System Approaches to Study Soybean Root Biology at Single-Cell Resolution
EMSL Project ID
49773
Abstract
The long-term goal of this project is to further basic understanding of the agronomically important Bradyrhizobium japonicum-soybean nitrogen fixing symbiosis. Soybeans are the major source of nitrogen for livestock feed and are also processed into protein-rich products for human consumption. In 2014, soybean was grown on more than 81 million acres across the U.S. with an estimated value of more than $35 billion. Soybean is a major crop worldwide due to its ability, as a legume, to fix atmospheric N2 through its symbiotic relationship with N2-fixing rhizobia. It has been estimated that more than 60 million metric tons of N2 are fixed by legumes annually with a fertilizer replacement value of $7- 10 billion. A unique focus of this project is the ability to sample the transcriptome, proteome and metabolome at a single-cell level. These methods, as well as sophisticated data analysis and cell modeling tools, will be applied to the intermediate stages of soybean nodulation; specifically, infection thread progression, bacterial release into nodule cells, as well as investigations of nutrient/solute allocation via the vascular tissues. These are key events in nodule formation that remain largely undefined. Data integration and system modeling of complex biological processes requires detailed, functional genomic data, preferably obtained in a cell-specific way in order to avoid the effects of signal dilution due to the presence of non-responding cells. Our vision is to utilize high-resolution sampling of single root cells to explore in detail the molecular mechanisms leading to establishment of a N2-fixing symbiosis. . We will use new transcriptomic and mass spectrometry techniques that enable imaging and analysis at single-cell resolution. These data will be used to construct predictive, computational models of the plant response to rhizobial infection thread initiation and growth. These are critical areas for understanding the N2-fixing symbiosis and, at present, remain largely an unexplored area. The ultimate goals will be to expand our basic understanding of the agronomically relevant N2-fixing symbiosis, develop new tools for plant functional analysis and continue our efforts to develop soybean genomic resources.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2017-10-01
End Date
2019-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Stopka SA, BJ Agtuca, DW Koppenaal, L Pasa Tolic, G Stacey, A Vertes, and CR Anderton. 2017. "Laser Ablation Electrospray Ionization Mass Spectrometry with Ion Mobility Separation Reveals Metabolites and Lipids in the Symbiotic Interactions of Soybean Roots and Rhizobia." The Plant Journal 91(2):340-354. doi:10.1111/tpj.13569
Velickovic D.S., B.J. Agtuca, S.A. Stopka, A. Vertes, D.W. Koppenaal, L. Pasa Tolic, and G. Stacey, et al. 2018. "Observed Metabolic Asymmetry Within Soybean Root Nodules Reflects Unexpected Complexity in Rhizobacteria-legume Metabolite Exchange." Nature. PNNL-SA-127419. doi:10.1038/s41396-018-0188-8