Phylogeny Based on 16S rRNA/DNA

Erko Stackebrandt, DSMZ‐German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

Published online: September 2009

DOI: 10.1002/9780470015902.a0000462.pub2

Polyphasic systematics of prokaryotes is guided by the results of comparative analysis of the evolutionary conservative 16S ribosomal ribonucleic acid (RNA) genes. Certain genes coding for ‘housekeeping’ proteins support the phylogenetic outline but most of these genes are either not ubiquitous or they are evolving too rapidly to embrace all higher taxa. Dendrograms of phylogenetic relatedness show the order at which organisms evolved in time, thus providing the frame for their classification. The delineation and circumscription of taxa should not be solely based on the topology of dendrograms but it is advised to include a wide range of molecular, chemical and metabolic properties, which need to be assessed and evaluated in the light of novel taxonomic information.

Key concepts:

  • The results of comparative 16S ribosomal ribonucleic acid (rRNA) gene sequence analysis shattered the dogma of the bifurcation of higher life form categories, that is prokaryotes versus eukaryotes.
  • The advantage of rRNA genes over genes coding for proteins is a combination of properties: universal presence, easy accessibility and polymerase chain reaction (PCR) amplification, rare lateral gene transfer and broad coverage of taxa between domain and species.
  • The only taxonomic category where the 16S rRNA gene sequence fails to unravel detailed evolutionary insights into the structure of its members is the taxon ‘species’.
  • Taxonomy of a strain is more than the analysis of a few sequences: it is a pragmatic concept that takes into account the results of its evolutionary history leading to changes at the genomic, epigenetic and phenotypic levels.
  • Classification is a process in which the database of a strain is compared to the network of strains already classified. Its place in the system is found when this dataset matches most closely the dataset of an already classified taxon. In this process the 16S rRNA sequence guides the affiliation to the genus level.

Keywords: semantides; evolution; phylogeny; taxonomy; systematics; classification

Figure 1. Secondary structure of a 16S rRNA molecule based on the Escherichia coli structure (Maidak et al., 1994; available in the public domain Ribosomal Database Project). Highly variable regions are red; highly conservative stretches are green. Binding sites of primers used in PCR amplification of the rRNA gene are blue, with the direction of amplification indicated by arrows. The other nucleotides are black.
Figure 2. Phylogenetic distribution of peptidoglycan amino acids as a salient chemotaxonomic property. Type strains of Microbacterium (M.) with ornithine in their peptidoglycan are indicated in red, those with lysine are indicated in blue. Neighbour-Joining dendrograms of relationship of genes coding for 16S rRNA (1A), rpoB (1B), recA (1C), gyrB (1D), ppk (1E) and a concatenated dataset (1F), containing the gene sequences that formed the basis for genes displayed in Figure 1A–1E. Bootstrap values of >30% are indicated at relevant branching points. Agromyces albus DSM 15934T served as a root. Scale bar indicates 2% inferred nucleotide changes. Reprinted from Richert et al. (2007), www.elsevier.com/locate/sam. Copyright (2007) with permission from Elsevier.
Figure 3. The phylogenetic tripartition of living organisms based on the analysis of genes coding for small subunit rRNA (16S and 18S rRNA). Within the prokaryotic domains most of the main lines of descent, called kingdoms in the domain Archaea, and phyla in the domain Bacteria, are indicated. The origin of the evolutionary lineages appears to be located close to the branching point of the lineage of the Bacteria (indicated by a circle). The bar represents 5 nucleotide substitutions per 100 nucleotides.
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 References
    Achtman M and Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nature Reviews Microbiology 6: 431–440.
    Adékambi T, Shinnick TM, Raoult DL and Drancourt M (2008) Complete rpoB gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation. International Journal of Systematic and Evolutionary Microbiology 58: 1807–1814.
    Barns SM, Delwiche CF, Palmer JD and Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proceedings of the National Academy of Sciences of the USA 93: 9188–9193.
    Cohan FM (2002) What are bacterial species? Annual Review of Microbiology 56: 457–487.
    book Danson MJ, Hough DW and Lunt GG (1992) The Archaebacteria: Biochemistry and Biotechnology. Biochemical Society Symposium 58. London: Portland Press.
    book Garrity GM, Brenner DJ, Krieg NR and Staley JT (2005) Bergey's Manual of Systematic Bacteriology, vol. 2. The Proteobacteria. New York: Springer.
    Gevers D, Cohan FM, Lawrence JG et al. (2005) Opinion: re-evaluating prokaryotic species. Nature Reviews Microbiology 3: 733–739.
    Gogarten JP, Doolittle WF and Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Molecular and Biological Evolution 19: 2226–2238.
    Ludwig W, Neumaier J, Klugbauer N et al. (1993) Phylogenetic relationships of bacteria based on comparative sequence analysis of elongation factor TU and ATP-synthase -subunit genes. Antonie van Leeuwenhoek 64: 285–305.
    Maidak BL, Larsen N, McCaughey MJ et al. (1994) The Ribosomal Database Project. Nucleic Acids Research 22: 3485–3487.
    McInerney JO and Wilkinson M (2005) New methods ring changes for the tree of life. Trends in Ecology and Evolution 20: 105–107.
    Ochman H, Elwyn S and Moran NA (1999) Calibrating bacterial evolution. Proceedings of the National Academy of Science of the USA 96: 12638–12643.
    Olsen GJ, Woese CR and Overbeek R (1994) The winds of (evolutionary) changes: breathing new life into microbiology. Journal of Bacteriology 178: 1–6.
    Richert K, Brambilla E and Stackebrandt E (2007) The phylogenetic significance of peptidoglycan types: Molecular analysis of the genera Microbacterium and Aureobacterium based upon sequence comparison of gyrB, rpoB, recA and ppk and 16SrRNA genes. Systematic and Applied Microbiology 30: 102–108.
    book Roselló-Mora R (2005) "DNA–DNA reassociation methods applied to microbial taxonomy and their critical evaluation". In: Stackebrandt E (ed.) Molecular Identification, Systematics, and Population Structure of Prokaryotes, pp. 23–50. Heidelberg: Springer.
    Roselló-Mora R and Amann R (2001) The species concept for prokaryotes. FEMS Microbiology Reviews 25: 39–67.
    book Stackebrandt E (2006) "Defining taxonomic ranks" In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E (eds) The Prokaryotes, 2nd edn, vol. 1. New York: Springer.
    Stackebrandt E and Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 4: 152–155.
    Stackebrandt E and Goebel BM (1994) A place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44: 846–849.
    Stackebrandt E, Frederiksen W, Garrity GM et al. (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology 52: 1043–1047.
    book Stackebrandt E and Rainey FA (1995) "Partial and complete 16S rDNA sequences, their use in generation of 16S rDNA phylogenetic trees and their implications in molecular ecological studies". In: Akkermans ADL, van Elsas JD and de Bruijn FJ (eds) Molecular Microbial Ecology Manual. Amsterdam: Kluwer Academic Publishers.
    Vandamme P, Pot B, Gillis M et al. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiological Reviews 60: 407–438.
    Wayne L, Brenner DJ, Colwell RR et al. (1987) International Committee on Systematic Bacteriology: report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology 37: 463–464.
    Woese CR (1987) Bacterial evolution. Microbiological Reviews 51: 221–271.
    Woese CR and Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the USA 74: 5088–5090.
    Woese CR, Kandler O and Wheelis ML (1990) Towards a natural system of organisms. Proposal for the domains archaea, bacteria, and eucarya. Proceedings of the National Academy of Sciences of the USA 87: 4576–4579.
    Zuckerkandl E and Pauling L (1965) Molecules as documents of evolutionary history. Journal of Theoretical Biology 8: 357–366.
 Further Reading
    book Atlas RM (1997) "Microbial systematics, evolution, phylogeny and classification". In: Atlas RM (ed.) Principles of Microbiology, 2nd edn, pp. 888–951. Chicago: Wm.C. Brown Publishers.
    Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 2124–2129.
    book Dworkin M, Falkow S, Rosenberg E, Schleifer K-H and Stackebrandt E (eds) (2006) The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 3rd edn. New York: Springer.
    Golding GB and Gupta RS (1995) Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Molecular Biology and Evolution 12: 1–6.
    book Goodfellow M and O'Donnell AG (1993) Handbook of New Bacterial Systematics. London: Academic Press.
    Konstantinidis KT and Tiedje JM (2005) Towards a genome based taxonomy for prokaryotes. Journal of Bacteriology 187: 6258–6264.
    Lake JA and Rivera MC (2004) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Molecular and Biological Evolution 21: 681–690.
    book Li W-H and Graur D (1991) Fundamentals of Molecular Evolution. Sunderland: Sinauer Associates.
    book Ludwig W and Klenk H-P (2001) "Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics". In: Boon DR, Castenholz RW and Garrity GM (eds) Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 49–65. New York: Springer.
    Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734–740.
    book Priest FG, Ramos-Cormenzana A and Tindall BJ (eds) (1995) Bacterial Diversity and Systematics. New York: Plenum Press.
    book Stackebrandt E (1992) "Unifying phylogeny and phenotypic properties". In: Balows A, Trüper HG, Dworkin M, Harder W and Schleifer KH (eds) The Prokaryotes, A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd edn. New York: Springer.
    Woese CR, Gutell R, Gupta R and Noller H (1983) Detailed analysis of the higher order structure of 16S like ribosomal ribonucleic acids. Microbiological Reviews 47: 621–669.
    Yarza P, Richter M, Peplies J et al. (2008) The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Systematic and Applied Microbiology 31: 241–250.
    Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. International Journal of Systematic and Evolutionary Microbiology 53: 1893–1900.

Related Sub-Topics:

Classification | Archaea | Bacteria | Microbial Evolution and Taxonomy
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Article Title: Phylogeny Based on 16S rRNA/DNA
 
How to Cite close
Stackebrandt, Erko(Sep 2009) Phylogeny Based on 16S rRNA/DNA. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000462.pub2]