Results for “rhizosphere microbiome” — Page 2

DOE OSTI2021

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization

Abstract Background Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome. Results In this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions. Conclusions Standardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid ( Adelges tsugae , HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii , that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

16S rRNA↗

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 OSTI2021

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Abstract Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants ( Panicum virgatum ) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

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

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

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

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

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

Favela, Alonso [School of Plant Sciences, Universi↗

DOE OSTI2021

Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions

The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Enzymatically hydrolyzed fluorescence-based chemical probe enables in situ mapping of chitinase activity in the rhizosphere

Rhizosphere microbiomes and root exudates play a pivotal biochemical role in helping to catalyze chitin catabolism. Chitin is a recalcitrant and ubiquitous soil biopolymer, estimated to be the second most abundant organic soil biopolymer on Earth. Despite its abundance, role as a source of C and N in soil, and importance to ecosystem function, the biochemical mechanisms controlling chitin fate in the rhizosphere are elusive and poorly understood. To enable spatial mapping of chitinase activity in the rhizosphere, we designed and synthesized an enzymatically activated fluorogenic substrate, chitotriose-TokyoGreen (chitotriose-TG), by incorporating a fluorescein derivative (TG) onto the trimeric unit of chitin. This non-fluorescent substrate is selectively hydrolyzed by chitinase to release TG and yield a high fluorescence signal, which can be used to spatially image and measure chitinase activity in the rhizosphere. To demonstrate the application of this technique, we grew switchgrass (Panicum virgatum) in rhizoboxes amended with a horizontal layer of chitin. We extracted mobile proteins from the rhizobox using a nitrocellulose membrane blotting technique which offer non-destructive enzyme extraction while preserving the 2D spatial position of the enzymes. We then subjected these membranes to the synthesized chitotriose-TG stain to spatially visualize the distribution of chitinase activity within the rhizosphere. Furthermore, we observed increased chitinase activity near plant roots and higher activity within the soil zone enriched in chitin, showing an adaptive response of chitinase activity with spatial focusing in areas of higher chitin abundance. Thus, the enzyme extraction and visualization strategy we describe here can help enlighten efforts to better understand spatial controls on chitin breakdown in rhizosphere, further elucidating the role of chitin as a C and N source in these systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Root exudate composition reflects drought severity gradient in blue grama (Bouteloua gracilis)

Abstract Plant survival during environmental stress greatly affects ecosystem carbon (C) cycling, and plant–microbe interactions are central to plant stress survival. The release of C-rich root exudates is a key mechanism plants use to manage their microbiome, attracting beneficial microbes and/or suppressing harmful microbes to help plants withstand environmental stress. However, a critical knowledge gap is how plants alter root exudate concentration and composition under varying stress levels. In a greenhouse study, we imposed three drought treatments (control, mild, severe) on blue grama ( Bouteloua gracilis Kunth Lag. Ex Griffiths), and measured plant physiology and root exudate concentration and composition using GC–MS, NMR, and FTICR. With increasing drought severity, root exudate total C and organic C increased concurrently with declining predawn leaf water potential and photosynthesis. Root exudate composition mirrored the physiological gradient of drought severity treatments. Specific compounds that are known to alter plant drought responses and the rhizosphere microbiome mirrored the drought severity-induced root exudate compositional gradient. Despite reducing C uptake, these plants actively invested C to root exudates with increasing drought severity. Patterns of plant physiology and root exudate concentration and composition co-varied along a gradient of drought severity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗