial populations, and find that dissolved metabolite distributions are not directly related to their particulate abundances.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial responses to long-term warming differ across soil microenvironments

Soil carbon loss is likely to increase due to climate warming, but microbiomes and microenvironments may dampen this effect. In a 30-year warming experiment, physical protection within soil aggregates affected the thermal responses of soil microbiomes and carbon dynamics. In this study, we combined metagenomic analysis with physical characterization of soil aggregates to explore mechanisms by which microbial communities respond to climate warming across different soil microenvironments. Long-term warming decreased the relative abundances of genes involved in degrading labile compounds (e.g. cellulose), but increased those genes involved in degrading recalcitrant compounds (e.g. lignin) across aggregate sizes. These changes were observed in most phyla of bacteria, especially for Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes. Microbial community composition was considerably altered by warming, leading to declined diversity for bacteria and fungi but not for archaea. Microbial functional genes, diversity, and community composition differed between macroaggregates and microaggregates, indicating the essential role of physical protection in controlling microbial community dynamics. Our findings suggest that microbes have the capacity to employ various strategies to acclimate or adapt to climate change (e.g. warming, heat stress) by shifting functional gene abundances and community structures in varying microenvironments, as regulated by soil physical protection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting

Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data for: Spatial access and resource limitations control carbon mineralization in soils

This dataset contains data and code used for the paper "Spatial access and resource limitations control carbon mineralization in soils", https://doi.org/10.1016/j.soilbio.2021.108427. Core-scale soil carbon fluxes are ultimately regulated by pore-scale dynamics of substrate availability and microbial access. These are constrained by physicochemical and biochemical phenomena (e.g. spatial access and hydrologic connectivity, physical occlusion, adsorption-desorption with mineral surfaces, nutrient and resource limitations). We conducted an experiment to determine how spatial access and resource limitations influence core-scale water-soluble soil organic matter (SOM) mineralization, and how these are regulated by antecedent moisture conditions. Intact soil cores were incubated at field-moist vs. drought conditions, after which they were saturated from above (to simulate precipitation) or below (to simulate groundwater recharge). Soluble carbon (acetate) and nitrogen (nitrate) forms were added to some cores during the rewetting process to alleviate potential nutrient limitations. Soil respiration was measured during the incubation, after which pore water was extracted from the saturated soils and analyzed for water soluble organic carbon concentrations and characterization. Our results showed that carbon (C) amendments increased the cumulative carbon dioxide (CO2) evolved from the soil cores, suggesting that the soils were C-limited. Drought and rewetting increased soil respiration, and there was a greater abundance of complex aromatic molecules in pore waters sampled from these soils. This newly available substrate appeared to alleviate nutrient limitations on respiration, because there were no further respiration increases with subsequent C and N amendments. We had hypothesized that respiration would be influenced by wetting direction, as simulated precipitation would mobilize C from the surface. However, as a main effect, this response was seen only in the C-amended soils, indicating that surface-C may not have been bioavailable. At the pore scale (pore water samples), drought and the C, N amendments caused a net loss of identified molecules when the soils were rewet from below, whereas wetting from above caused a net increase in identified molecules, suggesting that fresh inputs stimulated the C-and N-limited microbial populations present deeper in the soil profile. Our experiment highlights the complex and interactive role of antecedent moisture conditions, wetting direction, and resource limitations in driving core-scale C fluxes.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/kaizadp/TES_spatial_access_2021 (DOI: 10.5281/zenodo.5522938).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Biogeochemical Processes Across Aquatic Interfaces

The aquatic interfaces exposing terrestrial soils to oxic-anoxic regime shifts represent biogeochemical “hotspots” that are extremely sensitive to climate and environmental change. However, processes and interaction across theses aquatic interfaces are poorly understood and underrepresented in current Earth system models. In this project, we aim to develop predictive understanding of the feedbacks between microbial systems and geochemical environments that determine emergent ecosystem behaviors and resilience in response to disturbances. We use experimental, mechanistic modeling and meta-analysis tools to elucidate interactions among soil, water, geomorphology and microbiology that regulate the molecular transformations and fluxes of carbon, nutrients, and redox-sensitive compounds across aquatic interfaces.

58 GEOSCIENCES↗
DOE OSTI2023

Mineral reactivity determines root effects on soil organic carbon

Modern conceptual models of soil organic carbon (SOC) cycling focus heavily on the microbe-mineral interactions that regulate C stabilization. However, the formation of ‘stable’ (i.e. slowly cycling) soil organic matter, which consists mainly of microbial residues associated with mineral surfaces, is inextricably linked to C loss through microbial respiration. Therefore, what is the net impact of microbial metabolism on the total quantity of C held in the soil? To address this question, we constructed artificial root-soil systems to identify controls on C cycling across the plant-microbe-mineral continuum, simultaneously quantifying the formation of mineral-associated C and SOC losses to respiration. Here we show that root exudates and minerals interacted to regulate these processes: while roots stimulated respiratory C losses and depleted mineral-associated C pools in low-activity clays, root exudates triggered formation of stable C in high-activity clays. Moreover, we observed a positive correlation between the formation of mineral-associated C and respiration. This suggests that the growth of slow-cycling C pools comes at the expense of C loss from the system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Challenges in integrating dissolved organic matter chemodiversity into kinetic models of soil respiration

The chemodiversity of dissolved organic matter (DOM) in soil has been proposed to influence the microbial metabolism and fate of belowground organic carbon (C). However, integrating DOM chemistry into soil C cycle models to improve predictions of C stocks and fluxes—beyond simply considering DOM pool size—remains a challenge. While recent research suggests that incorporating DOM chemodiversity into models can improve predictions of microbial respiration, there is still a lack of mechanistic understanding describing how DOM chemodiversity affects microbial metabolism and soil respiration. Here, we evaluated whether DOM chemodiversity was a determinant of soil respiration using paired measurements of high-resolution DOM chemistry, obtained from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and potential soil respiration rates from across the United States (U.S.), all data provided by the Molecular Observation Network. Our objectives were to (1) assess statistical relationships between DOM chemodiversity and microbial respiration, and (2) evaluate the ability of kinetic models to leverage DOM chemistry to explain empirical relationships found in statistical models. Statistical regressions revealed that DOM chemodiversity (alpha diversity) was nonlinearly related to potential soil respiration rates, both independently and through its interactions with DOM and total C concentrations. In soils with relatively high DOM but low total C concentrations, potential soil respiration rates were negatively correlated with DOM alpha diversity, whereas in soils with relatively low DOM and high total C concentrations showed the opposite trend. However, when metabolic transition theory kinetic models were modified to include chemodiversity, their performance was comparable to traditional Monod kinetics approaches, which simulate respiration rates as a function of DOM concentration. The inability to account for nonlinearities in DOM chemodiversity–respiration relationships highlight an opportunity to advance substrate uptake kinetics by establishing causal links between DOM chemodiversity, microbial metabolism trade-offs, and potential interactions under varied environmental conditions.

Bioenergetic model↗
DOE OSTI2021

Spatial access and resource limitations control carbon mineralization in soils

Core-scale soil carbon fluxes are ultimately regulated by pore-scale dynamics of substrate availability and microbial access. These are constrained by physicochemical and biochemical phenomena (e.g. spatial access and hydrologic connectivity, physical occlusion, adsorption-desorption with mineral surfaces, nutrient and resource limitations). We conducted an experiment to determine how spatial access and resource limitations influence core-scale SOM mineralization, and how these are regulated by antecedent moisture conditions. Intact soil cores were incubated at field-moist vs. drought conditions, after which they were saturated from above (to simulate precipitation) or below (to simulate groundwater recharge). Soluble C (acetate) and N (nitrate) forms were added to some cores during the rewetting process to alleviate potential nutrient limitations. Respiration showed evidence of C-limitation, as C amendments increased the cumulative CO 2 evolved. Drought and rewetting increased soil respiration, and these soils also exhibited increased complex aromatic molecules in porewater. This newly available substrate appeared to alleviate nutrient limitations on respiration, because there were no further respiration increases with subsequent C and N amendments. We expected that respiration would be influenced by wetting direction, as simulated precipitation would mobilize C from the surface. However, as a main effect, this response was seen only in the C-amended soils, indicating that surface-C may not have been bioavailable. At the pore scale (porewater samples), compared to the baseline soils, drought and the C, N amendments caused a net loss of identified molecules when the soils were rewet from below, whereas wetting from above caused a net increase in identified molecules. This indicates that as soils were wet from below, the fresh inputs simulated the C-and N-limited microbial populations present deeper in the soil profile. Furthermore, our experiment highlights the complex and interactive role of antecedent moisture conditions, wetting direction, and resource limitations in driving core-scale C fluxes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Benefits of symbiotic ectomycorrhizal fungi to plant water relations depend on plant genotype in pinyon pine

Rhizosphere microbes, such as root-associated fungi, can improve plant access to soil resources, affecting plant health, productivity, and stress tolerance. While mycorrhizal associations are ubiquitous, plant–microbe interactions can be species specific. Here we show that the specificity of the effects of microbial symbionts on plant function can go beyond species level: colonization of roots by ectomycorrhizal fungi (EMF) of the genus Geopora has opposite effects on water uptake, and stomatal control of desiccation in drought tolerant and intolerant genotypes of pinyon pine (Pinus edulis Engelm.). These results demonstrate, for the first time, that microorganisms can have significant and opposite effects on important plant functional traits like stomatal control of desiccation that are associated with differential mortality and growth in nature. They also highlight that appropriate pairing of plant genotypes and microbial associates will be important for mitigating climate change impacts on vegetation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites

Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.

Klein, Matthew L↗
DOE OSTI2022

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate

Abstract Microbial predators such as choanoflagellates are key players in ocean food webs. Choanoflagellates, which are the closest unicellular relatives of animals, consume bacteria and also exhibit marked biological transitions triggered by bacterial compounds, yet their native microbiomes remain uncharacterized. Here we report the discovery of a ubiquitous, uncultured bacterial lineage we name Candidatus Comchoanobacterales ord. nov., related to the human pathogen Coxiella and physically associated with the uncultured marine choanoflagellate Bicosta minor . We analyse complete ‘Comchoano’ genomes acquired after sorting single Bicosta cells, finding signatures of obligate host-dependence, including reduction of pathways encoding glycolysis, membrane components, amino acids and B-vitamins. Comchoano encode the necessary apparatus to import energy and other compounds from the host, proteins for host-cell associations and a type IV secretion system closest to Coxiella’s that is expressed in Pacific Ocean metatranscriptomes. Interactions between choanoflagellates and their microbiota could reshape the direction of energy and resource flow attributed to microbial predators, adding complexity and nuance to marine food webs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid ( Adelges tsugae , HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii , that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

16S rRNA↗
DOE OSTI2020

Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient

Peatlands are important players in climate change–biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH 4 ). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO 2 ) and CH 4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. Finally, these findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Analysis of biofilm assembly by large area automated AFM

Biofilms are complex microbial communities critical in medical, industrial, and environmental contexts. Understanding their assembly, structure, genetic regulation, interspecies interactions, and environmental responses is key to developing effective control and mitigation strategies. While atomic force microscopy (AFM) offers critically important high-resolution insights on structural and functional properties at the cellular and even sub-cellular level, its limited scan range and labor-intensive nature restricts the ability to link these smaller scale features to the functional macroscale organization of the films. We begin to address this limitation by introducing an automated large area AFM approach capable of capturing high-resolution images over millimeter-scale areas, aided by machine learning for seamless image stitching, cell detection, and classification. Large area AFM is shown to provide a very detailed view of spatial heterogeneity and cellular morphology during the early stages of biofilm formation which were previously obscured. Using this approach, we examined the organization of Pantoea sp. YR343 on PFOTS-treated glass surfaces. Our findings reveal a preferred cellular orientation among surface-attached cells, forming a distinctive honeycomb pattern. Detailed mapping of flagella interactions suggests that flagellar coordination plays a role in biofilm assembly beyond initial attachment. Additionally, we use large-area AFM to characterize surface modifications on silicon substrates, observing a significant reduction in bacterial density. This highlights the potential of this method for studying surface modifications to better understand and control bacterial adhesion and biofilm formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Methane-derived carbon flows into host–virus networks at different trophic levels in soil

Significance The impact of soil viruses on prokaryotic hosts and their functional processes is largely unknown. While metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts, this does not necessarily identify contemporary interactions. To enable a detailed analysis of active virus–host interactions between individual populations, we focused on the critical biogeochemical process of methane (CH 4 ) oxidation and followed the transfer of carbon from hosts to their associated viruses in situ. Analysis of 13 C-enriched metagenomic DNA demonstrated that CH 4 -derived carbon is transferred into viral biomass via both primary and secondary utilizers of CH 4 and suggests viral predation is an important mechanism for releasing CH 4 -derived organic carbon into the soil matrix.

Lee, Sungeun↗