bacterial taxonomy bacterial taxonomy bacterial taxonomy is subfield of taxonomy devoted to the classification of bacteria specimens into taxonomic ranks. the hierarchy of biological classification's eight major taxonomic ranks. intermediate minor rankings are not shown. 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 main article: bacteria bacteria (prokaryotes, together with archaea) share many common features. these commonalities include the lack a of nuclear membrane, unicellularity, division by binary-fission and generally small size. the various species can be differentiated through the comparison of on 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 called them "animalcules" and 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); polyangium, by h. f. link (1809), the first bacterium still recognized today; serratia, by bizio (1823); and spirillum, spirochaeta and bacterium, by ehrenberg (1838). the term bacterium, introduced as a genus by ehrenberg in 1838, became a catch-all for rod-shaped cells. early formal classifications tree of life in generelle morphologie der organismen (1866) bacteria were first 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: die gymnomoneren (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 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" (plural "monera") in english and "eine moneren"(fem. pl. "moneres") 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 (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. 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, 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. cohn recognized four tribes: spherobacteria, microbacteria, desmobacteria, and spirobacteria. stanier and van neil recognized the kingdom monera with two phyla, myxophyta and schizomycetae, the latter comprising classes eubacteriae (three orders), myxobacteriae (one order), and spirochetae (one order). 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 established two orders: cephalotrichinae (seven families) and peritrichinae (presumably with only one family). bergey et al. 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) bacteria (cohn 1872 b) schizomycetaceae (detoni and trevisan 1889) 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 sorted out several problems. a. r. prévot's system) 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) linnaeus1735 haeckel1866 chatton1925 copeland1938 whittaker1969 woese et al.1990 cavalier-smith1998 cavalier-smith2015 2 kingdoms 3 kingdoms 2 empires 4 kingdoms 5 kingdoms 3 domains 2 empires, 6 kingdoms 2 empires, 7 kingdoms (not treated) protista prokaryota monera monera bacteria bacteria bacteria archaea archaea eukaryota protoctista protista eucarya protozoa protozoa chromista chromista vegetabilia plantae plantae plantae plantae plantae fungi fungi fungi animalia animalia animalia animalia animalia animalia 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 order 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 (gram-positive, subsequently corrected to firmicutes) 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) "archaic bacteria" and woese's reclassification main article: archaea phylogenetic tree showing the relationship between the archaea and other forms of life. eukaryotes are colored red, archaea green and bacteria blue. adapted from ciccarelli et al. 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's 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 (erroneously) 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 (regio in latin) which divided life into 3 domains: the eukaryota, the archaea and the bacteria. subdivisions main article: bacterial phyla in 1987 carl woese divided the eubacteria into 11 divisions based on 16s ribosomal rna (ssu) sequences, which with several additions are still used today. opposition while the three domain system is widely accepted, some authors have opposed it for various reasons. one prominent scientist who opposes the three domain system is thomas cavalier-smith, who proposed that the archaea and the eukaryotes (the neomura) stem from gram positive bacteria (posibacteria), which in turn derive from gram negative bacteria (negibacteria) based on several logical arguments, which are highly controversial and generally disregarded by the molecular biology community (c.f. reviewers' comments on, e.g. eric bapteste is "agnostic" regarding the conclusions) and are often not mentioned in reviews (e.g.) due to the subjective nature of the assumptions made. however, despite there being a wealth of statistically supported studies towards the rooting of the tree of life between the bacteria and the neomura by means of a variety of methods, including some that are impervious to accelerated evolution—which is claimed by cavalier-smith to be the source of the supposed fallacy in molecular methods—there are a few studies which have drawn different conclusions, some of which place the root in the phylum firmicutes with nested archaea. radhey gupta's molecular taxonomy, based on conserved signature sequences of proteins, includes a monophyletic gram negative clade, a monophyletic gram positive clade, and a polyphyletic archeota derived from gram positives. hori and osawa's molecular analysis indicated a link between metabacteria (=archeota) and eukaryotes. the only cladistic analyses for bacteria based on classical evidence largely corroborate gupta's results (see comprehensive mega-taxonomy). james lake presented a 2 primary kingdom arrangement (parkaryotae + eukaryotes and eocytes + karyotae) and suggested a 5 primary kingdom scheme (eukaryota, eocyta, methanobacteria, halobacteria, and eubacteria) based on ribosomal structure and a 4 primary kingdom scheme (eukaryota, eocyta, methanobacteria, and photocyta), bacteria being classified according to 3 major biochemical innovations: photosynthesis (photocyta), methanogenesis (methanobacteria), and sulfur respiration (eocyta). he has also discovered evidence that gram-negative bacteria arose from a symbiosis between 2 gram-positive bacteria. authorities