The Effect of the Microbiome on the Rice Transcriptome

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PI: Harsh P. Bais (University of Delaware)CoPIs: Venkatesan Sundaresan and Jonathan A. Eisen (University of California - Davis)Collaborators: Venu Kalavacharla (Delaware State University) and Gurdev Khush (University of California - Davis)Plants grow in close association with large communities of microbes collectively called the microbiome. Comparatively little is known about the diversity of microbes that associate with plants and their interactions and effects on performance and crop yields. Specific microbes have been extensively documented to provide beneficial effects to plants, such as those involving well-known symbiotic associations in legumes. Previous studies utilizing a single beneficial bacterial species in the model plant Arabidopsis thaliana demonstrate how plants actively recruit beneficial bacteria under biotic stress regimes. While valuable insights can be gained from studies with single microbial species, preliminary studies show a wide diversity of bacterial species associated with field grown rice (Oryza sativa) plants, whose biological significance is completely unknown. This project will utilize a combination of genomic and metagenomic approaches to dissect the impact of microbial associations on rice. Specifically, a controlled experimental system will be established, in which microbial populations will be characterized by metagenomic rRNA profiling, and plant responses by transcriptomic profiling. The expression profiles for localized and whole plant responses will be analyzed for global changes in gene expression, as well as for changes in the expression of specific functional classes of genes that would reflect changes in nutrient availability, or establishment of plant immunity. The proposed research will provide the foundations for future investigations into the impact of the microbiome on plant performance. All sequence and mapping data generated in this project will be accessible through a genome browser that will be developed specifically for this project. Allsequence data will be deposited for long-term dissemination in GenBank, GreenGenes (http://greengenes.lbl.gov), the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/), and NCBI's Short Read Archive (SRA; http://www.ncbi.nlm.nih.gov/Traces/home/). The broader impacts of this project stem, in part, from the interdisciplinary nature of the research. Training for students and postdoctoral associates will integrate quantitative approaches with applications to experimental biology. The project will also have broader impacts in the professional development and educational arenas. Professionally, the students and postdoctoral researcher involved in this project will benefit from experimental design training, the acquisition of technical expertise and interdisciplinary communication. In addition, the project will conduct a robust internship program for outstanding students from Delaware State University (DSU), an 1890 Historically Black University, and Delaware Technical & Community College (DTCC), a two-year institution with substantial numbers of first-generation college and minority students. The "Field to Lab" program will involve training in agricultural sampling, gene expression, metabolic profiling studies and bioinformatics.