Bacterial taxonomy is subfield of taxonomy devoted to the classification of bacteria specimens into taxonomic ranks. Archaeal taxonomy are governed by the same rules.
In the scientific classification established by Carl Linnaeus, each species is assigned to a genus resulting in a two-part name. This name denotes the two lowest levels in a hierarchy of ranks, increasingly larger groupings of species based on common traits. Of these ranks, domains are the most general level of categorization. Presently, scientists classify all life into just three domains, Eukaryotes, Bacteria and Archaea.
Bacterial taxonomy is the classification of strains within the domain Bacteria into hierarchies of similarity. This classification is similar to that of plants, mammals, and other taxonomies. However, biologists specializing in different areas have developed differing taxonomic conventions over time. For example, bacterial taxonomists name types based on descriptions of strains. Zoologists among others use a type specimen instead.
Diversity
Bacteria (prokaryotes, together with Archaea) share many common features. These commonalities include the lack of a nuclear membrane, unicellularity, division by binary-fission and generally small size. The various species can be differentiated through the comparison of several characteristics, allowing their identification and classification. Examples include: Phylogeny: All bacteria stem from a common ancestor and diversified since, and consequently possess different levels of evolutionary relatedness (see Bacterial phyla and Timeline of evolution) Metabolism: Different bacteria may have different metabolic abilities (see Microbial metabolism) Environment: Different bacteria thrive in different environments, such as high/low temperature and salt (see Extremophiles) Morphology: There are many structural differences between bacteria, such as cell shape, Gram stain (number of lipid bilayers) or bilayer composition (see Bacterial cellular morphologies, Bacterial cell structure)
History
First descriptions Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. He did not distinguish bacteria as a separate type of microorganism, calling all microorganisms, including bacteria, protists, and microscopic animals, "animalcules". He published his observations in a series of letters to the Royal Society.
Early described genera of bacteria include Vibrio and Monas, by O. F. Müller (1773, 1786), then classified as Infusoria (however, many species before included in those genera are regarded today as protists, which are eukaryotes); Polyangium, by H. F. Link (1809), the first bacterium still recognized today; Serratia, by Bizio (1823); and Spirillum, Spirochaeta and Bacterium, by Ehrenberg (1838).Murray, R.G.E., Holt, J.G. (2005). The history of Bergey's Manual. In: Garrity, G.M., Boone, D.R. & Castenholz, R.W. (eds., 2001). Bergey's Manual of Systematic Bacteriology, 2nd ed., Vol. 1, Springer-Verlag, New York, pp. 1–14. link. [See p. 2.]Pot, B., Gillis, M., and De Ley, J., The genus Aquaspirillum. In: Balows, A., Trüper, H.G., Dworkin, M., Harder, W., Schleifer, K.-H. (Eds.). The prokaryotes, 2nd ed, Vol. 3. Springer-Verlag. New York. 1991
The term Bacterium, introduced as a genus by Ehrenberg in 1838, became a catch-all for rod-shaped cells.
Early formal classifications
In 1857, bacteria were classified as plants constituting the class Schizomycetes, which along with the Schizophyceae (blue green algae/Cyanobacteria) formed the phylum Schizophyta.
Haeckel in 1866 placed the group in the phylum Moneres (from μονήρης: simple) in the kingdom Protista and defines them as completely structureless and homogeneous organisms, consisting only of a piece of plasma. He subdivided the phylum into two groups: (no envelope) Protogenes – such as Protogenes primordialis, now classed as a eukaryote and not a bacterium Protamaeba – now classed as a eukaryote and not a bacterium Vibrio – a genus of comma shaped bacteria first described in 1854Pacini, F.: Osservazione microscopiche e deduzioni patologiche sul cholera asiatico. Gazette Medicale de Italiana Toscano Firenze, 1854, 6, 405-412. Bacterium – a genus of rod shaped bacteria first described in 1828, that later gave its name to the members of the Monera, formerly referred to as "a moneron" (plural "monera") in English and ""(fem. pl. "") in German Bacillus – a genus of spore-forming rod shaped bacteria first described in 1835Ehrenberg, C. G. (1835). "Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes". Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften zu Berlin aus den Jahren 1833-1835, pp. 143–336. Spirochaeta – thin spiral shaped bacteria first described in 1835 Spirillum – spiral shaped bacteria first described in 1832Ehrenberg, C. G. (1830). "Beiträge zur Kenntnis der Organization der Infusorien und ihrer geographischen Verbreitung besonders in Sibirien". Abhandlungen der Koniglichen Akademie der Wissenschaften zu Berlin 1832, pp. 1–88. etc. (with envelope) Protomonas – now classed as a eukaryote and not a bacterium. The name was reused in 1984 for an unrelated genus of Bacteria Vampyrella – now classed as a eukaryote and not a bacterium
The classification of Ferdinand Cohn (1872) was influential in the nineteenth century, and recognized six genera: Micrococcus, Bacterium, Bacillus, Vibrio, Spirillum, and Spirochaeta.
The group was later reclassified as the Prokaryotes by Chatton in 1925.
The classification of Cyanobacteria (colloquially "blue green algae") has been fought between being algae or bacteria (for example, Haeckel classified Nostoc in the phylum Archephyta of Algae).
in 1905, Erwin F. Smith accepted 33 valid different names of bacterial genera and over 150 invalid names,Smith, Erwin F. (1905). Nomenclature and Classification in Bacteria in Relation to Plant Diseases, Vol. 1. and Vuillemin, in a 1913 study,Vuillemin (1913). "Genera Schizomycetum". Annales Mycologici, Vol. 11, pp. 512–527. concluded that all species of the Bacteria should fall into the genera Planococcus, Streptococcus, Klebsiella, Merista, Planomerista, Neisseria, Sarcina, Planosarcina, Metabacterium, Clostridium, Serratia, Bacterium, and Spirillum.
in 1875, CohnCohn, Ferdinand (1875). "Untersuchungen uber Bakterien, II". Beitrage zur Biologie der Pfanzen, Vol. 1: pp. 141–207 recognized four tribes: Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria. Stanier and van Neil in 1941Stanier and van Neil (1941). "The main outlines of bacterial classification". Journal of Bacteriology, Vol. 42, pp. 437– 466 recognized the kingdom Monera with two phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae (three orders), Myxobacteriae (one order), and Spirochetae (one order). In 1962, BissetBisset (1962). Bacteria, 2nd ed.; London: Livingston. distinguished 1 class and 4 orders: Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales. Walter Migula's system (1897),Migula, Walter (1897). System der Bakterien. Jena, Germany: Gustav Fischer. which was the most widely accepted system of its time and included all then-known species but was based only on morphology, contained the three basic groups Coccaceae, Bacillaceae, and Spirillaceae, but also Trichobacterinae for filamentous bacteria. Orla-Jensen in 1909Orla-Jensen (1909). "Die Hauptlinien des naturalischen Bakteriensystems nebst einer Ubersicht der Garungsphenomene". Zentr. Bakt. Parasitenk., Vol. II, No. 22, pp. 305–346 established two orders: Cephalotrichinae (seven families) and Peritrichinae (presumably with only one family). Bergey et al. in 1925Bergey's Manual of Determinative Bacteriology (1925). Baltimore: Williams & Wilkins Co. (with many subsequent editions). presented a classification which generally followed the 1920 Final Report of the Society of American Bacteriologists Committee (Winslow et al.), which divided class Schizomycetes into four orders: Myxobacteriales, Thiobacteriales, Chlamydobacteriales, and Eubacteriales, with a fifth group being four genera considered intermediate between bacteria and protozoans: Spirocheta, Cristospira, Saprospira, and Treponema.
However, different authors often reclassified the genera due to the lack of visible traits to go by, resulting in a poor state which was summarised in 1915 by Robert Earle Buchanan. By then, the whole group received different ranks and names by different authors, namely: Schizomycetes (Naegeli 1857) Bacteriaceae (Cohn 1872 a)Cohn, Ferdinand (1872 a). "Organismen in der Pockenlymphe". Virchow (ed.), Archiv, Vol. 55, p. 237. Bacteria (Cohn 1872 b)Cohn, Ferdinand (1872 b) "Untersuchungen ilber Bakterien". Beitrage zur Biologie der Pflanzen Vol. 1, No. 1, p. 136. Schizomycetaceae (DeToni and Trevisan 1889)Detoni, J. B.; Trevisan, V. (1889). "Schizomycetaceae". Saccardo (ed.), Sylloge Fungorum, Vol. 8, p. 923. Furthermore, the families into which the class was subdivided changed from author to author and for some, such as Zipf (1917), the names were in German and not in Latin.
The first edition of the Bacteriological Code in 1947 set a standardised system and authority for the classification of Bacteria.
A. R. Prévot's system (1958)Prévot, A. R. (1958). Manuel de classification et détermination des bactéries anaérobies. Paris: Masson.Prévot, A. R. (1963). Bactéries in Précis de Botanique. Paris: Masson. had four subphyla and eight classes, as follows: Eubacteriales (classes Asporulales and Sporulales) Mycobacteriales (classes Actinomycetales, Myxobacteriales, and Azotobacteriales) Algobacteriales (classes Siderobacteriales and Thiobacteriales) Protozoobacteriales (class Spirochetales)
Informal groups based on Gram staining Despite there being little agreement on the major subgroups of the Bacteria, Gram staining results were most commonly used as a classification tool. Consequently, until the advent of molecular phylogeny, the Kingdom Prokaryota was divided into four divisions, A classification scheme still formally followed by Bergey's manual of systematic bacteriology for tome orderGeorge M. Garrity: Bergey's manual of systematic bacteriology. 2. Auflage. Springer, New York, 2005, Volume 2: The Proteobacteria, Part B: The Gammaproteobacteria Gracilicutes (gram-negative) Photobacteria (photosynthetic): class Oxyphotobacteriae (water as electron donor, includes the order Cyanobacteriales=blue-green algae, now phylum Cyanobacteria) and class Anoxyphotobacteriae (anaerobic phototrophs), orders: Rhodospirillales and Chlorobiales Scotobacteria (non-photosynthetic, now the Proteobacteria and other gram-negative nonphotosynthetic phyla) Firmacutes [sic] (gram-positive, subsequently corrected to FirmicutesMURRAY (R.G.E.): The higher taxa, or, a place for everything...? In: N.R. KRIEG and J.G. HOLT (ed.) Bergey's Manual of Systematic Bacteriology, Vol. 1, The Williams & Wilkins Co., Baltimore, 1984, pp. 31–34) several orders such as Bacillales and Actinomycetales (now in the phylum Actinobacteria) Mollicutes (gram variable, e.g. Mycoplasma) Mendocutes (uneven gram stain, "methanogenic bacteria", now known as the Archaea)
Molecular era "Archaic bacteria" and Woese's reclassification