The Seed Microbiome

The plant microbiome comprising complex communities has shown to play an role for plant growth and health. So far, mostly endophyte communities colonizing roots and stems have been studied. Seeds, however, are also colonized by a small number and diversity of endophytic bacteria, which have been rarely investigated so far. Our hypothesis is that seed endophytes may play a vital role for plant development and adaptation. The aim of this project is to use Setaria viridis as model plant to study the diversity and functioning of seed endophytes. S. viridis is closely related to maize and other important C4 grasses and it has a small genome, which has been recently sequenced. It furthermore can be easily cultivated and S. viridis represents a plant, which occurs naturally in many locations worldwide as it easily adapts to various conditions and has a weedy character. The aim of the proposed work is to study the interaction between soil environment, plant genotype and seed endophyte communities as compared to stem endophyte communities. Seed endophytes are likely to be more conserved across sites and genotypes, whereas stem endophytes mostly derive from the soil environment. We furthermore aim to address transmission routes of endophytes and will explore to which extent seed endophytes are vertically transmitted or derive from the soil or flowers. In regard to colonization genome sequencing of individual closely related strains will be used to identify the features, which are important for colonization of or a life inside seeds. Finally, the role of naturally colonizing seed endophyte communities on plant growth, development, adaptation and competition will be addressed.

The plant microbiome comprising complex communities has shown to play a role for plant growth and health. So far, mostly endophyte communities colonizing roots and stems have been studied. Seeds, however, are also colonized by a small number and diversity of endophytic bacteria, which have been rarely investigated so far. Our hypothesis is that seed endophytes may play a vital role for plant development and adaptation. The aim of this project was to use Setaria viridis and Setaria pumila as model plants to study the diversity and functioning of seed endophytes. Setaria is closely related to maize and other important C4 grasses and is easily cultivated. S. viridis represents a plant, which occurs naturally in many locations worldwide as it easily adapts to various conditions and has a weedy character. In this project we studied the microbiome associated with different plant tissues, particularly roots as opposed to seeds and panicles to study to which extent the (soil) environment, the plant species and plant tissue shape microbiomes as well as whether bacterial endophytes are translocated to the next generation of seeds. We showed that different plant tissues host highly distinct microbial communities. Based on the fact that certain taxa are found in all both, roots and panicles, of plants grown at distinct sites, it can be concluded that some taxa are highly affiliated with plants and seem to be vertically transmitted. We also showed that seeds deprived of endophytes have a poor performance.