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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

The Freundlich isotherm equation best represents phosphate sorption across soil orders and land use types in tropical soils of Puerto Rico

Biomass production in the lowland wet tropical forest is greater than in any other biome, and it is typically limited by soil phosphorus (P) availability. However, the mechanisms involved in the P cycle remain poorly represented in Earth System Models (ESMs). Soil P sorption processes are key in the P cycle and for understanding the extent of P limitation for plant productivity. Currently, a few ESMs include isotherm equations to model these processes. Although the Langmuir equation is widely cited, other isotherm equations may better describe sorption in tropical soils. Here, we use a diverse range of soil samples from Puerto Rico to test the validity of the Langmuir, Freundlich, and Temkin equation. We found that across four soil orders (Inceptisols, Mollisols, Oxisols, Ultisols), and forested and cultivated land use types, the Freundlich equation best represented soil P sorption. Furthermore, the Langmuir and the Temkin equations poorly represent soil P adsorption, especially at low P concentrations. Specifically, the Langmuir equation underestimated soil P adsorption by 40% and the Temkin equation overestimated adsorption by 76%. We also found, as expected, that soil clay content and pH were the most important parameters explaining the variability of the Freundlich (K f ) constant. Greater clay content and lower pH, common in highly weathered Ultisols and Oxisols which are abundant in the tropics, led to greater K f values. Overall, our results suggest that a diversity of soils can prompt underestimation of P sorption when using the Langmuir isotherm, which leads to an overestimation of available P that can have repercussions on ESM predictions of the P cycle and tropical forest productivity.

Earth system models↗
DOE OSTI2025

Miscanthus × giganteus increases soil maximum water holding capacity compared to maize

Soil ecosystem services, like the ability to store water, have been depleted after a century of conventional, annual cropping, and perennial crops offer a solution to this and other agricultural environmental issues. We assessed the impact of Miscanthus × giganteus (miscanthus), a perennial biomass crop, on soil water holding capacity and structure compared to continuous maize (Zea mays L.) at two sites in Iowa. After three growing seasons, we measured the following: (1) maximum water holding capacity (MWHC) with and without soil structure, and (2) total porosity and pore size distribution (PSD) via micro-computed tomography (microCT). Miscanthus increased MWHC by 14.7% across both sites relative to maize (p = 0.002), and we attributed this to structural changes due to the lack of a crop effect when measured on structureless soils. No significant changes were detected in soil organic matter, texture, total porosity, or PSD that could explain the increase in MWHC under miscanthus. Our findings suggest that the increases in MWHC are primarily due to structural changes rather than increases in soil organic matter or porosity (at least porosity detectable by microCT). This study highlights miscanthus' potential to enhance soil water storage and underscores the need for further investigation to clarify the mechanisms through which this biomass crop influences soil structural properties.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

KS4A-Omics1.0_FspDS682

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. Here, we observed how a representative of common saprotrophic soil fungi, Fusarium sp. DS 682, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals.This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment, using a high-throughput multi-omic analysis approach. Data package KS4A-Omics.1.0_FspDS682 (Publication: Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization) contents reported here are the first version (1.0) and contain pre- and post-processed data using high throughput data capture technologies for multi-omic analysis and integration, this data package contains raw and post-processed experimental data for X-Ray Absorption Near Edge Structure Spectroscopy (XANES/XRF), Optical Microscopy, Proteomics, Scanning Electron Microscope (SEM), Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS), X-Ray Diffraction Spectroscopy (XRD) files, and X- Ray Photoelectron Spectroscopy (XPS) using EMSL capabilities. This data package DOI contains a comprehensive collection of high-throughput multi-omics data and process metadata catalog. Support files include additional data download contents “Read Me” with dataset descriptor information and data source method application ontologies (see data dictionary section). Reported data download content is structured for compliance with reported guidelines provided by community standard initiatives and publisher stakeholder policies supporting FAIR data principles.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Electrical Conductivity of Clayey Rocks and Soils: A Non-Linear Model

It is well-accepted that Archie's law is only applicable to “clean” rocks and soils but fails in “dirty” ones where clay minerals possess an additional component of surface conductivity. Although several models, for example, Waxman-Smits model, were presented to account for this phenomenon, surface conductivity is always inappropriately treated as constant, which actually only holds at high salinities. The essential non-linear characteristic differing over fluid salinities has not been physically or mathematically explained well in those models. Here, we scrutinize the conduction mechanism of clayey rocks and soils and ascribe this non-linear feature to (a) variation of the electrical double layer and (b) the intrinsic clay-and-water conduction pattern. With effective medium theory, we develop an easy-to-use non-linear model that both reflects electrochemical theories and explains the measurement data well. Our model can be used to produce more accurate results for laboratory- and field-scale petrophysical parameter evaluations than the previous models.

58 GEOSCIENCES↗
DOE OSTI2024

Reanalysis of NOAA H 2 observations: implications for the H 2 budget

Abstract. Hydrogen (H2) is a promising low-carbon alternative to fossil fuels for many applications. However, significant gaps in our understanding of the atmospheric H2 budget limit our ability to predict the impacts of greater H2 usage. Here we use NOAA H2 dry air mole fraction observations from air samples collected from ground-based and ship platforms during 2010–2019 to evaluate the representation of H2 in the NOAA GFDL-AM4.1 atmospheric chemistry-climate model. We find that the base model configuration captures the observed interhemispheric gradient well but underestimates the surface concentration of H2 by about 10 ppb. Additionally, the model fails to reproduce the 1–2 ppb yr−1 mean increase in surface H2 observed at background stations. We show that the cause is most likely an underestimation of current anthropogenic emissions, including potential leakages from H2-producing facilities. We also show that changes in soil moisture, soil temperature, and snow cover have most likely caused an increase in the magnitude of the soil sink, the most important removal mechanism for atmospheric H2, especially in the Northern Hemisphere. However, there remains uncertainty due to fundamental gaps in our understanding of H2 soil removal, such as the minimum moisture required for H2 soil uptake, for which we performed extensive sensitivity analyses. Finally, we show that the observed meridional gradient of the H2 mixing ratio and its seasonality can provide important constraints to test and refine parameterizations of the H2 soil sink.

Paulot, Fabien (ORCID:0000000175344922)↗
DOE OSTI2023

Numerical Study of Coupled Water and Vapor Flow, Heat Transfer, and Solute Transport in Variably-Saturated Deformable Soil During Freeze-Thaw Cycles

As climate change intensifies, soil water flow, heat transfer, and solute transport in the active, unfrozen zones within permafrost and seasonally frozen ground exhibit progressively more complex interactions that are difficult to elucidate with measurements alone. For example, frozen conditions impede water flow and solute transport in soil, while heat and mass transfer are significantly affected by high thermal inertia generated from water-ice phase change during the freeze-thaw cycle. To assist in understanding these subsurface processes, the current study presents a coupled two-dimensional model, which examines heat conduction-convection with water-ice phase change, soil water (liquid water and vapor) and groundwater flow, advective-dispersive solute transport with sorption, and soil deformation (frost heave and thaw settlement) in variably saturated soils subjected to freeze-thaw actions. This coupled multiphysics problem is numerically solved using the finite element method. The model's performance is first verified by comparison to a well-documented freezing test on unsaturated soil in a laboratory environment obtained from the literature. Then based on the proposed model, we quantify the impacts of freeze-thaw cycles on the distribution of temperature, water content, displacement history, and solute concentration in three distinct soil types, including sand, silt and clay textures. The influence of fluctuations in the air temperature, groundwater level, hydraulic conductivity, and solute transport parameters was also comparatively studied. The results show that (a) there is a significant bidirectional exchange between groundwater in the saturated zone and soil water in the vadose zone during freeze-thaw periods, and its magnitude increases with the combined influence of higher hydraulic conductivity and higher capillarity; (b) the rapid dewatering ahead of the freezing front causes local volume shrinkage within the non-frozen region when the freezing front propagates downward during the freezing stage and this volume shrinkage reduces the impact of frost heave due to ice formation. This gradually recovers when the thawed water replenishes the water loss zone during the thawing stage; and (c) the profiles of soil moisture, temperature, displacement, and solute concentration during freeze-thaw cycles are sensitive to the changes in amplitude and freeze-thaw period of the sinusoidal varying air temperature near the ground surface, hydraulic conductivity of soil texture, and the initial groundwater levels. Our modeling framework and simulation results highlight the need to account for coupled thermal-hydraulic-mechanical-chemical behaviors to better understand soil water and groundwater dynamics during freeze-thaw cycles and further help explain the observed changes in water cycles and landscape evolution in cold regions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A Model of Ice Wedge Polygon Drainage in Changing Arctic Terrain

As ice wedge degradation and the inundation of polygonal troughs become increasingly common processes across the Arctic, lateral export of water from polygonal soils may represent an important mechanism for the mobilization of dissolved organic carbon and other solutes. However, drainage from ice wedge polygons is poorly understood. We constructed a model which uses cross-sectional flow nets to define flow paths of meltwater through the active layer of an inundated low-centered polygon towards the trough. The model includes the effects of evaporation and simulates the depletion of ponded water in the polygon center during the thaw season. In most simulations, we discovered a strong hydrodynamic edge effect: only a small fraction of the polygon volume near the rim area is flushed by the drainage at relatively high velocities, suggesting that nearly all advective transport of solutes, heat, and soil particles is confined to this zone. Estimates of characteristic drainage times from the polygon center are consistent with published field observations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Plant Roots and the Fate of Mineral-Associated Soil Carbon (Final Report)

Atmospheric CO 2 concentrations continue to rise due to human activities, but there are also natural mechanisms operating in ecosystems that can store carbon in soil long-term. The organic carbon derived from organisms in soil becomes associated with minerals, where it can be protected for thousands of years. Plants are particularly important contributors of carbon belowground, via their roots. The long-term protection of carbon contributed to soil has great value to humans as climate change looms. But, to keep growing, living plants and soil microbes also need to be able to access and recycle soil nutrients that are stored along with the carbon. In this DOE-funded work, Cardon (MBL), Keiluweit (UMass Amherst/University of Lausanne), Malmstrom (MSU), and Riley (LBNL) used lab and greenhouse experiments coupled with mathematical modeling to determine mechanisms by which plant roots and their associated microbes can dislodge organic matter from soil minerals, making its components available for recycling, but also making its carbon vulnerable to re-release to the atmosphere as CO 2 .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome (Final Report for DE-SC0014395)

The specific project objectives were to: 1) Conduct deep census surveys of root microbiomes concurrent with phenotypic characterizations of a diverse panel of sorghum genotypes across multiple years to define the microbes associated with the most productive lines under drought and low nitrogen conditions. 2) Associate systems-level genotypic, microbial, and environmental factors with improved sorghum performance using robust statistical approaches. 3) Develop culture collections of sorghum root/leaf associated microbes that recapitulate root-enriched sequences defined in the census. 4) Perform controlled environment experiments for in-depth characterization and hypothesis testing of G sorghum x G microbe x E interactions . Validate physiological mechanisms, map genetic loci for stress tolerance, and determine the persistence of optimal microbial strains under greenhouse and field conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

KIN3 impacts arbuscular mycorrhizal symbiosis and promotes fungal colonisation in Medicago truncatula

Summary Arbuscular mycorrhizal fungi help their host plant in the acquisition of nutrients, and this association is itself impacted by soil nutrient levels. High phosphorus levels inhibit the symbiosis, whereas high nitrogen levels enhance it. The genetic mechanisms regulating the symbiosis in response to soil nutrients are poorly understood. Here, we characterised the symbiotic phenotypes in four Medicago truncatula Tnt1 ‐insertion mutants affected in arbuscular mycorrhizal colonisation. We located their Tnt1 insertions and identified alleles for two genes known to be involved in mycorrhization, RAM1 and KIN3 . We compared the effects of the kin3‐2 and ram1‐4 mutations on gene expression, revealing that the two genes alter the expression of overlapping but not identical gene sets, suggesting that RAM1 acts upstream of KIN3. Additionally, KIN3 appears to be involved in the suppression of plant defences in response to the fungal symbiont. KIN3 is located on the endoplasmic reticulum of arbuscule‐containing cortical cells, and kin3‐2 mutants plants hosted significantly fewer arbuscules than the wild type. KIN3 plays an essential role in the symbiotic response to soil nitrogen levels, as, contrary to wild‐type plants, the kin3‐2 mutant did not exhibit increased root colonisation under high nitrogen.

Irving, Thomas B.↗
DOE OSTI2022

Alternative stable states of the forest mycobiome are maintained through positive feedbacks

Most trees on Earth form a symbiosis with either arbuscular mycorrhizal or ectomycorrhizal fungi. By forming common mycorrhizal networks, actively modifying the soil environment and other ecological mechanisms, these contrasting symbioses may generate positive feedbacks that favour their own mycorrhizal strategy (that is, the con-mycorrhizal strategy) at the expense of the alternative strategy. Positive con-mycorrhizal feedbacks set the stage for alternative stable states of forests and their fungi, where the presence of different forest mycorrhizal strategies is determined not only by external environmental conditions but also mycorrhiza-mediated feedbacks embedded within the forest ecosystem. Here, in this work, we test this hypothesis using thousands of US forest inventory sites to show that arbuscular and ectomycorrhizal tree recruitment and survival exhibit positive con-mycorrhizal density dependence. Data-driven simulations show that these positive feedbacks are sufficient in magnitude to generate and maintain alternative stable states of the forest mycobiome. Given the links between forest mycorrhizal strategy and carbon sequestration potential, the presence of mycorrhizal-mediated alternative stable states affects how we forecast forest composition, carbon sequestration and terrestrial climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Metal (hydr)oxide surface precipitates and their effects on potassium sorption

Surface precipitation has been shown to occur on rapid time scales in clay and metal oxide mineral systems. The formation of surface precipitates is hypothesized to present new potential sorption sites for potassium (K), where K can become incorporated into newly formed interlayer spaces (e.g., between tetrahedral–octahedral–tetrahedral stacked sheets). The objective of this study is to determine the effects of newly formed mineral surface precipitates on K sorption. Potassium adsorption experiments were conducted by utilizing Al 2 O 3 and SiO 2 sorbents in the presence of various cations (magnesium, zinc, and nickel) that helped to catalyze the formation of surface precipitates. Dissolved concentrations of elements were monitored via inductively coupled plasma optical emission spectrometry (ICP-OES). Solids were characterized via X-ray diffraction (XRD), and K surface complexation was analyzed via X-ray absorption near edge structure (XANES) spectroscopy. X-ray diffraction analysis indicated bayerite, layered double hydroxides (LDH), and silicated LDH were formed as reaction products, thus creating new surface sites for potential K adsorption. The presence of Si increased K adsorption perhaps due to its role in the formation of LDH surface precipitates. When the differences between observed and theoretical surface area normalized K sorption densities were averaged, a 31% increase in K adsorption was observed in the presence of Si. XANES analysis indicated that the binding mechanism of K to Si is different than that of K to Al, perhaps due to the presence of inner-sphere complexation of K to Al-oxide. Samples reacted for one month versus one week yielded more intense XANES post-edge peaks which indicated that the K sorption complex changes over time. Altogether, our findings provide novel insights into the mechanisms of K fixation in soil and has high implication in providing improved K fertilizer recommendation to growers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Residence time determines invasiveness and performance of garlic mustard ( Alliaria petiolata ) in North America

Abstract While biological invasions have the potential for large negative impacts on local communities and ecological interactions, increasing evidence suggests that species once considered major problems can decline over time. Declines often appear driven by natural enemies, diseases or evolutionary adaptations that selectively reduce populations of naturalised species and their impacts. Using permanent long‐term monitoring locations, we document declines of Alliaria petiolata (garlic mustard) in eastern North America with distinct local and regional dynamics as a function of patch residence time. Projected site‐specific population growth rates initially indicated expanding populations, but projected population growth rates significantly decreased over time and at the majority of sites fell below 1, indicating declining populations. Negative soil feedback provides a potential mechanism for the reported disappearance of ecological dominance of A. petiolata in eastern North America.

Blossey, Bernd↗
DOE OSTI2022

Diversity of genomic adaptations to the post‐fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development

Summary Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire‐responsive fungal colonizers of post‐fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes. Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum , Pyronema omphalodes , Tricharina praecox , Geopyxis carbonaria , Morchella snyderi , and Peziza echinospora . A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. A comparative transcriptome analysis of P. domesticum under two conditions – growing on charcoal, and during sexual development – identified modules of genes that are co‐expressed in the charcoal and light‐induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition. Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Position-specific kinetic isotope effects for nitrous oxide: a new expansion of the Rayleigh model

Nitrous oxide (N 2 O) is a potent greenhouse gas and the most significant anthropogenic ozone-depleting substance currently being emitted. A major source of anthropogenic N 2 O emissions is the microbial conversion of fixed nitrogen species from fertilizers in agricultural soils. Thus, understanding the enzymatic mechanisms by which microbes produce N 2 O has environmental significance. Measurement of the 15 N/ 14 N isotope ratios of N 2 O produced by purified enzymes or axenic microbial cultures is a promising technique for studying N 2 O biosynthesis. Typically, N 2 O-producing enzymes combine nitrogen atoms from two identical substrate molecules (NO or NH 2 OH). Position-specific isotope analysis of the central (N α ) and outer (N β ) nitrogen atoms in N 2 O enables the determination of the individual kinetic isotope effects (KIEs) for N α and N β , providing mechanistic insight into the incorporation of each nitrogen atom. Previously, position-specific KIEs (and fractionation factors) were quantified using the Rayleigh distillation equation, i.e., via linear regression of δ 15 N α or δ 15 N β against [–f In f / (1 – f)], where f is the fraction of substrate remaining in a closed system. This approach, however, is inaccurate for N α and N β because it does not account for fractionation at N α affecting the isotopic composition of substrate available for incorporation into the β position (and vice versa). Therefore, we developed a new expansion of the Rayleigh model that includes specific terms for fractionation at the individual N 2 O nitrogen atoms. By applying this Expanded Rayleigh model to a variety of simulated N 2 O synthesis reactions with different combinations of normal, inverse, and/or no KIEs at N α and N β , we demonstrate that our new model is both accurate and robust. We also applied this new model to two previously published datasets describing N 2 O production from NH 2 OH oxidation in a methanotroph culture (Methylosinus trichosporium) and N 2 O production from NO by a purified Histoplasma capsulatum (fungal) P450 NOR, demonstrating that the Expanded Rayleigh model is a useful tool in calculating position-specific fractionation for N 2 O synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Long-term nitrogen loading alleviates phosphorus limitation in terrestrial ecosystems

Increased human-derived nitrogen (N) deposition to terrestrial ecosystems has resulted in widespread phosphorus (P) limitation of net primary productivity. However, it remains unclear if and how N-induced P limitation varies over time. Soil extracellular phosphatases catalyze the hydrolysis of P from soil organic matter, an important adaptive mechanism for ecosystems to cope with N-induced P limitation. In this study we show, using a meta-analysis of 140 studies and 668 observations worldwide, that N stimulation of soil phosphatase activity diminishes over time. Whereas short-term N loading (≤5 years) significantly increased soil phosphatase activity by 28%, long-term N loading had no significant effect. Nitrogen loading did not affect soil available P and total P content in either short- or long-term studies. Together, these results suggest that N-induced P limitation in ecosystems is alleviated in the long-term through the initial stimulation of soil phosphatase activity, thereby securing P supply to support plant growth. Our results suggest that increases in terrestrial carbon uptake due to ongoing anthropogenic N loading may be greater than previously thought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Influence of clay mineral weathering on green rust formation at iron-reducing conditions

Green rusts (GR) are important drivers for trace metal and nutrient cycling in suboxic environments. We investigated whether green rusts would incorporate aluminum (Al) or other elements from naturally-formed clay minerals containing easily-weatherable clay minerals (e.g. mica, interlayered clays). We isolated the clay minerals from a Matapeake silt loam soil by removal of silt and sand, organic matter, and reducible oxides to study mechanisms of interaction between Fe(II) and soil-sourced clay minerals. We conducted batch Fe(II) sorption experiments at multiple near-neutral pHs (6.5–7.5) and reaction times (2h–365 days). Mineral transformations were characterized by selective extractions, X-ray diffraction (XRD), and Fe X-ray absorption spectroscopy (XAS) analyzed by shell-fitting and linear combination fitting (LCF) with natural and synthetic standards. Clay mineral fraction contained a mixture of quartz, kaolinite, interlayered vermiculite, mica, and chlorite with significant structural Fe (2.6% wt). Uptake of Fe(II) increased with pH and kinetics were rapid until 5 days, followed by slow continuous Fe(II) uptake. Citrate-bicarbonate desorption kinetics from Fe(II) sorbed clay released more Al and silicon (Si) compared with unreacted soil clay fraction whereas magnesium (Mg) and potassium (K) were unaffected. Citrate-bicarbonate extracted Fe contained more Fe(II) than an ideal GR with an Fe(II)/Fe(III) molar ratio of 5.50. Analysis of the Fe EXAFS by both LCF and shell fitting was best modeled as a combination of Fe(III)-clay reduction to Fe(II) and precipitation of GR and Fe(II)-Al LDH. After 7 days of Fe(II) sorption, LCF identified 55.2% total Fe in clay, 33.4% GR(Cl) and 11.4% Fe(II)-Al LDH. Further, these results provide novel evidence of Fe(II)-Al LDHs precipitating on naturally-formed soil clay minerals as a minor phase to GR. The geochemical implications are that GRs formed in soils and sediments should be considered to have Al and Si as well as Mg substitutions affecting their structure and reactivity.

58 GEOSCIENCES↗