Search NASA⌕ Search

SEARCH · Search NASA

Results for “Soil functions”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Arbuscular Mycorrhizal Tree Communities Have Greater Soil Fungal Diversity and Relative Abundances of Saprotrophs and Pathogens than Ectomycorrhizal Tree Communities

Trees associating with different mycorrhizas often differ in their effects on litter decomposition, nutrient cycling, soil organic matter (SOM) dynamics, and plant-soil interactions. For example, due to differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree leaf and root traits, ECM-associated soil has lower rates of C and N cycling and lower N availability than AM-associated soil. These observations suggest that many groups of nonmycorrhizal fungi should be affected by the mycorrhizal associations of dominant trees through controls on nutrient availability. To test this overarching hypothesis, we explored the influence of predominant forest mycorrhizal type and mineral N availability on soil fungal communities using next-generation amplicon sequencing. Soils from four temperate hardwood forests in southern Indiana, United States, were studied; three forests formed a natural gradient of mycorrhizal dominance (100% AM tree basal area to 100% ECM basal area), while the fourth forest contained a factorial experiment testing long-term N addition in both dominant mycorrhizal types. We found that overall fungal diversity, as well as the diversity and relative abundance of plant pathogenic and saprotrophic fungi, increased with greater AM tree dominance. Additionally, tree community mycorrhizal associations explained more variation in fungal community composition than abiotic variables, including soil depth, SOM content, nitrification rate, and mineral N availability. Our findings suggest that tree mycorrhizal associations may be good predictors of the diversity, composition, and functional potential of soil fungal communities in temperate hardwood forests. These observations help explain differing biogeochemistry and community dynamics found in forest stands dominated by differing mycorrhizal types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Pore2Chip: All-in-one python tool for soil microstructure analysis and micromodel design

The Pore2Chip Python package is designed to create 2D micromodels using extracted data from 3D X-ray computed tomography (XCT) images. This package helps analyze soil structure and function, allowing for the investigation of hydro-biogeochemical processes that impact mineral extraction and reactivity, oxygen concentrations, and nutrient availability in disturbed or managed soils. Key metrics encompass pore size distributions, pore throat size distributions, and connectivity (pore coordination numbers). The final output is a 2D scalable SVG design representing a core or aggregate. Designs can be fabricated with methods such as laser etching, 3D printing, and photolithography.

lab-on-chip↗
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 OSTI2026

Cryo-EM visualization of viruses from partially irrigated soils

Viruses are numerically the most abundant forms on Earth, and most are present in soil. Even though viruses are highly abundant in soil and critical to rhizosphere function, visualizing the diverse morphotypes within soil has been challenging. The difficulty is primarily due to the heterogenous nature of isolated suspensions that typically contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and hinders cryo-electron microscopy due to ice thickness and contrast issues. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method employs common physical biochemical separation steps to remove large and small debris which dramatically improves image quality and preservation of structural features to permit visualizing morphotypes not typically seen with conventional negative stain approaches. In addition to tailed and non-tailed polyhedral phages, several under reported or novel morphotypes of soil viruses are directly visualized as a particle library with both 2D and 3D information.

cryo-EM↗
DOE OSTI2022

Inclusion of a cold hardening scheme to represent frost tolerance is essential to model realistic plant hydraulics in the Arctic–boreal zone in CLM5.0-FATES-Hydro

As temperatures decrease in autumn, vegetation of temperate and boreal ecosystems increases its tolerance to freezing. This process, known as hardening, results in a set of physiological changes at the molecular level that initiate modifications of cell membrane composition and the synthesis of anti-freeze proteins. Together with the freezing of extracellular water, anti-freeze proteins reduce plant water potentials and xylem conductivity. To represent the responses of vegetation to climate change, land surface schemes increasingly employ “hydrodynamic” models that represent the explicit fluxes of water from soil and through plants. The functioning of such schemes under frozen soil conditions, however, is poorly understood. Nonetheless, hydraulic processes are of major importance in the dynamics of these systems, which can suffer from, e.g., winter “frost drought” events. In this study, we implement a scheme that represents hardening into CLM5.0-FATES-Hydro. FATES-Hydro is a plant hydrodynamics module in FATES, a cohort model of vegetation physiology, growth, and dynamics hosted in CLM5.0. We find that, in frozen systems, it is necessary to introduce reductions in plant water loss associated with hardening to prevent winter desiccation. This work makes it possible to use CLM5.0-FATES-Hydro to model realistic impacts from frost droughts on vegetation growth and photosynthesis, leading to more reliable projections of how northern ecosystems respond to climate change.

58 GEOSCIENCES↗
DOE OSTI2025

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil

In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils—however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with 18 O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils—which are often more water limited and pulse driven—have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Microbial metabolic dependency and its impacts on the soil carbon cycle (Final Technical Report, DE-SC0016364)

The terrestrial biosphere contains a large fraction of global carbon (C) and nearly 70% of the organic C in terrestrial systems is found in soils. Global changes in atmospheric CO 2 , temperature, precipitation, and ecosystem N inputs, will impact primary production and carbon inputs to soils, but it remains difficult to predict soil responses to these environmental conditions. Our ability to predict C-cycle responses to global change remains limited by unexplained variability within the terrestrial C-cycle. Our difficulty in predicting responses of the soil C-cycle to environmental change suggests a need for a greater understanding of the biotic mechanisms that govern soil C-transformations. Changes in microbial community structure and function have been proposed to impact soil processes, but mechanistic connections between microbial activity and C-cycle transformations remain poorly described. We assembled an interdisciplinary team to conduct cross-scale examination of microbial contributions to C-cycle dynamics and C-fate in soils. We investigated microbial contributions to soil C-transformations using a suite of complementary isotopic techniques including DNA-Stable Isotope Probing (DNA-SIP), metagenomic-SIP, metabolomic-SIP, proteomic-SIP, and microspatial analysis of soil organic C. These techniques were deployed in experiments that tested fundamental assumptions that underlie terrestrial C-cycle models. We characterized the functional characteristics of soil microorganisms responsible for major C-transformations in soil, evaluated the metabolic and ecological interactions that underlie soil C-cycle dynamics, and evaluated the degree to which these interactions impact rates of C mineralization and stabilization in soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Analysis of RNA viral function from metatranscriptomic reads in drought simulated soils

Soil viruses have received increased interest in recent years because of their abundance and unelucidated potential as drivers for organic carbon derived from fungal and bacterial necromass. With decreasing levels of rainfall and climbing instances of unseasonal conditions, it becomes crucial to our goals for negative carbon emissions to understand how soil carbon flux is affected. Here we leveraged metatranscriptomic data from a section of research plot of Hopland Research and Extension in northern California with a suite of viral detection tools: VirSorter, DRAMv, and VContact2. We aimed to cross analyze moisture regiments with viral populations. We find that viral diversity is driven by site, like bacteria. We found that viral diversity at face value showed some differentiation but did not significantly differ by legacy moisture content. Additionally, there was detection of auxiliary metabolic genes in a viral sequence which may further support virus’s direct input into the soil carbon pool.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Using probability distribution function as a scaling approach to incorporate soil heterogeneity into biogeochemical models for greenhouse gas predictions (Final Technical Report)

The project investigated biogeochemical processes at terrestrial-aquatic interfaces (TAIs), focusing on soil microsite heterogeneity and its impact on greenhouse gas (GHG) fluxes. Using laboratory experiments, modeling, and data integration, researchers explored redox-driven microbial processes under fluctuating hydrological conditions. Key advancements included modifying the DAMM-GHG model to incorporateelectron acceptor availability and enhancing the AquaMEND model for improved microbial metabolism representation. Results highlighted microsite redox variability as a key driver of GHG fluxes, informing Earth system models. The project fostered interdisciplinary collaborations, student training, and the development of novel modeling frameworks to improve Earth'senergy budget.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Habitat specialization and edge effects of soil microbial communities in a fragmented landscape

Abstract Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or “edge effects.” To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats (“specialists”) and taxa that showed no habitat preference (“nonspecialists”). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore‐formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.

Winfrey, Claire C. [Department of Ecology and Evol↗
DOE OSTI2021

Long-term measurements in a mixed-grass prairie reveal a change in soil organic carbon recalcitrance and its environmental sensitivity under warming

Soil respiration, the major pathway for ecosystem carbon (C) loss, has the potential to enter a positive feedback loop with the atmospheric CO2 due to climate warming. For reliable projections of climate-carbon feedbacks, accurate quantification of soil respiration and identification of mechanisms that control its variability are essential. Process-based models simulate soil respiration as functions of belowground C input, organic matter quality, and sensitivity to environmental conditions. However, evaluation and calibration of process-based models against the long-term in situ measurements are rare. Here, we evaluate the performance of the Terrestrial ECOsystem (TECO) model in simulating total and heterotrophic soil respiration measured during a 16-year warming experiment in a mixed-grass prairie; calibrate model parameters against these and other measurements collected during the experiment; and explore whether the mechanisms of C dynamics have changed over the years. Calibrating model parameters against observations of individual years substantially improved model performance in comparison to pre-calibration simulations, explaining 79–86% of variability in observed soil respiration. Interannual variation of the calibrated model parameters indicated increasing recalcitrance of soil C and changing environmental sensitivity of microbes. Overall, we found that (1) soil organic C became more recalcitrant in intact soil compared to root-free soil; (2) warming offset the effects of increasing C recalcitrance in intact soil and changed microbial sensitivity to moisture conditions. Furthermore, these findings indicate that soil respiration may decrease in the future due to C quality, but this decrease may be offset by warming-induced changes in C cycling mechanisms and their responses to moisture conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Minimal Impacts of Microplastics on Soil Physical Properties under Environmentally Relevant Concentrations

Agricultural soils are a major reservoir of microplastics, and concerns have arisen about the impacts of microplastics on soil properties and functioning. In this report we measured the physical properties of a silt loam in response to the incorporation of polyester fibers and polypropylene granules over a wide range of concentrations. We further elucidated the underlying mechanisms through determining the role of microplastic shape and the baseline effects from the amendment of soil particles. The incorporation of microplastics into soil tended to increase contact angle and saturated hydraulic conductivity, decrease bulk density and water holding capacity, while did not affect aggregate stability. Polyester fibers affected soil physical properties more profoundly than polypropylene granules, due to the vastly different shape of fibers from that of soil particles. However, changes in soil properties were gradual, and significant changes did not occur until a high concentration of microplastics was reached (i.e., 0.5% w/w for polyester fibers and 2% w/w for polypropylene granules). Currently, microplastic concentrations in soils not heavily polluted with plastics are far below these concentrations, and results from this study suggest that microplastics at environmentally relevant concentrations have no significant effects on soil physical properties.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Innovative Biomonitoring and Remediation of Heavy Metals Using Phytotechnologies at the Savannah River Site (SRS) Coal Combustion Product (CCP) Impoundment Sites

The Savannah River Site (SRS) contains legacy coal combustion product (CCP) impoundments that are impacted by elevated concentrations of heavy metals and radionuclides, posing long-term risks to soil health, ecosystem functioning, and environmental sustainability. Traditional environmental monitoring approaches rely primarily on chemical analyses to quantify contaminant concentrations but often provide limited information regarding biological responses or ecosystem recovery. This project addressed these limitations by integrating environmental chemistry, microbial ecology, artificial intelligence (AI), and bioremediation into a comprehensive framework for environmental diagnostics and restoration of contaminated soils. The overarching goal of this collaborative project between Florida A&M University (FAMU) and the University of Georgia's Savannah River Ecology Laboratory (SREL) was to develop innovative biomonitoring and remediation strategies for heavy metal-contaminated CCP impoundment sites at the Savannah River Site. Specifically, the project sought to (i) characterize heavy metal contamination, (ii) determine microbial responses to contamination, (iii) isolate indigenous heavy metal-resistant microorganisms for remediation applications, (iv) develop a microbial ecological health index using machine learning, and (v) optimize fungal-mediated bioremediation using artificial intelligence.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2022

Editorial: Exogenous carbon-based materials in soil ecosystems

Various exogenous carbon-based materials (ECMs) such as crop straw, biochar, carbon-based nano-fertilizer, and microplastics have accumulated in soil ecosystems. These ECMs may cause direct and indirect impacts on soil properties, processes, productivity, and health, thus potentially changing the function and stability of soil ecosystems. However, large knowledge gaps still exist on ECMs in soil ecosystems, including their accumulation, interactions with soil components, and potential ecological impacts and risks. Therefore, more efforts are needed to further understand the impacts especially the long-term effects of ECMs in soil ecosystems. By generating new knowledge, this Research Topic aims to improve the understanding of the effects of ECMs on soil ecosystems, including soil quality, nutrient cycling, microbial ecology, crop growth, environmental health and ecological risk.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Modeling the processes of soil moisture in regulating microbial and carbon-nitrogen cycling

Soil carbon (C) and nitrogen (N) cycles and their complex responses to hydro-climatic forcing have gained increasing attention. While the temperature effects have been intensively studied, soil moisture response functions (SMRFs) are not well documented for various microbial and enzymatic processes due to the difficulties in directly measuring and differentiating the moisture effects on various processes. In this work we extended our C-only Microbial-ENzyme Decomposition (MEND) model to the C-N coupled MEND model with flexible element stoichiometry. Our model calibration showed good agreement between simulated and observed C:N ratios in soil organic matter and microbial biomass, as well as the ammonium and nitrate concentrations. We show that the selection of SMRFs for specific biogeochemical processes could result in significant differences in model simulated microbial and C-N processes. In particular, it is essential to account for the soil moisture effects on microbial dormancy and resuscitation, as the changes in microbial physiology under favorable or stressful conditions will exert strong controls on soil C and N dynamics. We also advocate the utilization of dynamic (time-variant) data (e.g., litter input, N deposition, soil temperature and moisture), instead of time-invariant data, to drive model simulations and analyses. Dynamic forcing data (particularly dynamic soil moisture) better represent the real-world climate and environmental conditions, which could facilitate more realistic modeling and understanding of soil C and nutrient cycling in a changing world.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Divergent species-specific impacts of whole ecosystem warming and elevated CO 2 on vegetation water relations in an ombrotrophic peatland

Boreal peatland forests have relatively low species diversity and thus impacts of climate change on one or more dominant species could shift ecosystem function. Despite abundant soil water availability, shallowly rooted vascular plants within peatlands may not be able to meet foliar demand for water under drought or heat events that increase vapor pressure deficits while reducing near surface water availability, although concurrent increases in atmospheric CO 2 could buffer resultant hydraulic stress. We assessed plant water relations of co-occurring shrub (primarily Rhododendron groenlandicum and Chamaedaphne calyculata) and tree (Picea mariana and Larix laricina) species prior to, and in response to whole ecosystem warming (0 to +9°C) and elevated CO 2 using 12.8-m diameter open-top enclosures installed within an ombrotrophic bog. Water relations (water potential [Ψ], turgor loss point, foliar and root hydraulic conductivity) were assessed prior to treatment initiation, then Ψ and peak sap flow (trees only) assessed after 1 or 2 years of treatments. Under the higher temperature treatments, L. laricina Ψ exceeded its turgor loss point, increased its peak sap flow, and was not able to recover Ψ overnight. In contrast, P. mariana operated below its turgor loss point and maintained constant Ψ and sap flow across warming treatments. Similarly, C. calyculata Ψ stress increased with temperature while R. groenlandicum Ψ remained at pretreatment levels. The more anisohydric behavior of L. laricina and C. calyculata may provide greater net C uptake with warming, while the more conservative P. mariana and R. groenlandicum maintained greater hydraulic safety. These latter species also responded to elevated CO 2 by reduced Ψ stress, which may also help limit hydraulic failure during periods of extreme drought or heat in the future. Along with Sphagnum moss, the species-specific responses of peatland vascular communities to drier or hotter conditions will shape boreal peatland composition and function in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Revisiting diffusion-based moisture functions: why do they fail?

Microbial activities in soil are controlled by the balance between physical and biological mechanisms that are currently implied by soil moisture-respiration relationships, but not explicitly represented. Diffusion based moisture functions focus on physical controls, while substrate kinetics based models primarily address biological drivers. How to harmonize these two types of models for robust predictions of soil respiration and other processes has not been addressed. Here we derived a generalizable analytical solution of diffusion-limited nonlinear microbial uptake kinetics, in which microbial metabolic rates were governed by both physical and biological drivers via substrate diffusion and microbial affinity. We proposed a soil trait concept to integrate both physical and biological perspectives into one unified function, and tested it using both laboratory and field based observations from a variety of soils. This approach provides a tractable and scalable approach that incorporates soil heterogeneity and functional complexity in macroscopic model descriptions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Soil pore network response to freeze-thaw cycles in permafrost aggregates

This dataset contains data used for the paper "Pore network response to freeze-thaw cycles in permafrost aggregates". The Related References field will be updated with a full citation when available.Climate change in Arctic landscapes may increase freeze-thaw frequency within the active layer as well as newly thawed permafrost. A highly disruptive process, freeze-thaw can deform soil pores and alter the architecture of the soil pore network with varied impacts to water transport and retention, redox conditions, and microbial activity. Our objective was to investigate how freeze-thaw cycles impacted the pore network of newly thawed permafrost aggregates to improve understanding of what type of transformations can be expected from warming Arctic landscapes. We measured the impact of freeze-thaw on pore morphology, pore throat diameter distribution, and pore connectivity with X-ray computed tomography (XCT) using six permafrost aggregates with sizes of 2.5 cm3 from a mineral soil horizon (Bw; 28-50 cm depths) in Toolik, Alaska. Freeze-thaw cycles were performed using a laboratory incubation consisting of five freeze-thaw cycles (-10˚C to 20˚C) over five weeks. Our findings indicated decreasing spatial connectivity of the pore network across all aggregates with higher frequencies of singly connected pores following freeze-thaw. Water-filled pores that were connected to the pore network decreased in volume while the overall connected pore volumetric fraction was not affected. Shifts in the pore throat diameter distribution were mostly observed in pore throats ranges of 100 microns or less with no corresponding changes to the pore shape factor of pore throats. Responses of the pore network to freeze-thaw varied with aggregate, suggesting that initial pore morphology may play a role in driving freeze-thaw response. Our research suggests that freeze-thaw alters the microenvironment of permafrost aggregates during the incipient stage of deformation following permafrost thaw, impacting soil properties and function in Arctic landscapes undergoing transition. 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/Erin-Rooney/XCT-freezethaw (DOI: 10.5281/zenodo.5816355).

54 ENVIRONMENTAL SCIENCES↗