The Effect of the Microbiome on the Rice Transcriptome

PI: Harsh P. Bais（特拉华大学）合作者：Venkatesan Sundaresan和Jonathan A. Eisen（加州大学戴维斯分校）合作者：Venu Kalavacharla（特拉华州立大学）和Gurdev Khush（加州大学戴维斯分校）植物生长与被称为微生物组的大型微生物群落密切相关。相对而言，我们对与植物有关的微生物的多样性及其相互作用和对生产性能和作物产量的影响知之甚少。特定的微生物已经被广泛地记录下来，为植物提供有益的影响，例如那些涉及众所周知的豆科植物共生关系的微生物。先前的研究利用模式植物拟南芥中的单一有益细菌物种，证明了植物如何在生物胁迫下积极招募有益细菌。虽然从单一微生物物种的研究中可以获得有价值的见解，但初步研究表明，与田间种植的水稻（Oryza sativa）植物相关的细菌物种具有广泛的多样性，其生物学意义是完全未知的。该项目将利用基因组学和宏基因组学相结合的方法来分析微生物对水稻的影响。具体来说，将建立一个受控的实验系统，其中微生物种群将通过宏基因组rRNA分析来表征，植物的反应将通过转录组分析来表征。将分析局部和整个植物反应的表达谱，以了解基因表达的全球变化，以及反映营养可利用性变化或植物免疫建立的特定功能类基因表达的变化。本研究将为进一步研究微生物组对植物生产性能的影响奠定基础。在这个项目中产生的所有序列和制图数据都可以通过一个专门为这个项目开发的基因组浏览器访问。所有序列数据将保存在GenBank、GreenGenes （http://greengenes.lbl.gov）、Gene Expression Omnibus （GEO）数据库（www.ncbi.nlm.nih.gov/geo/）和NCBI的Short Read Archive （SRA; http://www.ncbi.nlm.nih.gov/Traces/home/）中进行长期传播。这个项目更广泛的影响，部分源于研究的跨学科性质。对学生和博士后的培训将把定量方法与实验生物学的应用结合起来。该计划也将对专业发展和教育领域产生更广泛的影响。在专业方面，参与该项目的学生和博士后研究员将受益于实验设计培训、技术专长的获取和跨学科的交流。此外，该项目还将为特拉华州立大学（DSU）和特拉华州技术与社区学院（DTCC）的优秀学生提供一个强有力的实习计划。特拉华州立大学是一所1890年历史上的黑人大学，特拉华州技术与社区学院是一所两年制大学，拥有大量第一代大学生和少数族裔学生。“从田间到实验室”项目将包括农业取样、基因表达、代谢分析研究和生物信息学方面的培训。

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.