Plant microbiome manipulation: nitrogen as the key currency

氮的有效性是限制陆地生态系统生长的主要因素。不加区别地使用氮肥是绿色革命带来的产量提高的核心。然而，氮肥施肥现在是农业面临的环境和经济问题的前沿。鉴于其限制性的性质，我假设N的竞争是调节植物-微生物在土壤-根界面的相互作用的一个中心机制。我已经收集了初步的数据，表明植物通过在其根际分泌微小RNA（miRNAs）有意抑制细菌的氨基酸通透酶基因表达。这将导致土壤氨基酸库的大部分被路由到植物。此外，我已经表明，氨氧化剂在决定小麦产量和谷物品质方面发挥着关键作用，远远超过施肥量。氨氧化菌是将氨转化为硝酸盐的细菌和古细菌，以产生用于固定二氧化碳的能量（化学合成）。因此，它们完全独立于植物提供的碳，但它们需要来自肥料或有机氮降解的氨来满足其能量需求。与此同时，氨在能量上比硝酸盐更有利于植物生长，使植物和氨氧化剂的需求齐头并进。我的研究计划旨在1）理解和展示氮在植物-微生物相互作用中的关键作用，无论是有机和无机氮源，2）寻找新的方法来修改植物-微生物相互作用使用氮。更具体地说，我的短期目标是1）确定植物miRNA在根际氮竞争中的作用，2）确定氨基酸在根际氮竞争中的作用，3）通过改变氮竞争来操纵植物微生物组。我的研究计划将提供对植物-微生物相互作用规则的深入了解，从而找到新的方法来塑造植物微生物群，以优化作物产量和质量。创新实验与先进的分子方法相结合，如测序，生物信息学和多元统计学，将为参与我的计划的3名博士生，3名硕士生和10名本科生做好准备，以便在行业，政府或学术界担任核心职位。

Nitrogen (N) availability is the main factor limiting growth in terrestrial ecosystems. Indiscriminate use of nitrogen fertilization was central to the yield boost brought by the Green Revolution. However, N fertilization is now at the forefront of the environmental and economical issues facing agriculture. In view of its limiting nature, I hypothesize that competition for N is a central mechanism regulating plant-microbe interactions at the soil-root interface. I have gathered preliminary data that show that the plant intendedly inhibits the amino acid permease gene expression of bacteria through the secretion of micro RNAs (miRNAs) in its rhizosphere. This would result in a larger part of the soil amino acid pool being routed to the plant. Additionally, I have shown that ammonia-oxidizers have a key role in determining wheat yields and grain quality, much more than the amount of applied fertilizer. Ammonia oxidizers are bacteria and archaea that transform ammonia to nitrate in order to generate energy that they use to fix carbon dioxide (chemosynthesis). As such, they are completely independent from the carbon provided by the plant, but they need ammonia from fertilizer or from the degradation of organic nitrogen to fulfill their energy requirement. At the same time, ammonia is energetically more favorable for plant growth than nitrate, putting the needs of the plant and of the ammonia-oxidizers head-to-head. My research program aims at 1) understanding and demonstrating the key role of nitrogen in plant-microbe interactions, both for organic and inorganic nitrogen sources, and 2) finding novel ways to modify plant-microbe interactions using nitrogen. More specifically, my short-term objectives are to 1) Determine the role of plant miRNAs in the competition for N in the rhizosphere, 2) Determine the role of amino acids in the competition for N in the rhizosphere and 3) Manipulate the plant microbiome by changing the competition for N. My research program will provide an advanced understanding of the rules governing plant-microbe interactions, leading to novel approaches to shape the plant microbiota toward an optimization of crop yields and quality. The combination of innovative experiments combined with advanced molecular methods such as sequencing, bioinformatics and multivariate statistics will prepare the 3 PhD students, 3 MSc students and 10 undergraduate students involved in my program to take up central positions in the industry, the government or academia.