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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

Up until now, soil microbes that colonize plant roots and are responsive to differences in plant genotype remain to be ascertained for agronomically important crops. From a very large-scale longitudinal field study of 27 maize inbred lines planted in three fields, with partial replication 5 y later, we identify root-associated microbiota exhibiting reproducible associations with plant genotype. Analysis of 4,866 samples identified 143 operational taxonomic units (OTUs) whose variation in relative abundances across the samples was significantly regulated by plant genotype, and included five of seven core OTUs present in all samples. Plant genetic effects were significant amid the large effects of plant age on the rhizosphere microbiome, regardless of the specific community of each field, and despite microbiome responses to climate events. Seasonal patterns showed that the plant root microbiome is locally seeded, changes with plant growth, and responds to weather events. However, against this background of variation, specific taxa responded to differences in host genotype. If shown to have beneficial functions, microbes may be considered candidate traits for selective breeding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities

The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

Terrestrial plants benefit from many well-understood mutualistic relationships with root and leaf-associated microbiomes, but relatively little is known about these relationships for seagrass and other aquatic plants. We used 16S rRNA gene amplicon sequencing and metatranscriptomics to assess potential mutualisms between microorganisms and the seagrasses Zostera marina and Zostera japonica collected from mixed beds in Netarts Bay, OR, United States. The phylogenetic composition of leaf-, root-, and water column-associated bacterial communities were strikingly different, but these communities were not significantly different between plant species. Many taxa present on leaves were related to organisms capable of consuming the common plant metabolic waste product methanol, and of producing agarases, which can limit the growth of epiphytic algae. Taxa present on roots were related to organisms capable of oxidizing toxic sulfur compounds and of fixing nitrogen. Metatranscriptomic sequencing identified expression of genes involved in all of these microbial metabolic processes at levels greater than typical water column bacterioplankton, and also identified expression of genes involved in denitrification and in bacterial synthesis of the plant growth hormone indole-3-acetate. These results provide the first evidence using metatranscriptomics that seagrass microbiomes carry out a broad range of functions that may benefit their hosts, and imply that microbe–plant mutualisms support the health and growth of aquatic plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Root microbiota drive direct integration of phosphate stress and immunity

Plants live in biogeochemically diverse soils with diverse microbiota. Plant organs associate intimately with a subset of these microbes, and the structure of the microbial community can be altered by soil nutrient content. Plant-associated microbes can compete with the plant and with each other for nutrients, but may also carry traits that increase the productivity of the plant. Additionally, it is unknown how the plant immune system coordinates microbial recognition with nutritional cues during microbiome assembly. Here we establish that a genetic network controlling the phosphate stress response influences the structure of the root microbiome community, even under non-stress phosphate conditions. We define a molecular mechanism regulating coordination between nutrition and defence in the presence of a synthetic bacterial community. We further demonstrate that the master transcriptional regulators of phosphate stress response in Arabidopsis thaliana also directly repress defence, consistent with plant prioritization of nutritional stress over defence. In conclusion, our work will further efforts to define and deploy useful microbes to enhance plant performance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species

Panicum represents a large genus of many North American prairie grass species. These include switchgrass ( Panicum virgatum ), a biofuel crop candidate with wide geographic range, as well as Panicum hallii , a close relative to switchgrass, which serves as a model system for the study of Panicum genetics due to its diploid genome and short growth cycles. For the advancement of switchgrass as a biofuel crop, it is essential to understand host microbiome interactions, which can be impacted by plant genetics and environmental factors inducing ecotype-specific phenotypic traits. We here compared rhizosphere and root endosphere bacterial communities of upland and lowland P. virgatum and P. hallii genotypes planted at two sites in Texas. Our analysis shows that sampling site predominantly contributed to bacterial community variance in the rhizosphere, however, impacted root endosphere bacterial communities much less. Instead we observed a relatively large core endophytic microbiome dominated by ubiquitously root-colonizing bacterial genera Streptomyces , Pseudomonas , and Bradyrhizobium . Endosphere communities displayed comparable diversity and conserved community structures across genotypes of both Panicum species. Functional insights into interactions between P. hallii and its root endophyte microbiome could hence inform testable hypotheses that are relevant for the improvement of switchgrass as a biofuel crop.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Quantitative genetic-by-soil microbiome interactions in a perennial grass affect functional traits

Plants interact with diverse microbiomes that can impact plant growth and performance. Recent studies highlight the potential beneficial aspects of plant microbiomes, including the possibility that microbes facilitate the process of local adaptation in their host plants. Microbially mediated local adaptation in plants occurs when local host genotypes have higher fitness than foreign genotypes because of their affiliation with locally beneficial microbes. Here, plant adaptation results from genetic interactions of the host with locally beneficial microbes (e.g. host genotype-by-microbiome interactions). We used a recombinant inbred line (RIL) mapping population derived from upland and lowland ecotypes of the diploid C4 perennial bunch grass Panicum hallii to explore quantitative genetic responses to soil microbiomes focusing on functional root and shoot traits involved in ecotypic divergence. We show that the growth and development of ecotypes and their trait divergence depends on soil microbiomes. Moreover, we find that the genetic architecture is modified by soil microbiomes, revealing important plant genotype-by-microbiome interactions for quantitative traits. We detected a number of quantitative trait loci (QTL) that interact with the soil microbiome. Our results highlight the importance of microbial interactions in ecotypic divergence and trait genetic architecture in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fire alters plant microbiome assembly patterns: integrating the plant and soil microbial response to disturbance

Summary It is increasingly evident that the plant microbiome is a strong determinant of plant health. While the ability to manipulate the microbiome in plants and ecosystems recovering from disturbance may be useful, our understanding of the plant microbiome in regenerating plant communities is currently limited. Using 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) region amplicon sequencing, we characterized the leaf, stem, fine root, rhizome, and rhizosphere microbiome of < 1‐yr‐old aspen saplings and the associated bulk soil after a recent high‐intensity prescribed fire across a burn severity gradient. Consistent with previous studies, we found that soil microbiomes are responsive to fire. We extend these findings by showing that certain plant tissue microbiomes also change in response to fire. Differences in soil microbiome compositions could be attributed to soil chemical characteristics, but, generally, plant tissue microbiomes were not related to plant tissue elemental concentrations. Using source tracking modeling, we also show that fire influences the relative dominance of microbial inoculum and the vertical inheritance of the sapling microbiome from the parent tree. Overall, our results demonstrate how fire impacts plant microbiome assembly, diversity, and composition and highlights potential for further research towards increasing plant fitness and ecosystem recovery after fire events.

16rRNA↗
DOE OSTI2024

Bioenergy sorghum nodal root bud development: morphometric, transcriptomic and gene regulatory network analysis

Bioenergy sorghum’s large and deep nodal root system and associated microbiome enables uptake of water and nutrients from and deposition of soil organic carbon into soil profiles, key contributors to the crop’s resilience and sustainability. The goal of this study was to increase our understanding of bioenergy sorghum nodal root bud development. Sorghum nodal root bud initiation was first observed on the stem node of the 7 th phytomer below the shoot apex. Buds were initiated near the upper end of the stem node pulvinus on the side of the stem opposite the tiller bud, then additional buds were added over the next 6-8 days forming a ring of 10-15 nascent nodal root buds around the stem. Later in plant development, a second ring of nodal root buds began forming on the 17 th stem node immediately above the first ring of buds. Overall, nodal root bud development can take ~40 days from initiation to onset of nodal root outgrowth. Nodal root buds were initiated in close association with vascular bundles in the rind of the pulvinus. Stem tissue forming nascent nodal root buds expressed sorghum homologs of genes associated with root initiation (WOX4), auxin transport (LAX2, PIN4), meristem activation (NGAL2), and genes involved in cell proliferation. Expression of WOX11 and WOX5, genes involved in root stem niche formation, increased early in nodal root bud development followed by genes encoding PLTs, LBDs (LBD29), LRP1, SMB, RGF1 and root cap LEAs later in development. A nodal root bud gene regulatory network module expressed during nodal root bud initiation predicted connections linking PFA5, SPL9 and WOX4 to genes involved in hormone signaling, meristem activation, and cell proliferation. A network module expressed later in development predicted connections among SOMBRERO, a gene involved in root cap formation, and GATA19, BBM, LBD29 and RITF1/RGF1 signaling. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for understanding the regulation of sorghum nodal root bud formation and development.

09 BIOMASS FUELS↗
DOE OSTI2019

Nitrogen fertilizer affects the Populus microbiome

Plants are colonized by numerous microorganisms serving important symbiotic functions that aid in plant growth and success. Populus deltoides (Eastern Cottonwood) and Populus trichocarpa (Black Cottonwood) are potential biofuel crops that rely on microbial symbionts to complete essential tasks, such as nitrogen fixation. Often, in agricultural and biofuel production, exogenous nitrogen is added to soils, since nitrogen availability is the limiting factor for plant growth. However, these additions may alter the soil microbial communities and result in unintentional consequences if excess nitrogen escapes the setting. We sought to determine how nitrogen fertilization alters the microbial communities within the soil, roots, and leaves of two cottonwoods. We grew P. deltoides and P. trichocarpa in a greenhouse with and without added nitrogen fertilizer, in two soil types. The soils were from Oregon and West Virginia and had distinctive chemical properties and different initial soil microbial communities. We hypothesized that the abundance of diazotrophs within the soils would increase as nitrogen became limiting. Over the 2-month study, we assessed plant growth characteristics for over 160 Populus plants. We investigated the root, leaf, and soil microbiomes of selected plants using 16S rRNA gene and ITS2 PCR amplicon DNA sequencing. We then used bioinformatics tools to evaluate the composition and diversity of these microbiomes. The microbiomes differed significantly across all three experimental factors - nitrogen addition, Populus species, and soil type.

09 BIOMASS FUELS↗
DOE OSTI2022

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons

Abstract Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mucilage produced by aerial roots hosts diazotrophs that provide nitrogen in Sorghum bicolor

Sorghum ( Sorghum bicolor ) is an important food, feed, and fodder crop worldwide and is gaining popularity as an energy crop due to its high potential for biomass production. Some sorghum accessions develop many aerial roots and produce an abundant carbohydrate-rich mucilage after rain. This aerial root mucilage is similar to that observed in landraces of maize ( Zea mays ) from southern Mexico, which have been previously shown to host diazotrophs. In this study, we characterized the aerial root development of several sorghum accessions and the impact of humidity on this trait. We conducted a microbiome study of the aerial root mucilage of maize and sorghum and isolated numerous diazotrophs from field sorghum mucilage. We observed that the prevailing phyla in the mucilage were Pseudomonadota, Bacteroidota, and Bacillota. However, bacterial abundances varied based on the genotype and the location. Using acetylene reduction, 15 N 2 gas feeding, and 15 N isotope dilution assays, we confirmed that these sorghum accessions can acquire about 40% of their nitrogen from the atmosphere through these associations on aerial roots. Nitrogen fixation in sorghum aerial root mucilage offers a promising avenue to reduce reliance on synthetic fertilizers and promote sustainable agricultural practices for food, feed, fodder, and bioenergy production.

Venado, Rafael E.↗
DOE OSTI2022

16S rRNA squencing to identify microbiomes associated with different crops and different growing conditions

The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers.

16S rRNA sequencing↗
DOE OSTI2025

Linked nitrogen and carbon dynamics reveal distinct pools and patterns in a deep, weathered bedrock rhizosphere

Nitrogen is one of the most limiting nutrients to forest productivity worldwide. Recently, it has been established that diverse ecosystems source a substantial fraction of their water from weathered bedrock, leading to questions about whether root-driven nitrogen cycling extends into weathered bedrock as well. In this study, we specifically examined nitrogen dynamics using specialized instrumentation distributed across a 16 m weathered bedrock vadose zone (WBVZ) underlying an old growth forest in northern California where the rhizosphere—composed of plant roots and their associated microbiome—extends meters into rock. We documented total dissolved nitrogen (TDN), dissolved organic carbon (DOC), inorganic nitrogen (ammonium and nitrate), and CO 2 and O 2 gases every 1.5 m to 16 m depth for 2 y. We found that TDN concentrations increased with depth, were an order of magnitude greater at 15 m than in the upper 30 cm, and that the majority of TDN throughout the weathered bedrock vadose zone was organic. We also found that TDN concentrations are influenced by depth, season, and interannual precipitation patterns. Carbon isotope composition of the DOC suggests that dissolved organic matter in the WBVZ is primarily derived from plant sources, and not the nitrogen-rich bedrock. We conclude that nitrogen dynamics in the WBVZ may be driven, in part, by an active rhizosphere, meters below the base of soil, and we argue that weathered bedrock horizons may play a key role in C-N cycling in ecosystems with deep-rooted plants.

Science & Technology - Other Topics↗
DOE OSTI2024

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

Abstract Mitigating the effects of climate stress on crops is important for global food security. The microbiome associated with plant roots, the rhizobiome, can harbor beneficial microbes that alleviate stress, but the factors influencing their recruitment are unclear. We conducted a greenhouse experiment using field soil with a legacy of growing switchgrass and common bean to investigate the impact of short-term drought severity on the recruitment of active bacterial rhizobiome members. We applied 16S rRNA and 16S rRNA gene sequencing for both crops and metabolite profiling for switchgrass. We included planted and unplanted conditions to distinguish environment- versus plant-mediated rhizobiome drivers. Differences in community structure were observed between crops and between drought and watered and planted and unplanted treatments within crops. Despite crop-specific communities, drought rhizobiome dynamics were similar across the two crops. The presence of a plant more strongly explained the rhizobiome variation in bean (17%) than in switchgrass (3%), with a small effect of plant mediation during drought observed only for the bean rhizobiome. The switchgrass rhizobiome was stable despite changes in rhizosphere metabolite profiles between planted and unplanted treatments. We conclude that rhizobiome responses to short-term drought are crop-specific, with possible decoupling of plant exudation from rhizobiome responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Symbiosis Under Stress: How Arbuscular Mycorrhizal Fungi and Sorghum Metabolism Shift Under Drought

As drought becomes more prevalent across the globe, causing billions of dollars in agricultural loss, the need to maintain crop health and productivity grows increasingly important. Out of the most important cereal crops, sorghum shows the greatest drought tolerance, and plant-microbiome interactions at the root region play a crucial role in this. A key microbial player is arbuscular mycorrhizal fungi (AMF), which deliver water and nutrients to plants in exchange for nutrients they cannot produce. Using sorghum as a model plant, we combine mass-spectrometry based proteomics and metabolomics to examine metabolic interactions between sorghum roots and AMF under drought stress. With AMF, sorghum downregulated lipid-related biological processes involving fatty acid biosynthesis and metabolism. Similarly, amino acid biosynthesis pathways were also suppressed; however, metabolite analysis revealed increased amino acid abundance related to the phenylpropanoid pathway. AMF also enhanced the upregulation of drought-protective osmolytes, such as mannitol and sorbitol, suggesting their key role in mediating sorghum’s response to drought stress. AMF hyphal biomass also had an increased abundance of key osmoprotectant amino acids, indicating similar mechanisms of drought tolerance between sorghum and AMF. Metabolomic evidence also suggested that carbohydrate exchange between sorghum and AMF shifted under stress, indicating an altered exudation pattern likely driven by drought response. Our results demonstrate the molecular mechanisms through which AMF modulate sorghum metabolism under drought conditions, highlighting their promising role in improving crop resilience. By identifying the molecular targets that can improve drought tolerance, we can begin engineering drought resistant agricultural biosystems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Legacy Effects of Cropping System and Precipitation Influence the Core Camelina sativa Microbiome

Camelina ( Camelina sativa L.) is a potential biofuel crop and beneficial rotation crop in dryland cropping systems. Little is known about camelina microbiota or the legacy effect of soil origin/cropping system zones on camelina-associated microbiome assembly. To explore camelina-microbe associations, we grew camelina in the greenhouse using soil transplanted from 33 locations in the dryland wheat production area of eastern Washington. Bacterial, archaeal, and fungal communities from bulk soil, rhizosphere, and endosphere were characterized with 16S rRNA and internal transcribed spacer amplicon sequencing and were analyzed alongside site-specific climatic and edaphic data. We found that soil from the highest precipitation zone had higher alpha diversity than soil from the driest zone, but this effect was not seen in the greenhouse rhizosphere or endosphere. Plant compartment, cropping system zone, and soil origin all significantly influenced microbial composition, with soil pH and organic matter, as well as precipitation at origin, as major predictors. Analysis of abundance–occupancy distributions showed that the Actinobacteriota Aeromicrobium and Marmoricola and the fungus Pseudogymnoascus in the rhizosphere were plant-selected, while the endosphere was characterized by a number of Actinobacteriota, Rhizobium, and Clostridium. Sphingomonas amplicon sequence variants were also consistently enriched in the rhizosphere, suggesting that they are present in soils collected throughout eastern Washington and may represent good candidate biostimulants. Several lignin decomposing fungi had site-specific rhizospheric distributions, suggesting that they may be dispersal-limited or result from the legacy effect of long-term wheat cropping. Overall, this study contributes to our understanding of microbiome assembly in and on camelina roots while also highlighting the potential impact of cropping history on soil- and plant-associated microbiomes. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.

Barnes, Elle M↗
DOE OSTI2024

Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface

Abstract Aims Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere. Methods The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing. Results We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla ( Asteraceae ) were more similar than the perennial Solanum distichum ( Solanaceae ). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific. Conclusions The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

Wicaksono, Wisnu Adi (ORCID:0000000215561981)↗