Archives of Microbiology

, Volume 184, Issue 6, pp 353–361

Genotype versus phenotype in the circumscription of bacterial species: the case of Pseudomonas stutzeri and Pseudomonas chloritidismutans

  • Aina Maria Cladera
  • Elena García-Valdés
  • Jorge Lalucat
Original Paper

Abstract

The phenotypic characteristic of strain AW-1T of Pseudomonas chloritidismutans that is most relevant from the taxonomic point of view appears to be the capacity of growth under anaerobic conditions using chlorate as electron acceptor. This property is not restricted to this species only within the genus Pseudomonas, since it is also present in strains of genomovars 1 or 5, and 3 of Pseudomonas stutzeri. P. chloritidismutans has been described as a non-denitrifying species, but the isolation of variants that are able to grow anaerobically in the presence of nitrate is possible after subcultivation under selective conditions. The subdivision of P. stutzeri into a number of species on the basis of these characteristics does not help to clarify the phylogenetic relationships among the members of an otherwise coherent group of strains, and the considerations presented in this communication support the reclassification of the new species name P. chloritidismutans, which in our opinion, should be considered as a Junior name of P. stutzeri. A multilocus sequence analysis, together with a phenotypic analysis of the anaerobic oxidative metabolism, gives new insights into the phylogeny and evolution of the species.

Keywords

P. stutzeri P. chloritidismutans Denitrification Multilocus sequence analysis (MLSA) 

Supplementary material

203_2005_52_MOESM1_ESM.pdf (86 kb)
Supplementary material

References

  1. Achenbach LA, Michaelidou U, Bruce RA, Fryman J, Coates JD (2001) Dechloromonas agitata gen. nov., sp. nov. and Dechlorosoma suillum gen. nov., sp. nov., two novel environmentally dominant (per)chlorate-reducing bacteria and their phylogenetic position. Int J Syst Evol Microbiol 51:527–533PubMedGoogle Scholar
  2. Alef K (1995) Assay of denitrification. In: Alef K, Nannipieri P (eds) Methods in applied and soil microbiology and biochemistry. Academic, London, pp 283–284Google Scholar
  3. Bender KS, Rice MR, Fugate WH, Coates JD, Achenbach LA (2004) Metabolic primers for detection of (per)chlorate-reducing bacteria in the environment and phylogenetic analysis of cld gene sequences. Appl Environ Microbiol 70:5651–5658PubMedCrossRefGoogle Scholar
  4. Bennasar A, Rosselló-Mora R, Lalucat J, Moore ERB (1996) 16S rRNA gene sequence analysis relative to genomovars of Pseudomonas stutzeri; proposal of Pseudomonas balearica, sp. nov. Int J Syst Bacteriol 46:200–205PubMedGoogle Scholar
  5. Bennasar A, Guasp C, Lalucat J (1998a) Molecular methods for the detection and identification of Pseudomonas stutzeri in pure culture and environmental samples. Microbial Ecol 35:22–23CrossRefGoogle Scholar
  6. Bennasar A, Guasp C, Tesar M, Lalucat J (1998b) Genetic relationships among Pseudomonas stutzeri strains based on molecular typing methods. J Appl Microbiol 85:643–656CrossRefGoogle Scholar
  7. Bosch R, García-Valdés E, Moore ERB (2000) Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10. Gene 245:65–74PubMedCrossRefGoogle Scholar
  8. Cladera AM, Bennasar A, Barceló M, Lalucat J, García-Valdés E (2004) Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. J Bacteriol 186:5239–5248PubMedCrossRefGoogle Scholar
  9. Coates JD, Michaelidou U, Bruce RA, O’Connor SM, Crespi JN, Achenbach LA (1999) Ubiquity and diversity of dissimilatory (per)chlorate-reducing bacteria. Appl Environ Microbiol 65:5234–5241PubMedGoogle Scholar
  10. Coates JD, Achenbach LA (2004) Microbial perchlorate reduction: rocket-fuelled metabolism. Nature Rev Microbial 2:569–580CrossRefGoogle Scholar
  11. García-Valdés E, Castillo MM, Bennasar A, Guasp C, Cladera AM, Bosch R, Engesser KH, Lalucat J (2003) Polyphasic characterization of Pseudomonas stutzeri CLN100 which simultaneously degrades chloro and methylaromatics: A new genomovar within the species. Syst Appl Microbiol 26:390–403PubMedCrossRefGoogle Scholar
  12. Guasp C, Moore E, Lalucat J, Bennasar A (2000) Utility of internally-transcribed 16S–23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species. Int J Syst Evol Bacteriol 50:1629–1639Google Scholar
  13. Lan R, Reeves PL (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401PubMedCrossRefGoogle Scholar
  14. Logan BE, Zhang H, Mulvaney P, Milner MG, Head IM, Unz RF (2001) Kinetics of perchlorate- and chlorate-respiring bacteria. Appl Environ Microbiol 67:2499–2506PubMedCrossRefGoogle Scholar
  15. Miller JM (1972) Experiments in molecular genetics. Cold Spring Harbour, New YorkGoogle Scholar
  16. Nakamura Y, Gojobori T, Ikemura T (2000) Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucleic Acids Res 28:292PubMedCrossRefGoogle Scholar
  17. Palleroni NJ (1984) Genus I. Pseudomonas. In: Krieg JGHNR (eds) Bergey’s manual of systematic bacteriology. Williams and Wilkins Co., Baltimore, pp 141–199Google Scholar
  18. Palleroni NJ, Doudoroff M (1972) Some properties and taxonomic subdivisions of genus Pseudomonas. Ann Rev Phytopathol pp 73–78Google Scholar
  19. Rius N, Fusté M, Guasp C, Lalucat J, Lorén J (2001) Clonal population structure of Pseudomonas stutzeri: a species with exceptional genetic diversity. J Bacteriol 183:736–744PubMedCrossRefGoogle Scholar
  20. Rosselló R, García-Valdés E, Lalucat J, Ursing J (1991) Genotypic and phenotypic diversity of Pseudomonas stutzeri. Syst Appl Microbiol 14:150–157Google Scholar
  21. Rosselló-Mora RA, García-Valdés E, Lalucat J (1993) Taxonomic relationship between Pseudomonas perfectomarina strain ZoBell and Pseudomonas stutzeri. Int J Syst Bacteriol 43:852–854CrossRefGoogle Scholar
  22. Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67PubMedCrossRefGoogle Scholar
  23. Ruby EG, Wirsen CO, Jannasch W (1981) Chemolithotrophic sulfur-oxidizing bacteria from the Galapagos Rift Hydrotermal Vents. Appl Environ Microbiol 42:317–324PubMedGoogle Scholar
  24. Sikorski J, Rosselló-Mora R, Lorenz MG (1999) Analysis of genotypic diversity and relationships among Pseudomonas stutzeri strains by PCR-based genomic fingerprinting and multilocus enzyme electrophoresis. Syst Appl Microbiol 22:393–402PubMedGoogle Scholar
  25. Sikorski J, Teschner N, Wackernagel W (2002a) Highly different levels of natural transformation are associated with genomic subgroups within a local population of Pseudomonas stutzeri from soil. Appl Environ Microbiol 68:865–873CrossRefGoogle Scholar
  26. Sikorski J, Möhle M, Wackernagel W (2002b) Identification of complex composition, strong strain diversity and directional selection in local Pseudomonas stutzeri populations from marine sediments and soil. Environ Microbiol 4:465–476CrossRefGoogle Scholar
  27. Sikorski J, Lalucat J, Wackernagel W (2005) Genomovars 11 to 18 of Pseudomonas stutzeri, identified among isolates from soil and marine sediment. Int J Syst Evol Microbiol. In press DOI: 10.1099/ijs.0.63535-0Google Scholar
  28. Sorokin DY, Teske A, Robertson LA, Kuenen G (1999) Anaerobic oxidation of thiosulfate to tetrathionate by obligately heterotrophic bacteria, belonging to the Pseudomonas stutzeri group. FEMS Microbiol Ecol. 30:113–123PubMedCrossRefGoogle Scholar
  29. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Withman WB (2002) Report of the ad hoc committee for the re-evaluaton of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047PubMedCrossRefGoogle Scholar
  30. Tamegai H, Li L, Masui N, Kato C (1997) A denitrifying bacterium from the deep sea at 11,000 m depth. Extremophiles 1:207–211PubMedCrossRefGoogle Scholar
  31. Ursing JB, Rosselló-Mora RA, García-Valdés E, Lalucat J (1995) Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups. Int J Syst Bacteriol 45:604Google Scholar
  32. Vermeiren H, Willems A, Schoofs G, de Mot R, Keijers V, Hai W, Vanderleyden J (1999) The rice inoculant strain Alcaligenes faecalis A15 is a nitrogen-fixing Pseudomonas stutzeri. Syst Appl Microbiol. 22:215–224PubMedGoogle Scholar
  33. Wilson K (1987). Preparation of genomic DNA from bacteria. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 241–242Google Scholar
  34. Wolterink AFWM, Jonker AB, Kengen SWM, Stams AJM (2002) Pseudomonas chloritidismutans sp. nov., a non-denitrifying, chlorate-reducing bacterium. Int J Syst Evol Microbiol 52:2183–2190PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Aina Maria Cladera
    • 1
    • 2
  • Elena García-Valdés
    • 1
    • 2
  • Jorge Lalucat
    • 1
    • 2
  1. 1.Departament de Biologia, MicrobiologiaUniversitat de les Illes BalearsPalma de MallorcaSpain
  2. 2.Institut Mediterrani d’Estudis Avançats (CSIC-UIB)Palma de MallorcaSpain

Personalised recommendations