There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by

Carl Woese Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...

. The branching order proposed by Carl Woese was based on

molecular phylogeny Molecular phylogenetics () is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to ...

, which was considered revolutionary as all preceding models were based on discussions of morphology. (''v.''

Monera Monera (/məˈnɪərə/) (Greek - μονήρης (monḗrēs), "single", "solitary") is a biological kingdom that is made up of prokaryotes. As such, it is composed of single-celled organisms that lack a nucleus. The taxon Monera was first p ...

). Several models have been proposed since and no consensus is reached at present as to the branching order of the major bacterial lineages. The gene used was the 16S ribosomal DNA.

Tree

The names have been changed to reflect more current nomenclature used by molecular phylogenists.

Note on names

Despite the impact of the paper on bacterial classification, it was not a proposal for change of taxonomy. Consequently, many clades were given official names. Only subsequently, this occurred: for example, the "purple bacteria and relatives" were renamed

Proteobacteria Pseudomonadota (synonym Proteobacteria) is a major phylum of Gram-negative bacteria. The renaming of phyla in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature. The ...

Discussion

In 1987,

, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on

16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rR ...

(SSU) sequences, listed below. Many new phyla have been proposed since then. *

Purple Bacteria Purple bacteria or purple photosynthetic bacteria are Gram-negative proteobacteria that are phototrophic, capable of producing their own food via photosynthesis. They are pigmented with bacteriochlorophyll ''a'' or ''b'', together with various ...

and their relatives (later renamed

) ** alpha subdivision ( purple non-sulfur bacteria,

rhizobacteria Rhizobacteria are root-associated bacteria that can have a detrimental (parasitic varieties), neutral or beneficial effect on plant growth. The name comes from the Greek ''rhiza'', meaning root. The term usually refers to bacteria that form symbio ...

, ''

Agrobacterium ''Agrobacterium'' is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. '' Agrobacterium tumefaciens'' is the most commonly studied species in this genus. ''Agrobacterium'' i ...

'', '' Rickettsiae'', ''

Nitrobacter ''Nitrobacter'' is a genus comprising rod-shaped, gram-negative, and chemoautotrophic bacteria. The name ''Nitrobacter'' derives from the Latin neuter gender noun ''nitrum, nitri'', alkalis; the Ancient Greek noun βακτηρία'','' βακτ� ...

'') ** beta subdivision ('' Rhodocyclus'', (some) ''

Thiobacillus ''Thiobacillus'' is a genus of Gram-negative Betaproteobacteria. ''Thiobacillus thioparus'' is the type species of the genus, and the type strain thereof is the StarkeyT strain, isolated by Robert Starkey in the 1930s from a field at Rutgers Un ...

'', ''

Alcaligenes ''Alcaligenes'' is a genus of Gram-negative, aerobic, rod-shaped bacteria. The species are motile with amphitrichous flagella and rarely nonmotile. It is a genus of non-fermenting bacteria (in the family Alcaligenaceae). Additionally, some str ...

'', ''

Spirillum ''Spirillum'' is a genus of Gram-negative bacteria in the family '' Spirillaceae'' of the '' Nitrosomonadales'' of the ''Betaproteobacteria''.Garrity, George M.; Brenner, Don J.; Krieg, Noel R.; Staley, James T. (eds.) (2005). Bergey's Manual o ...

'', '' Nitrosovibrio'') ** gamma subdivision (enterics, fluorescent pseudomonads,

purple sulfur bacteria The purple sulfur bacteria (PSB) are part of a group of Pseudomonadota capable of photosynthesis, collectively referred to as purple bacteria. They are anaerobic or microaerophilic, and are often found in stratified water environments including ...

, ''

Legionella ''Legionella'' is a genus of pathogenic gram-negative bacteria that includes the species '' L. pneumophila'', causing legionellosis (all illnesses caused by ''Legionella'') including a pneumonia-type illness called Legionnaires' disease and a mil ...

'', (some) '' Beggiatoa'') ** delta subdivision (Sulfur and sulfate reducers (''

Desulfovibrio ''Desulfovibrio'' is a genus of Gram-negative sulfate-reducing bacteria. ''Desulfovibrio'' species are commonly found in aquatic environments with high levels of organic material, as well as in water-logged soils, and form major community member ...

''),

Myxobacteria The myxobacteria ("slime bacteria") are a group of bacteria that predominantly live in the soil and feed on insoluble organic substances. The myxobacteria have very large genomes relative to other bacteria, e.g. 9–10 million nucleotides except ...

, '' Bdellovibrio'') *

Gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bact ...

Eubacteria ** High-G+C species (later renamed

Actinobacteria The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to so ...

) (''

Actinomyces ''Actinomyces'' is a genus of the Actinomycetia class of bacteria. They all are gram-positive. ''Actinomyces'' species are facultatively anaerobic and they grow best under anaerobic conditions. ''Actinomyces'' species may form endospores, an ...

'', '' Streptomyces'', '' Arthrobacter'', ''

Micrococcus ''Micrococcus'' (mi’ krō kŏk’ Əs) is a genus of bacteria in the Micrococcaceae family. ''Micrococcus'' occurs in a wide range of environments, including water, dust, and soil. Micrococci have Gram-positive spherical cells ranging from abo ...

'', ''

Bifidobacterium ''Bifidobacterium'' is a genus of gram-positive, nonmotile, often branched anaerobic bacteria. They are ubiquitous inhabitants of the gastrointestinal tract though strains have been isolated from the vagina and mouth ('' B. dentium'') of mammal ...

'') ** Low-G+C species (later renamed

Firmicutes The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...

) ('' Clostridium'', '' Peptococcus'', ''

Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum '' Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacill ...

'', '' Mycoplasma'') ** Photosynthetic species (''

Heliobacteria Heliobacteria are a unique subset of prokaryotic bacteria that process light for energy. Distinguishable from other phototrophic bacteria, they utilize a unique photosynthetic pigment, bacteriochlorophyll ''g'' and are the only known Gram-posit ...

'') ** Species with Gram-negative walls (''

Megasphaera ''Megasphaera'' is a genus of Bacillota bacteria classified within the class Negativicutes. This classification has been reexamined.Yutin N, Galperin MY (2013) A genomic update on Clostridial phylogeny: Gram-negative spore formers and other mi ...

'', '' Sporomusa'') * Cyanobacteria and chloroplasts (''

Aphanocapsa ''Aphanocapsa'' is a genus of cyanobacteria belonging to the family Merismopediaceae The Merismopediaceae are a family of cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain ene ...

'', ''

Oscillatoria ''Oscillatoria'' is a genus of filamentous cyanobacterium which is often found in freshwater environments, such as hot springs, and appears blue-green. Its name refers to the oscillating motion of its filaments as they slide against each other ...

'', ''

Nostoc ''Nostoc'', also known as star jelly, troll’s butter, spit of moon, fallen star, witch's butter (not to be confused with the fungi commonly known as witches' butter), and witch’s jelly, is the most common genus of cyanobacteria found in var ...

'', ''

Synechococcus ''Synechococcus'' (from the Greek ''synechos'', in succession, and the Greek ''kokkos'', granule) is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 to 1.5 µm. The photosynthetic c ...

'', '' Gloeobacter'', ''

Prochloron ''Prochloron'' (from the Greek ''pro'' (before) and the Greek ''chloros'' (green) ) is a genus of unicellular oxygenic photosynthetic prokaryotes commonly found as an extracellular symbiont on coral reefs, particularly in didemnid ascidians (sea ...

'') *

Spirochetes A spirochaete () or spirochete is a member of the phylum Spirochaetota (), (synonym Spirochaetes) which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled (corkscrew-shaped or ...

and relatives ** Spirochetes (''

Spirochaeta ''Spirochaeta'' is a genus of bacteria classified within the phylum Spirochaetota.See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from See the NCBIbr>webpage on SpirochaetesData extracted from Phylogeny Taxono ...

'', ''

Treponema ''Treponema'' is a genus of spiral-shaped bacteria. The major treponeme species of human pathogens is ''Treponema pallidum'', whose subspecies are responsible for diseases such as syphilis, bejel, and yaws. '' Treponema carateum'' is the cause ...

'', ''

Borrelia ''Borrelia'' is a genus of bacteria of the spirochete phylum. Several species cause Lyme disease, also called Lyme borreliosis, a zoonotic, vector-borne disease transmitted by ticks. Other species of ''Borrelia'' cause relapsing fever, and are t ...

'') ** Leptospiras (''

Leptospira ''Leptospira'' ( grc, leptos, italics=yes, 'fine, thin' and la, spira, links=no, 'coil') is a genus of spirochaete bacteria, including a small number of pathogenic and saprophytic species. ''Leptospira'' was first observed in 1907 in kidney ti ...

'', '' Leptonema'') *

Green sulfur bacteria The green sulfur bacteria are a phylum of obligately anaerobic photoautotrophic bacteria that metabolize sulfur. Green sulfur bacteria are nonmotile (except ''Chloroherpeton thalassium'', which may glide) and capable of anoxygenic photosynthe ...

(''

Chlorobium ''Chlorobium'' is a genus of green sulfur bacteria. They are photolithotrophic oxidizers of sulfur and most notably utilise a noncyclic electron transport chain to reduce NAD+. Photosynthesis is achieved using a Type 1 Reaction Centre using b ...

'', '' Chloroherpeton'') *

Bacteroides ''Bacteroides'' is a genus of Gram-negative, obligate anaerobic bacteria. ''Bacteroides'' species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unus ...

Flavobacteria The class Flavobacteriia is composed of a single order of environmental bacteria. According to Bernardet ''et al''., Flavobacteriia are Gram-negative aerobic rods, 2–5 μm long, 0.3–0.5 μm wide, with rounded or tapered end ...

and relatives (later renamed

Bacteroidetes The phylum Bacteroidota (synonym Bacteroidetes) is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, a ...

** Bacteroides (''

'', ''

Fusobacterium ''Fusobacterium'' is a genus of anaerobic, Gram-negative, non-sporeforming bacteria belonging to Gracilicutes. Individual cells are slender, rod-shaped bacilli with pointed ends. Strains of ''Fusobacterium'' cause several human diseases, includi ...

'') ** Flavobacterium group (''

Flavobacterium ''Flavobacterium'' is a genus of Gram-negative, nonmotile and motile, rod-shaped bacteria that consists of 130 recognized species. Flavobacteria are found in soil and fresh water in a variety of environments. Several species are known to cause ...

'', ''

Cytophaga ''Cytophaga'' is a genus of Gram-negative, gliding, rod-shaped bacteria. This bacterium is commonly found in soil, rapidly digests crystalline cellulose ''C. hutchinsonii'' is able to use its gliding motility to move quickly over surfaces. A ...

'', '' Saprospira'', ''

Flexibacter ''Flexibacter'' is a genus of bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a f ...

'') * Planctomyces and relatives (later renamed

Planctomycetes The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammoniu ...

) ** Planctomyces group ('' Planctomyces'', '' Pasteuria'' 'sic'' ** Thermophiles ('' Isocystis pallida'') *

Chlamydiae The Chlamydiota (synonym Chlamydiae) are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of ...

(''

Chlamydia psittaci ''Chlamydia psittaci'' is a lethal intracellular parasite, intracellular bacterial species that may cause Endemism, endemic Bird, avian chlamydiosis, epizootic outbreaks in mammals, and respiratory psittacosis in humans. Potential hosts include ...

'', ''

Chlamydia trachomatis ''Chlamydia trachomatis'' (), commonly known as chlamydia, is a bacterium that causes chlamydia, which can manifest in various ways, including: trachoma, lymphogranuloma venereum, nongonococcal urethritis, cervicitis, salpingitis, pelvic infla ...

'') * Radioresistant micrococci and relatives (now commonly referred to as Deinococcus–Thermus or

Thermi Thermi ( el, Θέρμη) is a Southeastern suburb and a municipality in the Thessaloniki regional unit, Greece. Its population was 53,201 at the 2011 census. It is located over the site of ancient Therma. Municipality The municipality Ther ...

) ** Deinococcus group (''

Deinococcus radiodurans ''Deinococcus radiodurans'' is an extremophilic bacterium and one of the most radiation-resistant organisms known. It can survive cold, dehydration, vacuum, and acid, and therefore is known as a polyextremophile. It has been listed as the world' ...

'') ** Thermophiles (''

Thermus aquaticus ''Thermus aquaticus'' is a species of bacteria that can tolerate high temperatures, one of several thermophilic bacteria that belong to the ''Deinococcota'' phylum. It is the source of the heat-resistant enzyme ''Taq'' DNA polymerase, one of th ...

'') * Green non-sulfur bacteria and relatives (later renamed Chloroflexi) ** Chloroflexus group (''

Chloroflexus Chloroflexales is an order of bacteria in the class Chloroflexia. Taxonomy The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). * ...

'', ''

Herpetosiphon ''Herpetosiphon'' is a genus of bacteria in the family '' Herpetosiphonaceae''. Phylogeny References {{Taxonbar, from=Q16965551 Phototrophic bacteria Bacteria genera Chloroflexota ...

'') ** Thermomicrobium group ('' Thermomicrobium roseum'') *

Thermotogae The Thermotogota are a phylum of the domain (biology), domain Bacteria. The phylum Thermotogota is composed of Gram-negative staining, anaerobic organism, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.Gupta, RS (2014) The Phyl ...

(''

Thermotoga maritima ''Thermotoga maritima'' is a hyperthermophilic, anaerobic organism that is a member of the order Thermotogales. ''T. maritima'' is well known for its ability to produce hydrogen (clean energy) and it is the only fermentative bacterium that has b ...

'')

Last universal common ancestor

The root of the tree, ''i.e.'' the node of the

last universal common ancestor The last universal common ancestor (LUCA) is the most recent population from which all organisms now living on Earth share common descent—the most recent common ancestor of all current life on Earth. This includes all cellular organisms; th ...

, is placed between the domain ''

Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...

'' (or kingdom ''Eubacteria'' as it was then known) and the clade formed by the domains ''Archaea'' (formerly kingdom ''Archaebacteria'') and ''Eukaryotes''. This is consistent with all subsequent studies, bar the study by

Thomas Cavalier-Smith Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (21 October 1942 – 19 March 2021), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford. His research has led to discov ...

in 2002 and 2004, which was not based on molecular phylogeny. Eukaryotes are a mosaic of different lineages: * The genome in the nucleus descends from the first organelle-less eukaryote, the "urkaryote" a sister species to the ancestral archeon * The mitochondria are organelles that descended from the

proto-mitochondrion The proto-mitochondrion is the hypothetical ancestral bacterial endosymbiont from which all mitochondria in eukaryotes are thought to descend, after an episode of symbiogenesis which created the aerobic eukaryotes. Phylogeny The phylogenetic ana ...

, a species of ''

Rickettsiales The Rickettsiales, informally called rickettsias, are an order of small Alphaproteobacteria. They are obligate intracellular parasites, and some are notable pathogens, including ''Rickettsia'', which causes a variety of diseases in humans, and ' ...

'' (''Alphaproteobacteria'') (''v.'' ''

Reclinomonas ''Reclinomonas'' is a monotypic genus of jakobid eukaryotes containing the single species ''Reclinomonas americana''.Simpson, A. 2008''Reclinomonas'' Flavin & Nerad 1993. ''Reclinomonas americana'' Flavin & Nerad 1993.Version 05. The Tree of Life ...

'' and retortamonads). * The

chloroplasts A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...

are organelles of cyanobacterial origin. Consequently, in Woese (1987) the group is referred to as urkaryote. The clade composed of Archaea and the nuclear genome of eukaryotes is called Neomura by T. Cavalier-Smith

Footnotes

References

{{DEFAULTSORT:Bacterial Phyla Bacteriology Systems of bacterial taxonomy Carl Woese

Tree

Note on names

Discussion

Last universal common ancestor

See also

Footnotes

References