Abstract
Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes.
Zusammenfassung
Die Arten bilden die Grundlage des taxonomischen Modells. Sie sind die unterste taxonomische Kategorie und dienen als Einheit zur Beschreibung von Biodiversität und Evolution. In diesem Beitrag diskutieren wir den gegenwärtigen Artbegriff am Beispiel der Prokaryonten, also der Organismen, die als die am weitesten diversifizierten Lebewesen gelten. Der Begriff „Art“ wird derzeit wie folgt umschrieben: Eine Prokaryontenart ist eine Kategorie, die eine (vorzugsweise) genomisch kohärente Gruppe individueller Isolate/Stämme beschreibt, die in Vergleichstests unter hoch standardisierten Bedingungen einen hohen Grad von Ähnlichkeit hinsichtlich (vieler) voneinander unabhängiger Merkmale zeigen. Obwohl die Anzahl der beschriebenen Prokaryontenarten in der Welt des Lebenden unterrepräsentiert ist, gilt dieser phylophenetische oder polythetische Artbegriff, der heute benutzt wird, als pragmatisch, brauchbar, allgemeingültig und erfolgreich in seiner Anwendung in Identifikationsverfahren.
Résumé
Les espèces constituent la base du modèle taxinomique. Elles sont la catégorie taxinomique la plus basse et servent d’unités pour la description de la biodiversité et de l’évolution. Dans notre article, nous étudions le concept courant d’espèce en prenant l’exemple des procaryotes, qui sont considérés comme présentant la plus grande diversité parmi les organismes vivants. La notion d’espèce est actuellement délimitée comme suit : une espèce procaryote est une catégorie comprenant un groupe d’individus/de variétés (de préférence) cohérent du point de vue génomique et présentant un degré élevé de similarités pour de (nombreuses) caractéristiques indépendantes les unes des autres. Bien que le nombre d’espèces procaryotes décrites soit sous-représenté dans le monde vivant, ce concept phylo-phénétique ou polythétique d’espèce en usage aujourd’hui, est considéré comme pragmatique, opérationnel, universellement applicable et utilisé avec succès dans les procédés d’identification.
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References
Boucher Y, Nesbo CL, Doolitle WF (2001) Microbial genomes: dealing with diversity. Curr Opin Microbiol 4:285–289
Buchanan RE, John-Brooks RS, Breed RS (1948) International bacteriological code of nomenclature. J Bacteriol 55:287–306
Cohan FM (2002) What are bacterial species? Annu Rev Microbiol 56:457–487
Colwell RR, Clayton RA, Ortiz-Conde BA, Jacobs D, Russek-Cohen E (1995) The microbial species concept and biodiversity. In: Allsopp D, Colwell RR, Hawksworth DL (eds) Microbial diversity and ecosystems function. CAB International, Oxon, pp 3–15
Cowan ST (1965) Principles and practice of bacterial taxonomy—a forward look. J Gen Microbiol 39:48–159
Dykhuizen DE (1998) Santa Rosalia revisited: why are there so many species of bacteria? Ant van Leeuwen 73:25–33
Euzéby JP (1997) List of bacterial names with standing in nomenclature. Société de Bactériologie Systématique et Vétérinaire. http://www.bacterio.cict.fr/. Cited 2003
Goodfellow M, Minnikin DE (eds) (1985) Chemical methods in bacterial systematics. Academic, London
Goodfellow M, Jones D, Priest FG (eds) (1985) Computer-assisted bacterial systematics. Academic, London
Goodfellow M, Manfio GP, Chun J (1997) Towards a practical species concept for cultivable bacteria. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman & Hall, London, pp 25–60
Grimont PAD (1988) Use of DNA reassociation in bacterial classification. Can J Microbiol 34:541–546
Hey J (2001a) Genes, categories and species. Oxford University Press, New York
Hey J (2001b) The mind of the species problem. Trends Ecol Evol 16:326–329
Hughes JB, Hellmann JJ, Rickets TH, Bohannan BJM (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Env Microbiol 67:4399–4406
Hull DL (1997) The ideal species concept-and why we can’t get it. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman & Hall, London, pp 357–380
Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401
Lengeler JW, Drews G, Schlegel HG (eds) (1999) Biology of prokaryotes. Thieme, Stuttgart
Ludwig W, Schleifer KH (1994) Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15:155–173
Madigan MT, Martinko JM, Parker J (eds) (2001) Mikrobiologie, Spektrum Akademischer, Heidelberg
Mallet M (1995) A species definition for the modern synthesis. Trends Ecol Evol 10:294–299
Mayden RL (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman & Hall, London, pp 381–324
Mühlhardt C (2003) Der Experimentator: Molekularbiologie/Genomics. Spektrum Akademischer, Heidelberg
Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299–304
Rosselló-Mora (2003) Opinion: the species problem, can we achieve a universal concept? Syst Appl Microbiol 26:323–326
Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67
Rosselló-Mora R, Kämpfer P (2004) Defining microbial diversity—the species concept for prokaryotic and eukaryotic microorganisms. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington DC, pp 29–39
Sneath PHA (1983) Distortions of taxonomic structure from incomplete data on a restricted set of reference strains. J Gen Microbiol 129:1045–1073
Sneath PHA (1992) International code of nomenclature of bacteria. American Society for Microbiology. Washington DC
Sneath PHA (1993) Evidence fromAeromonasfor genetic crossing-over in ribosomal sequences. Int J Syst Bacteriol 43:626–629
Sneath PHA, Sokal RR (1973) Numerical taxonomy. W.H. Freeman, San Francisco
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
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, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047
Stahl DA (1996) Molecular approaches for the measurement of density, diversity and phylogeny. In: Hurst CJ, Knudsen GR, McInerney MJ, Stetzenbach LD, Walter MV (eds) Manual of environmental microbiology. ASM Press, Washington DC, pp 102–114
Strätz M, Mau M, Timmis KN (1996) System to study horizontal gene exchange among microorganisms without cultivation of recipients. Mol Microbiol 22:207–215
Trüper HG (1999) How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature. FEMS Microbiol Rev 23:231–249
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 45:604
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
Van Niel CB, Allen MB (1952) A note on Pseudomonas stutzeri. J Bacteriol 64:413–422
Van Regenmortel MHV (1997) Viral species. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman and Hall, London, pp 17–24
Ward DM (1998) A natural species concept for prokaryotes. Curr Opin Microbiol 1:271–277
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
Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons exist in the genome of the actinomyceteThermomonospora chromogenaand evidence for horizontal gene transfer of an entire rRNA operon. J Bacteriol 181:5210–5209
Young JM (2001) Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 51:945–953
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Kämpfer, P., Rosselló-Mora, R. The species concept for prokaryotic microorganisms—An obstacle for describing diversity?. Poiesis Prax 3, 62–72 (2004). https://doi.org/10.1007/s10202-004-0068-3
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DOI: https://doi.org/10.1007/s10202-004-0068-3