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Elucidation of plant-microbe interactions mechanisms in the rhizosphere

ABSTRACT: Scientific rationale. The plant microbiome includes beneficial microbiota that provide the plant host protection from pathogens, increased nutrient availability and resilience against abiotic stress. It is well established that the well characterized plant root-colonizing, growth-promoting rhizobacterium Pseudomonas simiae WCS417 conveys benefit to plant host Arabidopsis thaliana, but the mechanisms of this microbially mediated enhancement remains underexplored. In a pilot in vitro investigation, we observed that only providing root exudates in the absence of the plant failed to result in bacterial growth, suggesting that a key component of an in vivo plant-microbe interaction is essential. Here, we propose to use novel plant propagation techniques, namely fabricated ecosystems via ecoBoxes, to facilitate controlled and reproducible plant-microbe interaction over a four-week period. Through metabolomics analyses, we aim to identify the presence/absence of key metabolites observed in experimental treatments. Specific aim. Experimental characterization of root colonization mechanisms. Col-0 seeds will be surface sterilized and plated on mesh and ½ MS medium in square plates and left at 4oC for approximately 48 hours to allow for stratification. Two to 3-day old seedlings will be added to ecoBoxes and let to grow for 1-2 weeks with 60 ml 1/5 MS media (pH adjusted to ~ 5.7). Pseudomonas simiae WCS417 fluorescent strain, SB642 will be added to ‘with bacterium’ treatment and all samples will be subsequently collected at ~ 4 weeks. Each treatment will have 5 corresponding replicates. Exudate media will be processed for metabolomic analysis (15 samples total) while Arabidopsis will be used for confocal microscopy of plant root colonization (15 plants total). The work (proposal:https://doi.org/10.46936/10.25585/60008794) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Microbiome

SUBMITTER: Jonelle Basso

PROVIDER: MSV000098284 | MassIVE | Mon Jun 23 13:37:00 BST 2025

REPOSITORIES: MassIVE

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Project description:Scientific rationale. The plant microbiome includes beneficial microbiota that provide the plant host protection from pathogens, increased nutrient availability and resilience against abiotic stress. It is well established that the well characterized plant root-colonizing, growth-promoting rhizobacterium Pseudomonas simiae WCS417 conveys benefit to plant host Arabidopsis thaliana, but the mechanisms of this microbially mediated enhancement remains underexplored. In a pilot in vitro investigation, we observed that only providing root exudates in the absence of the plant failed to result in bacterial growth, suggesting that a key component of an in vivo plant-microbe interaction is essential. Here, we propose to use novel plant propagation techniques, namely fabricated ecosystems via ecoBoxes, to facilitate controlled and reproducible plant-microbe interaction over a four-week period. Through metabolomics analyses, we aim to identify the presence/absence of key metabolites observed in experimental treatments. Specific aim. Experimental characterization of root colonization mechanisms. Col-0 seeds will be surface sterilized and plated on mesh and ½ MS medium in square plates and left at 4oC for approximately 48 hours to allow for stratification. Two to 3-day old seedlings will be added to ecoBoxes and let to grow for 1-2 weeks with 60 ml 1/5 MS media (pH adjusted to ~ 5.7). Pseudomonas simiae WCS417 fluorescent strain, SB642 will be added to ‘with bacterium’ treatment and all samples will be subsequently collected at ~ 4 weeks. Each treatment will have 5 corresponding replicates. Exudate media will be processed for metabolomic analysis (15 samples total) while Arabidopsis will be used for confocal microscopy of plant root colonization (15 plants total). The work (proposal:https://doi.org/10.46936/10.25585/60008794) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

Project description:Part of the DOE’s strategy to ensure American energy independence is to produce biofuels from dedicated biomass crops. Achieving DOE’s ambitious goal of displacing 30 percent of 2004 gasoline demand with biofuels by 2030 will require major increases in plant productivity. Switchgrass has been championed as a promising bioenergy species, but few tools exist to facilitate its widespread commercial use. A major challenge has been its large, complex genome. As a close relative of agronomic switchgrass (Panicum virgatum) with a diploid genome and seed-to-seed time of 8 weeks, Panicum hallii offers researchers a model system for exploring Panicum genetics, genomics, and adaptation for agronomic improvement. Bacteria living in leaves and roots influence many aspects of plant health, especially rhizobacteria and mycorrhizae are known to impact plant aboveground phenotypes 1,2. To better understand P. halli-microbe ecosystems, we will conduct experiments at our Texas field site, in EcoCells at Desert Research Institute (DRI) and in growth chambers and the Ecopod at LBNL. Ecopods are enclosed environments that allow direct and intensive monitoring and manipulation of replicated plant-soil-microbe-atmosphere interactions over the complete plant life cycle. Specifically, we are interested in plant microbe ecosystem stress response with respect to soil drying. Despite its broad adaptation to marginal, droughty soils 3,4, a persistent issue in producing switchgrass has been the rapid and consistent establishment of strong stands, especially when drought occurs during implantation. The proposed study is aimed at disclosing biotic interactions modulating plant and microbial metabolism under globally relevant environmental conditions and provides an opportunity to benchmark the Ecopods at LBNL. The work (proposal:https://doi.org/10.46936/10.25585/60001211) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

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Elucidation of plant-microbe interactions mechanisms in the rhizosphere

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