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

根际是直接受根分泌物影响的狭窄土壤区域，与之相关的土壤微生物被称为根微生物群。根与其微生物群的相互作用有助于植物的健康和适应性。了解这些关系的分子和遗传基础将使植物在养分有效性差的农业土壤上保持优异的性能，从而减少矿物肥料的施用。该项目将首先通过整合根皮质和茎柱的转录组数据以及根发育过程中获得的根际微生物组基因组数据，揭示寄主根与土壤微生物相互作用的复杂性。为此，我们将对一组氮素利用效率差异较大的玉米遗传多样性自交系和在不同氮素条件下侧根和根毛发育缺陷明显的根突变体进行研究。基因共表达、微生物共发生/共丰度和跨界网络将确定与关键微生物otu（操作分类单位）相互作用的枢纽基因。此外，代谢信号从内圈到根际的传递将通过根渗出物代谢组谱来确定。通过MRI（磁共振成像）、PET（正电子发射断层扫描）和NanoSIMS（纳米级二次离子质谱）进行的无创根成像，将进一步跟踪根的结构和功能信息，以及根在不同区域和不同根类型中跨空间隔间的分泌物。此外，候选枢纽基因和关键微生物的空间模式将通过原位杂交和CARD-FISH（催化报告细胞沉积结合荧光原位杂交）实验来证明。最后，通过CRISPR/Cas9进行基因组编辑，敲除与微生物相互作用的调节次生代谢物生物合成的枢纽基因，产生新的突变体。同时，将分离培养具有代表性的关键微生物otu，并利用合成群落验证其在玉米基因调控中的潜在作用。综上所述，本项目的总体目标是了解根系和根际微生物在提高植物抗缺氮能力方面的作用机制。这将为作物育种应用和微生物合成群落的应用铺平道路，以确保未来的粮食生产和维持农业资源的有效利用。

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.