A three-year bacterial survey of onion fields across Pennsylvania and New York

Bacterial diseases cause annual onion yield losses of 5 to 40% in Pennsylvania (PA) and New York (NY). More comprehensive knowledge of the bacteria present and further characterization of pathogenic bacteria is important for developing effective diagnostic tools and management strategies. This survey aimed to identify the bacteria associated with symptomatic onion leaves and bulbs and evaluate their pathogenicity. From 2020 to 2022, 30 onion fields across PA and NY were sampled, and 589 symptomatic plants and bulbs were collected. A total of 1957 bacterial isolates were recovered from the samples, and 1165 isolates were characterized to genus level. Of the 53 bacterial genera identified, Burkholderia (22.1%) and Pantoea (16.8%) were the most prevalent. Additionally, 957 isolates from 43 genera were tested for pathogenicity using the red scale necrosis (RSN) assay. Of these, 264 isolates from eight bacterial genera produced necrosis. A subset of 187 RSN-negative isolates was further tested in foliar and whole onion bulb pathogenicity assays. Of these, 25 were pathogenic in both assays, 15 only in the foliar assay, and 28 only in the bulb assay. This survey revealed that numerous bacterial genera are associated with symptomatic onion leaves and bulbs. However, only about one-third of the bacterial genera tested were pathogenic on onion. Of those genera, about one-third of the isolates were pathogenic in at least one of the three assays. These results indicate that most bacteria associated with symptomatic onion tissues are non-pathogenic, highlighting the importance of accurate diagnosis to design effective disease management strategies.