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

Root genetics in the field to understand drought adaptation and carbon sequestration (Final Scientific/Technical Report)

For all crop plants, roots play a critical role in growth. Roots anchor the plants, and are the primary site of nutrient and water uptake. Roots are also the main source of C to soil in the form of root tissues and exudates, and thus greatly influence SOM stocks. To perform these functions, primary roots extend into soil, producing a network of branching roots of characteristic form, known as its root system architecture (RSA). RSA varies among species, and among varieties within a species that are adapted to different environments. Root traits are major targets for the second green revolution because of their potential to improve crop productivity, increase drought tolerance and nutrient acquisition, and increase C capture of soil. Improving the quality of roots in maize will be particularly valuable, since this crop is planted on over 92 million acres annually in the US. The future sustainability of agricultural systems relies on their ability to enhance soil organic matter (SOM) storage and reduce GHG emissions, while maintaining or enhancing productivity. This program had two components, Sensors and Models. For the first component, we designed and built a high-throughput phenotyping platform for root pulling of maize plants. This eliminated the physical labor of manually pulling up plants and reduced the number of personnel required down to one. The standardized pulling mechanism allowed recording force curves during the pulling process, providing additional information. We validated that the maximum force for pulling the root system was well-correlated with the root system mass and provided root crowns for further RSA analysis. These root crowns identified significant correlations with 2D root area and root depth, along with 3D root volume, total root length and number of root tips. We then used this system for field-based studies in maize on the genetics of root system architecture and its relation to nitrogen-use efficiency (NUE), including using lines relevant to the Corteva breeding program. Varieties were also evaluated at Corteva sites in the cornbelt and Danforth farm in Missouri, to establish responses across sites. From these studies we have identified genetic loci associated with root traits and created mutant lines for these loci and correlations of root traits with NUE. For the Models component, we worked to incorporate root and soil characteristics into the MEMS 2.0 soil and ecosystem biogeochemical model. Existing soil C models, such as Century, are unable to represent specific root trait interactions with the soil environment and therefore to accurately forecast the potential C sequestration benefits of root breeding under different climatic and soil type conditions. We have developed the MEMS 2.0 ecosystem biogeochemical model to improve quantification of farm-scale soil carbon and greenhouse gas emissions. The new knowledge and large datasets produced by this project will be used to develop and drive an innovative model capable of forecasting the impacts on soil C stocks and nutrient dynamics. An innovation was to use the empirical data from the field studies (in 1, above) to model genetic variation in nitrogen use efficiencies and soil C input. Our work demonstrated that maize root-derived C rapidly replaces existing soil C and after 3 years of continuous maize, up to 20% of soil organic C in the topsoil (0-15cm) and 3% in the subsoil (15-30cm) was contributed by maize. However, this contribution did not entirely represent a net increase. Root C contribution to soil was affected by maize genetics. We have analyzed soils derived from the CSU field trials for C and N stocks, in the different soil physical fractions represented by the MEMS model, using both physical fractionation with elemental analyses, and Fourier transformed infrared spectroscopy. Data will be used to link crop nitrogen use efficiencies with soil C sequestration and provide data to bridge the field trials with the model development, for verification of model predictions. The project had a number of successful outcomes: we have used the new phenotyping platform to identify new genetic loci that can enhance root phenotypes; we have partnered with multiple maize seed companies phenotype varieties in their breeding programs; we have developed the MEMS model that can help inform industry on the potential for carbon sequestration in the agricultural sector, and which is now available at the CSU Soil Carbon Solutions Center for use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Novel Membrane-Associated Protein Aids Bacterial Colonization of Maize

The soil environment affected by plant roots and their exudates, termed the rhizosphere, significantly impacts crop health and is an attractive target for engineering desirable agricultural traits. Engineering microbes in the rhizosphere is one approach to improving crop yields that directly minimizes the number of genetic modifications made to plants. Soil microbes have the potential to assist with nutrient acquisition, heat tolerance, and drought response if they can persist in the rhizosphere in the correct numbers. Unfortunately, the mechanisms by which microbes adhere and persist on plant roots are poorly understood, limiting their application. This study examined the membrane proteome shift upon adherence to roots in two bacteria of interest, Klebsiella variicola and Pseudomonas putida. From this surface proteome data, we identified a novel membrane protein from a non-laboratory isolate of P. putida that increases binding to maize roots using unlabeled proteomics. When this protein was moved from the environmental isolate to a common lab strain (P. putida KT2440), we observed increased binding capabilities of P. putida KT2440 to both abiotic mimic surfaces and maize roots. We observed a similar increased binding capability to maize roots when the protein was heterologously expressed in K. variicola and Stutzerimonas stutzeri. With the discovery of this novel binding protein, we outline a strategy for harnessing natural selection and wild isolates to build more persistent strains of bacteria for field applications and plant growth promotion.

rhizosphere, colonization, membrane proteome, plan↗
DOE OSTI2025

Root architectural plasticity optimizes nutrient acquisition in switchgrass under variable phosphorus forms

Aims Understanding the influence of different forms of phosphorus (P) over the different root traits and how those traits are related to increasing the efficiency of nutrient acquisition strategies. Methods Investigation of switchgrass (Panicum virgatum L.) root morphology responses to inorganic P (Pi) soluble (Potassium-P), insoluble (Aluminum-P), and organic P (Po) (Inositol Hexa-Phosphate, IHex-P) in rhizoboxes. Roots were traced over the root box and scanned using WinRhizoTM. The CRootbox model was employed to simulate root growth. Results Significant plasticity observed under IHex-P treatment, with a 46% increase in root branching, leading to a 74% rise in total root length and a 65% increase in root surface area compared to inorganic P forms. IHex-P resulted in a 73% higher root biomass than Aluminum-P and a 26% increase compared to Potassium-P. Most of the differences were attributed to the elongation of root branches. Conclusions Here, the study emphasizes the dynamic nature of switchgrass root architecture and morphology in response to varying P forms in the soil. The absence of Pi in the soil triggered increased plasticity in root traits, facilitating root access to Po and uptake of P. These findings offer valuable insights into the adaptive mechanisms of perennial plants, with significant implications for optimizing nutrient acquisition strategies in both agricultural and natural ecosystems.

Organic phosphorus↗
DOE OSTI2021

Nodal root diameter and node number in maize ( Zea mays L.) interact to influence plant growth under nitrogen stress

Under nitrogen limitation, plants increase resource allocation to root growth relative to shoot growth. The utility of various root architectural and anatomical phenotypes for nitrogen acquisition are not well understood. Nodal root number and root cross-sectional area were evaluated in maize in field and greenhouse environments. Nodal root number and root cross-sectional area were inversely correlated under both high and low nitrogen conditions. Attenuated emergence of root nodes, as opposed to differences in the number of axial roots per node, was associated with substantially reduced root number. Greater root cross-sectional area was associated with a greater stele area and number of cortical cell files. Genotypes that produced few, thick nodal roots rather than many, thin nodal roots had deeper rooting and better shoot growth in low nitrogen environments. Fewer nodal roots offset the respiratory and nitrogen costs of thicker diameter roots, since total nodal root respiration and nitrogen content was similar for genotypes with many, thin and few, thick nodal roots. We propose that few, thick nodal roots may enable greater capture of deep soil nitrogen and improve plant performance under nitrogen stress. Synergistic interactions between an architectural and anatomical trait may be an important strategy for nitrogen acquisition. Understanding trait interactions among different root nodes has important implications in for improving crop nutrient uptake and stress tolerance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize

Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4–40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions

Plant iron (Fe) nutritional status has a significant impact on rhizosphere microbial communities. While this effect has been attributed to alterations in the composition of root exudates, the underlying mechanisms are not known. Here, we investigated the effect of Fe deficiency on the interactions between the grass Brachypodium distachyon and the common soil bacteria Pseudomonas fluorescens SBW25. Increased phytosiderophore production was the most significant response of Brachypodium root exudation to Fe deficiency. We observed upregulated expression of phytosiderophore biosynthesis genes but lower accumulated exudate concentrations in the presence of Pseudomonas, indicating that the bacteria degrade these phytosiderophores. Pseudomonas did not produce endogenous siderophores under the low Fe conditions. Rather, the bacterial transcriptome revealed upregulation of four genes in response to Fe deficiency that contain motifs associated with cellular uptake of small molecules. Collectively, these results suggest that rhizosphere Pseudomonas fluorescens may take up phytosiderophores produced by grasses in response to Fe deficiency, and we propose target genes that may be involved. Our findings provide insight into the molecular basis for the exchange of C, N, and Fe between plants and bacteria under Fe deficient conditions. These interactions may contribute to differences in the rhizosphere microbial community structure across soil pH regimes.

Boiteau, Rene M.↗
DOE OSTI2024

Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome

Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama ( Bouteloua gracilis ), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota , Thermoproteota (formerly Thaumarchaeota ), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.

Goemann, Hannah M.↗
DOE OSTI2022

Arctic Shrub Expansion, Plant Functional Trait Variation, and Effects on Belowground Carbon Cycling (Final Technical Report)

Terrestrial ecosystems are undergoing dramatic changes in response to climate warming, and these changes are expected to feedback to the atmosphere, potentially altering the trajectory of future climate change. Feedbacks from Arctic ecosystems are a major concern because the Arctic is projected to warm significantly in the 21 st century and because >50% of global belowground organic carbon is stored in permafrost and overlying soils. Warming-driven release of this carbon could drastically increase atmospheric greenhouse gas concentrations and accelerate climate warming. Plant communities are also responding to warming, as evidenced by the widely documented increase in woody-shrub growth and “greening” across much of the Arctic tundra biome. This vegetation shift may offset or amplify warming by altering carbon cycling. The direction and magnitude of shrub effects remain highly uncertain, however, due to limited understanding of the consequences of shrub expansion for belowground carbon cycling and simplification of these relationships in models. The major shrubs expanding in the Arctic (Betula, Salix, and Alnus) vary widely with respect to aboveground and belowground traits (e.g., tissue production and chemistry, rooting depth, microbial symbionts), and may also exhibit substantial intraspecific variation in these traits in response to environmental conditions. Such variation is likely to have profound implications for soil carbon cycling. The overarching goal of this project was to improve process-based understanding of the influence of shrub expansion on carbon cycling to enable improved representation of carbon dynamics in ecosystem and Earth system models. We investigated how plant functional traits vary among shrub genera, respond to environmental conditions, and affect belowground carbon and nutrient cycling by quantifying relationships among functional traits and biogeochemical cycling along edaphic gradients nested within a climate gradient in the Alaskan tundra. We found consistent differences in leaf and root traits among shrub genera and between shrubs and a widespread sedge species, indicating diverse nutrient acquisition strategies and belowground impacts among different arctic shrubs. We also found striking differences in trait values among individuals within the same species or genera within sites. Soil parameters were more important than climate parameters for predicting size and leaf trait variation, and root trait responses were less dependent on climate overall. For all but one root trait, including parameters representing aboveground traits improved the predictive ability of models. These results demonstrate that tundra shrub traits vary considerably at local scales and soil factors drive this variation, especially belowground. Furthermore, leveraging information about aboveground traits and soil conditions can improve predictions of how belowground traits will respond to climate change. Despite these differences, soil carbon and nitrogen pools in the active layer did not vary among plots dominated by different shrub or sedge genera. Instead, pool sizes generally decreased from warmer to colder sites, consistent with a productivity gradient. Patterns of isotopic N composition indicate that shrubs tighten nitrogen cycling via nitrogen resorption or immobilization of shrub litter. Overall, these results suggest that further identifying the specific shrub genera in the tundra landscape will ultimately provide better predictions of belowground dynamics across the changing arctic. We also performed simulation experiments with the Terrestrial Ecosystem Model (TEM) incorporated in the Predictive Ecosystem Analyzer (PEcAn) framework, treats model parameters as probability distributions, estimates parameters based on a synthesis of available field data, and then quantifies both model sensitivity and uncertainty to a given parameter or suite of parameters. We performed simulations across different types of tundra, including shrub tundra. One key finding was that both model sensitivity and uncertainty to a given parameter could vary within the same type of tundra, but in a different geographical location, such as over the climate gradient of shrub tundra described above. We organized a special session at the annual meeting of the Ecological Society of America in August 2019 to disseminate our results, refine recommendations for model improvement, and initiate collaborations to implement these recommendations in existing models of tundra carbon dynamics at ecosystem to Earth system scales. Our results support DOE near-term priorities by providing mechanistic insights into the role of vegetation change in the terrestrial carbon cycle in a region that is inadequately represented in Earth system models. Current models reduce the complexity of Arctic vegetation to a small number of plant functional types (PFTs). This approach implicitly assumes that each PFT represents the average ecological function of its constituent species, thus ignoring the effects of trait variation on biogeochemical cycling and potentially leading to large uncertainty in the sign and magnitude of ecosystem feedbacks to climate. By quantifying variation of plant functional traits across broad gradients of climatic and edaphic conditions and elucidating the linkages of such variation with carbon and nutrient cycling, our results illustrate the need and create a foundation for further developing trait-based modeling approaches that allow the traits of PFTs to vary as a function of environmental conditions. These approaches should improve the capacity of simulation models to offer insights into ecosystem carbon dynamics associated with novel plant communities in a rapidly changing Arctic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Modeling Plant Nutrient Acquisition Strategies Alters Projections of Carbon and Nitrogen Dynamics in Bioenergy Agroecosystems

Plant strategies to acquire nutrients from limited environments help shape ecosystem carbon (C) and nitrogen (N) cycling and response to environmental change. The effects of plant strategies on ecosystem dynamics are largely uncharacterized in bioenergy agroecosystems, where the impacts could determine bioenergy's ability to meet its sustainability goals of storing C and reducing N loss. We used FUN-BioCROP (Fixation and Uptake of Nitrogen-Bioenergy Carbon, Rhizosphere, Organisms and Protection), a plant–microbe interaction model of coupled plant nutrient uptake and soil organic matter decomposition, to simulate the effects of nutrient acquisition strategies on soil microbial activity and ecosystem nutrient cycling in bioenergy feedstocks miscanthus (Miscanthus × giganteus) and sorghum (Sorghum bicolor (L.) Moench). We examined the model's ability to reproduce the relative effects of belowground nutrient uptake on microbial activity using a reanalysis of empirical data showing that miscanthus root exudation provoked a larger soil microbial response than sorghum. From baseline model simulations, we found that the ability of miscanthus to retranslocate N resulted in higher N uptake at a lower C cost than the sorghum/soybean rotation and that soil C and N pools increased under perennial (miscanthus) and decreased under annual (sorghum/soybean) cultivation. The model also predicted that greater root exudation increased soil C accumulation, highlighting the role of roots in forming stable soil C. Overall, the baseline model was unable to reproduce field observations of miscanthus root exudation stimulating microbial activity more than sorghum. To improve the model, we updated the soil microbial parameters in miscanthus to have faster decomposition, a higher C/N ratio, and greater carbon use efficiency. These changes improved the simulated soil microbial response to miscanthus root exudation, supporting the hypothesis that miscanthus soils foster a microbial community that is more responsive to root exudation than that of sorghum.

09 BIOMASS FUELS↗
DOE OSTI2026

Implementing belowground controls on nutrient uptake in ELMv2-SPRUCE improves representation of a boreal peatland ecosystem

Boreal peatlands store 13 %–32 % of the global soil carbon (C) stock, a service dependent on plant-mycorrhizal fungi associations. In these nutrient poor systems, ectomycorrhizal and ericoid mycorrhizal fungi supply up to >80 % of the nutrient requirements of their plant hosts, partly with mined nitrogen (N) and phosphorus (P) from soil organic matter that are otherwise inaccessible to plants. Despite the ecological significance, mycorrhizal associations are only represented in a few land surface or ecosystem models. We modify the peatland branch of version 2 of the Energy Exascale Earth System Land Model (ELMv2-SPRUCE) to replace the default photosynthesis-driven inorganic N and P (NP) uptake process with a more realistic representation of the process via three pathways: (1) direct inorganic NP uptake by uncolonized fine roots, (2) indirect inorganic NP acquisition and (3) indirect NP acquisition from organic sources by mycorrhizal roots. We systematically evaluated the performance of the default and modified models with field observations from a whole ecosystem warming and carbon dioxide fertilization experimental site: Spruce and Peatland Responses Under Changing Environment (SPRUCE), in northern Minnesota, USA. The modified model reduces the underestimation of the growth response of shrubs in the default model to warming from 40 %–80 % to 17 %–35 % and reduces the overall relative absolute error on C fluxes from 1.61 to 1.54 in calibration. Improvements on modeled shrub growths and shrub-moss community net ecosystem exchanges are also seen in validation. The improved growth response of shrubs to warming is accompanied by several-fold increase in direct inorganic NP uptake and decrease in fungal colonization rate. The modified model simulates a smaller magnitude of transition of the ecosystem from C sink to C source under warming due to alleviation of plant nutrient limitation. Equifinality analysis shows the newly added parameters in the modified model can be constrained by the observed C fluxes. Sensitivity analysis shows the newly added parameters have stronger statistical interactions than the preexisting parameters in the default model. Overall, the modified model is an improvement over the default ELMv2-SPRUCE and will be a useful tool for understanding boreal peatland change.

Wang, Yaoping [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2024

Connecting Nitrogen Transformations Mediated by the Rhizosphere Microbiome to Perennial Cropping System Productivity in Marginal Lands

The demand for energy from biofuel production is increasing, prompting concerns about the environmental impact and long-term sustainability of bioenergy cropping systems. These cropping systems will make up much of our future landscapes, and threaten to take the place of food cropping systems. Many life cycle analyses of bioenergy sustainability focus on carbon accrual and budgets, since they want to maximize carbon accrual while producing alternative fuel. Less attention has been given to nitrogen (N) dynamics in these systems. N is the most commonly limiting nutrient for plants, but applying nitrogen fertilizer- as we do for most cropping systems – is harmful to the environment, energetically costly, and produces greenhouse gases. In other words, adding nitrogen by fertilizer bioenergy systems could add to the very problems (climate change) it is trying to address. This is especially true for the areas that are proposed for bioenergy systems: marginal lands. These more degraded lands do not complete with food crops, but do have limited nitrogen. If we are to use these marginal lands for bioenergy, we need to understand the mechanisms regulating nutrient acquisition, and identify ways that bioenergy crops can get nitrogen in sustainable ways. Nutrient acquisition in the soil is performed by microbes in the root zone, or rhizosphere. Microbes can either mineralize nitrogen in the soil (from organic forms) or fix nitrogen from the air, in a process called nitrogen fixation. The goal of our project was thus to understand how the rhizosphere microbiome provides nutrients to bioenergy crops on marginal lands. We focus especially on the process of nitrogen fixation, since it has potential to get “fertilizer for free” that has much less environmental harm. We investigated this goal using sites from the DOE Great Lakes Bioenergy Research Center (GLBRC) in the upper Midwest, and associated lab and ‘omics methods. We group our findings into three major areas. First, we showed that nitrogen fixation, the conversion of N2 gas from the air to ammonium that is usable by plants, is performed in bioenergy soils, and benefits switchgrass crops. While more well-studied in leguminous plants, free-living nitrogen fixation can occur in some systems, and represents a potential opportunity to gain ‘free’ sustainable nitrogen source. We identified the nitrogen fixing bacteria that were most active in providing switchgrass with N, and showed that the drivers of nitrogen fixation occurred at a microscale; it is not well-predicted by bulk variables like soil moisture or plant phenology. Second, we showed that nitrogen fixation is not suppressed by long-term fertilizer. We expected that plentiful nitrogen would reduce the symbiotic relationship between nitrogen fixers and plants, and ‘downregulate’ fixation. We did not find evidence for this, either after long-term fertilizer in the field, or short-term fertilizer in the greenhouse. Finally, we identified the root exudates, carbon compounds that are emitted from the root, that best stimulate nitrogen fixation. We found that carbohydrates were better at stimulating fixation than organic acids. We expected these exudates to be emitted from the plant in periods of high N demand, but we found they are emitted when N is plentiful. This suggests that the stimulation of N fixation by plants is a passive process. Overall, we show that nitrogen fixation has potential to support bioenergy cropping system, and future management could develop ways to maximize it. However, this may not be best achieved via the plant – we found very little evidence of a ‘transactional’ system by which plants are controlling when and where nitrogen fixation is stimulated. It will be better to understand how management practices like planting and fertilizer application affect the microscale soil dynamics, which will determine nitrogen fixation rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Long-term compost amendment modulates wheat genotype differences in belowground carbon allocation, microbial rhizosphere recruitment and nitrogen acquisition

The implementation of soil health-promoting practices, such as cover cropping and compost application, has important implications for nutrient cycling and management in agroecosystems. At the same time, plant belowground carbon (C) allocation patterns can influence nutrient cycling and availability in soil through changes to the microbial community, but the effects may depend on the crop genotype and management practices in place. We evaluated belowground C allocation patterns using 13 C labeling and root architecture in two genotypes of winter wheat (Triticum aestivum) with different levels of exudation and belowground allocation strategies in soils with contrasting compost amendment legacy (108.7 Mg ha -1 every 2 years over 10 years vs. no compost). We also measured microbial community structure and function in the rhizosphere and quantified uptake of residue-derived N from 15 N-labelled cover crop residues. We found an interactive effect between soil management and genotype, where in the no-compost soil, the high-exudation genotype (Snowmass) increased exudation by over 4-fold, while the low-exudate genotype (Byrd) increased only 2-fold. While we did not observe genotype differences in rhizosphere enzyme activity or dissolved N pools, residue N uptake was 1.8 times greater for Snowmass in the compost-amended soil. There were more rhizosphere microbial taxa associated with the high-exudate genotype (Snowmass); nine bacterial and seven fungal families were indicative of Snowmass, versus one bacterial and four fungal families for Byrd. Our results suggest that the high-exudation strategy can influence the rhizosphere microbial community, and lead to greater short-term residue N uptake in high SOM soil. By directly linking root architecture, exudation, microbial communities, and N mineralization and uptake dynamics, this work demonstrates that plasticity in root C allocation is genotype-specific and influences microbial communities and nutrient cycling depending on the soil health context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Soil management legacy interacts with wheat genotype to determine access to organic N in a dryland system

Organic nutrient management through the application of compost and/or cover crops provides mineralizable sources of nutrients for plants while often building soil organic matter (SOM) and various aspects of soil health. Variability in nutrient acquisition strategies between crop genotypes may confer advantages under different soil health contexts and could be important for crop selection and breeding, but crop response under field conditions remains unexplored. We investigated the ability of different genotypes of winter wheat (Triticum aestivum L.) to access nitrogen (N) from newly added cover crop residues in two soils with contrasting levels of SOM and biological activity. We planted three previously characterized wheat genotypes in a long-term dryland compost amendment field trial: 1) Byrd (modern, deep roots, low exudation), 2) Cheyenne (historic, drought susceptible, intermediate exudation), and 3) Snowmass (modern, drought-susceptible, high exudation). 15 N-labelled cover crop residue was added to each plot and traced into wheat tissue. In the low SOM soil, the high exudate genotype Snowmass and historic genotype Cheyenne took up the most residue-derived N (6.4–8.1 kg N ha −1 ) compared to the low-exudate genotype Byrd (4.4 kg N ha −1 ), suggesting a strong exudate effect in the more carbon-limited soil. However, in the high SOM soil, the low-exudate, deep rooted genotype, Byrd, took up the most residue N (4.6 kg N ha −1 vs. 2.8 and 3.3 hg N ha −1 for Cheyenne and Snowmass, respectively), which indicated higher native N cycling activities and greater importance of drought resistance. Enzyme activity, inorganic N, and microbial communities were not influenced by genotype, though did show strong effects of compost application legacy. Furthermore, our results show that belowground allocation strategies that favor microbial stimulation may be less successful under water limitation, especially when high native SOM and biological activity can support mineralization of residue N without added investment in root inputs. Increased soil health through SOM-building management likely enhances nutrient cycling, and may better support root strategies that invest less in microbial stimulation in favor of other limiting resources.

Compost↗
DOE OSTI2024

Nutrient Dynamics in a Coupled Terrestrial Biosphere and Land Model (ELM-FATES-CNP)

We present a representation of nitrogen and phosphorus cycling in the Functionally Assembled Terrestrial Ecosystem Simulator, a demographic vegetation model within the Energy Exascale Earth System land model. This representation is modular, and designed to allow testing of multiple hypothetical approaches for carbon-nutrient coupling in plants. Novel model hypotheses introduced in this work include, (a) the controls on plant acquisition of aqueous mineralized nutrients in the soil and (b) fairly straight forward methods of allocating nutrients to specific plant organs and their losses through live plant turnover as well as litter fluxes generated through plant mortality. This combines the new with pre-existing hypotheses (such as nitrogen fixation and soil decomposition) into a system that can accommodate plant-soil dynamics for a large number of size- and functional-type-resolved plant cohorts within a time-since-disturbance-resolved ecosystem. Root uptake of nutrients is governed by fine root biomass, and plants vary in their fine root biomass allocation in order to balance carbon and nutrient limitations to growth. We test the sensitivity of the model to a wide range of parameter variations and structural representations, and in the context of observations at Barro Colorado Island, Panama. A key model prediction is that plants in the high-light-availability canopy positions allocate more carbon to fine roots than plants in low-light understory environments, given the widely different carbon versus nutrient constraints of these two niches within a given ecosystem. This model provides a basis for exploring carbon-nutrient coupling with vegetation demography within Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Quantitative phenotyping of crop roots with spectral electrical impedance tomography: a rhizotron study with optimized measurement design

Background: Root systems are key contributors to plant health, resilience, and, ultimately, yield of agricultural crops. To optimize plant performance, phenotyping trials are conducted to breed plants with diverse root traits. However, traditional analysis methods are often labour-intensive and invasive to the root system, therefore limiting high-throughput phenotyping. Spectral electrical impedance tomography (sEIT) could help as a non-invasive and cost-efficient alternative to optical root analysis, potentially providing 2D or 3D spatio-temporal information on root development and activity. Although impedance measurements have been shown to be sensitive to root biomass, nutrient status, and diurnal activity, only few attempts have been made to employ tomographic algorithms to recover spatially resolved information on root systems. In this study, we aim to establish relationships between tomographic electrical polarization signatures and root traits of different fine root systems (maize, pinto bean, black bean, and soy bean) under hydroponic conditions. Results: Our results show that, with the use of an optimized data acquisition scheme, sEIT is capable of providing spatially resolved information on root biomass and root surface area for all investigated root systems. We found strong correlations between the total polarization strength and the root biomass (R 2 = 0.82) and root surface area (R 2 = 0.8). Our findings suggest that the captured polarization signature is dominated by cell-scale polarization processes. Additionally, we demonstrate that the resolution characteristics of the measurement scheme can have a significant impact on the tomographic reconstruction of root traits. Conclusion: Our findings showcase that sEIT is a promising tool for the tomographic reconstruction of root traits in high-throughput root phenotyping trials and should be evaluated as a substitute for traditional, often time-consuming, root characterization methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tripartite interactions among free-living, N-fixing bacteria, arbuscular mycorrhizal fungi, and plants: Mutualistic benefits and community response to co-inoculation

Interactions between arbuscular mycorrhizal (AM) fungi and free-living nitrogen fixers (FLNF) occur in the rhizosphere where they can enhance plant nutrient acquisition, impact plant growth, and affect soil processes. Tripartite mutualism commonly occurs between nodule-forming plants, symbiotic diazotrophs, and AM fungi, and can occur between non-nodulating plants, FLNF, and AM fungi. However, information on the extent of, and controls on, tripartite mutualism in non-nodulating plant systems is limited to a small number of crop plants and culturable microbial inoculum, mostly in greenhouse growing conditions. We conducted a systematic literature review to synthesize the current understanding of the responses of plants, AM fungi, and FLNF to co-inoculation, as well as the conditions affecting tripartite mutualism and the magnitude and range of benefits conferred. Our review shows that plants generally benefit from co-inoculation with AM fungi and FLNF taxa, but benefits are highly variable and context dependent, ranging from 94% reduction in plant shoot biomass to 255% increase in total plant biomass. Additionally, the presence of AM fungi can increase abundance of FLNF and the presence of FLNF can increase AM fungal root colonization, but these responses also vary widely. Major factors influencing variation in response to co-inoculation by all organisms include plant phenology/age, soil type and nutrient availability, and partner pairing. There is potential for leveraging these tripartite mutualisms to improve plant productivity and soil microbial function, but successful application is more likely with a thorough understanding of the environmental and mechanistic controls on these relationships and testing of field-scale implementation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport

Nitrogen (N) is an essential nutrient that limits plant growth in many ecosystems. Here we investigate an overlooked component of the terrestrial N cycle – subsurface ammonia (NH 3 ) gas transport and its contribution to plant and mycorrhizal N acquisition. In this work, we used controlled mesocosms, soil incubations, stable isotopes, and imaging to investigate edaphic drivers of NH 3 gas efflux, track lateral subsurface N transport originating from 15 NH 3 gas or 15 N-enriched organic matter, and assess plant and mycorrhizal N assimilation from this gaseous transport pathway. NH3 is released from soil organic matter, travels belowground, and contributes to root and fungal N content. Abiotic soil properties (pH and texture) influence the quantity of NH 3 available for subsurface transport. Mutualisms with arbuscular mycorrhizal (AM) fungi can substantially increase plant NH 3 -N uptake. The grass Brachypodium distachyon acquired 6–9% of total plant N from organic matter-N that traveled as a gas belowground. Colonization by the AM fungus Rhizophagus irregularis was associated with a two-fold increase in total plant N acquisition from subsurface NH 3 gas. NH 3 gas transport and uptake pathways may be fundamentally different from those of more commonly studied soil N species and warrant further research.

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

Endophyte-Promoted Phosphorus Solubilization in Populus

Phosphorus is an important plant nutrient, but in soils the majority of phosphorus, present in the form of a phosphate, forms metal complexes in soil making it relatively unavailable to plants. Therefore, inorganic phosphate solubilization is an important process of plant growth promotion by plant associated bacteria and fungi. Non nodulating plant species have been shown to thrive in low-nutrient environments, in some instances by relying on plant associated microorganisms called endophytes. These microorganisms live within the plant and help supply nutrients for the plant. Despite their potential enormous environmental importance, there are a limited number of studies looking at the direct molecular impact of phosphate solubilizing endophytic bacteria on the host plant. In this work, we studied the impact of two endophyte strains of wild poplar (Populus trichocarpa) that solubilize phosphate. Using a combination of x-ray imaging, spectroscopy methods, and proteomics we report direct evidence of endophyte-promoted phosphorus uptake in poplar. We found that the solubilized phosphate inside the plant may react and become insoluble again suggesting that the phosphate could be re-released within the plant by endophytes. Using synchrotron x-ray fluorescence spectromicroscopy combined with x-ray absorption near-edge structure, we visualized the nutrient phosphorus inside poplar roots inoculated by the selected endophytes and found the phosphorus in both forms of organic and inorganic phosphates inside the root. Tomography-based root imaging revealed a markedly different root biomass and root architecture for poplar samples inoculated with the phosphate solubilizing bacteria strains. Proteomics characterization on poplar roots coupled with protein network analysis revealed novel proteins and metabolic pathways with possible involvement in endophyte enriched phosphorus uptake. These findings suggest an important role of endophytes for phosphorus acquisition and provide a deeper understanding of the critical symbiotic associations between poplar and the endophytic bacteria.

36 MATERIALS SCIENCE↗