Pectobacterium sinaloense sp. nov., a novel phytopathogenic species isolated from potato plants in Mexico

Abstract

As part of a broader effort to survey and characterize the diversity of pectolytic bacteria affecting potato crops in Mexico, phytopathogenic strains were isolated from soft rot symptoms in potato plants in Sinaloa. Among them, an atypical Pectobacterium-like strain, LFLA-215T, could not be confidently assigned to any known species through biochemical or molecular methods. To clarify its taxonomic position and explore its genomic and functional features, whole-genome sequencing and comparative analyses were conducted, accompanied by biochemical, morphological and pathogenicity evaluations. The strain LFLA-215T is Gram-stain-negative, with peritrichous flagella, catalase-positive, and oxidase-negative. Phylogenetic analyses based on the 16S rRNA operon, dnaJ, and 923 core genes, confirmed that strain LFLA-215T belongs to the genus Pectobacterium. However, genomic similarity values with other Pectobacterium species, ranging from 87.73-93.53% (ANIb), 87.63-93.46% (ANIu), and 34.0-52.1% (isDDH), fell below species delineation thresholds. Pectobacterium colocasium LJ1T showed the closest relationship to LFLA-215T, whereas Pectobacterium parmentieri RNS 08-42-1AT was the most distantly related. Although LFLA-215T fulfilled Kochs postulates and demonstrated pathogenicity in potato plants, its virulence on tubers was comparatively lower than that of other known Pectobacterium strains, which could be related to the size and the reduction of the total number of genes when analyzed its complete genome reported here. Taken all together, our findings support the classification of strain LFLA-215T as a novel species within the genus Pectobacterium, for which the name Pectobacterium sinaloense sp. nov. is proposed, with LFLA-215T designated as the type strain.