Microbial Metabarcoding highlights different Bacterial and Fungal PopulationsAuthor(s): Sudhansu Sekhar Patra
Globalization has a significant impact on seed, fruit, and vegetable trade and mobility, resulting in a rise in economic losses due to the introduction of transboundary plant infections. Current diagnostic procedures are a helpful and precise tool for enacting surveillance regimens for certain organisms, but they are very targeted, whereas metabarcoding and shotgun metagenomics might be utilised to concurrently detect all known diseases as well as potentially novel ones. The goal of this review is to present the current state of high-throughput sequencing (HTS) diagnostics for fungal and bacterial plant pathogens, discuss the challenges that must be overcome, and provide guidance for the development of methods for detecting a small number of related taxa (specific surveillance) or all of the microorganisms present in a sample (general surveillance). HTS approaches, particularly metabarcoding, may be beneficial for monitoring soilborne, seedborne, and airborne diseases, as well as finding new pathogens and pinpointing outbreak origins. Metabarcoding and shotgun metagenomics still have a lot of room for improvement but this issue can be limited by carefully choosing primers and bioinformatic algorithms. The use of metagenomics to address crucial areas of plant pathogen identification and surveillance in plant material and commodities will be substantially accelerated thanks to advances in bioinformatics.