RISE: Rice plants shaping their microbiome: Rice as host for endophytic diazotrophs

根部是陆地植物与微生物相互作用的主要场所。由于它们之间的相互依存关系，植物及其微生物群可以被认为是与肠道微生物群具有相似功能的超有机物质，以促进健康和营养吸收。然而，目前对根际有益细菌复杂相互作用的了解仍处于初级阶段。植物如何塑造这个重要的微生物群的研究才刚刚开始。根据不同的植物基因型，它们如何作为根群落的过滤器？因此，在一种简化论的方法中，将开展分析寄主植物突变的影响的研究，以更好地了解植物与微生物的相互作用，并最终在可持续农业中改善植物的健康、营养和产量。在根和根际微生物中，尤其是与寄主植物密切相互作用的内生细菌，如固氮菌(Azoarcus sp.)BH72，它驻留在活组织中。另一方面，由于植物细胞通常可以通过植物的天然免疫调节防御反应来检测细菌分子成分(MAMP)并对其做出反应，内生菌能否在组织内建立起来是令人费解的。在这个项目中，将分析固氮藻与水稻的相互作用，这可能是迄今为止在细菌分子相互作用机制方面研究得最好的细菌内生模型之一。通过这种方式，将获得关于世界上最重要的主食之一的植物-微生物相互作用的重要信息，它也是植物分子生物学中最先进的模式作物之一。我们将在这个项目中解决几个问题。内生定植对水稻基因表达有何影响？当内生菌侵染程度不同时，水稻根系反应的调节方式是否存在差异？水稻感染后基因表达的变化是否与代谢反应相关？当细菌病原体定植在根上时，植物的反应有什么不同？水稻的防御反应和激素途径如何影响内生菌的建立？这方面将在我们的实验室水稻-固氮菌模型系统中阐明，在那里我们将分析不同突变水稻品系的组织内细菌的建立。我们的研究还将确定内生菌特定的水稻候选基因，用于未来对与内生菌相互作用所需的植物因子的反向遗传方法。

The primary site of land plants for interactions with microbes are roots. Due to their interdependence, plants and their microbiomes can be considered as "superorganims" with similar functions as the gut microbiome for health and nutrient uptake. However, the current understanding of the complex interactions with beneficial bacteria in the rhizosphere is still in its infancy. Investigations have just begun how plants shape this important microbiome. How do they act as filters for root communities depending on the plant genotype? Thus, in a reductionist approach, studies analyzing the impact of mutations of the host plant will be undertaken to better understand plant-microbe interactions and ultimately to improve plant health, nutrition and yields in sustainable agriculture. Among the root and rhizosphere microbes, particularly tight interactions with the host plant can be expected from endophytic bacteria such as Azoarcus sp. BH72, which reside within the living tissue. On the other hand, as plant cells can commonly detect and react to bacterial molecular components (MAMPs) by the plant's innate immunity-regulated defense responses, it is puzzling that endophytes can establish inside tissues. In this project, the Azoarcus-rice interaction will be analyzed which is probably one of the best-studied bacterial endophyte models to date with respect to bacterial molecular interaction mechanisms. In this way, vital information on plant-microbe interactions for one of the worldwide most important staple foods will be obtained, which is also one of the most advanced model crops in plant molecular biology. We will address several questions in this project. How is gene expression in rice affected by endophytic colonization? Are there differences in the modulation of the rice root response when the degree of colonization by endophytes differs? Are rice gene expression changes upon infection correlated with metabolic responses? How does the plant reaction differ when bacterial pathogens colonize the root? How do rice defense responses and hormonal pathways affect establishment of endophytes? This aspect will be elucidated in our laboratory rice-Azoarcus model system, where we will analyze establishment of the bacteria inside tissue for different mutant rice lines. Our studies will also identify endophyte-specific rice candidate genes for future reverse genetic approaches on plant factors required for interactions with endophytes.