Plant Microbe Interfaces SFA

Exploring host-microbe relationships across temporal scales to understand selection and performance of the biological partners.

The Plant Microbe Interfaces (PMI) Science Focus Area (SFA) studies the dynamic interface between plants, their microbiome, and the environment. These interactions determine how plants detect and respond to changing conditions, with the goal of understanding how symbiotic relationships adapt to climate change, influence nutrient cycling and sequestration, and the possible management of these systems as renewal energy sources.

Collaborative Development Projects

Design and omics exploration of constructed microbial communities

Synthetic microbial communities can be designed to mimic the behavior of natural communities and can be engineered to increase plant growth and impart disease resistance. They can provide a deeper understanding of mechanisms that drive microbial community interactions and can be used to study bacterial processes involved in community establishment and function. Partnered with the capability to obtain data on microbial activities (e.g., protein or metabolite production) facilitates linking functional processes and improves the quality of annotation and predictive models.

The increase in complexity of experimental data and design necessitates computational modules and applications to support the rational design and iterative testing of synthetic communities based on desired functional and phenotypic characteristics and the ability of community members to survive together. KBase provides a wide range and increasing number of relevant tools for functional annotation, metabolic modeling, auxotrophy prediction, substrate utilization and production of byproducts, taxonomy information, and prediction of microbial traits (e.g., nitrogen fixation) that are essential considerations in the rational design of synthetic communities and its members. 

In this collaboration with the Plant-Microbe Interfaces (PMI) SFA at Oak Ridge National Laboratory, we add isolate genome data and multi-omics datasets derived from Populus-associated microbiome. Additionally, various applications will be added to the KBase platform to create workflows for the computationally-aided selection of isolates for synthetic community experiments. For designing the community, researchers can use these KBase apps to annotate genomes with plant growth-promoting traits and secondary metabolism classes and calculate metabolic dependencies between microbes of interest. The design process will be tested using experimental systems established in the PMI SFA for studying synthetic communities. Further, the results from these experiments will be integrated back into KBase to improve the mechanistic understanding of interactions and iteratively improve the design process. The resulting workflow will support the rational design and iterative testing for more productive synthetic community research and serve the growing community that leverages this powerful research platform.  

Functionality and Tools

Isolate phenotyping

The PMI and ENIGMA SFAs have embarked on a joint effort to characterize microbial isolates of interest across both projects. PMI works in surface soils, especially in and around the roots of high-priority plant stocks such as poplar tree (Populus). ENIGMA works in subsurface environments that share many of the same microbes, at least the genus level, but these microbes likely play very different roles and utilize different functions. By establishing joint protocols for measuring isolate growth across a range of culture environments, ENIGMA and PMI are able to form robust phenotype observations. These observations are used to test and validate KBase’s metabolic models of microbes, enhancing and improving our mechanistic understanding of microbial metabolism across a variety of conditions. Together a more detailed picture of microbial community composition in terrestrial and subsurface environments will be gained.

Additional Information

Meet the Members

SFA Manager and Principal Investigator: Mitchel J. Doktycz1
SFA co-PIs: Dale A. Pelletier1, Timothy J. Tschaplinski1
KBase Contact: Priya Ranjan1, 2
Lead Developers: Dileep Kishore1, 2, Andrew Freiburger4, Alexis Marsh3, Priya Ranjan1, 2
Affiliations: 1Oak Ridge National Laboratory, 2KBase, 3Iowa State University, 4Argonne National Laboratory