Genomics of Host-Microbiome Interactions in Rice

主要研究者：Venkatesan Sundaresan（University of California-Davis）CoPI：Jonathan Bucken and大卫麦吉尔（University of California-Davis），and Merle Anders（University of Arkansas-Fayetteville）合作者：James Garner（University of Arkansas-Pine海崖）植物生长与被称为微生物组的大型微生物群落密切相关，微生物组影响土壤中的营养成分和营养吸收，以及疾病易感性。在理解人类微生物组对健康影响方面的重大进展来自于使用无菌动物系统，其中无菌动物暴露于确定的微生物组以研究其影响。研究植物中微生物组功能的Gnotobiotic系统更难实施，因为植物微生物组是内部和外部（例如土壤）成分的组合。 该项目将使用为水稻植物开发的gnotobiotic系统，其中可以移植来自不同来源或条件的根相关微生物组，并在受控条件下生长的植物中建立。 该项目将能够在分子水平上发现植物微生物组的特定功能，并评估微生物组对植物性能的影响。 了解宿主植物与其微生物组的相互作用，以及随后对作物性能和产量的影响，为利用植物-微生物协会进行未来作物改良提供了可能性。该项目的第二个目标是解决农业是全球排放强效温室气体甲烷的主要来源这一问题。据估计，全球水稻种植通过促进产生甲烷的微生物的生长而贡献了近一半的排放量。该项目将研究不同水稻品种对甲烷产生微生物的影响，以及在水稻根相关微生物组中发现的甲烷消耗微生物。 这些发现可以导致减少稻田甲烷排放的策略，并减少水稻种植对气候变化的影响。除了对学生和博士后进行培训外，该项目还将为阿肯色大学派恩海崖分校（一所历史悠久的黑人大学）的部分本科生提供暑期研究实习机会。该项目将使用基因组方法来了解微生物协会对作物水稻（Oryza sativa）的影响。初步数据显示，土壤种植水稻植物的根微生物组受到几种环境因素的调节，包括土壤类型，栽培实践和干旱，这表明微生物组的变化构成了植物适应环境的一部分。水稻对半水生基质的生长偏好已经被利用来建立一个无菌水稻模型，使得在受控条件下生长的植物可以获得确定的微生物组。 在该项目中，用于移植的微生物组将通过16 SrDNA测序来鉴定组成分类群，并将使用RNAseq研究经处理的水稻植物的转录组。 将分析具有来自不同来源的移植微生物组和包括干旱胁迫在内的胁迫处理的gnotobiotic水稻植物的转录反应，以了解基因表达的全球变化，以及可能反映微生物组诱导的植物适应性反应的特定功能基因类别。最后，将研究古细菌与栽培水稻的关系，这是对全球甲烷排放的重大贡献，并可能导致气候变化。 具体而言，基因型对产甲烷古菌和甲烷氧化细菌的影响，以及计算确定的相关微生物网络在田间种植的水稻，将其特征在于，朝着培育低排放水稻的目标。该项目产生的植物转录组和微生物序列数据将通过公共数据库发布，包括NCBI基因表达综合数据库（GEO）和序列读取档案（SRA）。

PI: Venkatesan Sundaresan (University of California-Davis)CoPIs: Jonathan Eisen and David Mackill (University of California-Davis), and Merle Anders (University of Arkansas-Fayetteville)Collaborator: James Garner (University of Arkansas-Pine Bluff)Plants grow in close association with large communities of microbes called microbiomes, that influence nutrient composition and uptake of nutrients in the soil, as well as disease susceptibility. Major advances in understanding the health effects of human microbiomes have resulted from using gnotobiotic animal systems, in which germ-free animals are exposed to defined microbiomes to study their effects. Gnotobiotic systems to study microbiome function in plants are harder to implement because plant microbiomes are a combination of internal and external (e.g. soil) components. This project will use a gnotobiotic system developed for rice plants, in which root-associated microbiomes from different sources or conditions can be transplanted, and established in plants grown under controlled conditions. The project will enable the discovery of specific functions of plant microbiomes at the molecular level, and the evaluation of the impact of microbiomes on plant performance. Understanding the interactions of the host plant with its microbiome, and subsequent effects on crop performance and yields, provides possibilities for exploiting plant-microbe associations for future crop improvement. A second aim of the project addresses the concern that agriculture is a major source of global emissions of the potent greenhouse gas methane. Rice cultivation worldwide is estimated to contribute nearly half of these emissions by promoting the growth of methane producing microbes. The project will examine the effects of different rice varieties on methane producing microbes, as well as methane consuming microbes, found in rice root-associated microbiomes. The findings can lead to strategies for reducing methane emissions from paddy fields, and reduce the impacts of rice cultivation on climate change. In addition to the training of students and postdoctoral associates, the project will provide summer research internships for selected undergraduate students from University of Arkansas-Pine Bluff, a Historically Black University.The project will use genomic approaches to understand the impact of microbial associations on the crop plant rice (Oryza sativa). Preliminary data show that root microbiomes of soil grown rice plants are modulated by several environmental factors, including soil type, cultivation practice and drought, suggesting that changes to microbiomes constitute part of the plant adaptation to the environment. The growth preference of rice for semi-aquatic substrates has been exploited to establish a gnotobiotic rice model, such that plants grown under controlled conditions can acquire a defined microbiome. In this project, microbiomes used for transplantation will be characterized by 16SrDNA sequencing to identify the constituent taxa, and the transcriptomes of the treated rice plants will be studied using RNAseq. The transcriptional responses of gnotobiotic rice plants with transplanted microbiomes from different sources and stress treatments, including drought stress, will be analyzed for global changes in gene expression, as well as specific functional classes of genes that might reflect adaptive responses by the plant induced by the microbiome. Lastly, the association of archaea with cultivated rice, a significant contribution to planetary methane emissions, and potentially to climate change, will be investigated. Specifically, the effects of genotype on methanogenic archaea and methanotrophic bacteria, as well as computationally identified associated microbial networks in field grown rice, will be characterized, towards the goal of breeding low emission rice. Plant transcriptomic and microbial sequence data generated by the project will be released through public databases that include the NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA), respectively.