Bacterial taxonomy


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 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
  • Metabolism: Different bacteria may have different metabolic abilities
  • Environment: Different bacteria thrive in different environments, such as high/low temperature and salt
  • Morphology: There are many structural differences between bacteria, such as cell shape, Gram stain or bilayer composition

    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, then classified as Infusoria ; Polyangium, by H. F. Link, the first bacterium still recognized today; Serratia, by Bizio ; and Spirillum, Spirochaeta and Bacterium, by Ehrenberg.
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 formed the phylum Schizophyta.
Haeckel in 1866 placed the group in the phylum Moneres 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:
  • die Gymnomoneren
  • * 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 1854
  • * 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" in English and "eine Moneren" in German
  • * Bacillus – a genus of spore-forming rod shaped bacteria first described in 1835
  • * Spirochaeta – thin spiral shaped bacteria first described in 1835
  • * Spirillum – spiral shaped bacteria first described in 1832
  • * etc.
  • die Lepomoneren
  • * 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 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 has been fought between being algae or bacteria.
in 1905, Erwin F. Smith accepted 33 valid different names of bacterial genera and over 150 invalid names, and Vuillemin, in a 1913 study, 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, Cohn recognized four tribes: Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria. Stanier and van Neil in 1941 recognized the kingdom Monera with two phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae, Myxobacteriae, and Spirochetae. In 1962, Bisset distinguished 1 class and 4 orders: Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales. Walter Migula's system, 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 1909 established two orders: Cephalotrichinae and Peritrichinae. Bergey et al. in 1925 presented a classification which generally followed the 1920 Final Report of the Society of American Bacteriologists Committee, 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
  • Bacteriaceae
  • Bacteria
  • Schizomycetaceae
Furthermore, the families into which the class was subdivided changed from author to author and for some, such as Zipf, 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 had four subphyla and eight classes, as follows:
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 order
  • Gracilicutes
  • * Photobacteria : class Oxyphotobacteriae and class Anoxyphotobacteriae, orders: Rhodospirillales and Chlorobiales
  • * Scotobacteria
  • Firmacutes
  • *several orders such as Bacillales and Actinomycetales
  • Mollicutes
  • 'Mendocutes'''''

    Molecular era

"Archaic bacteria" and Woese's reclassification

Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. However, a few biologists argue that the Archaea and Eukaryota arose from a group of bacteria. In any case, it is thought that viruses and archaea began relationships approximately two billion years ago, and that co-evolution may have been occurring between members of these groups. It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared only later. Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote only surviving meaning is "not a eukaryote", limiting its value.
With improved methodologies it became clear that the methanogenic bacteria were profoundly different and were believed to be relics of ancient bacteria thus Carl Woese, regarded as the forerunner of the molecular phylogeny revolution, identified three primary lines of descent: the Archaebacteria, the Eubacteria, and the Urkaryotes, the latter now represented by the nucleocytoplasmic component of the Eukaryotes. These lineages were formalised into the rank Domain which divided Life into 3 domains: the Eukaryota, the Archaea and the Bacteria.
In 2023, the Prokaryotic Code added the ranks of domain and kingdom to the prokaryotic nomenclature. The names of Bacteria and Archaea are validly-published taxa following Oren and Goker's publication that use these new rules.

Subdivisions

In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA sequences, which with several additions are still used today.
Oren and Goker has also validly published a number of kingdoms as a layer higher than the division/phylum: