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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Nitrogen Fertilizer, Arbuscular Mycorrhizal Fungi, and Soil Nematodes Affect Lignin Quality and Quantity in Switchgrass (Panicum virgatum L.)

Plant lignin content and composition, which limit cell wall digestibility and efficiency of cellulose conversion to bioethanol, can be influenced by belowground biotic and abiotic factors. Switchgrass (Panicum virgatum L.) is a leading lignocellulosic biofuel crop and forms strong belowground associations with arbuscular mycorrhizal fungi (AMF), is susceptible to belowground plant-parasitic nematodes (PPN), and when grown in monoculture generally requires nitrogen (N) fertilization. The main objectives of the study were to investigate the effects of N fertilizer and belowground organisms on lignin content and composition of switchgrass. Here, leaf, stem, and root tissues were evaluated separately to test whether these factors had varying belowground (local) or aboveground (systemic) effects on plants. These factors were manipulated in a field study in 2017 using biocide applications to reduce soil fungi and nematodes. Combined biocide application reduced p-hydroxyphenyl (H) unit abundance in the leaves by 14% and increased the syringyl:guaiacyl (S:G) ratio in stems by 2%. Application of fungicide alone increased stem syringyl (S) unit by 12.4% as compared with control plots, and 11.1% as compared with nematicide plots. Overall, fertilizer increased total stem lignin by 3%, stem S unit by 6.7%, and stem S:G ratio by 10%, whereas it reduced the amount of H-unit in the roots by 11%. While the effects of N fertilizer were more pronounced in this study, changes to soil organisms had similar magnitudes of effect for some measures of lignin, indicating that these belowground interactions may be important for growers to consider in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phosphate Availability Modulates Root Exudate Composition and Rhizosphere Microbial Community in a Teosinte and a Modern Maize Cultivar

Domestication and breeding have affected interactions between plants and their microbiomes in ways that are only beginning to be understood but may have important implications for recruitment of rhizosphere microorganisms, particularly under stress conditions. We investigated the responses of a modern maize (Zea mays subsp. mays) cultivar and its wild relative, teosinte (Z. mays subsp. parviglumis), to different phosphate availabilities. We appraised responses of the plant-microbial holobiont to phosphate stresses by profiling root exudate metabolomes, and microbial communities in the root endosphere and rhizosphere. We also performed plate assays to quantify phosphate-solubilizing microorganisms from the rhizosphere. Although root exudate metabolite profiles were distinct between the teosinte and modern maize under high phosphate, both plants shifted exudate compositions in response to phosphate stress toward a common metabolite profile. Root and rhizosphere microbial communities also responded significantly to both plant type and the phosphate availability. A subset of bacterial and fungal taxa were differentially abundant under the different phosphate conditions, with each of the three conditions favoring different taxa. Both teosinte and maize rhizospheres harbored phosphate-solubilizing microorganisms under all growth conditions. These results suggest that the root exudation response to phosphate stress was conserved through the domestication of maize from teosinte, shifting exudation levels of specific metabolites. Although microbial communities also shifted, plate-based assays did not detect selective recruitment of phosphate solubilizers in response to phosphate availability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The nuclear charge radius of 13 C

The size is a key property of a nucleus. Accurate nuclear radii are extracted from elastic electron scattering, laser spectroscopy, and muonic atom spectroscopy. The results are not always compatible, as the proton-radius puzzle has shown most dramatically. Beyond helium, precision data from muonic and electronic sources are scarce in the light-mass region. The stable isotopes of carbon are an exception. We present a laser spectroscopic measurement of the root-mean-square (rms) charge radius of 13 C and compare this with ab initio nuclear structure calculations. Measuring all hyperfine components of the 2 3 S → 2 3 P fine-structure triplet in 13 C 4+ ions referenced to a frequency comb allows us to determine its center-of-gravity with accuracy better than 2 MHz although second-order hyperfine-structure effects shift individual lines by several GHz. We improved the uncertainty of R c ( 13 C) determined with electrons by a factor of 6 and found a 3σ discrepancy with the muonic atom result of similar accuracy.

Müller, Patrick [Technical Univ. of Darmstadt (Ger↗
DOE OSTI2022

Soil resistance and recovery during neotropical forest succession

The recovery of soil conditions is crucial for successful ecosystem restoration and, hence, for achieving the goals of the UN Decade on Ecosystem Restoration. Here, we assess how soils resist forest conversion and agricultural land use, and how soils recover during subsequent tropical forest succession on abandoned agricultural fields. Our overarching question is how soil resistance and recovery depend on local conditions such as climate, soil type and land-use history. For 300 plots in 21 sites across the Neotropics, we used a chronosequence approach in which we sampled soils from two depths in old-growth forests, agricultural fields (i.e. crop fields and pastures), and secondary forests that differ in age (1–95 years) since abandonment. We measured six soil properties using a standardized sampling design and laboratory analyses. Soil resistance strongly depended on local conditions. Croplands and sites on high-activity clay (i.e. high fertility) show strong increases in bulk density and decreases in pH, carbon (C) and nitrogen (N) during deforestation and subsequent agricultural use. Resistance is lower in such sites probably because of a sharp decline in fine root biomass in croplands in the upper soil layers, and a decline in litter input from formerly productive old-growth forest (on high-activity clays). Soil recovery also strongly depended on local conditions. During forest succession, high-activity clays and croplands decreased most strongly in bulk density and increased in C and N, possibly because of strongly compacted soils with low C and N after cropland abandonment, and because of rapid vegetation recovery in high-activity clays leading to greater fine root growth and litter input. Furthermore, sites at low precipitation decreased in pH, whereas sites at high precipitation increased in N and decreased in C : N ratio. Extractable phosphorus (P) did not recover during succession, suggesting increased P limitation as forests age. These results indicate that no single solution exists for effective soil restoration and that local site conditions should determine the restoration strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Numerical Modeling of Air-Blast Suppression as a Function of Explosive-Charge Burial Depth

As a chemical explosion is buried, the mechanism for acoustic wave generation transitions from fully gas-generated at the surface to completely spall-induced at full containment depth. The fully gas-generated and completely spall-induced signals in the acoustic waveform are well described; however, the transition between these two end-members eludes numerical modeling because of the complex phenomena that are involved. The phenomena of crater formation and explosive cloud evolution are simulated using an Eulerian hydrocode that incorporates geomaterials with strength and porosity. Having accurately modeled these phenomena, we can confidently predict the propagation and relative strength of the gas-generated and spall-induced pulses in the recorded acoustic waveform. The numerical predictions agree with observations from the historical Stagecoach experiment as well as modern recordings from the Source Physics Experiment. In particular, the peak pressure p generated by an explosion is initially due to the gas-generated mechanism and decays with scaled depth of burial d s (depth d scaled by the cube-root of explosive yield w 1/3 ) as exp(-d s ) but then transitions near a scaled depth of 6 m/ton 1/3 to the spall-generated mechanism in which the decay is d$_{s}^{-7/4}$. This decay form is related to the strong ground-motion attenuation relationship that affects spall strength. So these results can improve seismoacoustic inverse models for the explosive source that need to account for the gas-generated and spall-induced signals and their effect on peak pressures and other acoustic signal features.

58 GEOSCIENCES↗
DOE OSTI2023

Trichoderma harzianum transcriptome in response to the nematode Pratylenchus brachyurus

The root-lesion nematode Pratylenchus brachyurus causes extensive damage in several crops of economic importance. Fungi of Trichoderma genus have been highlighted as biopesticide agents in the control of several plant diseases. Although it is already widely used in agriculture, there are few studies, especially at the molecular level, that evaluate T. harzianum in the control of P. brachyurus . The aim of the present study was to investigate how interaction with the nematode P. brachyurus influences gene expression of T. harzianum , by using RNA-Seq analysis. Of the 13,932 predicted genes in the T. harzianum genome, 2,922 (21%) were differentially expressed in the presence of P. brachyurus , in relation to the absence of the nematode. Among the differentially expressed genes, we found genes encoding Carbohydrate Active EnZymes (CAZy), MEROPS peptidases, and proteins related to secondary metabolite synthesis. 118 pathways were identified as related to the biosynthesis of secondary metabolites. Additionally, the analysis identified 136 metabolic pathways related to these differentially expressed genes, among which we highlight: aminobenzoate degradation, xenobiotic metabolism by cytochrome P450, and sesquiterpenoid and triterpenoid biosynthesis. Our results contribute to a better understanding of the response of T. harzianum to the nematode P. bracyurus , the potential for biocontrol by this fungus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Changes in soil pore structure generated by the root systems of maize , sorghum and switchgrass affect in situ N 2 O emissions and bacterial denitrification

Due to the heterogeneous nature of soil pore structure, processes such as nitrification and denitrification can occur simultaneously at microscopic levels, making prediction of small-scale nitrous oxide (N 2 O) emissions in the field notoriously difficult. We assessed N 2 O+N 2 emissions from soils under maize (Zea mays L.), switchgrass (Panicum virgatum L.), and energy sorghum (Sorghum bicolor L.), three potential bioenergy crops in order to identify the importance of different N 2 O sources to microsite production, and relate N 2 O source differences to crop-associated differences in pore structure formation. The combination of isotopic surveys of N 2 O in the field during one growing season and X-ray computed tomography (CT) enabled us to link results from isotopic mappings to soil structural properties. Further, our methodology allowed us to evaluate the potential for in situ N 2 O suppression by biological nitrification inhibition (BNI) in energy sorghum. Our results demonstrated that the fraction of N 2 O originating from bacterial denitrification and reduction of N 2 O to N 2 is largely determined by the volume of particulate organic matter occluded within the soil matrix and the anaerobic soil volume. Bacterial denitrification was greater in switchgrass than in the annual crops, related to changes in pore structure caused by the coarse root system. This led to high N-loses through N 2 emissions in the switchgrass system throughout the season a novel finding given the lack of data in the literature for total denitrification. Isotopic mapping indicated no differences in N 2 O-fluxes or their source processes between maize and energy sorghum that could be associated with the release of BNI by the investigated sorghum variety. The results of this research show how differences in soil pore structures among cropping systems can determine both N 2 O production via denitrification and total denitrification N losses in situ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Soil nutrients affect biomass allocation at the individual tree level in Populus_deltoides

The allocation of carbon (C) to tree roots has implication for forest productivity and soil C storage. Here, we elucidated the factors affecting absolute and relative production of resource-acquiring absorptive fine roots (AFR) and other tree organs. We assessed soil properties, leaf (Leaves), stem and branch (Stem-Br), coarse root (CR), transport fine root (TFR), and AFR biomass, production, and allocation and leaf litterfall and AFR and TFR turnover for 12 trees in a youngPopulus deltoides plantation. On a biomass basis, standing crop of AFRs was significantly related to that of TFRs, but both were independent of biomass of leaves, CRs and Stem-Brs. Production (standing crop + turnover) as a proportion of total biomass (allocation) highlighted significant relationships between AFR%, TFR%, and tree and soil characteristics. AFR% and TFR% were negatively correlated with Stem-Br%, Leaf%, and total tree production. Spatial variation in soil nutrient gradients altered allocation withinP. deltoides.AFR% and TFR% were negatively correlated with CEC, N, and Ca but positively correlated with soil P, Fe, and Na. Stem-Br% was positively correlated with CEC and soil N but negatively correlated with P. AFR and TFR growth and death are tightly coupled at the individual tree level. AFR allocation, but not standing biomass, is highly correlated with allocation to leaves, suggesting tight regulation of the growth of these two resource-acquiring organs. Lower soil N and Ca increased allocation to AFRs at the cost of leaves, whereas allocation to AFRs and leaves increased with soil P. Such changes in response to soil P may control whole-tree production in the current study.

Biomass allocation↗
DOE OSTI2022

Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism

Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus antigravitropic offset (AGO) mechanisms. Here we report a root angle regulatory gene termed ENHANCED GRAVITROPISM1 ( EGT1 ) that encodes a putative AGO component, whose loss-of-function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes an F-box and Tubby domain-containing protein that is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wild-type. Transcript profiling revealed Hvegt1 roots deregulate reactive oxygen species (ROS) homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shows that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic force microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wild-type. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery’s known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Decentralized Approach for Modeling Organized Convection Based on Thermal Populations on Microgrids

Abstract In this study, a spectral model for convective transport is coupled to a thermal population model on a two‐dimensional horizontal “microgrid,” covering the typical gridbox size of general circulation models. The goal is to explore new ways of representing impacts of spatial organization in cumulus cloud fields. The thermals are considered the smallest building block of convection, with thermal life cycle and movement represented through binomial functions. Thermals interact through two simple rules, reflecting pulsating growth and environmental deformation. Long‐lived thermal clusters thus form on the microgrid, exhibiting scale growth and spacing that represent simple forms of spatial organization and memory. Size distributions of cluster number are diagnosed from the microgrid through an online clustering algorithm, and provided as input to a spectral multiplume eddy‐diffusivity mass flux scheme. This yields a decentralized transport system, in that the thermal clusters acting as independent but interacting nodes that carry information about spatial structure. The main objectives of this study are (a) to seek proof of concept of this approach, and (b) to gain insight into impacts of spatial organization on convective transport. Single‐column model experiments demonstrate satisfactory skill in reproducing two observed cases of continental shallow convection. Metrics expressing self‐organization and spatial organization match well with large‐eddy simulation results. We find that in this coupled system, spatial organization impacts convective transport primarily through the scale break in the size distribution of cluster number. The rooting of saturated plumes in the subcloud mixed layer plays a key role in this process.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Evaluating genetic and environmental controls on silicon accumulation in Populus trichocarpa leaves

Background and aims: Silicon (Si) accumulation and formation of non-crystalline silica particles (phytoliths) inside plant cells contribute to plant function, soil carbon storage, and Si reservoirs in soils. A better understanding of how genetic and environmental factors control Si accumulation may improve understanding of Si cycling between plants and soil and its impacts on other ecosystem processes. Methods: This study examined how genetic potential for Si uptake and silicification translated to Si concentrations and phytolith formation in Populus trichocarpa leaves. Leaves were collected from four different genotypes of cultivated poplar trees that were grown in a common garden and possess established differences in leaf-level gene expression related to Si transport and silicification. Scanning electron microscopy and subsequent image analysis were used to quantify Si concentrations and phytolith abundance and features. Results: Phytoliths were identified in nearly all leaves but were often absent at very low (< 0.5 wt.%) Si concentrations at the leaf surface. The proportion of leaf area occupied by phytoliths increased as Si content increased. Silicon content and phytolith abundance at the leaf surface did not vary across genotypes, but surface Si was weakly correlated with plant available Si in soil. Conclusion: Phytoliths were prevalent in P. trichocarpa leaves; however, the genetic potential for Si uptake and silicification at the leaf-level poorly predicted foliar Si and phytolith abundance. Uniformly low expression of Si uptake genes in the roots may have reduced differences across genotypes. Consequently, Si accumulation in leaves was likely more strongly influenced by soil Si bioavailability, phenology, or additional environmental factors.

Image analysis↗
DOE OSTI2025

Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics

Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is challenging to investigate in the field. In this study, we extend ecosystem fabrication (EcoFAB 2.0) approaches to study plant-bacteria-phage interactions by comparing the impact of virocell (phage-lysed) and uninfected 15 N-labelled bacterial necromass on plant nitrogen acquisition and rhizosphere exometabolites composition. We show that grass Brachypodium distachyon derives some nitrogen from amino acids in uninfected Pseudomonas putida necromass lysed by sonication but not from virocell necromass. Additionally, the bacterial necromass elicits the formation of rhizosphere exometabolites, some of which (guanosine), alongside tested aromatic acids ( p -coumaric and benzoic acid), show bacterium-specific effects on bacteriophage-induced lysis when tested in vitro. The study highlights the dynamic feedback between virocell necromass and plants and suggests that root exudate metabolites can impact bacteriophage infection dynamics.

Brachypodium↗
DOE OSTI2021

Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere

Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the rhizosphere microbiome. These interactions affect plant fitness and performance, soil health, and the belowground carbon budget.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Phenolic acid-degrading Paraburkholderia prime decomposition in forest soil

Abstract Plant-derived phenolic acids are catabolized by soil microorganisms whose activity may enhance the decomposition of soil organic carbon (SOC). We characterized whether phenolic acid-degrading bacteria enhance SOC mineralization in forest soils when primed with 13C-labeled p-hydroxybenzoic acid (pHB). We further tested whether pHB-induced priming could explain differences in SOC content among mono-specific tree plantations in a 70-year-old common garden experiment. pHB addition primed significant losses of SOC (3–13 µmols C g−1 dry wt soil over 7 days) compared to glucose, which reduced mineralization (-3 to -8 µmols C g−1 dry wt soil over 7 days). The principal degraders of pHB were Paraburkholderia and Caballeronia in all plantations regardless of tree species or soil type, with one predominant phylotype (RP11ASV) enriched 23-fold following peak pHB respiration. We isolated and confirmed the phenolic degrading activity of a strain matching this phylotype (RP11T), which encoded numerous oxidative enzymes, including secretion signal-bearing laccase, Dyp-type peroxidase and aryl-alcohol oxidase. Increased relative abundance of RP11ASV corresponded with higher pHB respiration and expression of pHB monooxygenase (pobA), which was inversely proportional to SOC content among plantations. pobA expression proved a responsive measure of priming activity. We found that stimulating phenolic-acid degrading bacteria can prime decomposition and that this activity, corresponding with differences in tree species, is a potential mechanism in SOC cycling in forests. Overall, this study highlights the ecology and function of Paraburkholderia whose associations with plant roots and capacity to degrade phenolics suggest a role for specialized bacteria in the priming effect.

54 ENVIRONMENTAL SCIENCES↗