Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes The GenBank accession numbers for the sequences determined in this work are: gyrB, D37926, D37297, D86005–D86019 and AB039381–AB039492; rpoD, D86020–D86036 and AB039493–AB039624.

Abstract

Phylogenetic analysis of the genus Pseudomonas was conducted by using the combined gyrB and rpoD nucleotide sequences of 31 validly described species of Pseudomonas (a total of 125 strains). Pseudomonas strains diverged into two major clusters designated intrageneric cluster I (IGC I) and intrageneric cluster II (IGC II). IGC I was further split into two subclusters, the ' P. aeruginosa complex ', which included P. aeruginosa, P. alcaligenes, P. citronellolis, P. mendocina, P. oleovorans and P. pseudoalcaligenes, and the ' P. stutzeri complex ', which included P. balearica and P. stutzeri. IGC II was further split into three subclusters that were designated the ' P. putida complex ', the ' P. syringae complex ' and the ' P. fluorescens complex '. The ' P. putida complex ' included P. putida and P. fulva. The ' P. syringae complex ' was the cluster of phytopathogens including P. amygdali, P. caricapapayae, P. cichorii, P. ficuserectae, P. viridiflava and the pathovars of P. savastanoi and P. syringae. The ' P. fluorescens complex ' was further divided into two subpopulations, the ' P. fluorescens lineage ' and the ' P. chlororaphis lineage '. The ' P. fluorescens lineage ' contained P. fluorescens biotypes A, B and C, P. azotoformans, P. marginalis pathovars, P. mucidolens, P. synxantha and P. tolaasii, while the ' P. chlororaphis lineage ' included P. chlororaphis, P. agarici, P. asplenii, P. corrugata, P. fluorescens biotypes B and G and P. putida biovar B. The strains of P. fluorescens biotypes formed a polyphyletic group within the ' P. fluorescens complex '.

Taxonomic heterogeneity, as shown by siderotyping, of strains primarily identified as Pseudomonas putida

“…28 corresponding to P. jessenii and P. mandelii. In contrast, P. putida biovar B strains preferentially contributed to the siderovars of the second group related to the P. fluorescens lineage, a correlation that is in full agreement with the numerous taxonomical studies that state that P. putida biovar B strains are phylogenetically closer to P. fluorescens than to P. putida biovar A strains (Stanier et al, 1966;Yamamoto & Harayama, 1998;Yamamoto et al, 2000;Hilario et al, 2004). deeply acknowledged for their helpful critical reading and improvement of the manuscript.…”

“…Biolog metabolic profiling, restriction fragment length polymorphism ribotyping, PCR ribotyping, repetitive element sequence-based PCR (rep-PCR), using BOX or enterobacterial repetitive intergenic consensus (ERIC) primers Dawson et al, 2002), effectively concluded that great taxonomic heterogeneity was the rule within the species P. fluorescens and P. putida. The need for a detailed revision at the biochemical and molecular levels was also shown by a combined dataset of four molecular sequences (atpD, carA, recA and 16S rRNA gene sequences; Hilario et al, 2004) and by sequence comparisons focused on gyrB and rpoD gene sequences (Yamamoto et al, 2000). Interestingly, all these studies, as well as a few others specifically focused on P. putida (Yamamoto & Harayama, 1995, 1998, concluded that P. putida strains belonging to biovar B are phylogenetically closer to P. fluorescens strains than to strains of P. putida biovar A.…”

MvaT proteins in Pseudomonas spp.: a novel class of H-NS-like proteins

“…are known for their extreme ecological and metabolic diversity. Indeed, such bacteria have been collected from environments as diverse as soil, water (marine or freshwater), plants and animals, but their taxonomical classification is still a matter of controversy (Yamamoto et al, 2000). Currently, the genome sequencing of six of them by different international consortia is underway (http://igweb.…”

Ruegeria pelagia is a later heterotypic synonym of Ruegeria mobilis

“…The gyrB genes of the two type strains were sequenced (about 1072 bp) (Yamamoto et al, 2000), and the similarity between strain R. pelagia NBRC 102038 T and R. mobilis NBRC 101030 T was 97.7 %; the deduced GyrB amino acid sequence identity between the two strains was 99.2 %. As shown in Supplementary Fig.…”