Unraveling rice - endophyte interactions: Genome-wide analyses of the endophytic lifestyle of the diazotroph Azoarcus sp. strain BH72

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Global climate change and increasing costs of fossil fuels demand worldwide a more sustainable use of resources in agriculture and foster the development of cropping systems requiring least possible petrochemical input. Endophytic bacteria reside within the living tissue of a plant without substantively harming it. Endophytic associations between beneficial bacteria and plants are of high interest for agro-biotechnological applications, e.g. for improvement of plant growth and health, or even as biofertilizer. Especially the supply of atmospheric N2 to cereal crops is an agronomically and ecologically important potential of N2-fixing grass endophytes. However, a deeper understanding of how endophytes interact with their host plants is required. Surveys of microbial communities in different root and soil compartments suggest, that the endophytic root community requires numerous bacterial adaptations, is more specialized and less diverse that rhizoplane or rhizosphere soil microbiomes. Together with knowledge on bacterial functions, it can be assumed that it is an active process for bacteria to establish themselves inside the roots. 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 in high numbers inside tissues.One of the best-studied model systems at the molecular level for bacterial endophytes and monocotyledonous plants is the Azoarcus sp. strain BH72 - rice interaction. Azoarcus sp. strain BH72 is a nitrogen-fixing endophyte of grasses such as Kallar grass and can contribute fixed nitrogen to its host. Also rice roots are colonized well. Since genome sequences of both partners, Oryza sativa (rice) and Azoarcus sp. strain BH72 are available, both organisms provide an excellent model system for functional genomic analyses to unravel initial interaction processes. Based on the global transcriptomic approach of the previous project phase, we aim to further identify bacterial characteristics that play a role in colonization and physiologically successful interaction with rice, and thus to unravel mechanisms of the endophytic lifestyle. Using cutting-edge technology, new foci will be on antisense RNA and newly developed approaches for single bacterial cell gene expression quantification in planta.