Environmental Molecular Sciences Laboratory

A DOE Office of Science User Facility

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Functional characterization of a defined Panicum rhizobiome

Tuesday, October 1, 2019
Principal Investigator: 
Esther Singer
Lead Institution: 
Lawrence Berkeley National Laboratory
Project ID: 

Nitrogen limitation is a global challenge for biofuel crop resilience and hence bioenergy security. Plant growth promoting bacteria (PGPB) can help to mitigate plant stress by forming symbiotic relationships with their host that are mediated by exometabolites. While a lot of research has been dedicated to recording plant response to nutrient limitation, it is largely unknown how the plant microbiome reacts to nutrient stress and what types of signaling and regulation pathways are activated that have a beneficial impact on plant resilience. In particular, the metabolomic activity of root colonizing bacteria at the community level is an unexplored realm that could significantly impact overall plant health and present opportunities to identify emerging model systems that can be manipulated.
In the proposed work, we will perform stable isotope labeling in a novel platform for plant microbiome research, the EcoPOD. This mesocosm allows the control, manipulation and monitoring of entire plant-microbe-soil-atmosphere ecosystem, bridging laboratory and real-world experimental setups. We will conduct a 13C-CO2 pulse label study with Panicum hallii, a model to agronomic switchgrass with short life cycle and small genome, under N limitation in sterile soils inoculated with a defined rhizobiome consisting of >100 isolates isolated from Panicum grasses in marginal soils. Changes in plant and microbial gene expression, metabolite synthesis, as well as nutrient turnover will be observed for the first time in complex, controlled and entirely replicable conditions provided in the EcoPOD. This study will disclose unprecedented mechanistic insights into plant microbiome interactions at the community level, such as strain-specific plant growth promoting functions, which will be used to generate a standardized microbial community that will contribute to increase consistency in plant microbiome research.