Pantoea Species Isolated from Onion Plants and Bulbs Across Different Regions of Chile

Onions are one of the main vegetables cultivated in Chile. In recent years, changing climate conditions have favored the emergence of new bacterial diseases, where Pantoea species have been reported as causal agents of onion leaf blight and bulb rot in central Chile. The objective of this work was to study the abundance of Pantoea spp. isolated from symptomatic onion plants sampled in different regions of Chile. The identification of Pantoea species was determined based on gyrB, leuS and rpoB genes sequences, revealing Pantoea agglomerans as the most frequently isolated species, followed by Pantoea ananatis and Pantoea eucalypti . Pathogenicity tests were performed. Only three of the 20 isolated strains showed clear symptoms of bulb damage, with P. ananatis exhibiting the most severe symptoms. The complete genome of a pathogenic strain of each identified species was sequenced. These genomes were used for the implementation of PCR-High Resolution Melting-based system determining characteristic profiles of each species in order to facilitate the identification of the isolates in onion samples. Six primer pairs of housekeeping genes previously used in multilocus analysis were used to test their ability to differentiate between Pantoea species. The primer pairs gyrB and leuS showed the greatest discrimination among the Pantoea species. In this study, the identification of Pantoea species isolated from onion crops in Chile, revealed that only a small proportion were pathogenic, even in diseased plants. This highlights complex plant–bacteria interactions and suggests PCR-HRM as a useful tool to study these populations and better understand disease development.