title: Pantoea allii sp. nov., isolated from onion plants and seed.
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 390(T), 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 390(T) ( = LMG 24248(T)).
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
authors.forename: Carrie L
authors.initials: CL
authors.lastname: Brady
authors.affiliation: Agricultural Research Council, Plant Protection Research Institute, Department of Microbiology and Plant Pathology, Private Bag X134, Queenswood 0121, Pretoria, South Africa.
authors.forename: Teresa
authors.initials: T
authors.lastname: Goszczynska
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
authors.forename: Stephanus N
authors.initials: SN
authors.lastname: Venter
authors.affiliation: BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
authors.forename: Ilse
authors.initials: I
authors.lastname: Cleenwerck
authors.affiliation: BCCM/LMG Bacteria Collection, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium.
authors.forename: Paul
authors.initials: P
authors.lastname: De Vos
authors.affiliation: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton, GA 31793, USA.
authors.forename: Ronald D
authors.initials: RD
authors.lastname: Gitaitis
authors.affiliation: Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
authors.forename: Teresa A
authors.initials: TA
authors.lastname: Coutinho
mesh_terms: D000332:Aerobiosis; D054458:Amplified Fragment Length Polymorphism Analysis; D000678:Amygdalin / Q000378:metabolism; D000693:Anaerobiosis; D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D008124:Locomotion; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D009693:Nucleic Acid Hybridization; D019697:Onions / Q000382:microbiology*; D010088:Oxidoreductases / Q000378:metabolism; D020636:Pantoea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D010802:Phylogeny; D010860:Pigments, Biological / Q000378:metabolism; D010935:Plant Diseases / Q000382:microbiology; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012255:Ribitol / Q000378:metabolism; D012639:Seeds / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D013012:Sorbitol / Q000378:metabolism; D013019:South Africa; D014481:United States
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D010860:Pigments, Biological; D012336:RNA, Ribosomal, 16S; D000678:Amygdalin; D012255:Ribitol; D013012:Sorbitol; D010088:Oxidoreductases