Taxonomy and Systematics
Introduction
Systematics may succinctly be described as "the cradle of comparative biology". It encompasses ☞ characterization, ☞ classification, and nomenclature. The term "taxonomy" is often used interchangeably with systematics. It appears to make more sense to regard taxonomy as the domain within systematics that is concerned with classification. As an aspect of systematics, taxonomy thus constitutes a kind of classification that uses names and by doing so is affected by the ☞ rules of nomenclature. Identification is often considered to be a part of taxonomy but may better be regarded as a ☞ separate kind of undertaking that depends on taxonomy.
Resources
Information on taxonomy and systematics available at LPSN:
A chronologically sorted selection of publications on the taxonomy of prokaryotes:
2001-2005
- MURRAY (R.G.E.), HOLT (J.G.), KRIEG (N.R.), GARRITY (G.M.), BRENNER (D.J.), STALEY (J.T.), SNEATH (P.H.A.), LUDWIG (W.), KLENK (H.P.), AMANN (R.), SCHLEIFER (K.H.), TRÜPER (H.G.), ZINDER (S.H.), SALYERS (A.A.) and LABEDA (D.P.): Introductory chapters. In: D. R. BOONE, R. W. CASTENHOLZ and G. M. GARRITY (eds), Bergey’s Manual of Systematic Bacteriology. The Archaea and the Deeply Branching and Phototrophic Bacteria, second edition, vol. 1, Springer, New York, 2001, pp. 1-166.
- STACKEBRANDT (E.), FREDERIKSEN (W.), GARRITY (G.M.), GRIMONT (P.A.D.), KÄMPFER (P.), MAIDEN (M.C.J.), NESME (X.), ROSSELLO-MORA (R.), SWINGS (J.), TRÜPER (H.G.), VAUTERIN (L.), WARD (A.C.) and WHITMAN (W.B.): Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology 2002, 52, 1043–1047.
- STACKEBRANDT (E.): Will we ever understand? The undescribable diversity of the prokaryotes. Acta Microbiologica et Immunologica Hungarica, 2004, 51, 449-462.
2006-2010
- STACKEBRANDT (E.): Defining Taxonomic Ranks. In: DWORKIN, M., FALKOW, S., ROSENBERG, E., SCHLEIFER, K.H. and STACKEBRANDT, E. (eds), The Prokaryotes, Springer, New York, 2006, pp. 29-57.
- STACKEBRANDT (E.) and EBERS (J.): Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 2006, 33, 152–155.
- BUCKLEY (M.) and ROBERTS (R. J.): Reconciling microbial systematics and genomics. American Academy of Microbiology, Washington DC, 2007, pp. 1-10.
- TINDALL (B.J.), SIKORSKI (J.), SMIBERT (R.A.) and KRIEG (K.R.): Phenotypic Characterization and the Principles of Comparative Systematics. In: C.A. REDDY, T.J. BEVERIDGE, J.A. BREZNAK, G. MARZLUF, T.M. SCHMIDT, L.R. SNYDER (editors), Methods for General and Molecular Microbiology, 3rd Edition, ASM Science, Washington (D.C.), 2007, p. 330-393.
- Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Systematic and Applied Microbiology 2010; 33:175-182.
- Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249-266.
2011-2015
- Schumann P. Peptidoglycan structure. In: Rainey FA, Oren A (eds), Taxonomy of Prokaryotes, Academic Press, Chennai, 2011, pp. 101-129.
- Kampfer P, Glaeser SP. Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited. Environ Microbiol 2012; 14:291-317.
- Sutcliffe IC, Trujillo ME, Goodfellow M. Special Issue on The BISMiS 2011 Prokaryotic Systematics, a vital discipline entering a period of transition. Antonie van Leeuwenhoek 2012; 101:1-2.
- Göker M, Klenk HP. Phylogeny-driven target selection for genome-sequencing (and other) projects. Standards in Genomic Sciences 2013; 8:360-374.
- Kämpfer P, Glaeser SP. Prokaryote Characterization and Identification. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds), The Prokaryotes. Prokaryotic Biology and Symbiotic Associations, fourth edition, vol. 1. Springer, Heidelberg, 2013, pp. 123-147.
- Konstantinidis KT, Stackebrandt E. Defining Taxonomic Ranks. In: Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F (eds), The Prokaryotes. Prokaryotic Biology and Symbiotic Associations, fourth edition, vol. 1. Springer, Heidelberg, 2013, pp. 229-254.
- Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy? Archives of Microbiology 2013; 195:413-418.
- Meier-Kolthoff JP, Hahnke L, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin A, Chertkov O, Reddy K, Pati A, Ivanova N, Markowitz V, Kyrpides C, Woyke T, Göker M, Klenk HP. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Standards in Genomic Sciences 2014; 10:2.
- Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of the G+C content and DNA:DNA hybridization in the genomic age. International Journal of Systematic and Evolutionary Microbiology 2014; 64:352-356.
- Oren A, Garrity GM. Then and now: a systematic review of the systematics of prokaryotes in the last 80 years. Antonie Van Leeuwenhoek 2014; 106:43-56.
- Vandamme P, Peeters C. Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 2014; 106:57-65.
Useful online tools concerning prokaryotic taxonomy: