Cyanobacteria The cyanobacteria deserve special emphasis because of their great ecological importance in the global carbon, oxygen and nitrogen cycles, as well as their evolutionary significance in relationship to plants. Photosynthetic cyanobacteria have chlorophyll a and carotenoids in addition to some unusual accessory pigments named phycobilins. The blue pigment, phycocyanin and the red one, phycoerythrin, absorb wavelengths of light for photosynthesis that are missed by chlorophyll and the carotenoids. Within the cytoplasm of cyanobacteria are numerous layers of membranes, often parallel to one another. These membranes are photosynthetic thylakoids that resemble those found in chloroplasts, which, in fact, correspond in size to the entire cyanobacterial cell. The main storage product of the cyanobacteria is glycogen, and glycogen inclusions may be seen in the cytoplasm of the cells. Cyanobacteria are thought to have given rise to eucaryotic chloroplasts during the evolutionary events of endosymbiosis. In biochemical detail, cyanobacteria are especially similar to the chloroplasts of red algae (Rhodophyta).

Most cyanobacteria have a mucilaginous sheath, or coating, which is often deeply pigmented, particularly in species that occur in terrestrial habitats. The colors of the sheaths in different species include light gold, yellow, brown, red, green, blue, violet, and blue-black. It is these pigments that impart color to individual cells and colonies as well as to "blooms" of cyanobacteria in aquatic environments

Figure 9. Some common cyanobacteria L to R: Oscillatoria, a filamentous species common in fresh water and hot springs; Nostoc, a sheathed communal species; Anabaena, a nitrogen-fixing species. The small cell with an opaque surface (third from right) in the anabaena filament is a heterocyst, a specialized cell for nitrogen fixation. The large bright cell in the filament is a type of spore called an akinete; Synechococcus,  a unicelluar species in marine habitats and hot springs. Synechococcus is among the most important photosynthetic bacteria in the marine environment, estimated to account for about 25 percent of the primary production that occurs in typical marine habitats.

Although thousands of cyanobacteria have been observed, only about 200 species have been identified as distinct, free-living, nonsymbiotic procaryotes. Relative to other oxygenic phototrophs, cyanobacteria often grow under fairly extreme environmental conditions such as high temperature and salinity. They are the only oxygenic phototrophs present in many hot springs of the Yellowstone ecosystem; and in frigid lakes and oceans of Antarctica, they form luxuriant mats 2 to 4 centimeters thick in water beneath more than five meters of permanent ice. However, cyanobacteria are absent in acidic waters where their eucaryotic counterparts, the algae, may be abundant.

Layered chalk deposits called stromatolites, which exhibit a continuous geologic record covering 2.7 billion years, are produced when colonies of cyanobacteria bind calcium-rich sediments. Today, stromatolites are formed in only a few places, such as shallow pools in hot dry climates. The abundance of cyanobacteria in the fossil record is evidence of the early development of the cyanobacteria and their important role in elevating the level of free oxygen in the atmosphere of the early Earth.

Cyanobacteria often form filaments and may grow in large masses or "tufts" one meter or more in length. Some are unicellular, a few form branched filaments, and a few form irregular plates or irregular colonies. Cyanobacterial cells usually divide by binary fission, and the resulting progeny cells may separate to form new colonies. In addition, filaments may break into fragments, called hormogonia, which separate and develop into new colonies. As in other filamentous or colonial bacteria, the cells of cyanobacteria may joined by their walls or by mucilaginous sheaths, but each cell is an independent unit of life.

As true Bacteria, cyanobacteria contain peptidoglycan or murein in their cell walls. Most cyanobacteria have a Gram-negative type cell wall that consists of an outer membrane component, even though they may show a distant phylogenetic relationship with certain Gram-positive bacteria. Some of the filamentous cyanobacteria are motile by means gliding or rotating around a longitudinal axis. Short segments (hormogonia) may break off from a cyanobacterial colony and glide away from their parent colony at rates as rapid as 10 micrometers per second. The mechanism for this movement is unexplained but may be connected to the extrusion of slime (mucilage) through small pores in their cell wall, together with contractile waves in one of the surface layers of the wall.

Cyanobacteria are found in most aerobic environments where water and light are available for growth. Mainly they live in fresh water and marine habitats. Those inhabiting the surface layers of water are part of a complex microbial community called plankton. Planktonic cyanobacteria usually contain cytoplasmic inclusions called gas vesicles which are hollow protein structures filled with various gases. The vesicles can be inflated or deflated with gases allowing the organisms to maintain buoyancy and to float at certain levels in the water. Thus, the cyanobacteria can regulate their position in the water column to meet their optimal needs for photosynthesis, oxygen, and light-shielding. When numerous cyanobacteria become unable to regulate their gas vesicles properly (for example, because of extreme fluctuations of temperature or oxygen supply), they may float to the surface of a body of water and form visible "blooms". A planktonic species related to Oscillatoria gives rise to the redness (and the name) of the Red Sea.

The cyanobacteria have very few harmful effects on plants or animals. They may be a nuisance if they bloom in large numbers and then die and decay in bodies of fresh water that are used for drinking or recreational purposes. Many cyanobacteria are responsible for the earthy odors and flavors of fresh waters, including drinking waters, due to the production of compounds called geosmins. Some cyanobacteria that form blooms secrete poisonous substances that are toxic for animals that ingest large amounts of the contaminated water.

Many marine cyanobacteria occur in limestone (calcium carbonate) or lime-rich substrates, such as coral algae and the shells of mollusks. Some fresh water species, particularly those that grow in hot springs, often deposit thick layers of lime in their colonies.

Some cyanobacteria can fix nitrogen. In filamentous cyanobacteria, nitrogen fixation often occurs in heterocysts, which are specialized, enlarged cells, usually distributed along the length of a filament or at the end of a filament. Heterocysts have intercellular connections to adjacent vegetative cells, and there is continuous movement of the products of nitrogen fixation moving from heterocysts to vegetative cells, and the products of photosynthesis moving from vegetative cells to heterocysts. Heterocysts are low in phycobilin pigments and have only photosystem I. They lack the oxygen-evolving photosystem II. Furthermore, they are surrounded in a thickened, specialized glycolipid cell wall that slows the rate of diffusion of O₂ into the cell. Any O₂ that diffuses into the heterocyst is rapidly reduced by hydrogen, a byproduct of N₂ fixation, or is expelled through the wall of the heterocyst. The process of nitrogen fixation, specifically the enzyme nitrogenase, only functions in anaerobic conditions so the organism must maintain these oxygen-free compartments in order for N2 fixation to occur.

In addition to the heterocysts, some cyanobacteria form resistant spores called akinetes enlarged cells around which thickened outer walls develop. Akinetes are resistant to heat, freezing and drought (desiccation) and thus allow the cyanobacteria to survive unfavorable environmental conditions. The are functionally analogous to bacterial endospores, but they bear little resemblance and lack the extraordinary resistance properties of endospores.

A few cyanobacteria are symbionts of liverworts, ferns, cycads, flagellated protozoa, and algae, sometimes occurring as endosymbionts of the eucaryotic cells. In the case of the water fern, Azolla, the cyanobacterial endophyte (a species of Anabaena) fixes nitrogen that becomes available to the plant. In addition, it is often the case that the photosynthetic partners of lichens are cyanobacteria.

The planktonic cyanobacteria fix an enormous amount of CO₂ during photosynthesis, and as "primary producers" they are the basis of the food chain in marine environments. Their type of photosynthesis, which utilizes photosystem II, generates a substantial amount of oxygen present in the earth's atmosphere. Since many cyanobacteria can fix N₂ under certain conditions, they are one of the most significant free-living nitrogen-fixing procaryotes. Cyanobacteria carried out plant-type (oxygenic) photosynthesis for at least a billion and a half years before the emergence of plants, and cyanobacteria are believed to be the evolutionary forerunners of modern-day plant and algal chloroplasts. A group of phototrophic procaryotes, called prochlorophytes contain chlorophyll a and b but do not contain phycobilins. Prochlorophytes, therefore, resemble both cyanobacteria (because they are procaryotic and contain chlorophyll a) and the plant chloroplast (because they contain chlorophyll b instead of phycobilins). Prochloron, the first prochlorophyte discovered, is phenotypically very similar to certain plant chloroplasts and is the leading candidate for the type of bacterium that might have undergone endosymbiotic events that led to the development of the plant chloroplast.