Open AccessElevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacterium odoriferum sp. nov., proposal of Pectobacterium brasiliense sp. nov. and Pectobacterium actinidiae sp. nov., emended description of Pectobacterium carotovorum and description of Pectobacterium versatile sp. nov., isolated from streams and symptoms on diverse plants
Author(s) -
Pérrine Portier,
Jacques Pédron,
Géraldine Taghouti,
Marion Fischer-Le Saux,
Emma Caullireau,
Claire Bertrand,
Angélique Laurent,
Khaoula Chawki,
Saïd Oulgazi,
Mohedine Moumni,
Didier Andrivon,
Cécile Dutrieux,
Denis Faure,
Valérie Helias,
MarieAnne Barny
Publication year - 2019
Publication title -
international journal of systematic and evolutionary microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.925
H-Index - 173
eISSN - 1466-5034
pISSN - 1466-5026
DOI - 10.1099/ijsem.0.003611
Subject(s) - pectobacterium , pectobacterium carotovorum , biology , housekeeping gene , subspecies , botany , 16s ribosomal rna , microbiology and biotechnology , genetics , gene , zoology , pathogen , gene expression
The Pectobacteriumcarotovorum species corresponds to a complex, including two subspecies with validly published names, two proposed subspecies and two new species, Pectobacterium polaris and Pectobacterium aquaticum. Recent studies suggested that this complex needed revision. We examined the taxonomic status of 144 Pectobacterium strains isolated from a wide range of plant species, various geographical origins and waterways. Sequences of the leuS , dnaX and recA housekeeping genes clustered 114 of these Pectobacterium strains together within a not yet described clade. We sequenced eight strains of this clade and analysed them together with the 102 Pectobacterium genomes available in the NCBI database. Phylogenetic analysis, average nucleotide identity calculation and in silico DNA-DNA hybridization allowed us to differentiate seven clades. This led us to propose the elevation of Pectobacterium carotovorum subsp. odoriferum to species level as Pectobacteriumodoriferum sp. nov. (type strain CFBP 1878 T =LMG 5863 T =NCPPB 3839 T =ICMP 11533 T ), the proposal of Pectobacteriumactinidiae sp. nov. (type strain KKH3=LMG 26003 T =KCTC 23131 T ) and Pectobacteriumbrasiliense sp. nov. (type strain CFBP 6617 T = LMG 21371 T =NCPPB 4609 T ), to emend the description of Pectobacterium carotovorum (type strain CFBP 2046 T =LMG 2404 T =NCPPB 312 T =ICMP 5702 T ), and to propose a novel species, Pectobacterium versatile sp. nov (type strain CFBP6051 T = NCPPB 3387 T =ICMP 9168 T ) which includes the strains previously described as 'Candidatus Pectobacterium maceratum '. Phenotypic analysis performed using Biolog GENIII plates on eight strains of P. versatile sp. nov. and related strains completed our analysis.