Taxonomic evaluation of the genus Pantoea based on a multigene approach

Abstract

The genus Pantoea contains seven validly-published species, which are primarily known as plant-associated or phytopathogenic bacteria, but some have also been linked with human infections. Over the past six years, there have been increasing isolations of Pantoea strains from a range of hosts and locations which can not be conclusively identified. In South America and Uganda, Pantoea strains were isolated from Eucalyptus infected with bacterial blight. In South Africa, Pantoea strains were isolated from maize suffering from brown stalk rot and from onion seed. This has highlighted the need for a rapid, molecular-based technique to conclusively characterize these Pantoea strains. In the literature, two key taxonomic problems were identified within the genus Pantoea. The first involves three species isolated from fruit and soil samples in Japan, namely P. citrea, P. punctata and P. terrea, known as the “Japanese” Pantoea species. A recent review of the genus noted that Pantoea can be separated into two groups: the Pantoea “core” containing P. agglomerans, P. ananatis, P. dispersa and P. stewartii and the “Japanese” species. It was also stated that more taxonomic work is required to justify the assignment of the “Japanese” species to the genus Pantoea. The second taxonomic issue raised concerns over four DNA hybridization groups from a study of a large number of clinical strains belonging to the Erwinia herbicola-Enterobacter agglomerans complex. It had been previously suggested that these four DNA hybridization groups should belong to the genus Pantoea. The phylogenetic relationship between the Pantoea “core” species, the “Japanese” species and the four DNA hybridization groups is not clear. Multilocus sequence analysis (MLSA) was selected for a taxonomic study of the genus Pantoea The MLSA scheme was based on the sequences of four housekeeping genes: rpoB, atpD gyrB and infB. It was found that a phylogenetic tree of the concatenated sequences could differentiate all seven validly-published species as well as ten groups of strains from Eucalyptus, maize, onion, flowering shrubs and clinical isolates. The phylogenetic trees also confirmed the separation of Pantoea into two groups of species and indicated a close affiliation of the “Japanese” species with the genus Tatumella The clusters observed in the MLSA phylogenetic trees were confirmed by DNA-DNA hybridization. Using the MLSA data for support, four novel species were proposed from plant hosts: Pantoea vagens, Pantoea eucalypti, Pantoea deleyii and Pantoea anthophila. Four additional species were proposed for the clinical strains from the Erwinia herbicola-Enterobacter agglomerans complex, contained in three DNA hybridization groups: Pantoea septica, Pantoea eucrina, Pantoea brenneri and Pantoea conspicua. Phenotypic information and DNA-DNA hybridization values confirmed that the “Japanese” species were more similar to Tatumella than to Pantoea. This was demonstrated phylogenetically in the MLSA trees and gave support to transfer the “Japanese” species to the genus Tatumella. Additionally, a novel species was proposed for strains thought to belong to T.citrea, causing pink disease of pineapple: Tatumella morbirosei. Therefore, MLSA was not only proven to rapidly and successfully identify Pantoea strains, but also resolved the two major taxonomic issues within the genus. Please cite as follows: Brady, CL 2008, Taxonomic evaluation of the genus Pantoea based on a multigene approach, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-09182008-142751/ > Copyright