This project aims to improve understanding of the risk associated with the diversity and role of viral and bacterial microorganisms in agricultural systems and at the interface between crops and surrounding wild vegetation. Agroscope research has shown that agrosystem interfaces serve as persistent reservoirs for bacterial or viral diseases of grapevines or crops, rendering global eradication strategies ineffective and favoring containment measures instead. In addition, recent high-throughput sequencing-based monitoring of tomato production systems has identified numerous emerging reservoir viruses, some of which are potentially dangerous, such as a newly discovered tobamovirus. The project focuses on assessing this microbial diversity in different agricultural systems (arable crops, arboriculture, horticulture) to assess the risks and prepare the monitoring of microorganisms with the potential to develop into diseases. In parallel, it aims to identify biological and environmental factors that trigger the shift of pathogens detected in agrosystems towards epidemic behavior.