Plant reproduction is essential to many key features of the biosphere. It is becoming evident that plants optimize most of their biological processes by recruiting specific microbes in different organs. The microbes contribute to plant reproduction but also improve the health of pollinators. Such findings led to the proposal that the genome of microbes and their host genome form a single entity, the hologenome, upon which evolutionary forces can act. The mechanisms by which the hologenome evolve in response to new selective pressures is, however, not fully understood. This project exploits a common transition in plant evolution, the transition from pollinator-mediated reproduction (outcrosser) to self-fertilization (selfer), to study the evolution of the hologenome, and its contribution to the optimization of plant reproductive strategies with implications for enhanced crop production. This interdisciplinary project will leverage plant genetics, and microbiomics to (1) identify the microbes co-evolving with the plant mating system, (2) isolate beneficial microbes for plants and their pollinators and (3) select plant genotypes that promote the presence of beneficial floral microbes. We will characterize the community structure of microbes associated with the selfing/outcrossing genotypes in the wild species Capsella. These outcrosser and selfer species were grown in the experimental field at SLU in Uppsala. Root, leaf and flower associated microbes were collected from each mating type for each species and analysed by microbiomics using host associated microbes PCR. In this method, host (gene in unique copy) and microbial genetic markers (16S rRNA for bacteria; internal transcribed spacer for fungi and oomycetes, and cytochrome oxidase I for insects) are co-amplified in a non staturating PCR before resequencing. As a result, microbial abundances will be normalized to the host DNA content allowing not only to determine microbial community structure but also to assess quantitative difference in the presence of microbes. This study will provide methods and recommendations for the design of sustainable ecosystems by promoting beneficial microbes for plants and their pollinators. It will help to face the challenges caused by global change and its consequences for biodiversity and food production.