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

Starting Fall 2021Design and omics exploration of constructed microbial communities

Constructed communities can provide a deeper understanding of mechanisms that drive microbial community interactions. Partnering this 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. 

However, as experimental data and design complexity grow, computational modules and applications are required to support rational design and iterative testing of constructed communities based on desired functional and phenotypic characteristics and the ability of members of the community 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 important considerations in the rational design of constructed communities and its members. 

The current development project will add Populus-associated microbiome and isolate genome data and Apps to KBase, which include: 1) Summarize functional potential of genome set, 2) Generate minimal microbial consortia similar to a metagenome, 3) Design constructed microbial communities with desired characteristics, and 4) Compare groups of genomes from constructed community experiments. The resulting workflow will support rational design and iterative testing for more productive constructed community research, and serve the growing community that leverages this powerful research platform. 

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: Alexis Marsh3, Priya Ranjan1, 2
Project Team: Paul E. Abraham1, Jia Wang1, David J. Weston1
Affiliations: 1Oak Ridge National Laboratory, 2KBase, 3Iowa State University

Resources

System maintenance May 25

We will be performing system maintenance on Wednesday, May 25, from 2-4pm PDT (4-6pm CDT).  narrative.kbase.us, compute jobs, and appdev.kbase.us may be unavailable or unstable for parts of this time.

We do not anticipate any interruption to www.kbase.us.