One of the greatest challenges in current plant science is to understand the diversity and dynamics of plant-living microbes. From which sources are the plants colonized? Which mechanisms determine the structure of microbial communities? What causes differences in microbiomes between plant organs, genotypes and species, and between different environments? Recent studies on microbial communities of the model species Arabidopsis thaliana have discovered a small subgroup of so-called 'hub' microbes, which are highly interconnected and have a major impact on microbial structure and diversity. These studies have also shown that the hub species are important for the links between host genotype, environment and microbiome. Nevertheless, our understanding of the origin and stability of this nuclear microbiome, and its variability in natural plant populations, is still very limited.

To fill these knowledge gaps, we need more studies on different plant species that are widely distributed and naturally occurring under different environmental conditions, and we also need to study these plant species in situ. Here we propose a project with the widely distributed legume Lotus corniculatus, which is an important element of Central European grasslands. For our project we will use the research platform of the Biodiversity Exploratories, where L. corniculatus populations occur on different soils and under different land use intensities. The unique metadata of this platform will allow us to include different environmental influences in our analyses of microbial networks of L. corniculatus rhizospheres, shoots, flowers and seeds, thus separating different factors of natural microbial variation.

A special focus will be on the two basic modes of microbial transmission: vertical transmission by seeds, and horizontal transmission by pollinators and other vectors, or by similar environmental conditions. We will also relate our microbial analyses to the fitness and genotype of the plants. Our project will combine large-scale field studies with modern analyses of microbial networks and a series of controlled experiments, thus providing an exceptionally comprehensive study of plant-living microbes in an ecological context.

The DECRyPT Core project forms part of the DFG priority programme: Deconstuction and Reconstruction of the Plant Microbiota, DECRyPT

The central scientific objectives of this priority programme (SPP) are to obtain deep and potentially predictive insights into plant-microbiota associations and to develop pioneering reductionist approaches towards a molecular understanding of plant microbiota functions. This SPP will elucidate genetic factors underlying plant microbiota establishment, test presumed community adaptation in ecological contexts and define community-associated emergent properties.