Molecular Analyses of Plant Root-Microbe Interaction

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Plant roots offer mechanical support and absorb water and nutrients from the soil; however, roots also help plants interact with the soil environment. Plants’ survival and productivity largely depends on the ability of the root system to sense and respond to biotic and abiotic factors in the soil. One group of organisms that interact with plant root in the rhizosphere (the soil zone extending to a few millimeters immediately surrounding the root) is bacteria, a group consisting of both pathogenic and beneficial forms. Bacteria in the rhizosphere influence physiology of the plant roots and overall health of the plant. Thus, there is potential to improve plant health and productivity by selectively increasing the population of beneficial bacteria and reducing pathogens in the rhizosphere. To achieve this objective a clear understanding of the bacterial and plant factors that mediates root-bacteria interaction is critical. My research focuses on understanding plant factors that mediate root-microbe interaction. One of the questions we are asking is: are there plant genes that allow selective colonization of roots by beneficial bacteria? To this end we are using the plant model Arabidospsis thaliana and bacteria Pseudomonas syringe pv tomato DC3000 [Pst DC3000] (pathogen) and Pseudomonas putida (beneficial). With the support from the previous Discovery grant funding we have identified Arabidopsis single gene mutants that exhibited two contrasting colonization pattern; 1. mutants that support growth of the pathogen Pst DC3000 and reduced colonization of the beneficial bacteria P. putida, 2. mutants that promote colonization by P. putida and reduced the growth of Pst DC3000. In silico analysis and supporting preliminary results suggest that the proteins encoded by these genes interact with a number of other Arabidopsis proteins that ultimately cause the differential root-colonization phenotype. The proposed research program will use the Arabidopsis mutant identified in the previous Discovery project to develop a systems biology approach to understand the molecular basis of root-microbe interaction. The objective of this research program are 1) to study the proteome of the mutants that are altered in root-colonization phenotype 2) to characterize the spatiotemporal expression of genes that affect root-microbe interaction identified in the previous project when exposed to pathogenic and the beneficial bacteria 3) to study plant protein-protein interaction in root-microbe interaction 4)to study the difference in the whole metabolome of the mutant plants in response to inoculation with the Pst DC3000 and P. putida and to compare with that of the wild type plant 5) integrating the transcriptomic, proteomic and metabolomics data to better understand the physiological networks that mediate plant root-microbe interaction. This proposed research program will add considerable new knowledge to the current understanding of rhizosphere plant-microbe interactions. The results of the genetic basis of root-microbe interaction will unravel molecular networks that promote plants’ interaction with beneficial bacteria while diminishing its association with pathogens. The genes identified in this research program will aid in the development of ‘designer’ crop varieties that have the enhanced ability to recruit beneficial microbes on to the root and rhizosphere . Development of such crop varieties will significantly reduce the use of agricultural inputs like fertilizer, pesticides and water ultimately promoting sustainable agriculture.