LEPAGE Elise

Thesis subject: Emergences at the agro-ecological interface: the role of natural reservoirs on the epidemic and evolutionary dynamics of pathogens

Abstract: The fight against pathogens affecting crops is a major concern for food security, as well as a priority area in the agroecological transition. While the past few years have been marked by the Covid-19 pandemic, the same observation applies to the health of both humans and plants: the emergence of new pathogenic organisms is highly damaging and difficult to predict. For effective crisis management in plant health, understanding the characteristics of the relevant pathogens is essential. In particular, the role of interfaces between natural areas and human-modified spaces remains poorly understood, despite its potentially crucial impact on the emergence and development of epidemics. Starting from the premise that diverse natural areas are generally more resilient to epidemics than monocultures, landscape diversification in space and time is a fundamental component of agroecological disease management. However, studies focusing on these management strategies often overlook the ambivalent role of wild hosts in close proximity to crops. And even when considered, the complexity of the wild component is greatly simplified. Moreover, many landscape strategies can be undermined by generalist pathogens (i.e., capable of infecting a wide range of hosts). Indeed, these pathogens are, on one hand, likely to be present in numerous plants in the wild component and, on the other hand, possess an evolutionary potential that enables them to quickly overcome plant resistance. This thesis project aims to address the following issue: What roles do natural reservoirs play in the epidemic and evolutionary dynamics of generalist agricultural pathogens, and what are the implications for management strategies? The thesis will be based on the study of the ongoing epidemic of the Cucumber mosaic virus (CMV) in the pepper cultivation in the Espelette region, a recent emergence whose causes are still unknown. A systemic approach, combining field and laboratory experiments, as well as modeling, in collaboration with the Espelette Pepper PDO Association, will enable (1) the study of the genetic-spatial-temporal structure of the virus in the Espelette territory, (2) the identification of key epidemic factors, and (3) the proposal of strategies to combat the virus.