Genomics of Host-Microbiome Interactions in Rice

PI: Venkatesan Sundaresan（加州大学戴维斯分校）合作者：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（阿肯色大学松布夫分校）植物生长与被称为微生物群的大型微生物群落密切相关，微生物群影响土壤中营养成分和营养物质的吸收，以及疾病易感性。在了解人类微生物组对健康的影响方面取得的重大进展是由于使用非生物动物系统，在该系统中，无菌动物暴露于特定的微生物组以研究其影响。研究植物微生物组功能的非生物系统更难实施，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植物共生系统，其中可以移植来自不同来源或条件的与根相关的微生物组，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。了解寄主植物与其微生物群的相互作用，以及对作物性能和产量的后续影响，为利用植物与微生物之间的联系进行作物改良提供了可能。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甲烷微生物的生长，贡献了近一半的温室气体排放。该项目将研究不同水稻品种对产生甲烷的微生物的影响，以及在水稻根系相关微生物群中发现的消耗甲烷的微生物。这些发现可能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。除了培养学生和博士后助理，该项目还将为阿肯色大学派恩布拉夫分校（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关联对作物水稻（Oryza sativa）的影响。初步数据表明，土壤类型、栽培方式和干旱等环境因素可调节水稻根系微生物组，表明微生物组的变化是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用来建立一个非生物水稻模型，这样在受控条件下生长的植物可以获得一个确定的微生物组。本项目将对用于移植的微生物组进行16SrDNA测序，鉴定其组成类群，并利用RNAseq对处理水稻植株的转录组进行研究。研究人员将分析不同来源的微生物组移植后水稻植株的转录反应，以及干旱胁迫等胁迫处理下基因表达的全球变化，以及可能反映植物在微生物组诱导下适应性反应的特定功能基因类别。最后，将调查古细菌与栽培水稻的关系，这是对全球甲烷排放的重要贡献，并可能对气候变化产生影响。具体来说，基因型对产甲烷古菌和甲烷营养细菌的影响，以及在田间种植水稻中计算鉴定的相关微生物网络，将被表征，以实现培育低排放水稻的目标。该项目生成的植物转录组学和微生物序列数据将分别通过NCBI基因表达Omnibus （GEO）和sequence Read Archive （SRA）等公共数据库发布。

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.