Abstract: Plants are colonized by a wide range of microbes that together constitute the plant microbiome. These plant-inhabiting microbes have been found to affect plant growth and nutrient uptake, environmental stress tolerance, as well as protection against pathogens. However, in spite of all progress, the complexity of plant microbiomes, and the intrinsic and extrinsic factor that shape its diversity and composition, remain poorly understood. Here, we studied natural microbiome variation in the common legume Lotus corniculatus. We collected Lotus plants in seven natural grassland populations in Southern Germany, across four consecutive years. To be able to test for potential influences of plant age and plant genotype, we genotyped all plants using ddRAD, and we determined their ages through herb chronology, i.e. counting annual growth rings in the hypocotyl of plants. Furthermore, to understand organ specificity of microbiomes, we separately sequenced the microbiome (bacteria, fungi and oomycetes) of roots, shoots, flowers and seeds. We found that, plant organs harbored distinct microbiomes, and that microbiome diversity generally decreased from root to shoot to flowers to seeds. The root microbiome has the greatest overlap with the soil microbiome, whereas the microbiomes of aboveground plant organs were generally more related – in particular with regard to bacteria of the genera Pseudomonas, Pantoea and Ralstonia - and also more differentiated between plant individuals and populations. A network analysis confirmed the reciprocal influences of aboveground plant organs. In addition to the organ specificity, the sampling year influenced the microbiome composition in the aboveground microbial communities of shoots, flowers, and seeds, and less in the roots, but the root microbiome was more influenced by the sampling site. This shows that the root microbiome is more stable than the microbiome of the aboveground plant tissue, which is exposed to more disturbances in the sampling sites. The analyses of plant age and genotype effects are currently ongoing, and the results of the full analysis will be presented at the conference.
