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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Time‐series multi‐omics analysis of micronutrient stress in Sorghum bicolor reveals iron and zinc crosstalk and regulatory network conservation

Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources in identifying genes for functional studies and trait improvement, such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limited and excess conditions over a 21-day period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and co-expression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point, and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limitation and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves. Several of the reduction (Strategy I) and chelation (Strategy II) strategy genes that improve bioavailability of Fe and Zn in plant roots often used by non-grass and grass species, respectively, were differentially expressed. Gene regulatory network (GRN) analysis of roots revealed enrichment of genes from Fe limiting and Zn excess which strongly connect to homologues of SbFIT, SbPYE, and SbBTS as hub genes. The GRN for leaf responses showed homologues of SbPYE and SbBTS as hubs connecting genes for chloroplast biosynthesis, Fe-S cluster assembly, photosynthesis, and ROS scavenging. Expression analyses suggest sorghum uses Strategy II genes for Fe and Zn uptake, as expected, but can also utilize Strategy I genes, which may be advantageous in variable moisture environments. We found strong overlap between Fe and Zn responsive GRNs, indicative of micronutrient crosstalk. We also found conservation of root and leaf GRNs, and known homologous genes suggest strong constraints on homeostasis networks in plants. These data will provide a resource for functional genetics to enhance micronutrient transport in sorghum, and opportunities to conduct further comparative GRN analysis across diverse crops species.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Space Magnets Attracting Interest on Earth: Applications of Physical and Biological Techniques In the Study of Gravisensing and Response System of Plants

The BioTube/Magnetic Field Apparatus (MFA) research is designed to provide insight into the organization and operation of the gravity sensing systems of plants and other small organisms. This experiment on STS-107 uses magnetic fields to manipulate sensory cells in plant roots, thus using magnetic fields as a tool to study gravity-related phenomena. The experiment will be located in the SPACEHAB module and is about the size of a household microwave oven. The goal of the experiment is to improve our understanding of the basic phenomenon of how plants respond to gravity. The BioTube/MFA experiment specifically examines how gravitational forces serve as a directional signal for growth in the low-gravity environment of space. As with all basic research, this study will contribute to an improved understanding of how plants grow and will have important implications for improving plant growth and productivity on Earth. In BioTube/MFA, magnetic fields will be used to determine whether the distribution of subcellular starch grains, called amyloplasts, within plant cells predicts the direction in which roots will grow and curve in microgravity.

Karl H Hasenstein↗
DOE OSTI2023

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of Thaumarch aeota and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). In conclusion, our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Improved Representations of Land‐Atmosphere Interactions Over the Continental U.S. Through Dynamic Root Modeling

Previous studies have identified the oversimplified root system representation as a key factor leading to inaccuracies in vegetation‐atmosphere feedbacks. In this study, a dynamic root water uptake scheme in the Noah‐MP land surface model has been coupled to the Weather Research and Forecasting (WRF) model to investigate its impact on the surface hydroclimate variables and land‐atmosphere interactions. To evaluate the impact of the dynamic root, two coupled simulations were conducted, one with the dynamic root water uptake scheme (DynRt) and one with the static root water uptake scheme (StcRt), which is based on the default root representation in Noah‐MP, with slight modifications, primarily in vegetation‐related parameters. Both DynRt and StcRt simulations were conducted with a small ensemble of three members to account for variations in physical parameterizations, initial and boundary forcing and model setup. When compared with reference data sets, the DynRt simulations show improved results than the StcRt simulations, reducing biases in the simulated leaf area index, surface energy fluxes, soil moisture and precipitation. Two different mechanisms through which roots affect land‐atmosphere coupling have been identified. Over the transitional climate zone between the dry and wet climate, the dynamic root scheme affects surface climate and land‐atmosphere coupling mainly through changes in soil moisture through hydraulic redistribution by plant root system. Over the energy‐limited mesic zone, the dynamic root affects regional land‐atmosphere coupling mainly through changes in carbon allocation. This work highlights the importance of dynamic root representation in improving vegetation‐atmosphere simulations by enhancing predictions of water, energy, and carbon fluxes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft 3 (1.27 m 3 ), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO 2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Houseplants, Indoor Air Pollutants, and Allergic Reactions

The technology of using houseplant leaves for reducing volatile organics inside closed facilities has been demonstrated with formaldehyde and benzene. Philodendrons are among the most effective plants tested to date. Philodendron domesticum had demonstrated the ability to remove formaldehyde from small experimental chambers at a rate of 4.31 micro-g/sq cm leaf surface area with initial starting concentrations of 22 ppm. At initial starting concentrations of 2.3 ppm a formaldehyde removal rate of 0.57 micro-g/sq cm was achieved during a 24 hour test. Aleo vera demonstrated a much higher formaldehyde efficiency removal rate than Philodendron domesticum at low formaldehyde concentrations. During a 24 hour exposure period 5 ppm of formaldehyde were reduced to 0.5 ppm demonstrating a removal efficiency rate of 3.27 micro-g/sq cm. Removal efficiency rates can be expected to decrease with concentration levels because fewer molecules of chemicals come in contact with the leaf surface area. Several centimeters of small washed gravel should be used to cover the surface of pot plants when large numbers of plants are kept in the home. The reason for this is to reduce the exposed area of damp potting soil which encourages the growth of molds (fungi). The leaves of Philodendron domesticum and golden pothos (Scindapsus aureus) have also demonstrated their ability to remove benzene and carbon monoxide from closed chambers. A combination of activated carbon and plant roots have demonstrated the greatest potential for removing large volumes of volatile organics along with smoke and possible radon from closed systems. Although fewer plants are required for this concept a mechanical blower motor must be used to pull or push the air through the carbon-root filter. NASA studies on motor sizes and bioregeneration rates should be completed by 1988.

Wolverton, B. C.↗
DOE OSTI2024

Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Abstract Root nodule symbiosis (RNS) is a complex trait that enables plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. Pinpointing the evolutionary origins of RNS is critical for understanding its genetic basis, but building this evolutionary context is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for the NFC and an RNS trait database to reconstruct the evolution of RNS. Our analysis identifies evolutionary rate heterogeneity associated with a two-step process: An ancestral precursor state transitioned to a more labile state from which RNS was rapidly gained at multiple points in the NFC. We illustrate how a two-step process could explain multiple independent gains and losses of RNS, contrary to recent hypotheses suggesting one gain and numerous losses, and suggest a broader phylogenetic and genetic scope may be required for genome-phenome mapping.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Hydraulic redistribution by deeply rooted grasses and its ecohydrologic implications in the southern Great Plains of North America

Perennial bioenergy crops with deep (>1 m) rooting systems, such as switchgrass (Panicum virgatum L.), are hypothesized to increase carbon storage in deep soil. Deeply rooted plants may also affect soil hydrology by accessing deep soil water for transpiration, which can affect soil water content and infiltration in deep soil layers, thereby affecting groundwater recharge. Using stable H and O isotope (δ 2 H and δ 18 O) and 3 H values, we studied the soil water conditions at 20–30 cm intervals to depths of 2.4–3.6 m in paired fields of switchgrass and shallow rooted crops at three sites in the southern Great Plains of North America. We found that soil under switchgrass had consistently higher soil water content than nearby soil under shallow-rooted annual crops by a margin of 15%–100%. Soil water content and isotopic depth profiles indicated that hydraulic redistribution of deep soil water by switchgrass roots explained these observed soil water differences. To our knowledge, these are the first observations of hydraulic redistribution in deeply rooted grasses, and complement earlier observations of dynamic soil water fluxes under shallow-rooted grasses. Hydraulic redistribution by switchgrass may be a strategy for drought avoidance, wherein the plant may actively prevent water limitation. Furthermore, this raises the possibility that deeply rooted grasses may be used to passively subsidize soil water to more shallow-rooted species in inter-cropping arrangements.

3H↗
DOE OSTI2023

Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes

The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. Furthermore, this work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Impacts of The Wetland Sedge Carex aquatilis on Microbial Community and Methane Metabolisms

Microbial activity in the soil of wetlands is responsible for the emission of more methane to the atmosphere than all other natural sources combined. This microbial activity is heavily impacted by plant roots, which influence the microbial community by exuding organic compounds and by leaking oxygen into an otherwise anoxic environment. This study compared the microbial communities of planted and unplanted wetland soil from an Alaskan bog to elucidate how plant growth influences populations and metabolisms of methanogens and methanotrophs. A common boreal wetland sedge, Carex aquatilis, was grown in the laboratory and DNA samples were sequenced from the rhizosphere, unplanted bulk soil, and a simulated rhizosphere with oxygen input but no organic carbon. The abundance of both methanogens and methanotrophs were positively correlated with methane emissions. Among the methanotrophs, both aerobic and anaerobic methane oxidizing microbes were more common in the rhizosphere of mature plants than in unplanted soil, while facultative methanotrophs capable of utilizing either methane or other molecules became relatively less common. Furthermore, these trends indicate that the roots in this experiment created an environment which favored highly specialized microbial metabolisms over generalist approaches. One aspect of this specialized microbiome is the presence of both aerobic and anaerobic metabolisms, which indicates that oxygen is present but is a limiting resource controlling competition.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2003

Ionic signaling in plant gravity and touch responses

Plant roots are optimized to exploit resources from the soil and as each root explores this environment it will encounter a range of biotic and abiotic stimuli to which it must respond. Therefore, each root must possess a sensory array capable of monitoring and integrating these diverse stimuli to direct the appropriate growth response. Touch and gravity represent two of the biophysical stimuli that plants must integrate. As sensing both of these signals requires mechano-transduction of biophysical forces to biochemical signaling events, it is likely that they share signal transduction elements. These common signaling components may allow for cross-talk and so integration of thigmotropic and gravitropic responses. Indeed, signal transduction events in both plant touch and gravity sensing are thought to include Ca(2+)- and pH-dependent events. Additionally, it seems clear that the systems responsible for root touch and gravity response interact to generate an integrated growth response. Thus, primary and lateral roots of Arabidopsis respond to mechanical stimuli by eliciting tropic growth that is likely part of a growth strategy employed by the root to circumvent obstacles in the soil. Also, the mechano-signaling induced by encountering an obstacle apparently down-regulates the graviperception machinery to allow this kind of avoidance response. The challenge for future research will be to define how the cellular signaling events in the root cap facilitate this signal integration and growth regulation. In addition, whether other stimuli are likewise integrated with the graviresponse via signal transduction system cross-talk is an important question that remains to be answered.

Review↗
NASA NTRS2004

Response of graywater recycling systems based on hydroponic plant growth to three classes of surfactants

Anionic (sodium laureth sulfate, SLES), amphoteric (cocamidopropyl betaine, CAPB) and nonionic (alcohol polyethoxylate, AE) surfactants were added to separate nutrient film technique (NFT) hydroponic systems containing dwarf wheat (Triticum aestivum cv. USU Apogee) in a series of 21 day trials. Surfactant was added either in a (1). temporally dynamic mode (1-3 g surfactant m(-2) growing area d(-1)) as effected by automatic addition of a 300 ppm surfactant solution to meet plant water demand, or (2). continuous mode (2 g surfactant m(-2) growing area d(-1)) as effected by slow addition (10 mLh(-1)) of a 2000 ppm surfactant solution beginning at 4d after planting. SLES showed rapid primary degradation in both experiments, with no accumulation 24 h after initial addition. CAPB and AE were degraded less rapidly, with 30-50% remaining 24 h after initial addition, but CAPB and AE levels were below detection limit for the remainder of the study. No reductions in vegetative growth of wheat were observed in response to SLES, but biomass was reduced 20-25% with CAPB and AE. Microbial communities associated with both the plant roots and wetted hardware surfaces actively degraded the surfactants, as determined by monitoring surfactant levels following pulse additions at day 20 (with plants) and day 21 (after plant removal). In order to test whether the biofilm communities could ameliorate phytotoxicity by providing a microbial community acclimated for CAPB and AE decay, the continuous exposure systems were planted with wheat seeds after crop removal at day 21. Acclimation resulted in faster primary degradation (>90% within 24h) and reduced phytotoxicity. Overall, the studies indicate that relatively small areas (3-5m(2)) of hydroponic plant systems can process per capita production of mixed surfactants (5-10 g x person(-1)d(-1)) with minimal effects on plant growth.

Hydroponics↗
DOE OSTI2024

Shifts in belowground processes along a temperate forest edge

Abstract Context Forests are increasingly fragmented, and as a result most forests in the United States are within one km of an edge. Edges change environmental conditions of the forest—especially radiation, roughness, temperature, and moisture—that can have consequences for plant productivity and ecosystem functions. However, edge effects on aboveground characteristics of plants and the environment are better understood relative to plant roots and soil in the belowground environment. Objectives Our main objectives were to determine if soil C pools and fluxes are higher at the edge relative to other landscape positions, and to understand how specific belowground processes contribute to bulk differences in pools and fluxes. Methods We measured environmental conditions, live and dead fine root traits, soil chemistry, and soil respiration along a 75 m transect from interior forest to meadow in Gaithersburg, MD. Results We observed differences in the soil chemical, biological and hydrological environment between the forest interior, edge and adjacent meadow. In some cases, the forest edge represented a mid-point in environmental or belowground characteristics between the forest interior and meadow ( e.g. , pH, C-to-N ratio [C:N], live fine root biomass, heterotrophic respiration), likely reflecting the change in litter type and quality associated with the transition from grass to woody species. In other cases, neighboring landscape positions were different from the forest edge, which was drier and had higher dead fine root biomass. Although soil C contents were not significantly different across landscape positions, there was a tendency towards higher average soil C content at the edge relative to other landscape positions, suggesting that increased C loss related to root decay and greater soil respiration at the edge relative to the forest interior may have been offset by increased C gain from high plant productivity and subsequent inputs to soil. Conclusions This research provides insight into how forest edge environments may differ from the interior and how concurrent processes above- and belowground may contribute to those differences.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Metabolome and RNA-seq Analysis of Responses to Nitrogen Deprivation and Resupply in Tea Plant (Camellia sinensis) Roots

Nitrogen (N) is an important contributor in regulating plant growth and development as well as secondary metabolites synthesis, so as to promote the formation of tea quality and flavor. Theanine, polyphenols, and caffeine are important secondary metabolites in tea plant. In this study, the responses of Camellia sinensis roots to N deprivation and resupply were investigated by metabolome and RNA-seq analysis. N deficiency induced content increase for most amino acids (AAs) and reduction for the remaining AAs, polyphenols, and caffeine. After N recovery, the decreased AAs and polyphenols showed a varying degree of recovery in content, but caffeine did not. Meanwhile, theanine increased in content, but its related synthetic genes were down-regulated, probably due to coordination of the whole N starvation regulatory network. Flavonoids-related pathways were relatively active following N stress according to KEGG enrichment analysis. Gene co-expression analysis revealed TCS2 , AMT1;1 , TAT2 , TS , and GOGAT as key genes, and TFs like MYB, bHLH, and NAC were also actively involved in N stress responses in C. sinensis roots. These findings facilitate the understanding of the molecular mechanism of N regulation in tea roots and provide genetic reference for improving N use efficiency in tea plant.

Xu, Wenluan↗
NASA NTRS1985

Aquatic Plants Aid Sewage Filter

Method of wastewater treatment combines micro-organisms and aquatic plant roots in filter bed. Treatment occurs as liquid flows up through system. Micro-organisms, attached themselves to rocky base material of filter, act in several steps to decompose organic matter in wastewater. Vascular aquatic plants (typically, reeds, rushes, cattails, or water hyacinths) absorb nitrogen, phosphorus, other nutrients, and heavy metals from water through finely divided roots.

Wolverton, B. C.↗
DOE OSTI2023

Rapid in situ nutrient element distribution in plants and soils using laser-induced breakdown spectroscopy ($\mathrm{LIBS}$)

The aim of this study is to develop and test the applicability of a rapid in situ plant chemistry profiling technique to determine elemental composition of small-volume plant and soil samples obtained from a woody bioenergy crop species, Populus trichocarpa. Expanding the research tools available to characterize the nutrient element correlations among plant tissue types and soil depths is a critical need in the path of understanding productivity and adaptation of plants to variations in external abiotic and biotic factors and developing sustainable perennial bioenergy crops that are co-optimized for biomass valorization aboveground and carbon sequestration belowground. Several plant root, stem, and soil samples were tested using laser-induced breakdown spectroscopy (LIBS) to evaluate the presence and distribution of nutrient elements. Samples were tested as collected and after being dried and cross sectioned to evaluate the effectiveness of using LIBS for in situ analysis on plant samples. The collected LIBS spectra show the elemental peaks were the same in both the as collected and prepared samples for roots and stems. Qualitative amounts of elements such as H, C, N, O, Li, Na, Mg, K, Ca, Fe, Al, and Si were able to be identified rapidly in raw samples. Here in this report we demonstrate suitability of LIBS in obtaining rapid, in situ, elemental distribution in plant and soil samples, utilizing only small sample volumes and minimal sample preparation. This demonstration opens up a new rapid phenotyping avenue necessary to fill the asymmetrical knowledge gaps in belowground performance of plant systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

2-D soil zymography: Accounting for the spatial variation of pH

Soil zymography is commonly used to quantify spatial distribution of hydrolytic enzyme activities on soil and plant root surfaces. It is recommended to adjust pH in zymography substrates and calibration solutions with respect to soil/root pH. However, pH values may vary greatly within a few mm of plant rhizosphere, potentially altering the distribution of pH in zymography membranes. Despite the fact that the effect of pH on the calibration of zymography membranes is generally known, its potential impact on zymography results is unaccounted for in processing zymography images and calculations of enzyme activity. In this study we assessed the effect of pH variations on the persistency of the methylumbelliferone (MUF) calibration. The studied pH values ranged from 4.5 to 7.5. The MUF calibration curves greatly deviated from that at a reference pH of 6.5, with a marked nonlinear increase of deviation with greater membrane brightness. We suggest that the problem can be partially alleviated by reducing the membrane incubation time. However, such deviations suggest the need for a more comprehensive resolution via mapping pH and using pH-specific calibrations to process zymography images. Here, we developed a MATLAB code to implement a pixel-based correction of enzyme activity for pH in processing time-lapse zymography images.

59 BASIC BIOLOGICAL SCIENCES↗