Metagenomic and Culture-Based Detection of <i>Pectobacterium</i> spp.: What You See Is Not Always What You Get

Bacteria from the genera Pectobacterium and Dickeya cause blackleg and soft rot in potatoes. Isolating these pathogens from symptomatic plant tissues presents challenges because of the cohabitation of multiple microbes and the limitations of traditional isolation methods. In this study, culture-dependent and culture-independent approaches were used to identify Pectobacterium species from symptomatic blackleg samples collected from Pennsylvania potato fields. Metagenomic classification tools were used to detect Pectobacterium spp. and compare the results with culture-based isolates. The findings showed concordance between culture-based and metagenomic analysis in identifying Pectobacterium species. Metagenomic approaches effectively detected Pectobacterium spp. in most samples; however, pathogen abundance varied significantly within and across fields, highlighting the stochastic nature of microbial distribution. These results underscore the importance of employing rigorous methodologies when using plant disease diagnostic tools. Integrating culture-dependent and metagenomic approaches enhances our understanding of pathogen diversity and spatial distribution, ultimately contributing to more effective disease monitoring and control strategies. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .