KINGDOM OF BACTERIA

The three domains of life

Main article: Domain (biology)

A phylogenetic tree based on rRNA data showing Woese's three-domain system. All smaller branches can be considered kingdoms.

From around the mid-1970s onwards, there was an increasing emphasis on comparisons of genes on the molecular level (initially ribosomal RNA genes) as the primary factor in classification; genetic similarity was stressed over outward appearances and behavior. Taxonomic ranks, including kingdoms, were to be groups of organisms with a common ancestor, whether monophyletic (all descendants of a common ancestor) or paraphyletic (only some descendants of a common ancestor). Based on such RNA studies, Carl Woese thought life could be divided into three large divisions and referred to them as the "three primary kingdom" model or "urkingdom" model.^[4] In 1990, the name "domain" was proposed for the highest rank.^[5] Woese divided the prokaryotes (previously classified as the Kingdom Monera) into two groups, called Eubacteria and Archaebacteria or Archaea, stressing that there was as much genetic difference between these two groups as between either of them and all eukaryotes.
According to genetic data, although eukaryote groups such as plants, fungi, and animals may look different, they are more closely related to each other than they are to either the Eubacteria or Archaea. It was also found that the eukaryotes are more closely related to the Archaea than they are to the Eubacteria. Although the primacy of the Eubacteria-Archaea divide has been questioned, it has been upheld by subsequent research.^[6] There is no consensus on how many kingdoms exist in the classification scheme proposed by Woese.

Kingdoms of the Eukaryota

Phylogenetic and symbiogenetic tree of living organisms, showing the origins of eukaryotes & prokaryotes

One hypothesis of eukaryotic relationships, modified from Simpson and Roger (2004).

In 2004, a review article by Simpson and Roger noted that the Protista were "a grab-bag for all eukaryotes that are not animals, plants or fungi". They held that only monophyletic groups should be accepted as formal ranks in a classification and that - while this approach had been impractical previously (necessitating "literally dozens of eukaryotic ‘kingdoms’") - it had now become possible to divide the eukaryotes into "just a few major groups that are probably all monophyletic".
On this basis, the diagram opposite (redrawn from their article) showed the real 'kingdoms' (their quotation marks) of the eukaryotes.^[7] A classification which followed this approach was produced in 2005 for the International Society of Protistologists, by a committee which "worked in collaboration with specialists from many societies". It divided the eukaryotes into the same six "supergroups".^[8] The published classification deliberately did not use formal taxonomic ranks, including that of "kingdom".

Life Domain Bacteria Bacteria Domain Archaea Archaea Domain Eukaryota Excavata — Various flagellate protozoa Amoebozoa — most lobose amoeboids and slime moulds Opisthokonta — animals, fungi, choanoflagellates, etc. Rhizaria — Foraminifera, Radiolaria, and various other amoeboid protozoa Chromalveolata — Stramenopiles (Brown Algae, Diatoms etc.), Haptophyta, Cryptophyta (or cryptomonads), and Alveolata Archaeplastida (or Primoplantae) — Land plants, green algae, red algae, and glaucophytes

In this system the multicellular animals (Metazoa) are descended from the same ancestor as both the unicellular choanoflagellates and the fungi which form the Opisthokonta.^[8] Plants are thought to be more distantly related to animals and fungi.
However, in the same year as the International Society of Protistologists' classification was published (2005), doubts were being expressed as to whether some of these supergroups were monophyletic, particularly the Chromalveolata,^[9] and a review in 2006 noted the lack of evidence for several of the supposed six supergroups.^[10]
As of 2010, there is widespread agreement that the Rhizaria belong with the Stramenopiles and the Alveolata, in a clade dubbed the SAR supergroup,^[11] so that Rhizaria is not one of the main eukaryote groups.^{[12][13][14][15][16]} Beyond this, there does not appear to be a consensus. Rogozin et al. in 2009 noted that "The deep phylogeny of eukaryotes is an extremely difficult and controversial problem."^[17] As of December 2010, there appears to be a consensus that the 2005 six supergroup model does not reflect the true phylogeny of the eukaryotes and hence how they should be classified, although there is no agreement as to the model which should replace it.^[13][14][18]

Historical development

The classification of living things into animals and plants is an ancient one. Aristotle (384–322 BC) classified animal species in his History of Animals, while his pupil Theophrastus (c. 371–c. 287 BC) wrote a parallel work, the Historia Plantarum, on plants.^[19]
Carl Linnaeus (1707–1778) laid the foundations for modern biological nomenclature, now regulated by the Nomenclature Codes, in 1735. He distinguished two kingdoms of living things: Regnum Animale ('animal kingdom') and Regnum Vegetabile ('vegetable kingdom', for plants). Linnaeus also included minerals in his classification system, placing them in a third kingdom, Regnum Lapideum.

	Life Regnum Vegetabile Regnum Animale

In 1674, Antonie van Leeuwenhoek, often called the "father of microscopy", sent the Royal Society of London a copy of his first observations of microscopic single-celled organisms. Until then, the existence of such microscopic organisms was entirely unknown. Despite this, Linnaeus did not include any microscopic creatures in his original taxonomy.

Haeckel's original (1866) conception of the three kingdoms of life, including the new kingdom Protista. Notice the inclusion of the cyanobacterium Nostoc with plants.

At first, microscopic organisms were classified within the animal and plant kingdoms. However, by the mid-19th century, it had become clear to many that "the existing dichotomy of the plant and animal kingdoms [had become] rapidly blurred at its boundaries and outmoded".^[20] In 1866, Ernst Haeckel proposed a third kingdom of life, the Protista, for "neutral organisms" which were neither animal nor plant. Haeckel revised the content of this kingdom a number of times before settling on a division based on whether organisms were unicellular (Protista) or multicellular (animals and plants).^[20]

	Life Kingdom Plantae Kingdom Protista Kingdom Animalia

The development of the electron microscope revealed important distinctions between those unicellular organisms whose cells do not have a distinct nucleus (prokaryotes) and those unicellular and multicellular organisms whose cells do have a distinct nucleus (eukaryotes). In 1938, Herbert F. Copeland proposed a four-kingdom classification, elevating the protist classes of bacteria (Monera) and blue-green algae (Phycochromacea) to phyla in the novel Kingdom Monera.^[20]
The importance of the distinction between prokaryotes and eukaryotes gradually became apparent. In the 1960s, Stanier and van Niel popularised Édouard Chatton's much earlier proposal to recognise this division in a formal classification. This required the creation, for the first time, of a rank above kingdom, a superkingdom or empire, later called a domain.^[21]

	Life Domain Bacteria Kingdom Monera Empire Eukaryota Kingdom Protista Kingdom Plantae Kingdom Animalia

The differences between fungi and other organisms regarded as plants had long been recognised by some; Haeckel had moved the fungi out of Plantae into Protista after his original classification,^[20] but was largely ignored in this separation by scientists of his time. Robert Whittaker recognized an additional kingdom for the Fungi. The resulting five-kingdom system, proposed in 1969 by Whittaker, has become a popular standard and with some refinement is still used in many works and forms the basis for new multi-kingdom systems. It is based mainly upon differences in nutrition; his Plantae were mostly multicellular autotrophs, his Animalia multicellular heterotrophs, and his Fungi multicellular saprotrophs. The remaining two kingdoms, Protista and Monera, included unicellular and simple cellular colonies.^[22] The five kingdom system may be combined with the two empire system:

Life	Empire Prokaryota Kingdom Monera Empire Eukaryota Kingdom Fungi Kingdom Protista Kingdom Plantae Kingdom Animalia

In the Whittaker system, Plantae included some algae. In other systems (e.g., Margulis system), Plantae included just the land plants (Embryophyta).
Despite the development from two kingdoms to five among most scientists, some authors as late as 1975 continued to employ a traditional two-kingdom system of animals and plants, dividing the plant kingdom into Subkingdoms Prokaryota (bacteria and cyanophytes), Mycota (fungi and supposed relatives), and Chlorota (algae and land plants).^[23]

Cavalier-Smith's systems

Eight kingdoms

See also: Archaebacteria, Chromista and Archezoa

Thomas Cavalier-Smith thought at first, as it was nearly consensually admitted at that time, that the difference between eubacteria and archaebacteria was so great (particularly considering the genetic distance of ribosomal genes) that they needed to be separated into two different kingdoms, hence splitting the empire Bacteria into two kingdoms. He then divided Eubacteria into two subkingdoms: Negibacteria (Gram negative bacteria) and Posibacteria (Gram positive bacteria).
Technological advances in electron microscopy allowed the separation of the Chromista from the Plantae kingdom. Indeed, the chloroplast of the chromists is located in the lumen of the endoplasmic reticulum instead of in the cytosol. Moreover, only chromists contain chlorophyll c. Since then, many non-photosynthetic phyla of protists, thought to have secondarily lost their chloroplasts, were integrated into the kingdom Chromista.
Finally, some protists lacking mitochondria were discovered.^[24] As mitochondria were known to be the result of the endosymbiosis of a proteobacterium, it was thought that these amitochondriate eukaryotes were primitively so, marking an important step in eukaryogenesis. As a result, these amitochondriate protists were separated from the protist kingdom, giving rise to the, at the same time, superkingdom and kingdom Archezoa. This was known as the Archezoa hypothesis. This superkingdom was opposed to the Metakaryota superkingdom, grouping together the five other eukaryotic kingdoms (Animalia, Protozoa, Fungi, Plantae and Chromista).

Six kingdoms

In 1998, Cavalier-Smith published a six-kingdom model,^[3] which has been revised in subsequent papers. The version published in 2009 is shown below.^[12] (Compared to the version he published in 2004,^[25] the alveolates and the rhizarians have been moved from Kingdom Protozoa to Kingdom Chromista.) Cavalier-Smith no longer accepts the importance of the fundamental eubacteria–archaebacteria divide put forward by Woese and others and supported by recent research.^[6] His Kingdom Bacteria includes Archaebacteria as a phylum of the subkingdom Unibacteria which comprises only one other phylum: the Posibacteria. The two subkingdoms Unibacteria and Negibacteria of kingdom Bacteria (sole kingdom of empire Prokaryota) are opposed according to their membrane topologies. The bimembranous-unimembranous transition is thought to be far more fundamental than the long branch of genetic distance of Archaebacteria, viewed as having no particular biological significance. Cavalier-Smith does not accept the requirement for taxa to be monophyletic ("holophyletic" in his terminology) to be valid. He defines Prokaryota, Bacteria, Negibacteria, Unibacteria and Posibacteria as valid paraphyletic (therefore "monophyletic" in the sense he uses this term) taxa, marking important innovations of biological significance (in regard of the concept of biological niche).
In the same way, his paraphyletic kingdom Protozoa includes the ancestors of Animalia, Fungi, Plantae and Chromista. The advances of phylogenetic studies allowed Cavalier-Smith to realize that all the phyla thought to be archezoans (i.e. primitively amitochondriate eukaryotes) had in fact secondarily lost their mitochondria, most of the time by transforming them into new organelles: hydrogenosomes. This means that all living eukaryotes are in fact metakaryotes, according to the significance of the term given by Cavalier-Smith. Some of the members of the defunct kingdom Archezoa, like the phylum Microsporidia, were reclassified into kingdom Fungi. Others were reclassified in kingdom Protozoa like Metamonada which is now part of infrakingdom Excavata.
The diagram below does not represent an evolutionary tree.

	Life Empire Prokaryota Kingdom Bacteria — includes Archaebacteria as part of a subkingdom Empire Eukaryota Kingdom Protozoa — e.g. Amoebozoa, Choanozoa, Excavata Kingdom Chromista — e.g. Alveolata, cryptophytes, Heterokonta (Brown Algae, Diatoms etc.), Haptophyta, Rhizaria Kingdom Plantae — e.g. glaucophytes, red and green algae, land plants Kingdom Fungi Kingdom Animalia

Viruses

There is ongoing debate as to whether viruses, obligate intracellular parasites that lack metabolism and are not capable of replication outside of a host, can be included in the tree of life.^[26][27] A principal reason for inclusion comes from the discovery of unusually large and complex viruses, such as Mimivirus, that possess typical cellular genes.^[28]

Summary

A summary of the different kinds of proposed classification schemes presented in this article is summarized in the table below.

Linnaeus 1735[29]	Haeckel 1866[30]	Chatton 1925[31][32]	Copeland 1938[33][34]	Whittaker 1969[35]	Woese et al. 1977[36][37]	Woese et al. 1990[38]	Cavalier-Smith 1993[39][40][41]	Cavalier-Smith 1998[42][43][44]
2 kingdoms	3 kingdoms	2 empires	4 kingdoms	5 kingdoms	6 kingdoms	3 domains	8 kingdoms	6 kingdoms
(not treated)	Protista	Prokaryota	Monera	Monera	Eubacteria	Bacteria	Eubacteria	Bacteria
					Archaebacteria	Archaea	Archaebacteria
		Eukaryota	Protista	Protista	Protista	Eucarya	Archezoa	Protozoa
							Protozoa
							Chromista	Chromista
Vegetabilia	Plantae		Plantae	Plantae	Plantae		Plantae	Plantae
				Fungi	Fungi		Fungi	Fungi
Animalia	Animalia		Animalia	Animalia	Animalia		Animalia	Animalia

The kingdom-level classification of life is still widely employed as a useful way of grouping organisms.

• There is no current consensus on how many kingdoms are present in the Eukarya. In 2009, Andrew Roger and Alastair Simpson emphasized the need for diligence in analyzing new discoveries: "With the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution."^[45]