Historical evolution and current status of the taxonomy of genus Pseudomonas

doi:10.1016/j.meegid.2009.08.001

Infection, Genetics and Evolution

Volume 9, Issue 6, December 2009, Pages 1132-1147

https://doi.org/10.1016/j.meegid.2009.08.001 Get rights and content

Abstract

The genus Pseudomonas was described in 1894 and is one of the most diverse and ubiquitous bacterial genera whose species have been isolated worldwide in all kinds of environments, from the Antarctica to the Tropics, present in sediments, clinical samples, plant, fungi and diseased animal specimens, water, soil, plant rhizosphere, sea, deserts, etc. The taxonomy of the genus has been controversial for years since a lot of bacterial taxa initially included in genus Pseudomonas have been reclassified in other genera or species from a different class of Proteobacteria over the years, as techniques for characterization and classification of microorganisms improved, aiming to set a phylogenetic classification of the species. In this review, the historical evolution of the taxonomy of Pseudomonas is described, and the currently valid criteria and future challenges for taxonomy of the genus and techniques used to achieve the necessary characterization for classifying the species are discussed. Finally, all the validly published Pseudomonas species at present are listed with an overview of their diversity and ecology.

Section snippets

History of Pseudomonas taxonomy

The genus Pseudomonas was described by Migula (1894) and therefore it was part of the history of Bacteriology since the beginning of this science. Walter Emil Friedrich August Migula was a Botanist devoted to plant taxonomy, a science started more than a century before bacterial taxonomy, which began when the compound microscope reached the resolution power required for the observation of these organisms (Palleroni, 2003). He was a contemporary of Ferdinand Cohn who published a bacterial code

Current criteria in Pseudomonas taxonomy

Since its discovery the genus Pseudomonas has undergone numerous taxonomic changes not only as far as the number of species included but also as far as the criteria used for their definition and delineation. In the current edition of Bergey's Manual of Systematic Bacteriology, an exhaustive list of methods used in Pseudomonas taxonomy was included (Palleroni, 2005). These methods reveal the efforts for characterizing Pseudomonas species and include cell morphology and structure, cell wall

Future challenges in taxonomy of the genus Pseudomonas

Microbial taxonomy is currently in evolution searching new methods to find the most suitable criteria for genera and species delineation. The bacterial species definition was re-evaluated in 2002 (Stackebrandt et al., 2002), being this specially important in the case of complex genera as occurs in the genus Pseudomonas that currently contains more than 100 species (Table 2). Most of these species are saprophytic inhabitants of water and soil related environments (Table 3) and they have

Acknowledgments

The authors wish to thank I. Geldart for revising the English version of the manuscript, and two anonymous reviewers for valuable comments.

References (209)

N. Baïda et al.
Pseudomonas brenneri sp. nov., a new species isolated from natural mineral waters
J. Res. Microbiol.
(2001)
G.V. Bloemberg et al.
Molecular basis of plant growth promotion and biocontrol by rhizobacteria
Curr. Opin. Plant Biol.
(2001)
J. Bodilis et al.
Phylogenetic relationships between environmental and clinical isolates of Pseudomonas fluorescens and related species deduced from 16S rRNA gene and OprF protein sequences
Syst. Appl. Microbiol.
(2004)
R.J. Carpenter et al.
Pseudomonas putida war wound infection in a US Marine: a case report and review of the literature
J. Infect.
(2008)
S. Choudhary et al.
Characterization of a metal resistant Pseudomonas sp. isolated from uranium mine for its potential in heavy metal (Ni(2+), Co(2+), Cu(2+), and Cd(2+)) sequestration
Bioresour. Technol.
(2009)
J. Esteban et al.
Pseudomonas oryzihabitans peritonitis in a patient on continuous ambulatory peritoneal dialysis
Clin. Microbiol. Infect.
(2002)
M. Farhadian et al.
In situ bioremediation of monoaromatic pollutants in groundwater: a review
Bioresour. Technol.
(2008)
L.R. Hoffman et al.
Pseudomonas aeruginosa lasR mutants are associated with cystic fibrosis lung disease progression
J. Cyst. Fibros.
(2009)
M.G. Höfle
Identification of bacteria by low molecular weight RNA profiles: a new chemotaxonomic approach
J. Microbiol. Methods
(1988)
J.D. Janse et al.
Classification of fluorescent soft rot Pseudomonas bacteria, including P. marginalis strains, using whole cell fatty acid analysis
Syst. Appl. Microbiol.
(1992)

K. Kersters et al.

Recent changes in the classification of pseudomonads: an overview

Syst. Appl. Microbiol.

(1996)

W. Achouak et al.

Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov, two root-associated bacteria from Brassica napus and Arabidopsis thaliana

Int. J. Syst. Evol. Microbiol.

(2000)

S.M. Andersen et al.

Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site

Int. J. Syst. Evol. Microbiol.

(2000)

Y. Anzai et al.

Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence

Int. J. Syst. Evol. Microbiol.

(2000)

Y. Anzai et al.

The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera

Int. J. Syst. Bacteriol.

(1997)

G. Auling et al.

Rapid differentiation, by polyamine analysis, of Xanthomonas strains from phytopathogenic pseudomonads and other members of the class Proteobacteria interacting with plants

Int. J. Syst. Bacteriol.

(1991)

B. Austin et al.

Recovery of Serratia plymuthica and presumptive Pseudomonas pseudoalcaligenes from skin lesions in rainbow trout, Oncorhynchus mykiss (Walbaum), otherwise infected with enteric redmouth

J. Fish Dis.

(1992)

F.K. Bahrani-Mougeot et al.

Molecular analysis of oral and respiratory bacterial species associated with ventilator-associated pneumonia

J. Clin. Microbiol.

(2007)

N. Baïda et al.

Pseudomonas grimontii sp. nov.

Int. J. Syst. Evol. Microbiol.

(2002)

P.A. Bakker et al.

Induced systemic resistance by fluorescent Pseudomonas spp.

Phytopathology

(2007)

J.G. Barr et al.

API-20NE and sensititre autoidentification systems for identifying Pseudomonas spp.

J. Clin. Pathol.

(1989)

S.E. Battle et al.

Genomic islands of Pseudomonas aeruginosa

FEMS Microbiol. Lett.

(2009)

U. Behrendt et al.

Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov.

Int. J. Syst. Evol. Microbiol.

(2003)

U. Behrendt et al.

A taxonomic study of bacteria isolated from grasses: a proposed new species Pseudomonas graminis sp. nov.

Int. J. Syst. Bacteriol.

(1999)

U. Behrendt et al.

Pseudomonas lurida sp. nov., a fluorescent species associated with the phyllosphere of grasses

Int. J. Syst. Evol. Microbiol.

(2007)

Beijerinck, M.W., 1921. Verzamelde Werken, vols. I–V, vol. VI, 1940. Nijhoff,...

D.H. Bergey et al.

Bergey's Manual of Determinative Bacteriology

(1923)

J. Bishara et al.

Prosthetic knee septic arthritis due to Pseudomonas stutzeri

Can. J. Infect. Dis.

(2000)

N. Bozal et al.

Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment

Int. J. Syst. Evol. Microbiol.

(2007)

G.R. Brown et al.

Reclassification of [Pseudomonas] doudoroffii (Baumann et al. 1983) into the genus Oceanomonas gen. nov as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov.

Int. J. Syst. Bacteriol.

(2001)

B. Cámara et al.

Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid

Int. J. Syst. Evol. Microbiol.

(2007)

J. Carratala et al.

Community-acquired pneumonia due to Pseudomonas stutzeri

Clin. Infect. Dis.

(1992)

J.P. Casalta et al.

Prosthetic valve endocarditis caused by Pseudomonas luteola

BMC Infect. Dis.

(2005)

C.Y. Chi et al.

Pseudomonas mendocina spondylodiscitis: a case report and literature review

Scand. J. Infect. Dis.

(2005)

L.L. Clark et al.

Pseudomonas otitidis sp. nov., isolated from patients with otic infections

Int. J. Syst. Evol. Microbiol.

(2006)

T. Coenye et al.

Genotypic and chemotaxonomic evidence for the reclassification of Pseudomonas woodsii as Burkholderia andropogonis

Int. J. Syst. Evol. Microbiol.

(2001)

F. Cohan

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

Philos. Trans. R. Soc. Lond. B. Biol. Sci.

(2006)

F. Cohn

Untersuchungen über Bakterien

Beitr. Biol. Pflanz.

(1872)

R.R. Colwell et al.

Deoxyribonucleic acid base composition and Adansonian analysis of heterotrophic aerobic pseudomonads

J. Bacteriol.

(1965)

R.R. Colwell et al.

Adansonian analysis and deoxyribonucleic acid base composition of some Gram-negative bacteria

J. Bacteriol.

(1964)

B.J. Connor et al.

Recurrent Pseudomonas luteola (CDC group Ve-1) peritonitis in a patient undergoing continuous ambulatory peritoneal dialysis

J. Clin. Microbiol.

(1987)

R. Costa et al.

Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses

Environ. Microbiol.

(2007)

J.M. Cruz-Sánchez et al.

Enhancement of resolution of low molecular weight RNA profiles by staircase electrophoresis

Electrophoresis

(1997)

B. Curran et al.

Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa

J. Clin. Microbiol.

(2004)

F. Dabboussi et al.

Pseudomonas mosselii sp. nov., a novel species isolated from clinical specimens

Int. J. Syst. Evol. Microbiol.

(2002)

M. Dalamaga et al.

Pseudomonas luteola cutaneous abscess and bacteraemia in a previously healthy man

Scand. J. Infect. Dis.

(2004)

N. Degand et al.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of nonfermenting gram-negative bacilli isolated from cystic fibrosis patients

J. Clin. Microbiol.

(2008)

S. Delorme et al.

Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils

Int. J. Syst. Evol. Microbiol.

(2002)

E.B.M. Denner et al.

Reclassification of Pseudomonas echinoides Heumann 1962, 343^AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov.

Int. J. Syst. Bacteriol.

(1999)

P. De Vos et al.

Intra- and intergeneric similarities of Pseudomonas and Xanthomonas ribosomal ribonucleic acid cistrons

Int. J. Syst. Bacteriol.

(1983)

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ReviewHistorical evolution and current status of the taxonomy of genus Pseudomonas

Abstract

Section snippets

History of Pseudomonas taxonomy

Current criteria in Pseudomonas taxonomy

Future challenges in taxonomy of the genus Pseudomonas

Acknowledgments

J. Res. Microbiol.

Curr. Opin. Plant Biol.

Syst. Appl. Microbiol.

J. Infect.

Bioresour. Technol.

Clin. Microbiol. Infect.

Bioresour. Technol.

J. Cyst. Fibros.

J. Microbiol. Methods

Syst. Appl. Microbiol.

Syst. Appl. Microbiol.

Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov, two root-associated bacteria from Brassica napus and Arabidopsis thaliana

Int. J. Syst. Evol. Microbiol.

Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site

Int. J. Syst. Evol. Microbiol.

Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence

Int. J. Syst. Evol. Microbiol.

The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera

Int. J. Syst. Bacteriol.

Rapid differentiation, by polyamine analysis, of Xanthomonas strains from phytopathogenic pseudomonads and other members of the class Proteobacteria interacting with plants

Int. J. Syst. Bacteriol.

Recovery of Serratia plymuthica and presumptive Pseudomonas pseudoalcaligenes from skin lesions in rainbow trout, Oncorhynchus mykiss (Walbaum), otherwise infected with enteric redmouth

J. Fish Dis.

Molecular analysis of oral and respiratory bacterial species associated with ventilator-associated pneumonia

J. Clin. Microbiol.

Pseudomonas grimontii sp. nov.

Int. J. Syst. Evol. Microbiol.

Induced systemic resistance by fluorescent Pseudomonas spp.

Phytopathology

API-20NE and sensititre autoidentification systems for identifying Pseudomonas spp.

J. Clin. Pathol.

Genomic islands of Pseudomonas aeruginosa

FEMS Microbiol. Lett.

Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov.

Int. J. Syst. Evol. Microbiol.

A taxonomic study of bacteria isolated from grasses: a proposed new species Pseudomonas graminis sp. nov.

Int. J. Syst. Bacteriol.

Pseudomonas lurida sp. nov., a fluorescent species associated with the phyllosphere of grasses

Int. J. Syst. Evol. Microbiol.

Bergey's Manual of Determinative Bacteriology

Prosthetic knee septic arthritis due to Pseudomonas stutzeri

Can. J. Infect. Dis.

Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment

Int. J. Syst. Evol. Microbiol.

Reclassification of [Pseudomonas] doudoroffii (Baumann et al. 1983) into the genus Oceanomonas gen. nov as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov.

Int. J. Syst. Bacteriol.

Pseudomonas reinekei sp. nov., Pseudomonas moorei sp. nov. and Pseudomonas mohnii sp. nov., novel species capable of degrading chlorosalicylates or isopimaric acid

Int. J. Syst. Evol. Microbiol.

Community-acquired pneumonia due to Pseudomonas stutzeri

Clin. Infect. Dis.

Prosthetic valve endocarditis caused by Pseudomonas luteola

BMC Infect. Dis.

Pseudomonas mendocina spondylodiscitis: a case report and literature review

Scand. J. Infect. Dis.

Pseudomonas otitidis sp. nov., isolated from patients with otic infections

Int. J. Syst. Evol. Microbiol.

Genotypic and chemotaxonomic evidence for the reclassification of Pseudomonas woodsii as Burkholderia andropogonis

Int. J. Syst. Evol. Microbiol.

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

Philos. Trans. R. Soc. Lond. B. Biol. Sci.

Untersuchungen über Bakterien

Beitr. Biol. Pflanz.

Deoxyribonucleic acid base composition and Adansonian analysis of heterotrophic aerobic pseudomonads

J. Bacteriol.

Adansonian analysis and deoxyribonucleic acid base composition of some Gram-negative bacteria

J. Bacteriol.

Recurrent Pseudomonas luteola (CDC group Ve-1) peritonitis in a patient undergoing continuous ambulatory peritoneal dialysis

J. Clin. Microbiol.

Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses

Environ. Microbiol.

Enhancement of resolution of low molecular weight RNA profiles by staircase electrophoresis

Electrophoresis

Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa

Review
Historical evolution and current status of the taxonomy of genus Pseudomonas

Reclassification of Pseudomonas echinoides Heumann 1962, 343^AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov.