Genetic control and nutrient-dependency of root-microbe interaction in maize

• Applicant: Dr. Peng Yu
• Subject Area: Plant Cultivation, Plant Nutrition, Agricultural Technology
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 444755415

The rhizosphere is the narrow region of soil that is directly influenced by root secretions and that is associated soil microorganisms known as the root microbiome. The interaction of roots with their microbiome is instrumental for plant health and fitness. Understanding the molecular and genetic basis of these relationships will enable to sustain plants with superior performance on agricultural soils with poor nutrient availability and thus reducing mineral fertilizer application.The project will start with uncovering the complexity of host root interactions with the soil microbes by integration of transcriptome data of the root cortex and stele and rhizosphere microbiome genomic data obtained during root development. To this end a panel of genetically diverse inbred lines with contrasting nitrogen use efficiencies and root mutants with distinct developmental defects of lateral roots and root hairs under different nitrogen conditions in maize will be surveyed. Gene co-expression, microbial co-occurrence/co-abundance and trans-kingdom networks will identify the hub genes interacting with the keystone microbial OTUs (operational taxonomic units). Moreover, metabolic signal transmission from the endosphere to the rhizosphere will be determined by profiling of the metabolome from root exudates. Non-invasive root imaging by MRI (Magnetic Resonance Imaging), dynamics of carbon and nitrogen imaging by PET (Positron Emission Tomography) and NanoSIMS (Nanometer-scale Secondary Ion Mass Spectrometry) will further track the architectural and functional information of the root and its exudates across spatial compartments in the different zones of a single root and among different root types. In addition, spatial patterning of candidate hub genes and keystone microbes will be demonstrated by in situ hybridization and CARD-FISH (catalyzed reporter deposition combined with fluorescence in situ hybridization) experiments. Finally, the hub genes regulating the biosynthesis of secondary metabolites interacting with microbes will be knocked out by genome editing via CRISPR/Cas9 to generate new mutants. In parallel, representative keystone microbial OTUs will be isolated and cultured and derived synthetic communities will be employed to validate their potential roles on gene regulation in maize. In summary, the overall objective of this project is the mechanistic understanding of the function of root and rhizosphere microbes to enhance plant tolerance to nitrogen deficiency. This will pave the way for crop breeding applications and the application of microbial synthetic communities to secure future food production and sustain efficient resource usage in agriculture.

• DFG Programme: Independent Junior Research Groups