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

陆地植物与微生物相互作用的主要场所是根。由于它们的相互依赖性，植物及其微生物组可以被认为是“超级有机体”，具有与肠道微生物组相似的健康和营养吸收功能。然而，目前对根际有益细菌的复杂相互作用的理解仍处于起步阶段。植物如何塑造这种重要的微生物组的研究刚刚开始。它们如何根据植物基因型作为根系群落的过滤器？因此，在还原论的方法中，将进行分析宿主植物突变影响的研究，以更好地了解植物-微生物相互作用，并最终改善植物健康，营养和可持续农业的产量。在根和根际微生物中，与宿主植物的特别紧密的相互作用可以预期来自内生细菌，如固氮菌属BH 72，其存在于活组织内。另一方面，由于植物细胞通常可以通过植物的先天免疫调节防御反应来检测细菌分子组分（MAMPs）并对其做出反应，因此内生菌可以在组织内建立是令人困惑的。在本项目中，Azoarcus-rice相互作用将被分析，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菌模型之一。通过这种方式，将获得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，这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。内生定殖如何影响水稻基因表达？内生真菌定殖程度不同，对水稻根系反应的调节是否存在差异？水稻基因表达的变化是否与代谢反应有关？当细菌病原体定植在根部时，植物的反应有何不同？水稻防御反应和激素途径如何影响内生菌的建立？这方面将阐明在我们的实验室水稻-固氮菌模型系统，在那里我们将分析不同的突变体水稻品系的组织内的细菌的建立。 我们的研究还将确定内生菌特异性水稻候选基因，为未来的反向遗传方法对植物因子所需的相互作用与内生菌。

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.