NSF Postdoctoral Fellowship in Biology FY 2021: Using DNA-barcode lineage tracking to study ecological and evolutionary dynamics in the cucumber pathogen Erwinia tracheiphila

Johnson, Milo, Cambridge MA

Investigators

Abstract

This action funds an NSF Postdoctoral Research Fellowship in Biology for FY 2021, Integrative Research Investigating the Rules of Life Governing Interactions Between Genomes, Environment and Phenotypes. The fellowship supports research and training of the Fellow that will contribute to the area of Rules of Life in innovative ways. This research aims to use new genetic tools to understand the “evolutionary natural history” of an economically important cucumber and squash pathogen, Erwinia tracheiphila. E. tracheiphila infects plants through wounds on leaves or flowers, divides in the xylem of the plant, and is transmitted between plants by striped cucumber beetles. It is an ideal system for studying how plant pathogens adapt to different plant host and insect vector environments. Through a series of infection experiments, the Fellow will observe the process of E. tracheiphila evolution and measure the effects of mutations in squash, cucumber, and beetle environments. This research will further our understanding of this agriculturally important pathogen’s biology and will serve as a first step towards building a new model system for understanding the evolution of pathogens more generally. The Fellow will also participate in the Promoting Inclusivity in Computing (PINC) program at San Francisco State University during this work as part of an effort to broaden participation in computational biology research. This experience will also provide valuable training in education and scientific mentorship. Specifically, this research will use existing E. tracheiphila strain collections and DNA-barcode tracking technologies to study how E. tracheiphila evolves in high resolution. The Fellow will conduct lineage-tracking evolution experiments and barcode-based fitness assays to measure the fitness effects of both naturally occurring and engineered (using transposon mutagenesis) mutations in in-vivo plant and insect environments with and without competitors (other E. tracheiphila strains) and predators (phage). This work will provide a comprehensive dataset on how the fitness effects of mutations depend on the intersection of the environment, the genetic background, and ecological interactions. To maximize the broader impacts of this project, the barcoded E. tracheiphila strain libraries will be made available to other scientists, along with an open-source interactive browser that researchers can use to explore the data and test their own hypotheses. Working with scientists at UC Berkeley and Lawrence Berkeley National Labs, the Fellow will gain training - in functional bacterial genetics, plant-microbial interactions, experimental design, and mentorship - that will be essential for a successful career as a scientist or research professor. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.