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 (which may or may not be endorsed by those responsible for LPSN) on the taxonomy of prokaryotes:
1986-1990
- Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 1987; 37:463-464.
- Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433-434.
- Wayne LG. International Committee on Systematic Bacteriology announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. J Appl Bacteriol 1988; 64:283-284.
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.
- Christensen H, Bisgaard M, Frederiksen W, Mutters R, Kuhnert P, Olsen JE. Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 Revision). Int J Syst Evol Microbiol 2001; 51:2221-2225.
- 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.
- Hedlund BP, Dodsworth JA, Staley JT. The changing landscape of microbial biodiversity exploration and its implications for systematics. Syst Appl Microbiol 2015; 38:231-236.
- Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes. Syst Appl Microbiol 2015; 38:217-222.
- Yilmaz P, Yarza P, Rapp JZ, Glockner FO. Expanding the World of Marine Bacterial and Archaeal Clades. Front Microbiol 2015; 6:1524.
2016-2020
- Overmann J, Abt B, Sikorski J. Present and future of culturing bacteria. Annual Review of Microbiology 2017; 71:711-730.
- Brown DR. Notice of impending dissolution of inactive Subcommittees on Taxonomy. Int J Syst Evol Microbiol 2018; 68:2102-2103.
- Chuvochina M, Rinke C, Parks DH, Rappe MS, Tyson GW, Yilmaz P, Whitman WB, Hugenholtz P. The importance of designating type material for uncultured taxa. Syst Appl Microbiol 2019; 42:15-21.
- Overmann J, Huang S, Nübel U, Hahnke RL, Tindall BJ. Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms. Systematic and Applied Microbiology 2019; 42:22-29.
- Stackebrandt E, Smith D. Paradigm shift in species description: the need to move towards a tabular format. Archives of Microbiology 2019; 201:143–145.
2021-2025
- Göker M. What can genome analysis offer for bacteria? In: Bridge P, Smith D, Stackebrandt E (eds), Trends in the systematics of bacteria and fungi, CAB International, Wallingford, 2021, pp. 255-281.
- Liu C, Du MX, Abuduaini R, Yu HY, Li DH, Wang YJ, Zhou N, Jiang MZ, Niu PX, Han SS, et al. Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank. Microbiome 2021; 9:119.
- Sanford RA, Lloyd KG, Konstantinidis KT, Loffler FE. Microbial Taxonomy Run Amok. Trends Microbiol 2021; 29:394-404.
Useful online tools concerning prokaryotic taxonomy: