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

全球气候变化和不断增加的化石燃料成本要求全世界在农业中更可持续地利用资源，并促进需要尽可能少的石化投入的种植系统的发展。内生细菌存在于植物的活组织中，对其没有实质性的伤害。有益细菌和植物之间的内生联系对农业生物技术应用具有很高的兴趣，例如改善植物生长和健康，甚至作为生物肥料。特别是对谷类作物的大气氮供应是固氮草内生菌在农艺学和生态学上的重要潜力。然而，内生菌如何与寄主植物相互作用的深入了解是必要的。对不同根区和土壤区室微生物群落的调查表明，内生根群落需要许多细菌适应，比根面或根际土壤微生物群落更专门化，多样性更低。结合对细菌功能的了解，可以假设细菌在根内扎根是一个活跃的过程。由于植物细胞通常可以通过植物的先天免疫调节的防御反应来检测细菌分子成分（MAMPs）并作出反应，因此内生菌能够在组织内大量建立令人困惑。在分子水平上对细菌内生菌和单子叶植物研究得最好的模式系统之一是Azoarcus sp.菌株BH72 -水稻相互作用。偶氮菌（Azoarcus sp.） BH72是禾草（Kallar grass）的固氮内生菌，可为寄主提供固氮。水稻的根也能很好地定植。由于水稻和偶氮稻属BH72菌株的基因组序列都是可用的，这两种生物都为功能基因组分析提供了一个很好的模型系统，以揭示最初的相互作用过程。基于上一个项目阶段的全球转录组学方法，我们的目标是进一步确定在定植和与水稻生理成功相互作用中发挥作用的细菌特征，从而揭示内生生活方式的机制。利用尖端技术，新的焦点将放在反义RNA和植物中单细胞基因表达定量的新方法上。

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.