User:Squidonius/userpage/history of microbiology

Natural history
The ancestors of modern bacteria, archeans and eukaryotes were single-celled microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, all organisms were microscopic, and bacteria and archaea were the dominant forms of life. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species. However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage.

Bacteria were also involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from ancient bacteria entering into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea. This involved the engulfment by proto-eukaryotic cells of alpha-proteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa). Later on, some eukaryotes that already contained mitochondria also engulfed cyanobacterial-like organisms. This led to the formation of chloroplasts in algae and plants. There are also some algae that originated from even later endosymbiotic events. Here, eukaryotes engulfed a eukaryotic algae that developed into a "second-generation" plastid. This is known as secondary endosymbiosis.

Antiquity
Diseases such as the Plague of Justinian was a pandemic that afflicted the Eastern Roman Empire (Byzantine Empire) in 541–542 AD caused in Yersinia pestis biovar. antiqua. Sanitation to combat diseases.

Brewing and wine making.

Discovery


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. The name Bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1828. In fact, Bacterium was a genus which contained non-spore forming rod-shaped bacteria, as opposed to Bacillus a genus of spore forming rod-shaped bacteria defined by Ehrenberg in 1835.

Louis Pasteur demonstrated in 1859 that the fermentation process is caused by the growth of microorganisms, and that this growth is not due to spontaneous generation. (Yeasts and molds, commonly associated with fermentation, are not bacteria, but rather fungi.) Along with his contemporary, Robert Koch, Pasteur was an early advocate of the germ theory of disease. Robert Koch was a pioneer in medical microbiology and worked on cholera, anthrax and tuberculosis. In his research into tuberculosis, Koch finally proved the germ theory, for which he was awarded a Nobel Prize in 1905. In Koch's postulates, he set out criteria to test if an organism is the cause of a disease, and these postulates are still used today.

Though it was known in the nineteenth century that bacteria are the cause of many diseases, no effective antibacterial treatments were available. In 1910, Paul Ehrlich developed the first antibiotic, by changing dyes that selectively stained Treponema pallidum—the spirochaete that causes syphilis—into compounds that selectively killed the pathogen. Ehrlich had been awarded a 1908 Nobel Prize for his work on immunology, and pioneered the use of stains to detect and identify bacteria, with his work being the basis of the Gram stain and the Ziehl-Neelsen stain.

A major step forward in the study of bacteria was the recognition in 1977 by Carl Woese that archaea have a separate line of evolutionary descent from bacteria. This new phylogenetic taxonomy was based on the sequencing of 16S ribosomal RNA, and divided prokaryotes into two evolutionary domains, as part of the three-domain system.

Haekel's classification
] Traditionally the natural world was classified as animal, vegetable, or mineral as in Systema Naturae. After the discovery of microscopy, attempts were made to fit microscopic organisms into either the plant or animal kingdoms. Antonie van Leeuwenhoek in 1676 discovered Bacteria and called them "animacules" and assigned them to the class Vermes of the Animalia. Due to the limited tools — the sole references for this group where shape behaviour and habitat — the description of genera and their classification was extremely limited which was accentuated by the perceived lack of importance of the group.

Ten years after the origin of species by Darwin, In 1866 Ernst Haeckel, a supporter of evolution, proposed a three kingdom system which added the Protista as a new kingdom that contained most microscopic organisms. One of his eight major divisions of Protista was composed of the monerans (called Moneres in German) and defines them as completely structureless and homogeneous organisms, consisting only of a piece of plasma. Haeckel's Monera included not only bacterial groups of early discovery, but also included several small eukaryotic organisms, in fact only the genus Vibrio is the only bacterial genus explicitly assigned to the phylum, while others are mentioned indirectly, which has lead Copeland to speculate that Haeckel considered all bacteria to belong to the genus Vibrio ignoring other bacterial genera. One notable exception were the members of the modern phylum Cyanobacteria, such as Nostoc, which were placed in the phylum Archephyta of Algae (vide infra: Blue-green algae).

The Neolatin noun Monera and the german noun Moneren/Moneres is derived from the ancient Greek noun moneres (μονήρης) which Haeckel states to mean "simple", however it actually means "single, solitary". Haeckel also describes the protist genus Monas in the two page about Monera in his 1866 book. The informal name of a member of the Monera was initially moneron, but later moneran was used.

The phylum due to its lack of features was not fully subdivided, but the genera therein where divided into two groups:
 * die Gymnomoneren (no envelope [sic.] ): Gymnomonera
 * Protogenes &mdash; such as Protogenes primordialis, an unidentified amaeba (eukaryote) and not a bacterium
 * Protamaeba &mdash; an incorrectly described/fabricated species
 * Vibrio &mdash; a genus of comma shaped bacteria first described in 1854
 * Bacterium &mdash; a genus of rod shaped bacteria first described in 1828. Haeckel does not explicitly assign this genus to the Monera.
 * Bacillus &mdash; a genus of spore-forming rod shaped bacteria first described in 1835 Haeckel does not explicitly assign this genus to the Monera.
 * Spirochaeta &mdash; thin spiral shaped bacteria first described in 1835 Haeckel does not explicitly assign this genus to the Monera.
 * Spirillum &mdash; spiral shaped bacteria first described in 1832 Haeckel does not explicitly assign this genus to the Monera.
 * etc.: Haeckel does provide a comprehensive list.
 * die Lepomoneren (with envelope): Lepomonera
 * Protomonas &mdash; identified to a synonym of Monas, a flagellated protozoan, and not a bacterium. The name was reused in 1984 for an unrelated genus of Bacteria
 * Vampyrella &mdash; now classed as a eukaryote and not a bacterium.

Subsequent classifications
Like Protista, the Monera classification was not fully followed at first and several different ranks were used and located with animals, plants, protists or fungi. Furthermore, Häkel's classification lacked specificity and was not exhaustive —it in fact covers only a few pages—, consequently a lot of confusion arose even to the point that the Monera did not contain bacterial genera and others according to Huxley. The most popular scheme was created in 1859 by C. Von Nägeli who classified non-phototrophic Bacteria as the class Schizomycetes.

The class Schizomycetes was then emended by Walter Migula (along with the coinage of the genus Pseudomonas in 1894) and others. This term was in dominant use even in 1916 as reported by Robert Earle Buchanan, as it had priority over other terms such as Monera. However, starting with Ferdinand Cohn in 1872 the term bacteria (or in German der Bacterien) became prominently used to informally describe this group of species without a nucleus: Bacterium was in fact a genus created in 1828 by Christian Gottfried Ehrenberg Additionally, Cohn divided the bacteria according to shape namely:
 * Spherobacteria for the cocci
 * Microbacteria for the short, non-filamentous rods
 * Desmobacteria for the longer, filamentous rods and Spirobacteria for the spiral forms.

Successively, Cohn created the Schizophyta of Plants which contained the non-photrophic bacteria in the family Schizomycetes and the phototrophic bacteria (blue green algae/Cyanobacteria) in the Schizophyceae This union of blue green algae and Bacteria was much later followed by Haeckel, who classified the two families in a revised phylum Monera in the Protista.

Rise to prominence
The term Monora, became well established in the 20s and 30s when to rightfully increase the importance of the difference between species with a nucleus and without, In 1925 Édouard Chatton divided all living organisms into two empires Prokaryotes and Eukaryotes: the Kingdom Monera being the sole member of the Prokaryotes empire.

The anthropic importance of the crown group of animals, plants and fungi was hard to depose consequently several other megaclassification schemes ignored on the empire rank, but maintained the kingdom Monera consisting of bacteria, such Copeland in 1938 and Whittaker in 1969. The latter classification system was widely followed and in which Robert Whittaker proposed a five kingdom system for classification of living organisms. Whittaker's system placed most single celled organisms into either the prokaryotic Monera or the eukaryotic Protista. The other three kingdoms in his system were the eukaryotic Fungi, Animalia, and Plantae. Whittaker, however, did not believe that all his kingdoms were monophyletic. Whittaker subdiveded the kingdom into two branches containing several phyla:
 * Myxomonera branch
 * Cyanophyta, now called Cyanobacteria
 * Myxobacteria
 * Mastigomonera branch
 * Eubacteriae
 * Actinomycota
 * Spirochaetae

Alternative ommonly followed subdivision systems were based on Gram stains. This culminated in the Gibbons and Murray classification of 1978:
 * Gracilicutes (gram negative)
 * Photobacteria (photosynthetic): class Oxyphotobacteriae (water as electron acceptor, 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 Fimicutes )
 * 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
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 (erroneous) 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 This scheme is still followed today.

Subdivisions
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
Some authors have opposed the three domain due to various reasons, often in favour of more traditional anthropocentric classifications.

One prominent scientist which opposes the three domain system is Thomas Cavalier-Smith, which 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 molecular biology community (c.f. reviewers' comments on,  e.g. Eric Bapteste is "agnostic" regarding the conclusions) and are often not even mention in reviews (e.g. ), due to the subjective nature of the assumptions made for logical arguments. 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

In 1977, a PNAS paper by Carl Woese and George Fox demonstrated that the archaea (initially called archaebacteria) are not significantly closer in relationship to the bacteria than they are to eukaryotes. The paper received front-page coverage in The New York Times and great controversy initially, but the conclusions have since become accepted, leading to replacement of the kingdom Monera with the two kingdoms Bacteria and Archaea. However, Thomas Cavalier-Smith has never accepted the importance of the division between these two groups, and has published classifications in which the archaebacteria are part of a subkingdom of the Kingdom Bacteria.

Tree from Rappe and Giovanoni 2004, based on Woese 1987 tree , location of Poribacteria determined from
 * cladogram=