Cyanobacteria

# Overview
Cyanobacteria (Greek: s (kyanos) = blue + bacterium) also known as Cyanophyta is a phylum (or "division") of Bacteria that obtain their energy through photosynthesis. They are often referred to as blue-green algae, although they are in fact prokaryotes, not algae. The description is primarily used to reflect their appearance and ecological role rather than their evolutionary lineage. The name "cyanobacteria" comes from the colour of the bacteria, cyan; the bacteria do not use or produce cyanide whose chemical prefix is cyano-.
Putative fossil traces of cyanobacteria have been found from around 3.8 billion years ago (b.y.a.). See: Stromatolite. They are a significant component of the marine nitrogen cycle and an important primary producer in many areas of the ocean. Their ability to perform oxygenic (plant-like) photosynthesis is thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the life forms on Earth and provoked an explosion of biodiversity. See: Oxygen Catastrophe.

# Forms
Cyanobacteria are found in almost every conceivable habitat, from oceans to fresh water to bare rock to soil. Most are found in fresh water, while others are marine, occur in damp soil, or even temporarily moistened rocks in deserts. A few are endosymbionts in lichens, plants, various protists, or sponges and provide energy for the host. Some live in the fur of sloths, providing a form of camouflage.
Cyanobacteria include unicellular and colonial species. Colonies may form filaments, sheets or even hollow balls.  Some filamentous colonies show the ability to differentiate into several different cell types: vegetative cells, the normal, photosynthetic cells that are formed under favorable growing conditions; akinetes, the climate-resistant spores that may form when environmental conditions become harsh; and thick-walled heterocysts, which contain the enzyme nitrogenase, vital for nitrogen fixation. Heterocysts may also form under the appropriate environmental conditions (anoxic) wherever nitrogen is necessary. Heterocyst-forming species are specialized for nitrogen fixation and are able to fix nitrogen gas, which cannot be used by plants, into ammonia (Template:Nh3), nitrites (Template:No2-) or nitrates (Template:No3-), which can be absorbed by plants and converted to protein and nucleic acids. The rice paddies of Asia, which produce about 75% of the world's rice, could not do so were it not for healthy populations of nitrogen-fixing cyanobacteria in the rice paddy fertilizer.
Many cyanobacteria also form motile filaments, called hormogonia, that travel away from the main biomass to bud and form new colonies elsewhere. The cells in a hormogonium are often thinner than in the vegetative state, and the cells on either end of the motile chain may be tapered. In order to break away from the parent colony, a hormogonium often must tear apart a weaker cell in a filament, called a necridium.
Each individual cell of a cyanobacterium typically has a thick, gelatinous cell wall. They differ from other gram-negative bacteria in that the quorum sensing molecules autoinducer-2 and acyl-homoserine lactones are absent. They lack flagella, but hormogonia and some unicellular species may move about by gliding along surfaces. In water columns some cyanobacteria float by forming gas vesicles, like in archaea.

# Photosynthesis
Cyanobacteria have an elaborate and highly organized system of internal membranes which function in photosynthesis. Photosynthesis in cyanobacteria generally uses water as an electron donor and produces oxygen as a by-product, though some may also use hydrogen sulfide as occurs among other photosynthetic bacteria. Carbon dioxide is reduced to form carbohydrates via the Calvin cycle. In most forms the photosynthetic machinery is embedded into folds of the cell membrane, called thylakoids. The large amounts of oxygen in the atmosphere are considered to have been first created by the activities of ancient cyanobacteria. Due to their ability to fix nitrogen in aerobic conditions they are often found as symbionts with a number of other groups of organisms such as fungi (lichens), corals, pteridophytes (Azolla), angiosperms (Gunnera) etc.
Cyanobacteria are the only group of organisms that are able to reduce nitrogen and carbon in aerobic conditions, a fact that may be responsible for their evolutionary and ecological success. The water-oxidizing photosynthesis is accomplished by coupling the activity of photosystem (PS) II and I (Z-scheme). In anaerobic conditions, they are also able to use only PS I  cyclic photophosphorylation  with electron donors other than water (hydrogen sulfide, thiosulphate, or even molecular hydrogen) just like purple photosynthetic bacteria. Furthermore, they share an archaebacterial property, the ability to reduce elemental sulfur by anaerobic respiration in the dark. Their photosynthetic electron transport shares the same compartment as the components of respiratory electron transport. Actually, their plasma membrane contains only components of the respiratory chain, while the thylakoid membrane hosts both respiratory and photosynthetic electron transport.
Attached to thylakoid membrane, phycobilisomes act as light harvesting antennae for the photosystems . The phycobilisome components (phycobiliproteins) are responsible for the blue-green pigmentation of most cyanobacteria. The variations to this theme is mainly due to carotenoids and phycoerythrins which give the cells the red-brownish coloration. In some cyanobacteria, the color of light influences the composition of phycobilisomes. In green light, the cells accumulate more phycoerythrin, whereas in red light they produce more phycocyanin. Thus the bacteria appear green in red light and red in green light. This process is known as complementary chromatic adaptation and is a way for the cells to maximize the use of available light for photosynthesis.
A few genera, however, lack phycobilisomes and have chlorophyll b instead (Prochloron, Prochlorococcus, Prochlorothrix). These were originally grouped together as the prochlorophytes or chloroxybacteria, but appear to have developed in several different lines of cyanobacteria. For this reason they are now considered as part of cyanobacterial group.

# Relationship to chloroplasts
Chloroplasts found in eukaryotes (algae and higher plants)  likely evolved from an endosymbiotic relation with cyanobacteria. This endosymbiotic theory is supported by various structural and genetic similarities. Primary chloroplasts are found among the green plants, where they contain chlorophyll b, and among the red algae and glaucophytes, where they contain phycobilins. It now appears that these chloroplasts probably had a single origin, in an ancestor of the clade called Primoplantae. Other algae likely took their chloroplasts from these forms by secondary endosymbiosis or ingestion.
It was once thought that the mitochondria in eukaryotes also developed from an endosymbiotic relationship with cyanobacteria; however, we now suspect that this evolutionary event occurred when aerobic Eubacteria were engulfed by anaerobic host cells. Mitochondria are believed to have originated not from cyanobacteria but from an ancestor of Rickettsia.

# Cyanobacteria and Earth History
The biochemical capacity to use water as the source for electrons in photosynthesis evolved once, in a common ancestor of extant cyanobacteria.  The geological record indicates that this transforming event took place early in our planet's history, at least 2450-2320 million years ago (Ma), and possibly much earlier.  Geobiological interpretation of Archean (>2500 Ma) sedimentary rocks remains a challenge; available evidence indicates that life existed 3500 Ma, but the question of when oxygenic photosynthesis evolved continues to engender debate and research.  A clear paleontological window on cyanobacterial evolution opened about 2000 Ma, revealing an already diverse biota of blue-greens.  Cyanobacteria remained principal primary producers throughout the Proterozoic Eon (2500-543 Ma), in part because the redox structure of the oceans favored photautotrophs capable of nitrogen fixation.  Green algae joined blue-greens as major primary producers on continental shelves near the end of the Proterozoic, but only with the Mesozoic (251-65 Ma) radiations of dinoflagellates, coccolithophorids, and diatoms did primary production in marine shelf waters take modern form.  Cyanobacteria remain critical to marine ecosystems as primary producers in oceanic gyres, as agents of biological nitrogen fixation, and, in modified form, as the plastids of marine algae.

# Cyanobacterial Evolution from Comparative Genomics
Recent high-throughput sequencing has provided DNA sequences at an unprecedented rate, posing considerable analytical challenges, but also offering insight into the genetic mechanisms of adaptation. Here we present a comparative genomics-based approach towards understanding the evolution of these mechanisms in cyanobacteria. Historically, systematic methods of defining morphological traits in cyanobacteria have posed a major barrier in reconstructing their true evolutionary history. The advent of protein, then DNA, sequencing - most notably the use of 16S rRNA as a molecular marker - helped circumvent this barrier and now forms the basis of our understanding of the history of life on Earth. However, these tools have proved insufficient for resolving relationships between closely related cyanobacterial species. The 24 cyanobacteria whose genomes have been compared occupy a wide variety of environmental niches and play major roles in global carbon and nitrogen cycles. By integrating phylogenetic data inferred for hundreds to nearly 1000 protein coding genes common to all or most cyanobacteria, we are able to reconstruct an evolutionary history of the entire phylum, establishing a framework for resolving how their metabolic and phenotypic diversity came about.

# Classification
The cyanobacteria were traditionally classified by morphology into five sections, referred to by the numerals I-V. The first three - Chroococcales, Pleurocapsales, and Oscillatoriales - are not supported by phylogenetic studies. However, the latter two - Nostocales and Stigonematales - are monophyletic, and make up the heterocystous cyanobacteria.
The members of Chroococales are unicellular and usually aggregated in colonies. The classic taxonomic criterion has been the cell morphology and the plane of cell division. In Pleurocapsales, the cells have the ability to form internal spores (baeocytes). The rest of the sections include filamentous species. In Oscillatorialles, the cells are uniseriately arranged and do not form specialized cells (akinets and heterocysts). In Nostocalles and Stigonematalles the cells have the ability to develop heterocysts in certain conditions. Stigonematales, unlike Nostocalles include species with truly branched trichome.
Most taxa included in the phylum or division Cyanobacteria have not yet been validly published under the Bacteriological Code. Except:
- The classes Chroobacteria, Hormogoneae and Gloeobacteria
- The orders Chroococcales, Gloeobacterales, Nostocales, Oscillatoriales, Pleurocapsales and Stigonematales
- The families Prochloraceae and Prochlorotrichaceae
- The genera Halospirulina, Planktothricoides, Prochlorococcus, Prochloron, Prochlorothrix.

# Biotechnology and applications
Certain cyanobacteria produce cyanotoxins like Anatoxin-a, Anatoxin-as, Aplysiatoxin, Cylindrospermopsin, Domoic acid, Microcystin LR, Nodularin R (from Nodularia), or Saxitoxin. Sometimes a mass-reproduction of cyanobacteria results in algal blooms.
The unicellular cyanobacterium Synechocystis sp. PCC6803 was the third prokaryote and first photosynthetic organism whose genome was completely sequenced. It continues to be an important model organism. The smallest genomes have been found in Prochlorococcus spp. (1.7 Mb) and the largest in Nostoc punctiforme (9 Mb). Those of Calothrix spp. are estimated at 12-15 Mb, as large as yeast.
At least one secondary metabolite, cyanovirin, has shown to possess anti-HIV activity.
See hypolith for an example of cyanobacteria living in extreme conditions.
Some cyanobacteria are sold as food, notably Aphanizomenon flos-aquae (E3live) and Arthrospira platensis (Spirulina). It has been suggested that they could be a much more substantial part of human food supplies, as a kind of superfood.
Along with algae, some hydrogen producing cyanobacteria are being considered as an alternative energy source, notably at Oregon State University, in research supported by the U.S. Department of Energy, Princeton University, Colorado School of Mines as well as at Uppsala University, Sweden

# Health Risks
Some species of cyanobacteria produce neurotoxins, hepatotoxins, cytotoxins, and endotoxins, making them dangerous to animals and humans.  Several cases of human poisoning have been documented but a lack of knowledge prevents an accurate assessment of the risks.