CAREER: Deciphering the roles of nodule-specific PLAT domain genes in the nitrogen-fixing symbiosis and host-strain specificity

This award is funded in whole or in part under the American Rescue Plan Act of 2021 (Public Law 117- 2)

Although nitrogen is the most abundant gas in the Earth’s atmosphere, it cannot be assimilated by plants and animals unless it is reduced to ammonium and other bioavailable forms, in a process called nitrogen fixation. The conventional way of growing most of the world’s crops is to apply reduced forms of nitrogen as fertilizer. Although it promotes crop yields, much of the fertilizer leaches out into groundwater, streams, and oceans, causing severe ecological disturbances, including overgrowth of plant life, oxygen depletion, and death of animal life.

Due to overuse, more than 500 sites of coastal waters worldwide are now declared ‘dead zones’. A group of soil bacteria collectively known as rhizobia can reduce (fix) nitrogen. Legumes establish mutually beneficial associations (symbioses) with compatible rhizobia, by allowing their selective entry into newly developed organs (root nodules), thus acquiring an internal source of fertilizer.

Nitrogen fixation efficiency varies in different legume-rhizobia associations; therefore, for high yields, fertilizer nitrogen needs to be applied on legume crops. This shuts down symbiotic nitrogen fixation (SNF). The project seeks to uncover new mechanisms of host-strain specificity to improve SNF efficiency, informing the development of crop varieties and engineered bacterial strains that can enhance the economic potential of SNF for low-input, sustainable agriculture.

Research activities from this project will be integrated into an inquiry- and project-based revamped graduate course-lab, and into various educational activities including training of undergraduate and graduate students, a postdoctoral researcher, and training disadvantaged middle- and high school girls from rural Texas.

An intriguing aspect of SNF is host-strain specificity, critical for efficient nitrogen fixation, but, still, poorly understood at the genetic and the molecular level. Because the rhizosphere contains multiple rhizobial strains at any time, it is critical for a legume host to distinguish between friend and foe, and, also, to distinguish between efficient and less efficient friends, for optimal nitrogen fixation.

The proposed research builds on the hypothesis that the Medicago truncatula MtNPD1 gene (nodule-specific polycystin-1, lipoxygenase, alpha-toxin domain-containing protein) orchestrates rhizobial selection in order to maintain effective nitrogen fixation in root nodules. The host-strain specific phenotype of the npd1 mutant implies that MtNPD1 may be interacting with certain bacterial factors to promote survival and normal function of compatible strains inside root nodules.

An assortment of molecular, genetic, proteomic, genomic, and microscopic approaches will be used to decipher the biological roles of MtNPD1 and the other four members of this nodule-specific gene family. The main goals of the project are to identify plant and/or bacterial protein partners of MtNPD1, refine intracellular MtNPD1 localization in a strain-dependent manner, and identify bacterial factors linked to the NPD1 gene function and host-strain specificity using pan-genome analysis and genomic library switching between strains with contrasting fate in npd1 nodules.

Altogether, the proposed work is poised to enhance our understanding of how M. truncatula selects favorable symbiotic partners, thus optimizing SNF with specific rhizobial strains.

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.