Plant pathogens represent a worldwide problem on the economic and life stability. Indeed, plant diseases caused by a variety of pathogens, including viruses, viroids, bacteria, fungi, and yeast, pose significant threats to agricultural ecosystems. Early and accurate detection of these pathogens is critical for effective management and control strategies.
We present optimized protocols for the molecular detection of key plant pathogens: Xylella fastidiosa (Xf), Rose Rosette Virus (RRV), and Citrus exocortis viroid (CEVd), each responsible for substantial agricultural losses. Our approach relies on automated techniques using paramagnetic beads, facilitating the isolation of high-quality pathogenic DNA or RNA from various plant parts, significantly reducing hands-on time. We also discuss the use of optimized amplification master mixes, to overcome potential inhibition, frequently observed with plant samples. Through these technological advancements, we aim to provide a robust framework for the global effort in combating plant diseases, safeguarding both our environment and economic well-being.