Systematics of prokaryotes: the state of the art
Tóm tắt
The term taxonomy is often used synonymously with systematics but it should be regarded more as a specific part of the latter and comprises the orderly arrangements of (defined) units in addition to the nomenclature, i.e. labelling of these units defined by classification, and also identification of these units defined by classification and labeled by nomenclature. Similar to all biological disciplines, taxonomic approaches in microbiology aim at the establishment of a system that mirrors the “order in nature” as closely as possible with the ultimate goal to describe the whole evolutionary order back to the origin of life. With the recognition of molecular markers present in all organisms (here in particular the small subunit rRNAs, ssRNSs), the achievement of this goal has become more and more feasible and the generation of gene and increasing numbers of genome sequences allow nowadays the generation of large amounts of data and often a very detailed insight into the genetic potential of prokaryotes. The possibility to generate whole genome sequences in a very short period of time leads to a strong tendency to base the taxonomic system more and more on sequence data. However, a comprehensive understanding of all the information behind sequence data is lagging far behind their accumulation. Genes and genomes may (or may not) function only in a given “environment”, with the cell as basic entity for the display of this potential. Prokaryotic taxonomy still has its focus on the whole organism. In this context, natural selection drives evolution selecting the existing phenotypes and it is the phenotype that “exhibits” this process both in a given cellular and also environmental context. The term polyphasic taxonomy, which was coined almost 40 years ago and aimed at the integration of many levels of information (from molecular to ecological data) thereby allowing a more holistic view, should be revisited in the light of the enormous potential of the novel information associated with large data sets.
Tài liệu tham khảo
Bapteste E, Boucher Y (2008) Lateral gene transfer challenges principles of microbial systematics. Trends Microbiol 16:200–207
Bapteste E, O’Malley MA, Beiko RG, Ereshefky M, Gogarten JP, Franklin-Hall L et al (2009) Prokaryotic evolution and the tree of life are two different things. Biology Direct 4:34. doi:101186/1745-6150-4-34
Brenner DJ, Staley JT, Krieg NR (2001) Classification of prokaryotic organisms and the concept of bacterial speciation. In: Garrity GM (ed) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn. Springer, New York, pp 27–31
Brenner S (2010) Sequences and consequences. Phil Trans R Soc B 365:207–212
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287
Cole JR, Konstinidis K, Farris RJ, Tiedje JM (2010) Microbial diversity phylogeny: extending from rRNAs to genomes. In: Liu W-T, Jackson JK (eds) Environmental molecular microbiology. Caister Academic Press, Norfolk, pp 1–19
Colwell RR (1970) Polyphasic taxonomy of bacteria. In: Iizuka H, Hazegawa T (eds) Culture collections of microorganisms. University of Tokyo Press, Tokyo, pp 421–436
Cowan ST (1978) A dictionary of microbial taxonomy. Cambridge University Press, Cambridge
Dagan T, Artzy-Rrandup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Nat Acad Sci USA 105:10039–10044
De Vos P, Trüper HG (2000) Judicial Commission of the International Committee of Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15, 18 August 1999, Sydney, Australia. Int J Syst Evol Microbiol 50:2239–2244
Doroghazi JR, Buckley DH (2010) Widespread homologous recombination within and between Streptomyces species. ISME J 4:136–1143
Euzéby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590–592
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ et al (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739
Giffard P (2010) Bioinformatics of microbial sequences. In: Sintchenko V (ed) Infectious diseases informatics. Springer, New York, pp 27–52
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91
Harayama S, Kasai H (2006) Bacterial phylogeny reconstruction from molecular sequences. In: Stackebrandt E (ed) Molecular identification, systematics, and population structure of prokaryotes. Springer, Berlin, pp 105–140
Kämpfer P (2010) Certificates of deposit—a key element of the bacteriological code and an indispensable prerequisite for comparative taxonomic research. Report of a case of falsification and a reply to the letter to the editor by Tindall (2008). Int J Syst Evol Microbiol 60:475–477
Kämpfer P, Glaeser S (2011a) Prokaryotic taxonomy in the sequencing era and the role of MLSA in classification. Microbiology Australia 32:66–70
Kämpfer P, Glaeser S. (2011b) Prokaryotic taxonomy in the sequencing era—the polyphasic approach revisited. Env Microbiol (in press)
Klenk H-P, Göker M (2010) En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 33:175–182
Konstantinidis KT, Ramette A, Tiedje JM (2006) The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361:1929–1940
Konstantinidis KT, Tiedje JM (2005) Genomic insights into the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572
Konstantinidis KT, Tiedje JM (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10:504–509
Koonin EV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1:27–136
Krichevsky MI (2011) What is a bacterial species? I will know it when I see it. The Bulletin of BISMiS 2:17–23
Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56:17–24
Labeda DP (2000) International committee on systematic bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14 and 17 August 1999, Sydney, Australia. Int J Syst Evol Microbiol 50:2245–2247
Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA (1992) International code of nomenclature of bacteria (1990 Revision). American Society for Microbiology, Washington
Ludwig W (2010) Molecular phylogeny of microorganisms: is rRNA still a useful marker? In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, Norfolk, pp 65–84
Ludwig W, Klenk H-P (2001) Overview: a phylogenetic backbone and taxonomic framework of prokaryotes. In: Garrity GM (ed) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 49–65
Maiden MC, Bygraves JA, Feil E, Morelli G, Russel JE, Urwin R et al (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145
Moore ERB, Mihaylova SA, Vandamme P, Krichevsky MI, Dijkshoorn L (2010) Microbial systematics and taxonomy: relevance for a microbial commons. Res Microbiol 161:430–438
Murray RGE, Brenner DJ, Colwell RR, De Vos P, Goodfellow M, Grimont PAD et al (1990) Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. Int J Syst Bacteriol 40:213–215
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 45:19126–19131
Sneath PHA (1989) Analysis and interpretation of sequence data for bacterial systematics—the view of a numerical taxonomist. Syst Appl Microbiol 12:15–31
Sneath PHA (2007) The species concept. Microbiol Today 34:45
Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ et al (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
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, Woese CR (1981) Towards a phylogeny of the actinomycetes and related organism. Curr Microbiol 5:197–202
Tindall BJ (2008) Confirmation of deposit, but confirmation of what? Int J Syst Evol Microbiol 58:1785–1787
Tindall BJ, De Vos P, Trüper HG (2008a) Judicial Commission of the International Committee of Systematics of Prokaryotes. XIth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 23, 24, 27 July 2005, San Francisco, CA, USA. Int J Syst Evol Microbiol 58:1737–1745
Tindall BJ, Garrity GM (2008) Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic research. Int J Syst Evol Microbiol 58:1987–1990
Tindall BJ, Kämpfer P, Euzéby JP, Oren A (2006) Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. Int J Syst Evol Microbiol 56:2715–2720
Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266
Tindall BJ, Sikorski J, Smibert RA, Krieg NL (2008b) Phenotypic characterization and the principles of comparative systematics. In: Garrity GM (ed) Methods for general and molecular microbiology, 3rd Ed. ASM Press, Washington, pp 330–393
Vinuesa P (2010) Multilocus sequence analysis and bacterial species phylogeny estimation. In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, norfolk, pp 41–64
Wayne LG, 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. Int J Syst Bacteriol 37:463–464
Welker M, Moore ER (2011) Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 34:2–11
Williams D, Andam CP, Gogarten JP (2010) Horizontal gene transfer and the formation of groups of microorganisms. In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, Norfolk, pp 167–184
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Woese CR, Fox E (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Nat Acad Sci USA 74:5088–5090
Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250
Young JM (2001) Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 51:945–953