EDGE CMT: NSF-BSF: High-throughput discovery and testing of microbial genes modulating specificity and microbial load on plant roots.

Plant roots contain a diverse community of microbes that help the plant grow, uptake nutrients, and resist stress. Therefore, there has been a lot of interest in using these microbes to improve the growth and productivity of agricultural plants. Unfortunately, in many cases these microbial products fail to provide long-term benefits to the crop.

This is because scientists still lack a basic understanding of what makes a microbe able to survive on the plant root. To overcome this challenge, this project will implement novel genetic engineering techniques to discover genes that, when added to a microbe that cannot survive on plant roots, enable that microbe to survive longer on the roots. This research will be performed on several different types of plants under several different nutrient conditions and with several different types of plant-associated microbes.

Together, this project will allow the identification of microbes with the potential for long-term benefits to crop growth and productivity. In parallel, this project will implement a two weeklong summer program to introduce high school students to the importance of microbes in agriculture and organize reciprocal research exchange visits between graduate students at North Carolina State University, University of Kansas, and the Hebrew University of Jerusalem.

Our understanding of the genes and mechanisms that modulate bacterial abundance in/on roots remains incomplete, because prior work has either focused on correlative relationships between genes in root-associated versus non-root-associated bacteria, or genes that are “necessary” for colonization in an already good colonizer. Much less studied are genes that are “sufficient” to improve colonization in a poor colonizer.

To identify and study such genes, the project will 1) generate functional metagenomic libraries using soil and rhizosphere DNA, and apply these libraries to plants to explore the effects of host genotype on genetic functions enhancing microbial load on and in the root, 2) investigate the impact of microbial community composition on the functions enhancing microbial load on and in the plant root, 3) investigate the impact of abiotic stressors on the functions that enhance microbial load on and in the root, and 4) test whether load-enhancing functions are enriched in root-associated metagenomes and that removal of these genes from soil microbes reduces their load on and in roots. Taken together, this work will identify colonization-enhancing factors for the plant root, thus opening the door to other valuable phenotypes including pathogen resistance and nutrient provision.

It will also reveal to what extent the functions encoded within these genes are specific to certain plant varieties, species, microbiome compositions, and abiotic conditions.

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.