Genomics of Host-Microbiome Interactions in Rice

Pi：Venkatesan Sundaresan(加州大学戴维斯分校)Copis：Jonathan Eisen和David Mackill(加州大学戴维斯分校)和Merle Anders(阿肯色大学费耶特维尔分校)合作者：James Garner(阿肯色州大学松林分校)植物与被称为微生物群落的大型微生物群落密切相关，微生物群落影响土壤中的营养成分和养分吸收以及疾病易感性。在理解人类微生物群对健康的影响方面取得了重大进展，这是由于使用了灵知菌动物系统，在这种系统中，无菌动物暴露在定义的微生物群中，以研究它们的影响。由于植物微生物群是内部和外部(例如土壤)成分的组合，因此研究植物微生物群功能的灵生系统更难实现。该项目将使用为水稻植株开发的共生系统，在该系统中，来自不同来源或条件的根相关微生物可以被移植，并在受控条件下生长的植株中建立。该项目将能够在分子水平上发现植物微生物群的特定功能，并评估微生物群对植物性能的影响。了解寄主植物与其微生物群的相互作用，以及随后对作物表现和产量的影响，为利用植物与微生物之间的关系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人们的担忧，即农业是全球温室气体甲烷排放的主要来源。据估计，全世界的水稻种植通过促进产生甲烷的微生物的生长，贡献了近一半的排放。该项目将研究不同水稻品种对水稻根部相关微生物群中甲烷产生微生物和甲烷消耗微生物的影响。这些发现可能会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。除了培训学生和博士后，该项目还将为历史悠久的黑人大学阿肯色州大学松布拉夫分校的本科生提供暑期研究实习机会。该项目将使用基因组学方法来了解微生物协会对作物水稻(Oryza Sativa)的影响。初步数据表明，土壤种植的水稻根部微生物群落受到土壤类型、栽培措施和干旱等多种环境因素的调节，这表明微生物群落的变化是植物对环境适应的一部分。利用水稻对半水生基质的生长偏好，建立了一种灵生水稻模型，使在可控条件下生长的植物可以获得特定的微生物群。在这个项目中，用于移植的微生物群将通过16SrDNA测序来鉴定组成类群，并将使用RNAseq研究处理后的水稻植株的转录本。将分析来自不同来源和胁迫处理(包括干旱胁迫)的共生水稻植株的转录反应，以寻找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反应的特定功能类别的基因。最后，将调查古生菌与栽培水稻的关系，这是对全球甲烷排放的重大贡献，并可能对气候变化产生影响。具体地说，基因对产甲烷古生菌和甲烷营养细菌的影响，以及在大田种植的水稻中通过计算机识别的相关微生物网络，将朝着培育低排放水稻的目标进行表征。该项目产生的植物转录和微生物序列数据将通过公共数据库发布，其中分别包括NCBI基因表达总览(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.