Modification of the tomato seed microbiome for sustainable production (MoToMi)

Tomato, a crop belonging to the Solanaceae family, originates from South America and has been cultivated and domesticated for seven millennia. This domestication resulted in the modern varieties we know today. While domestication primarily aimed to improve yield and flavor, it also led to a decrease of important traits like stress resilience and a loss of beneficial plant-associated microorganisms. Advanced microscopy and high-throughput sequencing techniques provide the means to explore the world of microorganisms on a community level. These methods enable us to perform so-called microbiome studies a specific field in microbial ecology. Through microbiome studies, it became apparent that plants, including tomatoes, harbour distinct, diverse, and abundant communities of microorganisms in various niches, such as the above-ground plant parts (phyllosphere), the root-associated soil (rhizosphere), the leaf surfaces (epiphyllosphere), and the internal plant tissues (endosphere). These microorganisms play a crucial role in promoting plant growth and in the protection against invading pests and pathogens. Interestingly, recent findings have shown that seeds harbour a several species of microorganisms in their internal tissues, the so-called endophytes. These microorganisms along with their associated gene products collectively form the seed microbiome. The microbiome complements the host genome and is often referred to as the hosts secondary genome. The seed microbiome is primarily derived from the mother plant and is regarded as the primary source of the subsequently assembled plant microbiome. Modifications of the seed microbiome have the potential to positively affect the future development of the plant, as well as to increase its resilience towards environmental stress without requiring plant genetic modifications. In this project, we aim to (i) get new insights into the structure and function of tomato seed endophyte communities; (ii) identify the biotic and abiotic factors shaping the seed microbiome; (iii) characterize the plant growth promotion and biological control potential of bacterial seed endophytes; (iv) and decipher chemical signals of tomato that contribute to the assembly of a beneficial plant and/or seed microbiome. The results of these investigations will jointly contribute toward designing strategies for the delivery of beneficial bioproducts and their transgenerational monitoring in tomato breeding. The findings from this project will serve as the foundation for utilizing seed endophytes in sustainable agricultural practices, e.g., the reduction of synthetic pesticides usage. We consider the tomato crop as the ideal model for our research due to (i) its global economic and nutritional importance, (ii) its reliance on chemical inputs such as fertilizers and pesticides for sufficient yield, and (iii) the availability of curated genome data as well as relevant microbiome and biocontrol data from previous studies. The project will be implemented in the frame of the Schrödinger postdoctoral fellowship, funded by the Austrian Science Fund (FWF), and will be implemented in collaboration with the University of Southampton (United Kingdom) and Graz University of Technology (Austria).