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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

An integrated Imaging and Modeling Toolbox for Accelerated Development of Root-focused Crops at Field Scales

This project, led by Yuxin Wu at the LBNL, was proposed to develop an integrated imaging-modeling toolbox allowing for accelerated development of root-focused crops at field scales. Our approach is based on a novel root phenotyping method we termed Tomographic Electrical Rhizosphere Imaging (TERI), which provides advanced phenotyping of key root traits by sensing the electrical impedance response of roots and soil to external electrical excitations, and mapping these responses to root and soil properties. The role of Noble Research Institute in this project is to assist TERI model establishment and validation by collecting various above- and below-ground traits data from container- and field-grown plants (mainly wheat). Over the last three years, Noble Research Institute has conducted 3 phases of experiments as proposed including: (Phase 1) greenhouse and hoop-house experiments in wheat and pecan plants grown under controlled container-grown conditions; (Phase 2) space-planted individual plant field experiment using different wheat varieties; and (Phase 3) small-plot planted field experiment using different wheat varieties, as well as using different small grains species including wheat, rye, triticale, oat and barley for increasing plant variation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Bioenergy Underground: Challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production

Abstract Bioenergy production often focuses on the aboveground feedstock production for conversion to fuel and other materials. However, the belowground component is crucial for soil carbon sequestration, greenhouse gas fluxes, and ecosystem function. Roots maximize feedstock production on marginal lands by acquiring soil resources and mediating soil ecosystem processes through interactions with the microbial community. This belowground world is challenging to observe and quantify; however, there are unprecedented opportunities using current methodologies to bring roots, microbes, and soil into focus. These opportunities allow not only breeding for increased feedstock production but breeding for increased soil health and carbon sequestration as well. A recent workshop hosted by the USDOE Bioenergy Research Centers highlighted these challenges and opportunities while creating a roadmap for increased collaboration and data interoperability through standardization of methodologies and data using F.A.I.R. principles. This article provides a background on the need for belowground research in bioenergy cropping systems, a primer on root system properties of major U.S. bioenergy crops, and an overview of the roles of root chemistry, exudation, and microbial interactions on sustainability. Crucially, we outline how to adopt standardized measures and databases to meet the most pressing methodological needs to accelerate root, soil, and microbial research to meet the pressing societal challenges of the century.

09 BIOMASS FUELS↗
DOE OSTI2023

Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range

A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. Furthermore, this study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Soil oxidoreductase zymography: Visualizing spatial distributions of peroxidase and phenol oxidase activities at the root-soil interface

Decomposition of organic material in the rhizosphere – the most dynamic microbial habitat in soil – involves arrays of oxidoreductase and hydrolytic enzymes. Spatial distributions of various hydrolytic activities in soil have already been explored by zymographic techniques. However, the distribution of oxidative activity in the rhizosphere remains to be studied. Thus, we extended a Time-Lapse Zymography technique, using Amplex Red® reagent, to visualize and quantify distributions of phenol oxidase and peroxidase activities in the rhizosphere of Zea mays L. growing in a Haplic Phaeozem and the non-rhizospheric soil. The gross oxidative activity was greatest at the root surfaces, and fell to background soil levels 1.26 and 0.73 mm from seminal (>1 mm diameter) and lateral (<0.5 mm diameter) roots, respectively. The rhizosphere extent relative to the root radius was 59% broader around lateral than around seminal roots. The greatest activities, up to 30 nmol cm –2 min –1 , were peroxidase-dominated and closely associated with roots. Here, the results confirm the utility of the approach for studying spatio-temporal distributions of oxidative activities in soil. However, actual activity of oxidoreductases in the field will be strongly controlled by fluctuating environmental conditions such as soil aeration and the gradient of reactive oxygen species, which need to be considered especially in anoxic soils.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Root and Microbial Soil CO 2 and CH 4 Fluxes Respond Differently to Seasonal and Episodic Environmental Changes in a Temperate Forest

Upland forest soils are typically major atmospheric carbon dioxide (CO 2 ) sources and methane (CH 4 ) sinks, but the contributions of root and microbial processes, as well as their separate temporal responses to environmental change, remain poorly understood. This 2-year study was conducted in a temperate, deciduous forest located on the Chesapeake Bay in Maryland, USA. We used temporal CO 2 and CH 4 flux measurements, exclusion-source partitioning, and an ecosystem-scale flooding experiment to understand how carbon (C) fluxes, and their root and microbial sources, respond to seasonal and episodic environmental change. Here, we show that the root-and-rhizosphere component of soil CO 2 and CH 4 flux is significant and that its dependence on soil temperature and volumetric water content (VWC) influences soil C dynamics at seasonal timescales. Experimental flooding shows that CO 2 and CH 4 flux responses to episodic moisture change were driven by suppression of soil heterotrophs, while root respiration did not respond to transient hydrologic disturbance. Methane uptake responded strongly to episodic inundation, reinforcing the important role of soil moisture in the short-term control of the forest soil CH 4 sink. However, despite the clear seasonality of CH 4 uptake, as well as its strong response to short-term experimental inundation, temperature and VWC were weak predictors of CH 4 uptake at a seasonal timescale. We suggest that CH 4 consumption in the long-term may be determined by vegetation, nutrients, microbial communities, or other factors correlated with seasonal changes. Our results indicate that root and microbial sources of both CO 2 and CH 4 flux respond differently in timing and magnitude to seasonal and episodic environmental change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Root Dynamics Mitigate Warm and Dry Biases over the Central United States

The central United States frequently exhibits warm and dry biases in simulations of summertime conditions, a persistent feature that remains unresolved. While previous studies linked these biases to misrepresented surface energy exchanges, the role of belowground processes remains poorly understood. Here, we demonstrate that inadequate representation of root water uptake in land surface models contributes to this bias. Using both offline Noah-MP and coupled WRF-Noah-MP simulations with static and dynamic root water uptake schemes, we show that the inclusion of dynamic root processes reduces 2-m air temperature biases and enhances precipitation, primarily by increasing the rain rate of convective systems. Offline and coupled simulations further reveal that the cooling effects and precipitation increases are amplified through positive land-atmosphere feedback, active only in the coupled model. These findings highlight an important role of root in modulating land-atmosphere interactions and underscore the need to refine root-zone processes to improve regional atmospheric simulations.

Yang, Zhao (ORCID:0000000288027130)↗
DOE OSTI2021

Genetic determinants of endophytism in the Arabidopsis root mycobiome

The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species

Abstract Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana , Brachypodium distachyon , and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Strikingly high amount of tricin-lignin observed from vanilla (Vanilla planifolia) aerial roots

Lignin has attracted tremendous interest as a renewable resource for biofuels, biomaterials, and chemicals especially in the era of bio-based refineries. The structural studies of lignin play an essential role in both understanding the nature and biosynthesis of these polymers and optimizing their valorization values. In this study, we have investigated the structures of lignin from different tissues—aerial roots, nodes, internodes, and seeds, from vanilla (Vanilla planifolia) by using gel permeation chromatography (GPC), heteronuclear single-quantum coherence (HSQC) nuclear magnetic resonance (NMR), and 31P NMR. An unusual tricin-lignin was observed in the aerial roots of vanilla with an strikingly high level of tricin unit, whereas the lignin from the nodes and internodes displayed traditional S/G type lignin with only 4–10% tricin abundance. The aerial roots lignin is primarily composed of β-O-4' alkyl-aryl ether substructures (96% of linkages) in comparison to 65 and 73% in the nodes and internodes lignin, respectively. Additionally, thioacidolysis quantification results showed that lignin from aerial roots has 29.1 mg g -1 tricin, about 3- to 5-fold higher than the lignins isolated from nodes (10.1 mg g -1 ) and internodes (6.9 mg g -1 ). This communication of a particularly high level of tricin-lignin in vanilla plant has important impacts including: (1) the presence of the high amount of tricin as part of lignin from aerial roots could play a vital role for the valorization of lignin, even tricin itself, as a feedstock for value-added chemicals and commodities; and (2) it could open new ways to scientists to design and engineer the structure of tricin-lignin, or lignin in general, to confer plants with new or improved properties due to the plasticity of lignification.

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

Evolution of the ROOT Tree I/O

The ROOT TTree data format encodes hundreds of petabytes of High Energy and Nuclear Physics events. Its columnar layout drives rapid analyses, as only those parts (“branches”) that are really used in a given analysis need to be read from storage. Its unique feature is the seamless C++ integration, which allows users to directly store their event classes without explicitly defining data schemas. In this contribution, we present the status and plans of the future ROOT 7 event I/O. Along with the ROOT 7 interface modernization, we aim for robust, where possible compile-time safe C++ interfaces to read and write event data. On the performance side, we show first benchmarks using ROOT’s new experimental I/O subsystem that combines the best of TTrees with recent advances in columnar data formats. A core ingredient is a strong separation of the high-level logical data layout (C++ classes) from the low-level physical data layout (storage backed nested vectors of simple types). We show how the new, optimized physical data layout speeds up serialization and deserialization and facilitates parallel, vectorized and bulk operations. This lets ROOT I/O run optimally on the upcoming ultra-fast NVRAM storage devices, as well as file-less storage systems such as object stores.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Adventitious rooting (AR) is critical to the propagation, breeding, and genetic engineering of trees. The capacity for plants to undergo this process is highly heritable and of a polygenic nature; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of AR, we performed a genome-wide association study (GWAS) using 1148 genotypes of Populus trichocarpa. GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, reactive oxygen species signaling, and other processes with known roles in root development. Numerous genes with uncharacterized functions and/or cryptic roles were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of AR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A temperature-sensitive FERONIA mutant allele that alters root hair growth

Abstract In plants, root hairs undergo a highly polarized form of cell expansion called tip-growth, in which cell wall deposition is restricted to the root hair apex. In order to identify essential cellular components that might have been missed in earlier genetic screens, we identified conditional temperature-sensitive (ts) root hair mutants by ethyl methanesulfonate mutagenesis in Arabidopsis thaliana. Here, we describe one of these mutants, feronia-temperature sensitive (fer-ts). Mutant fer-ts seedlings were unaffected at normal temperatures (20°C), but failed to form root hairs at elevated temperatures (30°C). Map based-cloning and whole-genome sequencing revealed that fer-ts resulted from a G41S substitution in the extracellular domain of FERONIA (FER). A functional fluorescent fusion of FER containing the fer-ts mutation localized to plasma membranes, but was subject to enhanced protein turnover at elevated temperatures. While tip-growth was rapidly inhibited by addition of rapid alkalinization factor 1 (RALF1) peptides in both wild-type and fer-ts mutants at normal temperatures, root elongation of fer-ts seedlings was resistant to added RALF1 peptide at elevated temperatures. Additionally, at elevated temperatures fer-ts seedlings displayed altered reactive oxygen species (ROS) accumulation upon auxin treatment and phenocopied constitutive fer mutant responses to a variety of plant hormone treatments. Molecular modeling and sequence comparison with other Catharanthus roseus receptor-like kinase 1L (CrRLK1L) receptor family members revealed that the mutated glycine in fer-ts is highly conserved, but is not located within the recently characterized RALF23 and LORELI-LIKE-GLYCOPROTEIN 2 binding domains, perhaps suggesting that fer-ts phenotypes may not be directly due to loss of binding to RALF1 peptides.

Plant Sciences↗
DOE OSTI2024

Toward a coordinated understanding of hydro‐biogeochemical root functions in tropical forests for application in vegetation models

Summary Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest–climate feedbacks for these carbon‐rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine‐root strategies for soil resource exploration, (2) coupling and trade‐offs in fine‐root water vs nutrient acquisition, and (3) aboveground–belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground–belowground hydro‐nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO 2 . The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.

Plant Sciences↗
DOE OSTI2021

Future roots for future soils

Abstract Mechanical impedance constrains root growth in most soils. Crop cultivation changed the impedance characteristics of native soils, through topsoil erosion, loss of organic matter, disruption of soil structure and loss of biopores. Increasing adoption of Conservation Agriculture in high‐input agroecosystems is returning cultivated soils to the soil impedance characteristics of native soils, but in the low‐input agroecosystems characteristic of developing nations, ongoing soil degradation is generating more challenging environments for root growth. We propose that root phenotypes have evolved to adapt to the altered impedance characteristics of cultivated soil during crop domestication. The diverging trajectories of soils under Conservation Agriculture and low‐input agroecosystems have implications for strategies to develop crops to meet global needs under climate change. We present several root ideotypes as breeding targets under the impedance regimes of both high‐input and low‐input agroecosystems, as well as a set of root phenotypes that should be useful in both scenarios. We argue that a ‘whole plant in whole soil’ perspective will be useful in guiding the development of future crops for future soils.

Lynch, Jonathan P.↗
DOE OSTI2023

Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions

On the roots of wetland plants such as rice, Fe(II) oxidation forms Fe(III) oxyhydroxide-rich plaques that modulate plant nutrient and metal uptake. The microbial roles in catalyzing this oxidation have been debated and it is unclear if these iron-oxidizers mediate other important biogeochemical and plant interactions. To investigate this, we studied the microbial communities, metagenomes, and geochemistry of iron plaque on field-grown rice, plus the surrounding rhizosphere and bulk soil. Plaque iron content (per mass root) increased over the growing season, showing continuous deposition. Analysis of 16S rRNA genes showed abundant Fe(II)-oxidizing and Fe(III)-reducing bacteria (FeOB and FeRB) in plaque, rhizosphere, and bulk soil. FeOB were enriched in relative abundance in plaque, suggesting FeOB affinity for the root surface. Gallionellaceae FeOB Sideroxydans were enriched during vegetative and early reproductive rice growth stages, while a Gallionella was enriched during reproduction through grain maturity, suggesting distinct FeOB niches over the rice life cycle. FeRB Anaeromyxobacter and Geobacter increased in plaque later, during reproduction and grain ripening, corresponding to increased plaque iron. Metagenome-assembled genomes revealed that Gallionellaceae may grow mixotrophically using both Fe(II) and organics. The Sideroxydans are facultative, able to use non-Fe substrates, which may allow colonization of rice roots early in the season. FeOB genomes suggest adaptations for interacting with plants, including colonization, plant immunity defense, utilization of plant organics, and nitrogen fixation. Taken together, our results strongly suggest that rhizoplane and rhizosphere FeOB can specifically associate with rice roots, catalyzing iron plaque formation, with the potential to contribute to plant growth.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Fonseca-Garcia, Citlali↗
DOE OSTI2024

Tropical root traits in response to global changes from 1984 to 2023

This dataset is a compilation of tropical root traits data in response to different global changes in tropical sites, considering 23.50N and S as latitudinal boundaries. The global changes considered are warming, drought, flooding, cyclones, nitrogen addition, CO2 fertilization, and fire. This dataset contains 266 root trait observations from 93 studies across 24 tropical countries. The full citation from where the data was taken from is provided in the dataset, as well as the global change, the ecosystem type, location, coordinates, the root traits measured, and the direction of their response after the global change. Additional information such as the duration of the experiment, the intensity of the global change, the soil layers from where the roots were collected, the root orders, and the type of experiment are also shown. We obtained this dataset by performing a systematic literature review on Web of Science using standardized keywords in English, Spanish, and Portuguese (Yaffar, Lugli et al. in press).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using MicroED

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain uncharacterized in plants and microbes. Approximately 90% of the metabolites in root exudate profiles are unknown compounds, despite the importance of root exudate composition in plant-microbe interactions. We need advanced analytical capabilities that will support rapid discovery and structural elucidation of metabolites from biological samples that may be limited in quantity and high in complexity. To fill this gap, this project aimed to develop an integrated workflow involving metabolite extraction, separation, and crystallization from plant root exudates followed by characterization using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and microcrystal electron diffraction (MicroED). Using crude root exudates from sorghum, this project successfully developed higher throughput exudate fractionation strategies to obtain pure compounds for crystallization and identified crystals in multiple fractions that diffracted. Additional efforts to increase the throughput of high-quality crystal generation for MicroED, such as crystallization screening and crystallization chaperone exploration, will be needed to further advance root exudate metabolite identification. The overall optimized sample preparation process can then be integrated with the existing data collection and data analysis pipelines for MicroED at PNNL to facilitate more rapid natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗