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
- Calculate Metabolic Interaction Scores (Beta-only)
- Run Antismash analysis (still in development)
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
Project Team: Paul E. Abraham1, Jia Wang1, David J. Weston1
Affiliations: 1Oak Ridge National Laboratory, 2KBase, 3Iowa State University, 4Argonne National Laboratory
- ORNL Plant Microbe Interfaces SFA Project Website
- GitHub Repository – coming soon