Curtobacterium flaccumfaciens pv. flaccumfaciens: an integrated multidisciplinary approach as a model for the control of neglected EU quarantine bacterial plant pathogens

As climate change accelerates and the global population approaches 10 billion, ensuring food security is a critical challenge. Leguminous crops, essential for their high protein content and adaptability, are increasingly threatened by Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff), a quarantine pathogen in the EU that spreads through asymptomatic seeds, making detection and management difficult. Despite its official status, Cff has been largely neglected in European research, even as its presence expands due to insufficient regulations and rising international trade. This thesis investigates Cff’s impact on Phaseolus vulgaris (common bean) and Glycine max (soybean), two key legumes. It aims to enhance diagnostic tools and management strategies using an integrated, multidisciplinary approach. Given the limitations of traditional detection methods, the study develops a highly sensitive qRT-PCR assay capable of detecting minimal Cff DNA amounts. Additionally, innovative non-invasive detection techniques are explored, including photoacoustic spectroscopy (PAS) and volatile organic compound (VOC) profiling. PAS exploits Cff’s pigmentation for optical differentiation, while VOC analysis identifies unique metabolic markers for rapid, cost-effective pathogen detection. These methods show potential for large-scale application, enabling early intervention and reducing pathogen spread. Furthermore, this research pioneers gene expression analysis in Cff, identifying stable reference genes and investigating virulence-related genes to understand host-pathogen interactions. These insights could support breeding programs for disease-resistant beans and facilitate targeted pathogen control strategies. By combining molecular, optical, and chemical diagnostic approaches, this thesis provides a comprehensive framework for Cff detection and management. The proposed techniques address critical gaps in current diagnostic protocols and have already attracted industry interest for potential commercialization. Beyond Cff, these findings contribute to the broader field of plant pathology, offering new perspectives for the control of seed-borne bacterial diseases in legume crops.