AQUIFICAE

The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents. Members of the genus Aquifex, for example, are productive in water between 85 to 95 C. They are the dominant members of most terrestrial neutral to alkaline hot springs above 60 degrees celsius. They are autotrophs, and are the primary carbon fixers in these environments. They are true bacteria (domain bacteria) as opposed to the other inhabitants of extreme environments, the Archaea. Taxonomy There is currently no consensus regarding the taxonomy of genera within Aquificae. One standard text claims that only the genera Aquifex, Calderobacterium, Hydrogenobacter, and Thermocrinis belong in the Aquificales order. Another claims that, in addition to genera within the Aquificaceae and Hydrogenothermaceae families, the following genera are incertae sedis(unclassified), but within Aquificae: Balnearium, Desulfurobacterium, EX-H1 group, and Thermovibrio. Cavalier-Smith has postulated that Aquificae is part of the Proteobacteria. Along with Thermotogae, members of Aquificae are thermophilic eubacteria.

THERMOTOGAE

Thermotogae is a phylum of the domain "Bacteria". This phylum comprises merely the class "Thermotogae", with the order "Thermotogales" and the family "Thermotogaceae". It has been suggested that may be deeply branched within the bacteria, and may have much in common with species inArchaea. It has been suggested that it has many genes in common with Synergistetes, Firmicutes, Actinobacteria, Deferribacteres,Chloroflexi, DeinococcusThermus, and Fusobacteria. Along with Aquificae, members of Thermotogae are thermophilic eubacteria.

CHRYSIOGENES ARSENATIS

Chrysiogenes arsenatis is a species of bacterium given its own phylum, called the Chrysiogenetes. It has a unique lifestyle and biochemistry. Instead of respiring with oxygen, it respires using the most oxidized form of arsenic, arsenate. It uses arsenate as its terminal electron acceptor. Arsenic is usually toxic to life. Bacteria like Chrysiogenes arsenatis are found in anoxic arsenic-contaminated environments.

NITROSPIRA

Nitrospira is a genus of bacteria in the phylum Nitrospirae. The first member of this genus was discovered in 1995 from a corroded iron pipe in a Moscow heating system. The bacteria was named Nitrospira moscoviensis and is a gram-negativenitrite-oxidising organism with a helical to vibroid morphology 0.9-2.2 x 0.2-0.4 micrometres in size. The phylum Nitrospirae includes thermophilic bacteria that fix nitrogen to nitrogen gas (N2).

DEFERRIBACTERACEAE

The Deferribacteraceae are a family of bacteria, given their own phylum (Deferribacteres).

CHLOROFLEXI

Chloroflexi or Chlorobacteria (formerly known as green non-sulfur bacteria) is one of four classes of bacteria in thephylum Chloroflexi. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes. Chloroflexi are typically filamentous, and can move about through bacterial gliding. They are facultatively aerobic, but do not produce oxygen in the process of producing energy from light, or phototrophy. Additionally Chloroflexi have a different method of phototrophy (photoheterotrophy) than true photosynthetic bacteria. Phylogenetic analysis indicates that they had a separate origin.

THERMOMICROBIA

The Thermomicrobia are a group of thermophilic green non-sulfur bacteria. Until 2004, they were classified as a distinctphylum. It has recently been proposed, on the basis of an analysis of genetic affiliations, that the thermomicrobia should more properly be reclassified as a class belonging to the phylum chloroflexi.

FIBROBACTERES

Fibrobacteres is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla. The genus Fibrobacter(the only genus of Fibrobacteres) was divided from the genus Bacteroides in 1988

DEINOCOCCUS-THERMUS

The Deinococcus-Thermus are a small group of bacteria composed of cocci highly resistant to environmental hazards. There are two main groups. The Deinococcales include two families, each with a single genus, Deinococcus and Truepera, the former with several species that are resistant to radiation; they have become famous for their ability to eat nuclear waste and other toxic materials, survive in the vacuum of space and survive extremes of heat and cold. The Thermales include several genera resistant to heat (Marinithermus, Meiothermus, Oceanithermus, Thermus,Vulcanithermus). Thermus aquaticus was important in the development of the polymerase chain reaction where repeated cycles of heating DNA to near boiling make it advantageous to use a thermo-stable DNA polymerase enzyme. Though these two groups evolved from a common ancestor, the two mechanisms of resistance appear to be largely independent. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria. Cavalier-Smith calls this clade Hadobacteria (from Hades, the Greek underworld).

PROTEOBACTERIA

The Proteobacteria are a major group (phylum) of bacteria. They include a wide variety of pathogens, such asEscherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera. Others are free-living, and include many of the bacteria responsible for nitrogen fixation. Because of the great diversity of forms found in this group, the Proteobacteria are named after Proteus, a Greek god of the sea, capable of assuming many different shapes. Characteristics All proteobacteria are Gram-negative, with an outer membrane mainly composed of lipopolysaccharides. Many move about using flagella, but some are non-motile or rely on bacterial gliding. The last include the myxobacteria, a unique group of bacteria that can aggregate to form multicellular fruiting bodies. There is also a wide variety in the types of metabolism. Most members are facultatively or obligately anaerobic, chemoautotrophs, and heterotrophic, but there are numerous exceptions. A variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. These are called purple bacteria, referring to their mostly reddish pigmentation.

PLANCTOMYCETES

Planctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, and marine and fresh water. They reproduce by budding. In structure, the organisms of this group are ovoid and have a holdfast, called the stalk, at the nonreproductive end that helps them to attach to each other during budding. Cavalier-Smith has postulated that the Planctomycetes are within the clade Planctobacteria in the larger clade Gracilicutes. Structure The organisms belonging to this group lack murein in their cell wall. Murein is an important heteropolymer present in mostbacterial cell walls that serves as a protective component in the cell wall skeleton. Instead their walls are made up ofglycoprotein rich in glutamate. Planctomycetes have internal structures that are more complex than would be typically expected in prokaryotes. While they do not have a nucleus in the eukaryotic sense, the nuclear material can sometimes be enclosed in a double membrane. In addition to this nucleoid, there are two other membrane-separated compartments; the pirellulosome or riboplasm, which contains the ribosome and related proteins, and the ribosome-free paryphoplasm. OnlyEpixenosomes, in Verrucomicrobia, have a more complex structure. Genome RNA sequencing shows that the planctomycetes are related to the Verrucomicrobia and possibly the Chlamydiae. A number of essential pathways are not organised as operons, which is unusual for bacteria. A number of genes have been found (through sequence comparisons) that are similar to genes found in eukaryotes. One such example is a gene sequence (in Gemmata obscuriglobus) that was found to have significant homology to the integrin alpha-V, a protein that is important in transmembrane signal transduction in eukaryotes. Life cycle The life cycle of many planctomycetes involves alternation between sessile cells and flagellated swarmer cells. The sessile cells bud to form the flagellated swarmer cells which swim for a while before settling down to attach and begin reproduction.

CHLAMYDIAE

Chlamydiae is a bacterial phylum and class whose members are obligate intracellular pathogens. Many Chlamydiae coexist in an asymptomatic state within specific hosts, and it is widely believed that these hosts provide a natural reservoir for these species. All known Chlamydiae only grow by infecting eukaryotic host cells. They are as small or smaller than many viruses. Chlamydiae replicate inside the host cells and are termed intracellular. Most intracellular Chlamydiae are located in an inclusion body or vacuole. Outside of cells they survive only as an extracellular infectious form. Chlamydiae can grow only where their host cells grow. Therefore, Chlamydiae cannot be propagated in bacterial culture media in the clinical laboratory. Chlamydiae are most successfully isolated while still inside their host cell. Cavalier-Smith has postulated that the Chlamydiae fall into the clade Planctobacteria in the larger clade Gracilicutes. History Chlamydia-like disease affecting the eyes of people was first described in ancient Chinese and Egyptian manuscripts. A modern description of Chlamydia-like organisms was provided by Halberstaedter and von Prowazek in 1907. Chlamydial isolates cultured in the yolk sacs of embryonating eggs were obtained from a human pneumonitis outbreak in the late 1920s and early 1930s, and by the mid-20th Century isolates had been obtained from dozens of vertebrate species. The term Chlamydia (a cloak) appeared in the literature in 1945, although other names continued to be used, including Bedsonia, Miyagawanella, ornithosis-, TRIC-, and PLT-agents. Nomenclature In 1966, Chlamydiae were recognized as bacteria and the genus Chlamydia was validated. The Order Chlamydiales was created by Storz and Page in 1971. Between 1989 and 1999, new families, genera, and species were recognized. The phylum Chlamydiae was established in Bergey's Manual of Systematic Bacteriology. By 2006, genetic data for over 350 chlamydial lineages had been reported, four chlamydial families had been recognized (Chlamydiaceae, Parachlamydiaceae,Simkaniaceae, and Waddliaceae), and another family had been proposed (Rhabdochlamydiaceae).

SPIROCHAETE

Spirochaetes (also spelled Spirochetes) belong to a phylum of distinctive Gramnegative bacteria, which have long,helically coiled (spiral-shaped) cells. Spirochetes are chemoheterotrophic in nature, with lengths between 5 and 250 m and diameters around 0.10.6 m. Spirochaetes are distinguished from other bacterial phyla by the location of their flagella, sometimes called axial filaments, which run lengthwise between the cell wall and outer membrane. These cause a twisting motion which allows the spirochaete to move about. When reproducing, a spirochaete will undergo asexual transverse binary fission. Most spirochaetes are free-living and anaerobic, but there are numerous exceptions. Classification The spirochetes are divided into three families (Brachyspiraceae, Leptospiraceae, and Spirochaetaceae), all placed within a single order (Spirochaetales). Disease-causing members of this phylum include the following: Leptospira species, which causes leptospirosis Borrelia burgdorferi, which causes Lyme disease Borrelia recurrentis, which causes relapsing fever Treponema pallidum, which causes syphilis Treponema pertenue, which causes yaws Cavalier-Smith has postulated that the Spirochaetes belong in a larger clade called Gracilicutes. Historical Salvarsan, the first antibiotic in medical history, was effective against spirochaetes only and was primarily used to curesyphilis. It has been suggested by biologist Lynn Margulis that eukaryotic flagella were derived from symbiotic spirochaetes, but few biologists accept this, as there is no close structural similarity between the two.

BACTEROIDETES

The phylum Bacteroidetes is composed of three large classes of bacteria that are widely distributed in the environment, including in soil, in sediments, sea water and in the guts and on the skin of animals. By far, the ones in the Bacteroidetes class are the most well-studied, including the genus Bacteroides (an abundant organism in the feces of warm-blooded animals including humans), and Porphyromonas, a group of organisms inhabiting the human oral cavity. Members of the genus Bacteroides are opportunistic pathogens. Rarely are members of the other two classes pathogenic to humans. Researcher Jeffrey Gordon and his colleagues found that obese humans and mice had intestinal flora (gut flora) with a lower percentage of Bacteroidetes and relatively more bacteria from the Firmicutes family. However, they are unsure if Bacteroidetes prevent obesity or if these intestinal flora are merely preferentially selected by intestinal conditions in those who are not obese. It has been proposed by Cavalier-Smith to be part of the Sphingobacteria phylum.

GREEN SULFUR BACTERIA

The green sulfur bacteria are a family of obligately anaerobic photoautotrophic bacteria. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum. Green sulfur bacteria are non-motile (except Chloroherpeton thalassium, which may glide) and come in spheres, rods, and spirals. Photosynthesis is achieved using bacteriochlorophyll (BChl) c, d, or e, in addition to BChl aand chlorophyll a, in chlorosomes attached to the membrane. They use sulfide ions, hydrogen or ferrous iron as an electron donor and the process is mediated by the type I reaction centre and Fenna-Matthews-Olson complex. Elemental sulfur deposited outside the cell may be further oxidized. By contrast, the photosynthesis in plants uses water as electron donor and produces oxygen. Chlorobium tepidum has emerged as a model organism for the group, and although only ten genomes have been sequenced, these are quite comprehensive of the family's biodiversity. Their 2-3 Mb genomes encode 1750-2800 genes, 1400-1500 of which are common to all strains. The apparent absence of two-component histidine-kinases and response regulators suggest limited phenotypic plasticity. Their small dependence on organic molecule transporters andtranscription factors also indicate that these organisms are adapted to a narrow range of energy-limited conditions, anecology shared with the simpler cyanobacteria, Prochlorococcus and Synechococcus A species of green sulfur bacteria has been found living near a black smoker off the coast of Mexico at a depth of 2,500 meters beneath the surface of the Pacific Ocean. At this depth, the bacterium, designated GSB1, lives off the dim glow of the thermal vent since no sunlight can penetrate to that depth. Green sulfur bacteria appear in Lake Matano, Indonesia, at a depth of approximately 110120 meters. The population may include the species, Chlorobium ferrooxidans.

ACTINOBACTERIA

Actinobacteria are a group of Gram-positive bacteria with high G+C ratio. They can be terrestrial or aquatic. Use of the ferric uptake regulator (fur) has been suggested for classification. Analysis of glutamine synthetase has also been suggested. A Siberian example is said to be the oldest living organism on Earth, at around half a million years old. Characteristics They include some of the most common soil life, freshwater life, and marine life, playing an important role in decomposition of organic materials, such as cellulose and chitin, and thereby playing a vital part in organic matter turnover and carbon cycle. This replenishes the supply of nutrients in the soil and is an important part of humusformation. Other Actinobacteria inhabit plants and animals, including a few pathogens, such as Mycobacterium,Corynebacterium, Nocardia, Rhodococcus and a few species of Streptomyces. Actinobacteria are well known as secondary metabolite producers and hence of high pharmacological and commercial interest. In 1940 Selman Waksman discovered that the soil bacteria he was studying made actinomycin, a discovery for which he received a Nobel Prize. Since then, hundreds of naturally occurring antibiotics have been discovered in these terrestrial microorganisms, especially from the genus Streptomyces. Some Actinobacteria form branching filaments, which somewhat resemble the mycelia of the unrelated fungi, among which they were originally classified under the older name Actinomycetes. Most members are aerobic, but a few, such as Actinomyces israelii, can grow under anaerobic conditions. Unlike the Firmicutes, the other main group of Gram-positive bacteria, they have DNA with a high GC-content, and some Actinomycetes species produce external spores. Some types of Actinobacteria are responsible for the peculiar odor emanating from the soil after rain (Petrichor), mainly in warmer climates. The chemical that produces this odour is known as Geosmin.

CYANOBACTERIA

Cyanobacteria ( /sa no bk t ri /; also known as blue-green algae, blue-green bacteria, andCyanophyta) is a phylum of bacteria that obtain their energy through photosynthesis. The name "cyanobacteria" comes from the color of the bacteria (Greek: (kyans) = blue). The ability of cyanobacteria to perform oxygenic photosynthesis is thought to have converted the early reducingatmosphere into an oxidizing one, which dramatically changed the composition of life forms on Earth by stimulatingbiodiversity and leading to the near-extinction of oxygenintolerant organisms. According to endosymbiotic theory,chloroplasts in plants and eukaryotic algae have evolved from cyanobacterial ancestors via endosymbiosis.

FIRMICUTES

The Firmicutes (Latin: firmus, strong, and cutis, skin, referring to the cell wall) are a phylum of bacteria, most of which have Gram-positive cell wall structure.[1] A few however, such as Megasphaera, Pectinatus, Selenomonas, and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative. Scientists once classified the Firmicutes to include all Gram-positive bacteria, but have recently defined them to be of a core group of related forms called the low-G+C group, in contrast to the Actinobacteria. They have round cells, called cocci (singular coccus), or rod-shaped forms. Many Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions. They are found in various environments, and the group includes some notable pathogens. Those in one family, the heliobacteria, produce energy through photosynthesis. Firmicutes play an important role in beer, wine, and cider spoilage.

FUSOBACTERIUM

Fusobacterium is a genus of filamentous, anaerobic, Gram-negative bacteria, similar to Bacteroides. Fusobacteriumcontribute to several human diseases, including periodontal diseases, Lemierre's syndrome, and topical skin ulcers. Although older resources have stated that Fusobacterium is a common occurrence in the human oropharynx, the current consensus is that Fusobacterium should always be treated as a pathogen. In contrast to Bacteroides spp., Fusobacteria have a potent lipopolysaccharide.

VERRUCOMICROBIA

Verrucomicrobia is a recently described phylum of bacteria. This phylum contains only a few described species (Verrucomicrobium spinosum, is an example, the phylum is named after this). The species identified have been isolated fromfresh water and soil environments and human feces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes. While verrucae is another name for the warts often found on hands and feet, this phylum is so called not because it is a causative agent thereof, but because of its wart-like morphology. Evidence suggests that verrucomicrobia are abundant within the environment, and important (especially to soil cultures). This phylum is considered to have two sister phyla: Chlamydiae and Lentisphaerae. Cavalier-Smith has postulated that the Verrucomicrobia belong in the clade Planctobacteria in the larger clade Gracilicutes. 16S rRNA data corroborate that view. Recently the whole genome of Methylacidiphilum infernorum was sequenced (2.3 Mbp). On the single circular chromosome, 2473 predicted proteins were found, 731 of which had no detectable homologs. These analyses also revealed many possible homologies with Proteobacteria

ACIDOBACTERIA

Acidobacteria are a newly devised phylum of Bacteria, whose members are physiologically diverse and ubiquitous, expecially in soils, but are under-represented in culture. Members of this phylum are physiologically diverse, some being acidophilic, and were first recognized as a novel division in 1997. The first species, Acidobacterium capsulatum, of this phylum was discovered in 1991. Other notable species areHolophaga foetida, Geothrix fermentans, Acanthopleuribacter pedis and Bryobacter aggregatus. Since they have only recently been discovered and the large majority have not been cultured, the ecology and metabolism of these bacteria is not well understood. However, these bacteria may be an important contributor to ecosystems, since they are particularly abundant within soils.