Identifying mechanisms that facilitate or prevent microbial community invasion

University Of Pittsburgh, Pittsburgh PA

Investigators

Abstract

Plants associate with beneficial bacteria that help protect them from pathogens and facilitate nutrient uptake. As a result, they have the potential to supplement pesticides and fertilizers for use in agriculture. However, attempts to use beneficial bacteria in agriculture have had limited success, often due to poor survival of introduced strains. This project will enhance our understanding of the ecological, molecular, genetic, and genomic mechanisms that make some beneficial bacteria strong colonizers of plants and the mechanisms by which they protect plants from pathogens. The project will use synthetic microbial communities consisting of closely related plant-beneficial and pathogenic strains of bacteria, coupled with genetic and genomic approaches to find the molecular mechanisms that allow some beneficial microbes to successfully colonize plants and exclude pathogens. The use of established microbial communities, genome-sequenced community members and high throughput assays will enable rapid screening of many combinations of microbes. The project will also provide training opportunities for a breadth of career stages including graduate students and postdoctoral fellows, as well as undergraduate students through course-based research experiences. With the rise of emergent pathogens, understanding the mechanisms by which bacteria facilitate or prevent disease will aid in rapid and cost-effective solutions. Microbiome community engineering has proven difficult, in part, due to priority effects where existing communities result in poor invasion of introduced strains. The goal of this project is to facilitate understanding of the molecular, ecological, genetic, and genomic mechanisms that allow or prevent microbial community invasion. The project uses synthetic communities to understand the mechanisms that allow beneficial strains to exclude pathogens and invade a community via three objectives that query the molecular and genomic rules driving priority effects and microbial community assembly. First, strains that show strong priority effects and strains that can invade a community will be identified to determine the ecological and genomic features that contribute to priority effects. Comparative genomics will then be used to identify genes and traits that allow or prevent community invasion. Second, mechanisms by which a beneficial strain can exclude a closely related opportunistic pathogen will be examined using a pathogen-beneficial strain pair. A genetic screen will be used to identify novel genes required for plant colonization and pathogen exclusion. Genes essential for pathogen exclusion will be identified and tested in the presence of complex synthetic communities. Finally, genetic strategies for community invasion and overcoming priority effects will be engineered by building a Pseudomonas fosmid library containing large inserts representing the Pseudomonas pan-genome and iteratively passaging engineered P. fluorescens on roots of pathogen-infected plants. Collectively, these objectives will reveal the mechanisms by which communities exclude invaders and allow a beneficial strain to compete with an existing community. 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.