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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays)

Abstract Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges, including interactions with soil-dwelling microbial communities. However, the role of specialized metabolites in modulating plant-microbiome interactions often remains elusive. In this study, we report that maize ( Zea mays ) diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 ( anther ear 2 ), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. The Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other large-scale metabolome alterations. Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Worth More Dead than Alive? Quantifying Necromass Persistence for Terrestrial Carbon Storage

The continuous cycle of plant-associated microbial biomass growth, death, and decay provides a consistent supply of necromass-C throughout the rooting zone of the soil profile. These inputs are obviously important for resource allocation and soil quality, but microbial necromass-C may play a critical, but currently unknown, role in mitigating the impacts of climate change through atmospheric decarbonization. Microbial necromass is the largest terrestrial sink of persistent carbon in soils, thus its fate and preservation will have a major impact on global C budgets. Our current understanding of the ecosystem controls on necromass generation, biogeochemical transformation, and stabilization is lacking. The objective of this project is to explore the specific influence of rhizosphere and necromass inputs on soil carbon pools.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). Here, the rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere–bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Active microbial biomass decreases, but microbial growth potential remains similar across soil depth profiles under deeply-vs. shallow-rooted plants

Climate-smart land management practices that replace shallow-rooted annual crop systems with deeply-rooted perennial plants can contribute to soil carbon sequestration. However, deep soil carbon accrual may be influenced by active microbial biomass and their capacity to assimilate fresh carbon at depth. Incorporating active microbial biomass, dormancy, and growth in microbially-explicit models can improve our ability to predict soil's capacity to store carbon. But, so far, the microbial parameters that are needed for such modeling are poorly constrained, especially in deep soil layers. Here, we used a lab incubation experiment and growth kinetics model to estimate how microbial parameters vary along 240 cm of soil depth in profiles under shallow- (soy) and deeply-rooted (switchgrass) plants 11 years after plant cover conversion. We also assessed resource origin and availability (total organic carbon, 14 C, extractable organic carbon, specific UV absorbance of K 2 SO 4 extractable organic C, total nitrogen, total dissolved nitrogen) along the soil profiles to examine associations between soil chemical and biological parameters. Even though root biomass was greater and rooting depth was deeper under switchgrass than soy, resource availability and microbial growth parameters were generally similar between vegetation types. Instead, depth significantly influenced soil chemical and biological parameters. For example, resource availability and total and relative active microbial biomass decreased with soil depth. Decreases in the relative active microbial biomass coincided with increased lag time (response time to external carbon inputs) along the soil profiles. Even at a depth of 210–240 cm, microbial communities were activated to grow by added resources within a day. Maximum specific growth rate decreased to a depth of 90 cm and then remained consistent in deeper layers. Our findings show that >10 years of vegetation and rooting depth changes may not be long enough to alter microbial growth parameters, and suggest that at least a portion of the microbial community in deep soils can grow rapidly in response to added resources. Our study determined microbial growth parameters that can be used in microbially-explicit models to simulate carbon dynamics in deep soil layers.

14C↗
DOE OSTI2023

Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots

Abstract For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.

Acharya, Shwetha M.↗
DOE OSTI2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass ( Panicum virgatum L.) significantly impacts plant microbiomes

Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome.

09 BIOMASS FUELS↗
DOE OSTI2020

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil

Phenolic compounds perform various functions in soil ranging from microbial substrate to toxin and form the basis of several plant-mediated processes. The aim of this study was to investigate how phenolics commonly exuded by tree roots influence soil organic matter (SOM) decomposition and interact with other labile forms of carbon (C) abundant in root exudates. Therefore, we performed a 38-day incubation experiment and assessed whether phenolic compounds (benzoic acid, caffeic acid and catechin) facilitated or inhibited SOM decomposition in a glucose-amended forest soil. Changes in decomposition, substrate use, fungal and bacterial community composition, and microbial abundance and activity were measured over time using 13 C-stable-isotope tracing, DNA-based molecular methods and enzyme assays. Our findings showed that phenolics inhibited microbial activity and abundance to varying degrees. Yet, benzoic acid was the only compound producing a substantial priming effect leading to a 21% increase in SOM decomposition, which was amplified in glucose-amended soils. This stimulation in microbial activity was associated with an increase in β-1,4-glucosidase activity and the bacterial genera Paraburkholderia and Caballeronia of the Burkholderiaceae family. Phenolics drove microbial community shifts in glucose-amended soils with negligible interactive effects. In conclusion, phenolic priming of SOM decomposition is associated with microbial community shifts and amplified in the presence of glucose. This evidence emphasizes the need for considering phenolics and interactions among root exudates as priming mechanisms in the rhizosphere and other soil environments where aromatics and phenolic compounds are abundant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability

Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Lost and Found: Rediscovering Microbiome-Associated Phenotypes that Reshape Agricultural Sustainability

Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. Our findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture. ---- These maize root exduate metabolomics data are a subset of this larger project and make up a phenotyping for candidate lines.

Favela, Alonso [School of Plant Sciences, Universi↗
DOE OSTI2024

Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral‐associated organic matter

Summary Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two‐chamber microcosms where an air gap isolated AMF from roots, we 13 CO 2 ‐labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13 C enrichment. SOM density fractionation, 13 C NMR, and IRMS showed AMF transferred 0.77 mg C g −1 of soil (increasing total C by 2% relative to non‐mycorrhizal controls); 33% was found in occluded or mineral‐associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)‐enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF‐imported 13 C (> 20 atom%). Mapping sequences from 13 C‐SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13 C‐enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.

13C SIP↗
DOE OSTI2020

Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars

Microbial communities help plants access nutrients and tolerate stress. Some microbiomes are specific to plant genotypes and, therefore, may contribute to intraspecific differences in plant growth and be a promising target for plant breeding. Switchgrass (Panicum virgatum L.) is a potential bioenergy crop with broad variation in yields and environmental responses; recent studies suggest that associations with distinct microbiomes may contribute to variation in cultivar yields. We used a common garden experiment to investigate variation in 12 mature switchgrass cultivar soil microbiomes and, further, to examine how root traits and soil conditions influence microbiome structure. Here, we found that average root diameter varied up to 33% among cultivars and that they associated with distinct soil microbiomes. Cultivar had a larger effect on the soil bacterial than fungal community, but both were strongly influenced by soil properties. Root traits had a weaker effect on microbiome structure, but root length contributed to variation in the fungal community. Unlike the soil communities, the root bacterial communities did not group by cultivar, based on a subset of samples. Microbial biomass carbon and nitrogen and the abundance of several dominant bacterial phyla varied between ecotypes, but overall the differences in soil microbiomes were greater among cultivars than between ecotypes. Our findings show that there is not one soil microbiome that applies to all switchgrass cultivars, or even to each ecotype. These subtle but significant differences in root traits, microbial biomass, and the abundance of certain soil bacteria could explain differences in cultivar yields and environmental responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Differential Exudation Creates Biogeochemically Distinct Microenvironments during Rhizosphere Evolution

Plant roots and associated microbes release a diverse range of functionally distinct exudates into the surrounding rhizosphere with direct impacts on soil carbon storage, nutrient availability, and contaminant dynamics. Yet mechanistic linkages between root exudation and emergent biogeochemical processes remain challenging to measure nondestructively, in real soil, over time. Here we used a novel combination of in situ microsensors with high-resolution mass spectrometry to measure, nondestructively, changing exudation and associated biogeochemical dynamics along single growing plant roots (Avena sativa). We found that metabolite and dissolved organic carbon (DOC) concentrations as well as microbial growth, redox potential (EH), and pH dynamics vary significantly among bulk soil, root tip, and more mature root zones. Surprisingly, the significant spike of rhizosphere DOC upon root tip emergence did not significantly correlate with any biogeochemical parameters. However, the presence of sugars significantly correlated with declines in EH following the arrival of the root tip, likely due to enhanced microbial oxygen demand. Similarly, the presence of organic acids significantly correlated to declines in pH upon root tip emergence. Altogether, our in situ measurements highlight how different exudates released along growing roots create functionally distinct soil microenvironments that evolve over time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Plant-microbial interplay for organic nitrogen mediated by functional specificity of root compartments

The organic form of nitrogen (N) is a critical intermediate in mutualistic and competitive root-microbial interactions, mediated by extracellular enzymes. Visualization of the hotspots of organic N and proteolytic activity might be valuable for revealing root functional specificity in N acquisition and transformation at the level of individual roots and compartments. For the first time, we used time-lapse amino-mapping and zymography to co-localize and map the spatial distribution of amino-N and leucine aminopeptidase (LAP) activity in the soil and different root parts of maize (Zea mays L.). Amino-N distribution was mainly associated with seminal roots and root tips, where it overlapped with LAP activity hotspots. In the lateral roots and bulk soil, however, LAP activity was decoupled from amino-N. Distinct functional traits revealed themselves as the highest amino-N content and LAP activity in seminal root tips and as the largest relative extent of the rhizosphere in lateral root tips. Co-localized amino-N and LAP activities highlighted different nutrient acquisition strategies mediated by root-microbe interactions, depending on the root compartment. Seminal roots and their tips appeared to adopt mutualistic strategies, potentially attracting root-associated microorganisms through releasing oligo- and polypeptides. In contrast, lateral roots, with amino-N detected only at their tips, demonstrated stronger N competition, relying on the enzyme activity of the rhizosphere microbial community for N acquisition. These insights emphasized the role of root functional specialization in shaping plant-microbe interactions, offering pathways to enhance nutrient use efficiency.

Maize (Zea mays L.)↗
DOE OSTI2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Abstract Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa . Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Nutrient Cycling at a Coastal Terrestrial‐Aquatic Interface

Abstract The complex interactions among soil, vegetation, and site hydrologic conditions driven by precipitation and tidal cycles control the biogeochemical transformations and bi‐directional exchange of carbon and nutrients across the terrestrial–aquatic interfaces (TAIs) in coastal regions. This study uses a highly mechanistic model, Advanced Terrestrial Simulator (ATS)‐PFLOTRAN, to explore how these interactions affect exchanges of materials and carbon and nitrogen cycling. We used a transect in the Chesapeake Bay region that spans zones of open water, coastal wetland, transition, and upland forest. We designed several simulation scenarios to parse the effects of the individual controlling factors and the sensitivity of carbon cycling to reaction rate parameters derived from laboratory experiments. Our simulations reveal an active zone for carbon cycling under the transition zones between the wetland and the upland. Evapotranspiration is found to enhance the exchange fluxes between the surface and subsurface domains, resulting in a higher dissolved oxygen concentration in the TAIs. The transport of organic carbon derived from plant leaves and roots provide an additional source of organic carbon needed for the aerobic respiration and denitrification processes in the TAIs. The variability in reaction rate parameters associated with microbial activities is also found to play a dominant role in controlling the heterogeneity and dynamics of the simulated redox conditions. This modeling‐focused exploratory study enabled us to better understand the complex interactions among soil, water and microbes that govern the hydro‐biogeochemical processes at the TAIs, which is an important step toward representing coastal ecosystems in larger‐scale Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Global pine tree invasions are linked to invasive root symbionts

Symbiotic soil microbes can facilitate plant invasions, yet it is unclear whether the invasive capacity of plants can be explained by the invasiveness of their microbial symbionts. After compiling a global dataset on associations between non-native invasive pine trees and ectomycorrhizal fungi (EMF), here we found that the interaction with invasive EMF is an important predictor of pine invasion success that acts in concert with aboveground plant traits, questioning the way we currently predict plant invasions.

59 BASIC BIOLOGICAL SCIENCES↗