Abstract:
Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively
anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant
exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on
the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus
sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the
allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates
represented a novel species, which was phylogenetically most closely related to Pantoea ananatis
and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates
into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of
the genus Pantoea that showed .97% 16S rRNA gene sequence similarity with strain BD 390T,
the isolates exhibited 11–55% whole-genome DNA–DNA relatedness, which confirmed the
classification of the isolates in a novel species. The most useful phenotypic characteristics for the
differentiation of the isolates from their closest phylogenetic neighbours are production of acid
from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is
proposed, with type strain BD 390T (5LMG 24248T).
