Plant microbiome manipulation: nitrogen as the key currency

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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.