A Systems Analysis of Plant Growth Promotion by the Rhizosphere Microbiome

土壤微生物群落代表了作物产量提高的一个很大程度上尚未开发的来源。与土壤中没有微生物生长的植物相比，当植物在土壤微生物的充分补充下生长时，产量可以增加一倍。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生长所需的糖。为了确定微生物如何改善植物生长，目前的研究检查了1。微生物如何改变土壤化学，2。什么样的植物基因被选择性地打开，以响应微生物的存在，3。光合作用等植物过程如何对微生物作出反应，以及4.土壤微生物的身份和功能。这四组数据的连接结果将揭示从土壤到整株植物水平促进植物生长的原因。这项研究还包括当向土壤中添加不同量的氮时，预测植物生长和产量对土壤微生物的反应的方法，这应该能够减少肥料的使用。正在研究的植物是芜菁，它在世界各地作为根（芜菁），叶（卷心菜，白菜）和油籽（油菜）作物种植;由于这种作物的多种用途，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，并将植物与物理环境联系起来。虽然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科普干旱或缺乏氮等不良生长条件知之甚少。目前的研究填补了这些知识空白，并将为如何管理有益微生物的土壤提供建议。对这项工作的更广泛影响包括在怀俄明州大学的威廉姆斯温室、地质博物馆和贝瑞生物多样性中心内开发导游图尔斯，以及与进化和作物驯化研究有关的教学模块。土壤微生物提供一系列生态系统服务，促进植物在非生物胁迫条件下的生长，包括氮限制。然而，土壤微生物群落代表了一个很大程度上尚未开发的来源，提高作物品种的产量。分析植物转录组和生理反应的分类和功能多样的土壤微生物组将提供见解的机制，微生物促进植物生长。此外，贝叶斯系统模拟植物转录组，水力和气体交换对土壤微生物环境的反应，可以提供一个预测性的理解植物生长促进微生物在可变的氮修正案。当在完整的土壤微生物组与减少的土壤微生物组中生长时，芜菁作物上调气体交换并使生物量积累增加高达两倍，这表明植物对土壤微生物的转录组反应与最终的植物生物量积累之间存在一种生理联系。因为B。芜菁被驯化为根、叶和油籽作物，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B根际相关的微生物组。芜菁是高度分化的，从散装土壤更远离根，这表明该物种是一个有效的模式，用于研究组装动力学，身份和功能的有益植物相关的土壤微生物。利用下一代扩增子和根际DNA宏基因组测序，结合植物基因组学、转录组学和生理学实验，该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。该研究涉及PGRP 2014的重点领域：开发作物基因和生理功能之间的基因组水平联系，并开发植物与环境相互作用的系统水平理解的基因组，特别是在非生物胁迫方面。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图尔斯和教学模块，以及开发有益微生物的管理做法。有关该项目的信息可在www.RendezBiomics.org上查阅。

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.