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

• Applicant: Professorin Dr. Barbara Reinhold-Hurek
• Subject Area: Plant Cultivation, Plant Nutrition, Agricultural Technology
• Term: from 2014 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 253028022

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.

• DFG Programme: Research Grants