A Systems Analysis of Plant Growth Promotion by the Rhizosphere Microbiome

土壤微生物群落在很大程度上代表着作物增产的未开发来源。与土壤中没有微生物生长的植物相比，当植物生长时土壤微生物数量充足时，产量可能会增加一倍。微生物可以通过使土壤中的氮更容易被植物利用来促进植物的生长。从植物生长和最终产量的角度来看，氮是重要的，因为它是一种酶Rubisco的关键成分，Rubisco从空气中吸收二氧化碳，并通过光合作用将其转化为糖以供生长。为了确定微生物是如何促进植物生长的，目前的研究包括：1.微生物如何改变土壤化学；2.哪些植物基因被选择性地激活以响应微生物的存在；3.植物的光合作用等过程如何对微生物做出反应；以及4.土壤微生物的身份和功能是什么。将这四组数据的结果联系起来，将揭示从土壤到整个植物水平，是什么促进了植物的生长。这项研究还包括当土壤中添加不同数量的氮素时，预测植物生长和产量的方法，这将有助于减少化肥的使用。正在研究的植物是Brassica Rapa，它作为根(萝卜)、叶(卷心菜、白菜)和油籽(油菜籽)作物在世界各地种植；由于这种作物的不同用途，来自该物种的结果预计将适用于广泛的其他作物。土壤微生物是生态系统的重要组成部分，将植物与自然环境联系起来。虽然人们对自然和农业环境中的植物了解很多，但对有益土壤微生物的分布、类型和功能，以及它们如何帮助作物应对干旱或缺氮等恶劣生长条件的了解较少。目前的研究填补了这些知识空白，并将就如何管理土壤中有益微生物提供建议。对这项工作的更广泛影响包括在威廉姆斯音乐学院、地质博物馆和怀俄明大学贝里生物多样性中心开发导游，以及与进化和作物驯化研究相关的教学模块。土壤微生物为一系列生态系统服务，在包括氮素限制在内的应激非生物条件下促进植物生长。然而，土壤微生物群落在很大程度上代表着作物品种产量提高的未开发来源。分析植物对分类和功能不同的土壤微生物群的转录和生理反应将有助于深入了解微生物促进植物生长的机制。此外，对植物对土壤微生物环境的转录、水力和气体交换响应的贝叶斯系统建模可以提供对不同氮素改良剂下微生物促进植物生长的预测性理解。在土壤微生物群落完整和减少的情况下，白菜作物的气体交换增强，生物量积累增加两倍，这表明植物对土壤微生物的转录反应与最终的植物生物量积累之间存在生理联系。由于油菜被驯化为根、叶和油籽作物，因此该物种特有的促进生长的机制可以转化为一系列其他作物。此外，与油菜根际相关的微生物群与距离根较远的散装土壤的微生物群高度不同，这表明该物种是研究有益的植物相关土壤微生物的组装动力学、身份和功能的有效模型。利用下一代根际DNA扩增子和亚基因组测序，结合植物基因组学、转录组和生理学实验，本研究将表征土壤微生物促进植物生长的机制，并测试预测系统模型。这项研究针对的是PGRP 2014年的重点领域：在作物基因和生理功能之间建立基因组水平的联系，并从基因组到系统水平理解植物与环境的相互作用，特别是关于非生物胁迫。对这项工作的更广泛影响包括开发与作物驯化和改良有关的导游和教学模块，以及制定有益微生物的管理做法。有关该项目的信息，请访问www.RhizoBiomics.org。

Soil microbial communities represent a largely untapped source for yield improvement in crops. In comparison to plants grown without microbes in the soil, yields can be twice as great when plants are grown with their full complement of soil microbes. Microbes may improve plant growth by making soil nitrogen more available to plants. From the point of view of plant growth and eventual yield, nitrogen is important as it is a critical component of one enzyme, Rubisco, which takes carbon dioxide from the air and converts it to sugars for growth through the process of photosynthesis. To identify how microbes improve plant growth, the current research examines 1. how microbes modify soil chemistry, 2. what plant genes are selectively turned on in response to the presence of microbes, 3. how plant processes like photosynthesis respond to microbes, and 4. what the identity and functions are of the soil microbes. Connecting results from these four sets of data will reveal what it is that promotes plant growth, from the soil to the whole-plant level. This research also includes ways to predict plant growth and yield in response to soil microbes when different amounts of nitrogen are added to the soil, which should enable reduced use of fertilizers. The plant being studied is Brassica rapa, which is grown around the world as root (turnip), leaf (cabbage, pak choi), and oilseed (canola) crops; because of the diverse uses of this crop, results from this species are expected to apply to a wide range of other crops. Soil microbes are an important part of the ecosystem, and connect plants to the physical environment. While much is known about the plants in natural and agricultural settings, less is known about the distributions, types, and functions of beneficial soil microbes, and how they help crops cope with poor growing conditions such as drought or lack of nitrogen. The current research fills these knowledge gaps, and will provide recommendations on how to manage soils for beneficial microbes. Broader impacts to this work include development of guided tours within the Williams Conservatory, Geology Museum, and Berry Center for Biodiversity at the University of Wyoming as well as teaching modules related to the study of evolution and crop domestication. Soil microorganisms serve a range of ecosystem services that promote plant growth under stressful abiotic conditions, including nitrogen limitation. Yet, soil microbial communities represent a largely untapped source for yield improvement in crop species. Analyzing plant transcriptomic and physiological responses to taxonomically and functionally diverse soil microbiomes will provide insights as to the mechanisms by which microbes enhance plant growth. Further, Bayesian systems modeling of plant transcriptomic, hydraulic, and gas-exchange responses to the soil microbial environment can provide a predictive understanding of plant growth promotion by microbes under variable nitrogen amendments. When grown with an intact vs. reduced soil microbiome, crops of Brassica rapa upregulate gas-exchange and increase biomass accumulation up to two-fold, suggesting one physiological link between plant transcriptomic responses to soil microbes and eventual plant biomass accumulation. Because B. rapa is domesticated as root, leaf, and oilseed crops, mechanisms of growth promotion characterized in this species could translate to a range of other crops. Further, the microbiome associated with the rhizosphere of B. rapa is highly differentiated from that of bulk soils more distant from the roots, suggesting the species is an effective model for studying the assembly dynamics, identity, and function of beneficial plant-associated soil microbes. Using next-generation amplicon and metagenome sequencing of rhizosphere DNA in combination with plant genomic, transcriptomic, and physiological experiments, the research will characterize mechanisms of plant growth promotion by soil microbes and test predictive systems models. The research addresses the PGRP 2014 focal areas: to develop a genome-level link between genes and physiological functions in crop plants and to develop a genome to systems-level understanding of plant-environmental interactions, especially with respect to abiotic stress. Broader impacts to this work include development of guided tours and teaching modules related to crop domestication and improvement as well as development of management practices for beneficial microbes. Information on this project can be accessed at www.RhizoBiomics.org.