Prokaryotic Intraspecies Diversity

Johannes Sikorski, DSMZ—Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany

Published online: March 2009

DOI: 10.1002/9780470015902.a0020377

Abstract

Intraspecies prokaryotic diversity is a multifaceted research field with widespread connections to other biological disciplines. The dynamics of intraspecies diversity can be understood within models of bacterial microevolution, as population genetics is the basic theoretic foundation for explaining the mechanisms of evolution and speciation. Also, it directly relates to functional molecular biology, physiology and metabolism. Last, but not least, intraspecies diversity is inseparably linked to systematics and taxonomy, and to the current discussions on the prokaryotic species concept.

Key concepts

The field of prokaryotic intraspecies diversity is inseparably linked to the issue of species concepts. Currently, there is a strong debate as to whether further apply the historically evolved and pragmatic but in several aspects dissatisfying operational‐based species definition, or to develop theory‐based species concepts leading to new definitions. Any theory‐based species concepts that might be implemented must respect the current set of rules of naming species, the Bacteriological Code, to avoid substantial confusion.

Although this may seem on the first spot trivial and self‐evident, it must become clear that strains within a so‐called species can be fundamentally different from each other. The theoretical foundation for understanding such intraspecies diversity is the field of population genetics, which is based on analytical mathematics. Intraspecies diversity can be analysed using three principal approaches (i) theoretical studies including computer simulation, (ii) Experimental Evolution and (iii) the study of natural populations. Ideally, these approaches should be combined. Each of these principal approaches should be based on three equivalent pillars (i) genetic markers, (ii) phenotypic traits and (iii) a solid knowledge on the habitat in which the bacterial strains most probably evolved.

Keywords: population genetics; microevolution; theory‐based species concepts; prokaryote taxonomy; prokaryote nomenclature

Figure 1.

This figure summarizes the interrelationship of intraspecies diversity to other biological disciplines.
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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.

Achtman M, Morelli G, Zhu P et al. (2004) Microevolution and history of the plague bacillus, Yersinia pestis. Proceedings of the National Academy of Sciences of the USA 101: 17837–17842.

Adami C (2006a) Digital genetics: unravelling the genetic basis of evolution. Nature Reviews. Genetics 7: 109–118.

Adami C (2006b) Reducible complexity. Science 312: 61–63.

Bergstrom CT, Lipsitch M and Levin BR (2000) Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155: 1505–1519.

Brigulla M, Hoffmann T, Krisp A et al. (2003) Chill induction of the SigB‐dependent general stress response in Bacillus subtilis and its contribution to low‐temperature adaptation. Journal of Bacteriology 185: 4305–4314.

Buckley M and Roberts RJ (2006) Reconciling Microbial Systematics & Genomics: American Academy of Microbiology. Washington, DC: ASM.

Choi K‐H, Heath RJ and Rock CO (2000) β‐ketoacyl‐acyl carrier protein synthase III (FabH) is a determining factor in branched‐chain fatty acid biosynthesis. Journal of Bacteriology 182: 365–370.

Cohan FM (1994) The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. American Naturalist 143: 965–986.

Cohan FM and Perry EB (2007) A systematics for discovering the fundamental units of bacterial diversity. Current Biology 17: R373–R386.

Dekel E and Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588–592.

Elena SF and Lenski RE (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Reviews. Genetics 4: 457–469.

Excoffier L and Heckel G (2006) Computer programs for population genetics data analysis: a survival guide. Nature Reviews. Genetics 7: 745–758.

Falush D, Kraft C, Taylor NS et al. (2001) Recombination and mutation during long‐term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proceedings of the National Academy of Sciences of the USA 98: 15056–15061.

Hartl DL and Clark AG (2007) Principles of Population Genetics, 4 edn. Sunderland, MA: Sinauer Associates.

Herbeck JT, Funk DJ, Degnan PH and Wernegreen JJ (2003) A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL. Genetics 165: 1651–1660.

Jessup CM, Kassen R, Forde SE et al. (2004) Big questions, small worlds: microbial model systems in ecology. Trends in Ecology and Evolution 19: 189–197.

Kassen R, Llewellyn M and Rainey PB (2004) Ecological constraints on diversification in a model adaptive radiation. Nature 431: 984–988.

Koeppel A, Perry EB, Sikorski J et al. (2008) Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proceedings of the National Academy of Sciences of the USA 105: 2504–2509.

Konstantinidis KT and Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proceedings of the National Academy of Sciences of the USA 102: 2567–2572.

Lapage SP, Sneath PHA, Lessel EF et al. (1992) International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code. Washington, DC: American Society for Microbiology.

Lenski RE, Ofria C, Collier TC and Adami C (1999) Genome complexity, robustness and genetic interactions in digital organisms. Nature 400: 661–664.

Lenski RE, Ofria C, Pennock RT and Adami C (2003) The evolutionary origin of complex features. Nature 423: 139–144.

Lynch M (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proceedings of the National Academy of Sciences of the USA 104: 8597–8604.

MacLean RC, Bell G and Rainey PB (2004) The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proceedings of the National Academy of Sciences of the USA 101: 8072–8077.

Maharjan R, Seeto S, Notley‐McRobb L and Ferenci T (2006) Clonal adaptive radiation in a constant environment. Science 313: 514–517.

Mayr E (1997) The objects of selection. Proceedings of the National Academy of Sciences of the USA 94: 2091–2094.

de Mendoza D, Schujman GE and Aguilar PS (2002) Biosynthesis and function of membrane lipids. In: Sonenshein AL, Hoch JA and Losick R (eds) Bacillus Subtilis and Its Closest Relatives: From Genes to Cells, pp. 43–55. Washington, DC: ASM Press.

Mutch LA and Young JPW (2004) Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Molecular Ecology 13: 2435–2444.

Nei M (2007) The new mutation theory of phenotypic evolution. Proceedings of the National Academy of Sciences of the USA 104: 12235–12242.

Orr HA (2005a) The genetic theory of adaptation: a brief history. Nature Reviews. Genetics 6: 119–127.

Orr HA (2005b) Theories of adaptation: what they do and don't say. Genetica 123: 3–13.

Papke RT and Ward DM (2004) The importance of physical isolation to microbial diversification. FEMS Microbiology Ecology 48: 293–303.

Papke RT, Zhaxybayeva O, Feil EJ et al. (2007) Searching for species in haloarchaea. Proceedings of the National Academy of Sciences of the USA 104: 14092–14097.

Rainey PB and Travisano M (1998) Adaptive radiation in a heterogeneous environment. Nature 394: 69–72.

Rasko DA, Rosovitz MJ, Okstad OA et al. (2007) Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus‐group plasmids, including Bacillus anthracis pXO1. Journal of Bacteriology 189: 52–64.

Sikorski J (2008) Populations under microevolutionary scrutiny: what will we gain? Archives of Microbiology 189: 1–5.

Sikorski J, Brambilla E, Kroppenstedt RM and Tindall BJ (2008a) The temperature adaptive fatty acid content in Bacillus simplex strains from “Evolution Canyon”, Israel. Microbiology 154: 2416–2426.

Sikorski J and Nevo E (2005) Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at “Evolution Canyons” I and II, Israel. Proceedings of the National Academy of Sciences of the USA 102: 15924–15929.

Sikorski J and Nevo E (2007) Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of “Evolution Canyon” I and II, Israel. Environmental Microbiology 9: 716–726.

Sikorski J, Pukall R and Stackebrandt E (2008b) Carbon source utilization patterns of Bacillus simplex ecotypes do not reflect their adaptation to ecologically divergent slopes in “Evolution Canyon”, Israel. FEMS Microbiology Ecology 66: 38–440.

Smith NH, Kremer K, Inwald J et al. (2006) Ecotypes of the Mycobacterium tuberculosis complex. Journal of Theoretical Biology 239: 220–225.

Stackebrandt E (2002) From species definition to species concept: population genetics is going to influence the systematics of Prokaryotes. WFCC Newsletter 35: 1–4.

Stoltzfus A (2006) Mutationism and the dual causation of evolutionary change. Evolution & Development 8: 304–317.

Tanaka MM, Bergstrom CT and Levin BR (2003) The evolution of mutator genes in bacterial populations: the roles of environmental change and timing. Genetics 164: 843–854.

Tenaillon O, Le Nagard H, Godelle B and Taddei F (2000) Mutators and sex in bacteria: conflict between adaptive strategies. Proceedings of the National Academy of Sciences of the USA 97: 10465–10470.

Thompson JR, Pacocha S, Pharino C et al. (2005) Genotypic diversity within a natural coastal bacterioplankton population. Science 307: 1311–1313.

Vos M and Velicer GJ (2008) Isolation by distance in the spore‐forming soil bacterium Myxococcus xanthus. Current Biology 18: 386–391.

Ward DM, Cohan FM, Bhaya D et al. (2008) Genomics, environmental genomics and the issue of microbial species. Heredity 100: 207–219.

Wiehlmann L, Wagner G, Cramer N et al. (2007) Population structure of Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the USA 104: 8101–8106.

Wilke CO, Wang JL, Ofria C, Lenski RE and Adami C (2001) Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412: 331–333.

Further Reading

Kimura M (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.

Oren A (2004) Prokaryote diversity and taxonomy: present status and future challenges. Philosophical Transactions of the Royal Society. Series B 559: 623–638.

Page RDM and Holmes EC (1998) Molecular Evolution: A Phylogenetic Approach. Oxford: Blackwell Science.

Stackebrandt E (2003) The richness of prokaryotic diversity: there must be a species somewhere. Food Technology and Biotechnology 41: 17–22.

Tindall BJ, Kämpfer P, Euzéby JP and Oren A (2006) Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. International Journal of Systematic and Evolutionary Microbiology 56: 2715–2720.

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

Related Sub-Topics:

Evolution of Species | Diversity of Life | Classification | Microbial Evolution and Taxonomy | Population Structure and Genetics
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Article Title: Prokaryotic Intraspecies Diversity
 
How to Cite close
Sikorski, Johannes(Mar 2009) Prokaryotic Intraspecies Diversity. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020377]