Systematics has been defined in many ways but may be succinctly described as "the cradle of comparative biology."
Taxonomy can be clearly defined as encompassing characterization, classification, and nomenclature.
The characterization of an organism is no longer bounded by methodological barriers, and it is now possible to fully sequence the whole genome of a strain, to study individual genes, or to examine the genetic information by using amplified fragment length polymorphism, random amplification of polymorphic DNA (RAPD), and G+C content analysis. However, genes do not exist on their own, and it is becoming increasingly clear that the study of the biochemical pathways of an organism, the roles structural elements (proteins and lipopolysaccharides, etc.) may play in morphology, or the chemical composition of the cell should be correlated with the underlying genetic information.
Classification is the arrangement of prokaryotes into groups. Different forms of classification may have different goals. Organisms may be grouped according to their pathogenic potentials (biological safety levels) or in an arrangement based on more complex theories (i.e., the course of evolution). Nomenclature is the naming of those groups. When the groups are species, genera, and families, etc., then the way they are named or the links between names which have been used in the past are governed by an International Code of Nomenclature (147).
Identification is often considered to be a part of taxonomy but is concerned with comparing unknown organisms with organisms which have already been classified. As such, identification can be carried out only once a taxonomy has been established. Typically, identification protocols have the goal of quickly assigning an organism to a known group by using the minimum number of methods. In contrast, a novel organism should be characterized as fully as possible in order for subsequent identification systems to have a reliable basis on which to work. The more reliable the characterization and classification, the greater chance one will have of being able to pick identification methods which both are accurate and have a long-term future.
Nomenclature is regulated in prokaryote systematics by an official system of registering (or indexing) those names which may be used in prokaryote taxonomy via a centralized system. The formal term for registering a name is "valid publication [of a name]." This system was unique to the International Code of Nomenclature of Bacteria (but virology has followed this principle) and was introduced in 1980 to combat uncertainties in the application of some 40,000 names; which had accumulated over the previous ~200 years. With the introduction of the Approved Lists of Bacterial Names (240), only 2,000+ names made the grade into the modern system. While nomenclature is formally regulated, it is important to be aware that taxonomy is not regulated by the code. Thus, the code recognizes a "valid published species name," but the term "validly published species" has no meaning, despite being frequently met with in some of the literature. In order for a name to be validly published, the proposal for the name must be accompanied by a number of criteria (147, 247, 248). Among these criteria - is the designation of a nomenclatural type. Just as physics has reference points for the meter or the kilogramm - so too does biology, with the nomenclatural types being the reference points for a taxon. In the cases of the species and subspecies, these reference points are represented by type strains (147). Given the central importance of type strains, it is important that they be made available as widely as possible. The best course of action would appear to be to deposit type strains in a suitable culture collection, which should be able to maintain the distribution of the strain in the future (83, 141). Clearly, depositing a type strain in such a way that it is not easy to access is counterproductive to the principle behind the deposit of type strains, that of making them widely and easily available for comparative purposes."
Excerpt from: Phenotypic Characterization and the Principles of Comparative Systematics. Brian J. Tindall, Johannes Sikorski, Robert A. Smibert, and Noel R. Krieg (2007). Methods for General and Molecular Microbiology, 3rd Edition. Editors: C. A. Reddy, Terry J. Beveridge, John A. Breznak, George Marzluf, Thomas M. Schmidt, Loren R. Snyder. Book ISBN or Item Number: 978-1-55581-223-2
- Kämpfer, P. & Glaeser, S. P. (2013) Prokaryote Characterization and Identification. In: The Prokaryotes, Volume 1: Prokaryotic Biology and Symbiotic Associations. 4th edn. (Eds. E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt & F. Thompson), pp. 123-147. Springer Heidelberg; ISBN: 978-3-642-30193-3 (Print) 978-3-642-30194-0 (Online).
- Konstantinidis, K. T. & Stackebrandt, E. (2013) Defining Taxonomic Ranks. dto, pp. 229-254.
- Several authors (2006). Introductory chapters in Bergey's Manual of Systematic Bacteriology, Vol. I, The Archaea and the Deeply Branching and Phototrophic Bacteria, 2nd edn. (Eds. D. R. Boone, R. W. Castenholz & G. M. Garrity). Springer, New York.
- Stackebrandt, E., Tindall, B., Ludwig, W. & Goodfellow, M. (1999). Prokaryotic diversity and systematics. In: Biology of the Prokaryotes (eds. J. Lengeler, G., Drews & H. Schlegel), pp. 675–720. G. Thieme, Stuttgart.
- Several authors (2012). Special Issue on The BISMiS 2011 Prokaryotic Systematics, Antonie van Leeuwenhoek, volume 101, January 2012. ISSN: 0003-6072 (Print) 1572-9699 (Online).
- American Academy of Microbiology (2007): Reconciling Microbial Systematics & Genomics
During the last decades bacterial taxonomy has undergone remarkable changes. Phylogenetic relationships have become an important basis in the classification of bacteria. New categories of information of taxonomic value have become available, e.g. chemotaxonomic markers, DNA base composition, DNA-DNA hybridisation, gene and genome sequencing. These pieces of information are collected and evaluated in a "polyphasic approach". This integrated use of phenotypic and genotypic characteristics had great influence on prokaryotic classification and nomenclature and will continue to do so in the future.
The naming of bacteria is controlled by the International Code of Nomenclature of Bacteria (Lapage et al., 1992). The correct name of a bacterial taxon is based on:
- Valid publication
- Priority of publication.
Since 1 January 1980, priority of bacterial names is based upon the APPROVED LISTS OF BACTERIAL NAMES (Skerman et al., 1980). Names that were not included in the APPROVED LISTS at that time lost standing in bacterial nomenclature.
Valid publication of new names and new nomenclatural combinations can only be made by publication in the INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROCBIOLOGY (IJSEM), either as an original article or in the "VALIDATION LISTS" regularly appearing in that journal. The VALIDATION LISTS constitute valid publications of new names and new combinations that were previously effectively published outside the IJSEM.The prerequisite for the acceptance of a description of a new taxon in the IJSEM is the deposit and free availabilty of the designated type strain in two open collections.
Names not considered to be validly published should no longer be used or should be used in quotation marks (e.g."Bacillus mesentericus") to denote that the name is not validly published.
A more detailed overview of the mechanisms of valid publication of a name according to the Bacteriological Code can be found at: dx.doi.org/10.1099/ijs.0.64780-0.
Below you will find several useful links concerning prokaryotic taxonomy:
- List of Prokaryotic names with Standing in NomenclatureJ. P. Euzéby, Ecole Nationale Vétérinaire de Toulouse, France (until June 2013), and A. Parte, Bergey's Manual Trust
- TOBA - Taxonomic Outline of the Bacteria and Archaea
- LTP - The All-Species Living Tree Project
- Key to Peptidoglycan Types
- GGDC (Genome-To-Genome Distance Calculator) Web Server