Skip to main content

Microbial Systematics

  • Chapter
  • First Online:
Environmental Biotechnology

Part of the book series: Handbook of Environmental Engineering ((HEE,volume 10))

Abstract

This chapter aims at presenting an overview of different aspects of the classification and nomenclature of the prokaryotes, i.e., the domains Bacteria and Archaea. Concepts of systematics, taxonomy, classification, nomenclature, and identification are discussed. The number of species of prokaryotes – Bacteria and Archaea combined – is surprisingly small, 8,226 as of November 2009. It is obvious that the true number of different species much larger: we probably know less than 1% of the types of prokaryotes in Nature. Classification of prokaryotes and description of species based on a polyphasic approach that includes phenotypic as well as genotypic properties. Nomenclature is governed by the rules of the Bacteriological Code (International Code of Nomenclature of Prokaryotes), as determined by the International Committee on Systematics of Prokaryotes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Euzéby J (1997) List of bacterial names with standing in nomenclature: a folder available on the internet (URL: http://www.bacterio.cict.fr). Int J Syst Bacteriol 47:590–592

    Article  Google Scholar 

  2. Oren A (2008) Systematics of Archaea and Bacteria, In: Biological Science. Fundamentals and Systematics, Vol. 2. Encyclopedia of Life Support Systems (Minelli A, Contrafatto G, eds). United Nations Educational, Scientific and Cultural Organization, pp. 164–188

    Google Scholar 

  3. Brenner DJ, Staley JT, Krieg NR (2001) Classification of procaryotic organisms and the concept of bacterial speciation. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 27–31

    Chapter  Google Scholar 

  4. Lapage SP, Sneath PHA, Lessel EF Jr, Skerman VBD, Seelinger HPR, ClarkWA (eds) (1992) International Code of Nomenclature of Bacteria (1990 revision). American Society of Microbiology, Washington, DC

    Google Scholar 

  5. Garrity GM (editor-in-chief), Boone DR, Castenholz RW (eds) (2001) Bergey’s Manual of Systematic Bacteriology, 2nd ed., Vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria. Springer-Verlag, New York

    Google Scholar 

  6. Sneath PHA (2001) Bacterial nomenclature. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 83–88

    Chapter  Google Scholar 

  7. Stackebrandt E (2000) Defining taxonomic ranks. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The Prokaryotes: an evolving electronic resource for the microbiological community, 3rd edn, release 3.1, 20 January 2000. Springer, New York, http://link.springer-ny.com/link/service/books/10125/

  8. Oren A (2004) Prokaryote diversity and taxonomy: present status and future challenges. Philos Trans R Soc Lond B Biol Sci 559:623–638

    Article  Google Scholar 

  9. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  10. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosseló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1045–1047

    Google Scholar 

  11. Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    Article  Google Scholar 

  12. Cowan ST (1968) A dictionary of microbial taxonomic usage. Oliver & Boyd, Edinburgh

    Google Scholar 

  13. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438

    Google Scholar 

  14. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    Google Scholar 

  15. Woese CR (1992) Prokaryote systematics: the evolution of a science. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K-H (eds) The Prokaryotes. A handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, 2nd edn, vol 1. Springer, Berlin, pp 3–18

    Google Scholar 

  16. Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal of the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579

    Article  Google Scholar 

  17. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  Google Scholar 

  18. Fox GE, Wisotzkey JD, Jurtshuk P Jr (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170

    Article  Google Scholar 

  19. Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420

    Article  Google Scholar 

  20. Gillis M, Vandamme P, De Vos P, Swings J, Kersters K (2001) Polyphasic taxonomy, In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 43–48

    Chapter  Google Scholar 

  21. Ventosa A, Gutiérrez MC, Kamekura M, Zvyagintseva IS, Oren A (2004) Taxonomic study of Halorubrum distributum and proposal of Halorubrum terrestre sp. nov. Int J Syst Evol Microbiol 54:389–392

    Article  Google Scholar 

  22. Krieg NR (2001) Identification of Prokaryotes. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 33–38

    Chapter  Google Scholar 

  23. Sneath PHA (2001) Numerical taxonomy. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 39–42

    Chapter  Google Scholar 

  24. Trüper HG (1999) How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryotic nomenclature. FEMS Microbiol Rev 23:231–249

    Google Scholar 

  25. Trüper HG (2001) Etymology in nomenclature of procaryotes. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 89–99

    Chapter  Google Scholar 

  26. Labeda DP (2001) Culture collections: an essential resource for microbiology. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 111–113

    Chapter  Google Scholar 

  27. Ludwig W, Schleifer K-H (1994) Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15:155–173

    Article  Google Scholar 

  28. Gupta RS (1998) What are archaebacteria: life’s third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol Microbiol 29:695–707

    Article  Google Scholar 

  29. Madigan MT, Martinko JM, Dunlap PV, Clark DP (2009) Brock Biology of Microorganisms. 12th ed. Pearson-Benjamin Cummings, San Francisco

    Google Scholar 

  30. Karner MB, DeLong EF, Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409:507–510

    Article  Google Scholar 

  31. Ludwig W, Klenk H-P (2001) Overview: a phylogenetic backbone and taxonomic framework for procaryotic systematics. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 49–65

    Chapter  Google Scholar 

  32. Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) (2006) The Prokaryotes. 3rd ed. Springer, New York

    Google Scholar 

  33. Trüper HG, Schleifer K-H (2006) Prokaryote characterization and identification, In: The Prokaryotes. (Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E eds), Springer, New York, Vol. 1, pp. 58–79

    Google Scholar 

  34. Amann RI, Ludwig W, Schleifer K-H (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    Google Scholar 

  35. von Wintzingerode F, Göbel U, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

  36. Torsvik V, Sørheim R, Goksøyr J (1996) Total bacterial diversity in soil and sediment communities – a review. J Ind Microbiol 17:170–178

    Article  Google Scholar 

  37. Dykhuizen DE (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73:25–33

    Article  Google Scholar 

  38. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single microbial cells. Science 243:1360–1363

    Article  Google Scholar 

  39. Amann R, Schleifer K-H (2001) Nucleic acid probes and their application in environmental microbiology. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York, pp 67–82

    Chapter  Google Scholar 

  40. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    Google Scholar 

  41. Morris RM, Rappé MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806–810

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Oren, A. (2010). Microbial Systematics. In: Wang, L., Ivanov, V., Tay, JH. (eds) Environmental Biotechnology. Handbook of Environmental Engineering, vol 10. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-140-0_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-140-0_3

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-58829-166-0

  • Online ISBN: 978-1-60327-140-0

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics