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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Breeding of microbiomes conferring salt tolerance to plants

Microbiome breeding through host-mediated selection is a technique to artificially select for microbiomes conferring beneficial properties to plants. Using a systematic selection protocol that maximises the heritability of microbiome effects, transmission fidelity, and microbiome stability through multiple selection cycles, we previously developed root-associated microbial communities conferring sodium and aluminium tolerance to Brachypodium distachyon, a model for cereal crops. Here, we explore the physiological mechanisms underlying our selected microbiomes’ effect on plant fitness and analyse how our selection protocol shaped the composition and structure of these microbiomes. We analysed the effects of our selected microbiomes on plant fitness and tissue-nutrient concentration, then used 16S rRNA amplicon sequencing to examine microbial community composition and co-occurrence network patterns. Our sodium-selected microbiomes reduced leaf sodium concentration by ~ 50%, whereas the aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying the microbiome-mediated stress tolerance. By testing the selected microbiomes in a cross-fostering experiment, we show that our artificially selected microbiomes attained (a) ecological robustness contributing to transplantability (i.e. inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting salt-stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated artificial selection as a framework to breed microbiomes with targeted benefits for plants under salt stresses, with significant implications for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome

Plants associate with diverse microbiomes that impact their fitness, yet the contribution of the microbiome to plant adaptation is uncertain. As plant recruitment of its microbiome can be both highly variable and genetically determined, we hypothesized this recruitment process may be the result of adaptive evolution, and contributing to plant local adaptation. We investigated the evolution and adaptive benefit of plant–microbiome recruitment by characterizing the rhizosphere communities across a genotypic panel of Brachypodium distachyon in a common garden experiment. By linking microbial communities to their host genotype's historic environment, we identified signatures of selection on plant–microbiome recruitment. Plant–microbiome composition was significantly correlated with the host genotype's historic environment, with enrichment of microbial traits aligned to local resource conditions. For example, genotypes from low-nitrogen environments recruited communities enriched in nitrogen acquisition traits. In a complementary experiment evaluating plant nitrogen response, these same genotypes were well-adapted to low-nitrogen environments, contingent on the presence of key nitrogen-cycling microbes. These results suggest that local adaptation in plants may partially be mediated by recruitment of beneficial microbiomes. This perspective suggests that plant adaptation may be an emergent property of host–microbe interactions, where evolutionary responses favor traits that promote recruitment of locally beneficial microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning

Microbiome assembly, structure, and dynamics significantly influence plant health. Secreted microbial signaling molecules initiate and mediate symbiosis by binding to structurally compatible plant receptors. For example, lipo-chitooligosaccharides (LCOs), produced by nitrogen-fixing rhizobial bacteria and various fungi, are recognized by plant lysin motif receptor-like kinases (LysM-RLKs), which activate the common symbiotic pathway. Accurately predicting these molecular interactions could reveal complementary signatures underlying the initial stages of endosymbiosis. Despite the breakthrough in protein-ligand structure prediction with deep learning-based tools, such as AlphaFold3, the large size and highly flexible nature of signaling compounds like LCOs present major challenges for detailed structural characterization and binding-affinity prediction. Typical structure-/physics-based methods of ligand virtual screening are designed for small, drug-like molecules, often rely on high-resolution, experimentally determined structures of the protein receptors, and rarely achieve sufficient sampling to obtain converged thermodynamic quantities with large ligands. In this study, we developed a hybrid molecular dynamics/machine learning (MD/ML) approach capable of predicting binding affinity rankings with high accuracy in systems involving large, flexible ligands, despite limited experimental structural information. Using coarse initial structural models, the predictions using the MD/ML workflow achieved strong alignment with experimental trends, particularly in the top-affinity tier for four legume LysM-RLKs (LYR3) binding to LCOs and a chitooligosaccharide. Furthermore, the MD-based conformation selection protocol provided critical structural insights into substrate specificity and binding mechanisms. This study demonstrates a powerful method to screen for challenging cognate ligand-receptors and advance our understanding of the molecular basis of microbial colonization in plants.

Lipo-chitooligosaccharides↗
DOE OSTI2025

Microbially mediated nitrification improves modeled temperate forest responses to declining nitrogen deposition

As nitrogen deposition declines across the US, uncertainty remains in whether temperate forests will continue to sequester carbon. This uncertainty is amplified by ecosystem models that inaccurately capture the microbial mechanisms that drive soil carbon sequestration and nitrogen loss. Further, even soil process models that represent decomposer microbes and better capture soil carbon retention under nitrogen deposition broadly underrepresent microbial nitrogen transformations. To address this limitation, we leveraged three decades of biogeochemical cycling data from a whole-watershed nitrogen fertilization experiment to incorporate microbially-driven nitrification in the FUN-CORPSE (Fixation and Uptake of Nitrogen-Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment) model. Our objectives include: 1) Reproducing key ecosystem responses to fertilization, 2) Integrating microbially-explicit nitrification in FUN-CORPSE, and 3) Assessing modeled soil C and N under projected N deposition shifts. FUN-CORPSE accurately represented soil C and streamwater N losses under ambient N deposition and captured how fertilization induced a 25 % decline in plant C cost of N acquisition, reducing decomposition and increasing soil C. Furthermore, with microbially-explicit nitrification, FUN-CORPSE captured the 100 % increase in nitrification rates and the 50 % increase in streamwater nitrate loss under N fertilization. Specifically, incorporating microbial nitrification improved modeled streamwater N leaching from R 2 = 0.01 to R 2 = 0.57. Under declining N deposition, FUN-CORPSE simulates that N losses recover more quickly than soil C pools. However, the predicted return of soil C to pre-fertilized levels suggests that additional C sequestered due to N deposition may be vulnerable to loss over the next century.

Microbial nitrification model↗
DOE OSTI2026

Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid

Agrobacterium is not only a costly plant pathogen but is also an essential tool for plant transformation. Though Agrobacterium-mediated transformation (AMT) has been heavily studied, its polygenic nature and complex transcriptional regulation make identification of the genetic basis of transformational efficiency difficult through traditional genetic and bioinformatic approaches. Here, we use a bottom-up synthetic approach to systematically engineer the tumor-inducing plasmid (pTi), wherein the majority of virulence machinery is encoded. Using a validated toolkit to control Agrobacterium gene expression in planta, we perform a quantitative dissection of AMT to investigate the contributions of critical vir-genes at different expression levels. We construct a synthetic pTi capable of transient plant and stable fungal transformation and characterize bottlenecks and solutions for complex polygenic synthetic pTi designs. Our reductionist approach demonstrates how bottom-up engineering can be used to dissect and elucidate the genetic underpinnings of complex biological traits, laying the foundation for future engineering to establish full synthetic control over the critical process of AMT.

Agrobacterium-mediated transformation↗
DOE OSTI2024

Bridging 20 Years of Soil Organic Matter Frameworks: Empirical Support, Model Representation, and Next Steps

Abstract In the past few decades, there has been an evolution in our understanding of soil organic matter (SOM) dynamics from one of inherent biochemical recalcitrance to one deriving from plant‐microbe‐mineral interactions. This shift in understanding has been driven, in part, by influential conceptual frameworks which put forth hypotheses about SOM dynamics. Here, we summarize several focal conceptual frameworks and derive from them six controls related to SOM formation, (de)stabilization, and loss. These include: (a) physical inaccessibility; (b) organo‐mineral and ‐metal stabilization; (c) biodegradability of plant inputs; (d) abiotic environmental factors; (e) biochemical reactivity and diversity; and (f) microbial physiology and morphology. We then review the empirical evidence for these controls, their model representation, and outstanding knowledge gaps. We find relatively strong empirical support and model representation of abiotic environmental factors but disparities between data and models for biochemical reactivity and diversity, organo‐mineral and ‐metal stabilization, and biodegradability of plant inputs, particularly with respect to SOM destabilization for the latter two controls. More empirical research on physical inaccessibility and microbial physiology and morphology is needed to deepen our understanding of these critical SOM controls and improve their model representation. The SOM controls are highly interactive and also present some inconsistencies which may be reconciled by considering methodological limitations or temporal and spatial variation. Future conceptual frameworks must simultaneously refine our understanding of these six SOM controls at various spatial and temporal scales and within a hierarchical structure, while incorporating emerging insights. This will advance our ability to accurately predict SOM dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Host Species–Microbiome Interactions Contribute to Sphagnum Moss Growth Acclimation to Warming

Sphagnum moss is the dominant plant genus in northern peatlands responsible for long-term carbon accumulation. Sphagnum hosts diverse microbial communities (microbiomes), and its phytobiome (plant host + constituent microbiome + environment) plays a key role in nutrient acquisition along with carbon cycling. Climate change can modify the Sphagnum -associated microbiome, resulting in enhanced host growth and thermal acclimation as previously shown in warming experiments. However, the extent of microbiome benefits to the host and the influence of host–microbe specificity on Sphagnum thermal acclimation remain unclear. Here, we extracted Sphagnum microbiomes from five donor species of four peatland warming experiments across a latitudinal gradient and applied those microbiomes to three germ-free Sphagnum species grown across a range of temperatures in the laboratory. Using this experimental system, we test if Sphagnum 's growth response to warming depends on the donor and/or recipient host species, and we determine how the microbiome's growth conditions in the field affect Sphagnum host growth across a range of temperatures in the laboratory. After 4 weeks, we found that the highest growth rate of recipient Sphagnum was observed in treatments of matched host–microbiome pairs, with rates approximately 50% and 250% higher in comparison to maximum growth rates of non-matched host–microbiome pairs and germ-free Sphagnum , respectively. We also found that the maximum growth rate of host–microbiome pairs was reached when treatment temperatures were close to the microbiome's native temperatures. Our study shows that Sphagnum's growth acclimation to temperature is partially controlled by its constituent microbiome. Strong Sphagnum host–microbiome species specificity indicates the existence of underlying, unknown physiological mechanisms that may drive Sphagnum 's ability to acclimatize to elevated temperatures. Together with rapid acclimation of the microbiome to warming, these specific microbiome–plant associations have the potential to enhance peatland resilience in the face of climate change.

acclimation↗
DOE OSTI2025

Evolutionary and functional relationships between plant and microbial C 1 metabolism in terrestrial ecosystems

One-carbon (C 1 ) metabolism, centered on the universal methyl donor S-adenosyl methionine (SAM), plays critical roles in biosynthesis, redox regulation, and stress responses across plants and microbes. A recently proposed photosynthetic C 1 pathway links SAM methyl groups directly to RuBisCO-mediated CO 2 assimilation and integrates with nitrogen and sulfur metabolism. Light-dependent SAM synthesis may regulate the methylation of biopolymers and specialized metabolites and help mitigate photorespiratory stress under elevated temperature and drought. Phylogenetic analysis of two core enzymes suggests evolutionary continuity from methylotrophic microbes to land plants, supporting microbial origins via endosymbiotic gene transfer. Beyond intracellular roles, C 1 metabolism drives biosphere–atmosphere exchange via gases such as methane, methanol, formic acid, and formaldehyde, and numerous specialized volatiles synthesized through SAM methylation. S-methylmethionine, a mobile C 1 metabolite, may mediate phloem transport of reduced sulfur, nitrogen, and methyl groups, linking above- and belowground C 1 cycling in plants. Advances in real-time gas sensing now allow the high-frequency quantification of C 1 fluxes from leaves, stems, and soils, highlighting C 1 metabolism as a critical and underrecognized component of terrestrial carbon and nutrient cycling. Given its microbial ancestry and the production of diverse volatile biosignatures, C 1 metabolism may also offer unique insights into life's origins and biosignature detection on exoplanets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Dynamic Rhizodeposition in the Woody Perennial Populus trichocarpa

Plants undergo physiological and metabolic changes that release specific molecules into the surrounding soil, a process collectively known as rhizodeposition. These compounds play crucial roles in plant‐microbe‐soil interactions, such as supporting plant development and resilience in changing environments. Under nutrient‐limited conditions, these plant‐derived compounds modify the rhizosphere environment, mobilizing otherwise inaccessible nutrients and recruiting stress‐adaptive microbial communities that support stress resilience. Currently, the chemical diversity of rhizodeposition has yet to be fully realized but is expected to be a complex mixture that includes soluble organic compounds excreted from root cells, along with products of root cell turnover, sloughed‐off root cap and border cells, and mucilage. Here, we developed a methodological and conceptual framework for an in‐depth measurement of rhizodeposition through critical advancements in untargeted metabolomics. Further, this approach provided foundational insights into the dynamic changes in rhizodeposition for the woody perennial Populus trichocarpa and rhizodeposit profiles varying by genotype, time, location, and environment. More broadly, this study provides a framework that will help formulate the next steps to effectively study rhizodeposition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Eucalyptus grandis MYB‐Like and RAN‐Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis Pathways

Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending on the lifestyle of the associated fungus. Using co-expression network analysis, we identified hypothetical pathways correlated to these genes. We functionally validated these predictions using plants with transgenic roots with increased or decreased transcription of these genes, thereby showing the power of co-expression networks as an a priori approach to identify key immune response pathways in plants. Overall, our results demonstrate that prior to physical contact with microbes, MYB-like and RAN-like zinc finger proteins are key regulators of plant immune signaling that respond to fungal signals and enable or repress symbiotic establishment.

mycorrhizal fungi↗
DOE OSTI2024

Catabolic pathway acquisition by rhizosphere bacteria readily enables growth with a root exudate component but does not affect root colonization

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally simulated the consequences of one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol between rhizosphere isolates from the Pseudomonas genus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to the existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferable but is selectively neutral under environmentally relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting because the selective benefits are small.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hyaloscypha finlandica Metabolome Repository

This repository provides the curated data tables, manuscript figure and table exports, dependency records, and workflow scripts supporting an integrated comparative genomics and untargeted LC-MS/MS metabolomics analysis of Hyaloscypha finlandica strain PMI 746, a root-associated dark septate endophyte of poplar. The repository includes genome-mining summaries from antiSMASH, FunBGCeX, BGC-Prophet, and BiG-SCAPE; processed metabolomics inputs; metabolite annotation evidence; statistical outputs; and publication-facing figures and tables. Raw LC-MS/MS spectra, full genome/protein downloads, and large generated tool outputs are referenced through public archive/accession records and are not stored in Git.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2006

An Axenic Plant Culture System for Optimal Growth in Long-Term Studies: Design and Maintenance

The symbiotic co-evolution of plants and microbes leads to difficulties in understanding which of the two components is responsible for a given environmental response. Plant-microbe studies greatly benefit from the ability to grow plants in axenic (sterile) culture. Several studies have used axenic plant culture systems, but experimental procedures are often poorly documented, the plant growth environment is not optimal, and axenic conditions are not rigorously verified. We developed a unique axenic system using inert components that promotes plant health and can be kept sterile for at least 70 d. Crested wheatgrass (Agropyron cristatum cv. DII) plants were grown in sand within flow-through glass columns that were positively pressured with filtered air. Plant health was optimized by regulating temperature, light level, CO2 concentration, humidity, and nutrients. The design incorporates several novel aspects, such as pretreatment of the sand with Fe, graduated sand layers to optimize the air-water balance of the root zone, and modification of a laminar flow hood to serve as a plant growth chamber. Adaptations of several sterile techniques were necessary for maintenance of axenic conditions. Axenic conditions were verified by plating and staining leachates as well as rhizoplane stain. This system was designed to study nutrient and water stress effects on root exudates, but is useful for assessing a broad range of plant-microbe-environment interactions. Based on total organic C analysis, 74% of exudates was recovered in the leachate, 6% was recovered in the bulk sand, and 17% was recovered in the rhizosphere sand. Carbon in the leachate after 70 d reached 255 micro-g/d. Fumaric, malic, malonic, oxalic, and succinic acids were measured as components of the root exudates.

Henry, Amelia↗
DOE OSTI2025

Five PMI Isolates from Populus Deltoides and Populus Trichocarpa

Five bacterial isolates were isolated from the roots of poplar trees (Populus deltoides and P. trichocarpa), which are model organisms and a main focus of the Plant-Microbe Interfaces (PMI) project at ORNL. These strains belong to genera are not well represented and give a more complete view of the microbial community and bacterial interactions with poplar trees. These strains will support future studies and contribute to the broader PMI goal of understanding microbe-microbe and plant-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unraveling plant–microbe symbioses using single-cell and spatial transcriptomics

Plant-microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant-microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbial community dynamics in the soil-root continuum are linked with plant species turnover during secondary succession

Grazing exclusion and land abandonment are commonly adopted to restore degraded ecosystems in semiarid and arid regions worldwide. However, the temporal variation in the soil- versus root-associated microbiome over plant species turnover during secondary succession has rarely been quantified. Using the chronosequence restored from fenced grassland and abandoned farmlands on the Loess Plateau of China, we characterized the dynamics of the soil- and root-associated microbiome of host plant with different dominance statuses during secondary succession from 0 to 40 years. Our results revealed that the root microhabitat, the host plant and their interactions were the main contributors to the bacterial community shift (R 2 = 15.5%, 8.1%, and 22.3%, respectively), and plant interspecies replacement had a greater effect on the shift in the root-associated microbial community than intraspecies replacement did during succession. The root-associated bacterial community of pioneer plants was particularly responsive to succession, especially the endosphere community. Endosphere microbial diversity was positively correlated with host plant coverage change, and the diversity and abundance of taxon recruitment into the endosphere of pioneer plants from the surrounding environment decreased as succession progressed. The community assembly processes also indicated that the endosphere microbiota are strongly selected in younger host plants, whereas stochastic processes dominate in aged host plants. Our study provides evidence of the unique response of the root-associated microbiome to the replacement of plant species during secondary succession, and the function of endosphere microbes should be considered when studying plant–microbe feedback.

59 BASIC BIOLOGICAL SCIENCES↗