Advancing Plant Health: The Role of Metagenomics Technology in Early Detection and Identification of Pathogens

Verinder Virk ^1,2* Sadhana Giri ^1,2* Rishita Srivastava ²

• ¹ Faculty of Sciences, Gurukul Kangri University, Haridwar, India
• ² Gurukul Kangri University, Haridwar, Uttarakhand, India

Effective management of plant diseases and the reduction of agricultural losses hinges on the timely detection and accurate identification of plant pathogens. Traditional methods have largely relied on protein and nucleic acid analyses, with enzyme-linked immunosorbent assays (ELISA) standing out for their high throughput and cost-effectiveness. However, ELISA's sensitivity often falls short in the early stages of infection, limiting its utility for preemptive disease control. Nucleic acid-based technologies have brought significant improvements in pathogen identification, particularly for those that resist conventional culturing. Portable diagnostic tools, such as polymerase chain reaction (PCR) assays and lateral flow systems, have enabled rapid field detection. Despite their promise, these methods still face challenges related to sensitivity and specificity. The increasing impact of plant pathogens on global crop yields underscores the critical need for precise and robust diagnostic solutions. Recent breakthroughs in genomic technologies specifically shotgun metagenomics, amplicon-based metagenomics, and meta transcriptomics offer transformative potential. These techniques not only enable the accurate identification of diverse pathogens but also facilitate the analysis of their metabolic pathways, providing valuable insights into pathogen ecology and evolution. This review delves into the emerging role of metagenomic sequencing in plant pathogen detection, highlighting its advantages over traditional approaches and discussing its future implications for sustainable disease management in agriculture.